WorldWideScience

Sample records for biological aquatic system

  1. Aquatic biology studies

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Aquatic biology studies focused on studying the hydrothermal effects of Par Pond reservoir on periphyton, plankton, zooplankton, macrophytes, human pathogens, and microbial activity; the variability between the artificial streams of the Flowing Streams Laboratory and Upper Three Runs Creek; and the bacterial production of methane in Savannah River Plant aquatic systems

  2. Novel aquatic modules for bioregenerative life-support systems based on the closed equilibrated biological aquatic system (c.e.b.a.s.)

    Science.gov (United States)

    Bluem, Volker; Paris, Frank

    2002-06-01

    The closed equilibrated biological aquatic system (C.E.B.A.S) is a man-made aquatic ecosystem which consists of four subcomponents: an aquatic animal habitat, an aquatic plant bioreactor, an ammonia oxidizing bacteria filter and a data acquisition/control unit. It is a precursor for different types of fish and aquatic plant production sites which are disposed for the integration into bioregenerative life-support systems. The results of two successful spaceflights of a miniaturized C.E.B.A.S version (the C.E.B.A.S. MINI MODULE) allow the optimization of aquatic food production systems which are already developed in the ground laboratory and open new aspects for their utilization as aquatic modules in space bioregenerative life support systems. The total disposition offers different stages of complexity of such aquatic modules starting with simple but efficient aquatic plant cultivators which can be implemented into water recycling systems and ending up in combined plant/fish aquaculture in connection with reproduction modules and hydroponics applications for higher land plants. In principle, aquaculture of fishes and/or other aquatic animals edible for humans offers optimal animal protein production under lowered gravity conditions without the tremendous waste management problems connected with tetrapod breeding and maintenance. The paper presents details of conducted experimental work and of future dispositions which demonstrate clearly that aquaculture is an additional possibility to combine efficient and simple food production in space with water recycling utilizing safe and performable biotechnologies. Moreover, it explains how these systems may contribute to more variable diets to fulfill the needs of multicultural crews.

  3. Application of vascular aquatic plants for pollution removal, energy and food production in a biological system

    Science.gov (United States)

    Wolverton, B. C.; Barlow, R. M.; Mcdonald, R. C.

    1975-01-01

    Vascular aquatic plants such as water hyacinths (Eichhornia crassipes) (Mart.) Solms and alligator weeds (Alternanthera philoxeroides) (Mart.) Griesb., when utilized in a controlled biological system (including a regular program of harvesting to achieve maximum growth and pollution removal efficiency), may represent a remarkably efficient and inexpensive filtration and disposal system for toxic materials and sewage released into waters near urban and industrial areas. The harvested and processed plant materials are sources of energy, fertilizer, animal feed, and human food. Such a system has industrial, municipal, and agricultural applications.

  4. Animal protein production modules in biological life support systems: Novel combined aquaculture techniques based on the closed equilibrated biological aquatic system (C.E.B.A.S.)

    Science.gov (United States)

    Blüm, V.; Andriske, M.; Kreuzberg, K.; Schreibman, M. P.

    Based on the experiences made with the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) which was primarily deveoloped for long-term and multi-generation experiments with aquatic animals and plants in a space station highly effective fresh water recycling modules were elaborated utilizing a combination of ammonia oxidizing bacteria filters and higher plants. These exhibit a high effectivity to eliminate phosphate and anorganic nitrogen compounds and arc. in addidition. able to contribute to the oxygen supply of the aquatic animals. The C.E.B.A.S. filter system is able to keep a closed artificial aquatic ecosystem containing teleost fishes and water snails biologically stable for several month and to eliminate waste products deriving from degraded dead fishes without a decrease of the oxygen concentration down to less than 3.5 mg/l at 25 °C. More advanced C.E.B.A.S. filter systems, the BIOCURE filters, were also developed for utilization in semiintensive and intensive aquaculture systems for fishes. In fact such combined animal-plant aquaculture systems represent highly effective productions sites for human food if proper plant and fish species are selected The present papers elucidates ways to novel aquaculture systems in which herbivorous fishes are raised by feeding them with plant biomass produced in the BIOCURE filters and presents the scheme of a modification which utilizes a plant species suitable also for human nutrition. Special attention is paid to the benefits of closed aquaculture system modules which may be integrated into bioregenerative life support systems of a higher complexity for, e. g.. lunar or planetary bases including some psychologiccal aspects of the introduction of animal protein production into plant-based life support systems. Moreover, the basic reproductive biological problems of aquatic animal breeding under reduced gravity are explained leading to a disposition of essential research programs in this context.

  5. Interactions between physical, chemical and biological processes in aquatic systems - impacts on receiving waters with different contents of treated wastewater

    International Nuclear Information System (INIS)

    Kreuzinger, N.

    2000-08-01

    Two scenarios have be chosen within this PhD Thesis to describe the integrative key-significance of interactions between most relevant physical, chemical and biological processes in aquatic systems. These two case studies are used to illustrate and describe the importance of a detailed synthesis of biological, physical and chemical interactions in aquatic systems in order to provide relevant protection of water resources and to perform a sound water management. Methods are described to allow a detailed assessment of particular aspects within the complexity of the overall integration and therefore serve as a basis to determine the eventual necessity of proposed water management measures. Regarding the anthropogenic influence of treated wastewater on aquatic systems, one case study focuses on the interactions between emitted waters from a wastewater treatment plant and the resulting immission situation of its receiving water (The receiving water is quantitatively influenced by the treated wastewater by 95 %). This thesis proves that the effluent of wastewater treatment plants operated by best available technology meets the quality standards of running waters for the nutrients nitrogen and phosphorus, carbon-parameters, oxygen-regime and ecotoxicology. Within the second case study the focus is put on interactions between immissions and water usage. The general importance of biological phosphorus precipitation on the trophic situation of aquatic systems is described. Nevertheless, this generally known but within the field of applied limnology so far unrespected process of immobilization of phosphorus could be shown to represent a significant and major impact on phytoplannctotic development and eutrification. (author)

  6. C.E.B.A.S., a closed equilibrated biological aquatic system as a possible precursor for a long-term life support system?

    Science.gov (United States)

    Blüm, V.

    C.E.B.A.S.-AQUARACK is a long-term multi-generation experimental device for aquatic organisms which is disposed for utlizitation in a space station. It results from the basic idea of a space aquarium for maintaining aquatic animals for longer periods integrated in a AQUARACK which consists of a modular animal holding tank, a semi-biological/physical water recycling system and an electronical control unit. The basic idea to replace a part of the water recycling system by a continuous culture of unicellular algae primarily leads to a second system for experiments with algae, a botanical AQUARACK consisting of an algal reactor, a water recycling and the electronical control unit. The combination of the zoological part, and the botanical part with a common control system in the AQUARACK, however, results in a ``Closed Equilibrated Biological Aquatic System'' (C.E.B.A.S.) representing an closed artificial ecosystem. Although this is disposed primarily as an experimental device for basic zoological, botanical and interdisciplinary research it opens the theoretical possibility to adapt it for combined production of animal and plant biomass on ground or in space. The paper explains the basic conception of the hardware construction of the zoological part of the system, the corresponding scientific frame program including the choice of the experimental animals and gives some selected examples of the hardware-related resrearch. It furtheron discusses the practical and economical relevance of the system in the development of a controlled aquatical life support system in general.

  7. Antimony in aquatic systems

    OpenAIRE

    Filella, Montserrat; Belzile, Nelson; Chen, Yuwei; Elleouet, C.; May, P. M.; Mavrocordatos, D.; Nirel, P.; Porquet, A.; Quentel, F.; Silver, S.

    2003-01-01

    Antimony is ubiquitous in the environment. In spite of its proven toxicity, it has received scant attention so far. This communication presents an overview of current knowledge as well as the early results of a concerted, multidisciplinary effort to unveil antimony behaviour and fate in natural aquatic systems.

  8. Applying four principles of headwater system aquatic biology to forest management

    Science.gov (United States)

    Robert J. Danehy; Sherri L. Johnson

    2013-01-01

    Headwater systems, including the channel and the adjacent riparian forest, are a dominant landscape feature in forested watersheds, draining most of the watershed area, and comprising the majority of channel length in drainage networks. Being at the upper extent of watersheds, these systems are smaller and steeper than large streams, and create microhabitats that...

  9. Biological indication in aquatic ecosystems. Biological indication in limnic and coastal ecosystems - fundamentals, techniques, methodology

    International Nuclear Information System (INIS)

    Gunkel, G.

    1994-01-01

    Biological methods of water quality evaluation today form an integral part of environmental monitoring and permit to continuously monitor the condition of aquatic ecosystems. They indicate both improvements in water quality following redevelopment measures, and the sometimes insidious deterioration of water quality. This book on biological indication in aquatic ecosystems is a compendium of measurement and evaluation techniques for limnic systems by means of biological parameters. At present, however, an intense discussion of biological evaluation techniques is going on, for one thing as a consequence of the German reunification and the need to unify evaluation techniques, and for another because of harmonizations within the European Community. (orig./EF) [de

  10. Book review: Aquatic insect ecology: 1. Biology and habitat

    OpenAIRE

    Arnett, Ross H.

    2010-01-01

    Book Review: A comprehensive treatment of the ecology of aquatic insects in one place is needed for both students and researchers. Professor Ward is doing this in two volumes. The first volume covers the biology and habitats, as indicated in the subtitle, of the 13 insect orders that are either entirely aquatic at some stage, or those with some members aquatic at some stage. The second volume will be devoted entirely to the feeding ecology of these aquatic species.

  11. Study of a multitrophical integrated aquatic system for the teaching-learning of the subjects physics, chemistry and biology in the bachelor

    Science.gov (United States)

    Ramirez, Eva; Espinosa, Cecilia

    2017-04-01

    In Mexico exist due to the lack of water in the City, which is where the College of Sciences and Humanities Orient (at UNAM) is located. This is because a point of view from the Chemical, Physics and Biology subjects is important to find learning strategies that motivate students to seek solutions to problems such as these. As Science Mentors, students were asked to propose water treatment from the homes they live in. From these investigations the students concluded that it was necessary to study in depth the wetlands like Multi-trophic Aquatic System that allow the treatment of gray water, so that a prototype of Micro-scale Multitrophic Aquatic System was set up in the laboratory, where the pH was measured , The concentration of oxygen, phosphates, from a Chemical perspective. As for the subject of Biology, we worked on the search for mycorrhizal fungi associated with the growth of plants for the purification of water. In physics we worked the sedimentation system. Artificial wetlands are man-made zones in which, in a controlled manner, mechanisms for the removal of contaminants present in wastewater, occurring in natural wetlands through physical, biological and chemical processes, are constructed mechanically and Is waterproofed to prevent losses of water to the subsoil, the use of substrates different from the original land for rooting the plants and their selection that will colonize the wetland benefit the recovery of water. The present project aims to structure an Artificial Wetland to carry out didactic strategies, activities with students, as well as work on research projects in the sciences of Chemistry, Physics and Biology. Through the application of chemical, biological and physical concepts and processes, so that students of the different semesters of the College of Sciences and Humanities Plantel Oriente, appropriate the relevant knowledge in the area of experimental sciences, developing thinking skills and achieve Significant learning, which are

  12. Biota and biological principles of the aquatic environment

    International Nuclear Information System (INIS)

    Greeson, P.E.

    1982-01-01

    The first of several compilations of briefing papers on water quality prepared by the U.S. Geological Survey is presented. Each briefing paper is prepared in a simple, nontechnical, easy to understand manner. This U.S. Geological Survey Circular contains papers on selected biota and biological principles of the aquatic environment. Briefing papers are included on Why biology in water quality studies , Stream biology, Phytoplankton, Periphyton, Drift organisms in streams, Family Chironomidae (Diptera), Influences of water temperature on aquatic biota, and Stream channelization: Effects on stream fauna

  13. Freshwater ecosystems and aquatic insects: a paradox in biological invasions.

    Science.gov (United States)

    Fenoglio, Stefano; Bonada, Núria; Guareschi, Simone; López-Rodríguez, Manuel J; Millán, Andrés; Tierno de Figueroa, J Manuel

    2016-04-01

    Biological invasions have increased significantly in response to global change and constitute one of the major causes of biodiversity loss. Insects make up a large fraction of invasive species, in general, and freshwaters are among the most invaded ecosystems on our planet. However, even though aquatic insects dominate most inland waters, have unparalleled taxonomic diversity and occupy nearly all trophic niches, there are almost no invasive insects in freshwaters. We present some hypotheses regarding why aquatic insects are not common among aquatic invasive organisms, suggesting that it may be the result of a suite of biological, ecological and anthropogenic factors. Such specific knowledge introduces a paradox in the current scientific discussion on invasive species; therefore, a more in-depth understanding could be an invaluable aid to disentangling how and why biological invasions occur. © 2016 The Author(s).

  14. Modeling dynamics of biological and chemical components of aquatic ecosystems

    International Nuclear Information System (INIS)

    Lassiter, R.R.

    1975-05-01

    To provide capability to model aquatic ecosystems or their subsystems as needed for particular research goals, a modeling strategy was developed. Submodels of several processes common to aquatic ecosystems were developed or adapted from previously existing ones. Included are submodels for photosynthesis as a function of light and depth, biological growth rates as a function of temperature, dynamic chemical equilibrium, feeding and growth, and various types of losses to biological populations. These submodels may be used as modules in the construction of models of subsystems or ecosystems. A preliminary model for the nitrogen cycle subsystem was developed using the modeling strategy and applicable submodels. (U.S.)

  15. DNA barcodes for assessment of the biological integrity of aquatic ecosystems

    Science.gov (United States)

    Water quality regulations and aquatic ecosystem monitoring increasingly rely on direct assessments of biological integrity. Because these aquatic “bioassessments” evaluate the incidence and abundance of sensitive aquatic species, they are able to measure cumulative ecosystem eff...

  16. Modeling Aquatic Toxicity through Chromatographic Systems.

    Science.gov (United States)

    Fernández-Pumarega, Alejandro; Amézqueta, Susana; Farré, Sandra; Muñoz-Pascual, Laura; Abraham, Michael H; Fuguet, Elisabet; Rosés, Martí

    2017-08-01

    Environmental risk assessment requires information about the toxicity of the growing number of chemical products coming from different origins that can contaminate water and become toxicants to aquatic species or other living beings via the trophic chain. Direct toxicity measurements using sensitive aquatic species can be carried out but they may become expensive and ethically questionable. Literature refers to the use of chromatographic measurements that correlate to the toxic effect of a compound over a specific aquatic species as an alternative to get toxicity information. In this work, we have studied the similarity in the response of the toxicity to different species and we have selected eight representative aquatic species (including tadpoles, fish, water fleas, protozoan, and bacteria) with known nonspecific toxicity to chemical substances. Next, we have selected four chromatographic systems offering good perspectives for surrogation of the eight selected aquatic systems, and thus prediction of toxicity from the chromatographic measurement. Then toxicity has been correlated to the chromatographic retention factor. Satisfactory correlation results have been obtained to emulate toxicity in five of the selected aquatic species through some of the chromatographic systems. Other aquatic species with similar characteristics to these five representative ones could also be emulated by using the same chromatographic systems. The final aim of this study is to model chemical products toxicity to aquatic species by means of chromatographic systems to reduce in vivo testing.

  17. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

  18. Biological conservation of aquatic inland habitats: these are better days

    Directory of Open Access Journals (Sweden)

    Ian J. Winfield

    2013-08-01

    Full Text Available The biodiversity of aquatic inland habitats currently faces unprecedented threats from human activities. At the same time, although much is known about the functioning of freshwater ecosystems the successful transfer of such knowledge to practical conservation has not been universal. Global awareness of aquatic conservation issues is also hampered by the fact that conditions under the water surface are largely hidden from the direct experience of most members of society. Connectivity, or lack of it, is another challenge to the conservation of freshwater habitats, while urban areas can play a perhaps unexpectedly important positive role. Freshwater habitats frequently enjoy benefits accruing from a sense of ownership or stewardship by local inhabitants, which has led to the development of conservation movements which commonly started life centred on the aquatic inland habitat itself but of which many have now matured into wider catchment-based conservation programmes. A demonstrable need for evidence-based conservation management in turn requires scientific assessments to be increasingly robust and standardised, while at the same time remaining open to the adoption of technological advances and welcoming the rapidly developing citizen science movement. There is evidence of real progress in this context and conservation scientists are now communicating their findings to environmental managers in a way and on a scale that was rarely seen a couple of decades ago. It is only in this way that scientific knowledge can be efficiently transferred to conservation planning, prioritisation and ultimately management in an increasingly scaled-up, joined-up and resource-limited world. The principle of ‘prevention is better than cure’ is particularly appropriate to most biological conservation issues in aquatic inland habitats and is inextricably linked to educating and/or nudging appropriate human behaviours. When prevention fails, some form of emergency

  19. The neurotoxin BMAA in aquatic systems

    NARCIS (Netherlands)

    Faassen, E.J.

    2016-01-01

    Eutrophication is a major water quality issue and in many aquatic systems, it leads to the proliferation of toxic phytoplankton species. The neurotoxin β-N-methylamino-L-alanine (BMAA) is one of the compounds that can be present in phytoplankton. BMAA has been suggested to play a role in

  20. Arsenic in the aquatic environment - speciation and biological effects

    Energy Technology Data Exchange (ETDEWEB)

    Landner, L [Swedish Environmental Research Group (MFG)

    1998-03-01

    The present report is a contribution to EC Commission`s undertaking to review existing EC provisions on the substances for which Sweden has been granted transitional provisions. The provisions imply that Sweden may maintain more stringent regulations on four substances until the end of 1998. The present report deals with speciation and biological effects of arsenic in three types of aquatic environments - marine water, estuarine or brackish water and freshwater. The similarity between arsenate and phosphate and the interference in phosphorylation reactions is discussed. It is clear that in Scandinavian inland waters the concentration of phosphorous is on average lower than in most inland waters in continental Europe. However, in most inland waters phosphorus is the limiting factor for phytoplankton development and eutrophication, which means that there is a clear risk for detrimental effects in the great majority of inland waters, also eutrophic waters 167 refs, 27 figs, 12 tabs. Exemption Substances Project (Directive 89/677/EEC)

  1. Aquatic worms eating waste sludge in a continuous system

    NARCIS (Netherlands)

    Hendrickx, T.L.G.; Temmink, B.G.; Elissen, H.J.H.; Buisman, C.J.N.

    2009-01-01

    Aquatic worms are a biological approach to decrease the amount of biological waste sludge produced at waste water treatment plants. A new reactor concept was recently introduced in which the aquatic oligochaete Lumbriculus variegatus is immobilised in a carrier material. The current paper describes

  2. Monitoring aquatic environments with autonomous systems

    DEFF Research Database (Denmark)

    Christensen, Jesper Philip Aagaard

    High frequency measurements from autonomous sensors have become a widely used tool among aquatic scientists. This report focus primarily on the use of ecosystem metabolism based on high frequency oxygen measurements and relates the calculations to spatial variation, biomass of the primary producers...... and in shallow systems the macrophytes can completely dominate primary production. This was despite the fact that the plants in the studied system were light-saturated most of the light hours and occasionally carbon limited. It was also shown that the GPP and the total phytoplankton biomass in a nutrient...

  3. Biological conservation of aquatic inland habitats: these are better days

    OpenAIRE

    Ian J. Winfield

    2013-01-01

    The biodiversity of aquatic inland habitats currently faces unprecedented threats from human activities. At the same time, although much is known about the functioning of freshwater ecosystems the successful transfer of such knowledge to practical conservation has not been universal. Global awareness of aquatic conservation issues is also hampered by the fact that conditions under the water surface are largely hidden from the direct experience of most members of society. Connectivity, or lack...

  4. The development of a classification system for inland aquatic ...

    African Journals Online (AJOL)

    A classification system is described that was developed for inland aquatic ecosystems in South Africa, including wetlands. The six-tiered classification system is based on a top-down, hierarchical classification of aquatic ecosystems, following the functionally-oriented hydrogeomorphic (HGM) approach to classification but ...

  5. The biological control of aquatic weeds in South Africa: Current status and future challenges

    Directory of Open Access Journals (Sweden)

    Martin P. Hill

    2017-03-01

    Full Text Available Background: Aquatic ecosystems in South Africa are prone to invasion by several invasive alien aquatic weeds, most notably, Eichhornia crassipes (Mart. Solms-Laub. (Pontederiaceae (water hyacinth; Pistia stratiotes L. (Araceae (water lettuce; Salvinia molesta D.S. Mitch. (Salviniaceae (salvinia; Myriophyllum aquaticum (Vell. Conc. Verd. (parrot’s feather; and Azolla filiculoides Lam. (Azollaceae (red water fern. Objective: We review the biological control programme on waterweeds in South Africa. Results: Our review shows significant reductions in the extent of invasions, and a return on biodiversity and socio-economic benefits through the use of this method. These studies provide justification for the control of widespread and emerging freshwater invasive alien aquatic weeds in South Africa. Conclusions: The long-term management of alien aquatic vegetation relies on the correct implementation of biological control for those species already in the country and the prevention of other species entering South Africa.

  6. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  7. VASCULAR PLANTS AS ENGINEERS OF OXYGEN IN AQUATIC SYSTEMS

    Science.gov (United States)

    The impact of organisms on oxygen is one of the most dramatic examples of ecosystem engineering on Earth. In aquatic systems, which have much lower oxygen concentrations than the atmosphere, vascular aquatic plants can affect oxygen concentrations significantly not only on long t...

  8. Aquatics Systems Branch: transdisciplinary research to address water-related environmental problems

    Science.gov (United States)

    Dong, Quan; Walters, Katie D.

    2015-01-01

    The Aquatic Systems Branch at the Fort Collins Science Center is a group of scientists dedicated to advancing interdisciplinary science and providing science support to solve water-related environmental issues. Natural resource managers have an increasing need for scientific information and stakeholders face enormous challenges of increasing and competing demands for water. Our scientists are leaders in ecological flows, riparian ecology, hydroscape ecology, ecosystem management, and contaminant biology. The Aquatic Systems Branch employs and develops state-of-the-science approaches in field investigations, laboratory experiments, remote sensing, simulation and predictive modeling, and decision support tools. We use the aquatic experimental laboratory, the greenhouse, the botanical garden and other advanced facilities to conduct unique research. Our scientists pursue research on the ground, in the rivers, and in the skies, generating and testing hypotheses and collecting quantitative information to support planning and design in natural resource management and aquatic restoration.

  9. Carbon nanomaterials in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Pu Chun Ke [Laboratory of Single-Molecule Biophysics and Polymer Physics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 (United States); Qiao Rui [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634 (United States)

    2007-09-19

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  10. Carbon nanomaterials in biological systems

    International Nuclear Information System (INIS)

    Pu Chun Ke; Qiao Rui

    2007-01-01

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  11. Procedure to select test organisms for environmental risk assessment of genetically modified crops in aquatic systems.

    Science.gov (United States)

    Hilbeck, Angelika; Bundschuh, Rebecca; Bundschuh, Mirco; Hofmann, Frieder; Oehen, Bernadette; Otto, Mathias; Schulz, Ralf; Trtikova, Miluse

    2017-11-01

    For a long time, the environmental risk assessment (ERA) of genetically modified (GM) crops focused mainly on terrestrial ecosystems. This changed when it was scientifically established that aquatic ecosystems are exposed to GM crop residues that may negatively affect aquatic species. To assist the risk assessment process, we present a tool to identify ecologically relevant species usable in tiered testing prior to authorization or for biological monitoring in the field. The tool is derived from a selection procedure for terrestrial ecosystems with substantial but necessary changes to adequately consider the differences in the type of ecosystems. By using available information from the Water Framework Directive (2000/60/EC), the procedure can draw upon existing biological data on aquatic systems. The proposed procedure for aquatic ecosystems was tested for the first time during an expert workshop in 2013, using the cultivation of Bacillus thuringiensis (Bt) maize as the GM crop and 1 stream type as the receiving environment in the model system. During this workshop, species executing important ecological functions in aquatic environments were identified in a stepwise procedure according to predefined ecological criteria. By doing so, we demonstrated that the procedure is practicable with regard to its goal: From the initial long list of 141 potentially exposed aquatic species, 7 species and 1 genus were identified as the most suitable candidates for nontarget testing programs. Integr Environ Assess Manag 2017;13:974-979. © 2017 SETAC. © 2017 SETAC.

  12. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  13. Removal of pharmaceuticals and personal care products in aquatic plant-based systems: A review

    International Nuclear Information System (INIS)

    Zhang, Dongqing; Gersberg, Richard M.; Ng, Wun Jern; Tan, Soon Keat

    2014-01-01

    Pharmaceuticals and personal care products (PPCPs) in the aquatic environment are regarded as emerging contaminants and have attracted increasing concern. The use of aquatic plant-based systems such as constructed wetlands (CWs) for treatment of conventional pollutants has been well documented. However, available research studies on aquatic plant-based systems for PPCP removal are still limited. The removal of PPCPs in CWs often involves a diverse and complex set of physical, chemical and biological processes, which can be affected by the design and operational parameters selected for treatment. This review summarizes the PPCP removal performance in different aquatic plant-based systems. We also review the recent progress made towards a better understanding of the various mechanisms and pathways of PPCP attenuation during such phytoremediation. Additionally, the effect of key CW design characteristics and their interaction with the physico-chemical parameters that may influence the removal of PPCPs in functioning aquatic plant-based systems is discussed. -- Highlights: • Investigation of the removal performance of PPCPs in CW systems. • Investigation of the mechanisms and pathways contributing to PPCP removal in CWs. • Investigation of the effect of CW design parameters on PPCP removal. • Investigation of the correlation between physico-chemical parameters and PPCP removal. -- This review gives an overview of the present state of research on the removal of pharmaceutical and personal care products by means of constructed wetlands

  14. The use of aquatic macrophytes in monitoring and in assessment of biological integrity

    Science.gov (United States)

    Stewart, P.M.; Scribailo, R.W.; Simon, T.P.; Gerhardt, A.

    1999-01-01

    Aquatic plant species, populations, and communities should be used as indicators of the aquatic environment, allowing detection of ecosystem response to different stressors. Plant tissues bioaccumulate and concentrate toxin levels higher than what is present in the sediments; and this appears to be related to organic matter content, acidification, and buffering capacity. The majority of toxicity studies, most of these with heavy metals, have been done with several Lemna species and Vallisneria americana. Organic chemicals reviewed include pesticides and herbicides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other industrial contaminants. The use of aquatic plant communities as bioindicators of environmental quality was evaluated for specific characteristics and indices that may assess biological integrity. Indices such as the floristic quality index (FQI) and coefficient of conservatism (C) are pioneering efforts to describe the quality of natural areas and protect native biodiversity. Our case study in the Grand Calumet Lagoons found that 'least-impacted' sites had the greatest aquatic plant species richness, highest FQI and C values, and highest relative abundance. Lastly, we introduce the concepts necessary for the development of a plant index of biotic integrity. Development of reference conditions is essential to understanding aquatic plant community structure, function, individual health, condition, and abundance. Information on guild development and tolerance definition are also integral to the development of a multi-metric index.

  15. Monitoring aquatic environments with autonomous systems

    DEFF Research Database (Denmark)

    Christensen, Jesper Philip Aagaard

    High frequency measurements from autonomous sensors have become a widely used tool among aquatic scientists. This report focus primarily on the use of ecosystem metabolism based on high frequency oxygen measurements and relates the calculations to spatial variation, biomass of the primary producers...... and environmental variables. The results can be formulated in three main conclusions. 1) Primary production and respiration in stratified lakes are not evenly distributed in the water column. Generally you can expect the net production to decreases with depth as gross primary production (GPP) decreases with depth......, unless it is a very clear lake, while respiration is relatively stable. Metabolism estimates based on data from the epilimnion will only represent a minor proportion of the whole lake metabolism under conditions of strong stratification and high water transparency. At a low depth of the upper mixed layer...

  16. Ecological implications of mercury pollution in aquatic systems

    Energy Technology Data Exchange (ETDEWEB)

    Harriss, R C

    1971-07-01

    Mercury compounds discharged into the environment from industrial, agricultural, and domestic sources have contaminated a substantial portion of the hydrosphere and other parts of the biosphere. Their effects on aquatic ecosystems are a result of their low solubility in water, chemical stability in sediments, and accumulation through biological concentration and magnification in food-webs. The limited data available on the environmental chemistry and toxicity of mercurials prevent the establishment of adequate standards for the protection of biotic communities.

  17. Biological Control of Aquatic Plants with Pathogenic Fungi

    Science.gov (United States)

    1981-01-01

    methods have not been entirely satisfactory because of cost, overall ineffectiveness, or environmental pollution . The energy problem as it relates to...canal system near Cocoa, Florida, and in Palm Beach and Broward counties. With the exception of the Palm Beach and Broward areas, all the waterways in...Marvel’ 11 Phaseolus limensis MacF.* Butter Bean, ’Henderson’ 0 NT P. limensis* Lima Bean, ’Fordhook’ 5 3 d P. limensis* Lima Bean, ’Thorogreen’ 100

  18. Moving beyond a descriptive aquatic toxicology: the value of biological process and trait information.

    Science.gov (United States)

    Segner, Helmut

    2011-10-01

    In order to improve the ability to link chemical exposure to toxicological and ecological effects, aquatic toxicology will have to move from observing what chemical concentrations induce adverse effects to more explanatory approaches, that are concepts which build on knowledge of biological processes and pathways leading from exposure to adverse effects, as well as on knowledge on stressor vulnerability as given by the genetic, physiological and ecological (e.g., life history) traits of biota. Developing aquatic toxicology in this direction faces a number of challenges, including (i) taking into account species differences in toxicant responses on the basis of the evolutionarily developed diversity of phenotypic vulnerability to environmental stressors, (ii) utilizing diversified biological response profiles to serve as biological read across for prioritizing chemicals, categorizing them according to modes of action, and for guiding targeted toxicity evaluation; (iii) prediction of ecological consequences of toxic exposure from knowledge of how biological processes and phenotypic traits lead to effect propagation across the levels of biological hierarchy; and (iv) the search for concepts to assess the cumulative impact of multiple stressors. An underlying theme in these challenges is that, in addition to the question of what the chemical does to the biological receptor, we should give increasing emphasis to the question how the biological receptor handles the chemicals, i.e., through which pathways the initial chemical-biological interaction extends to the adverse effects, how this extension is modulated by adaptive or compensatory processes as well as by phenotypic traits of the biological receptor. 2011 Elsevier B.V. All rights reserved.

  19. 3. A Closed Aquatic System for Space and Earth Application

    Science.gov (United States)

    Slenzka, K.; Duenne, M.; Jastorff, B.; Ranke, J.; Schirmer, M.

    Increased durations in space travel as well as living in extreme environments are requiring reliable life support systems in general and bioregenerative ones in detail. Waste water management, air revitalization and food production are obviously center goals in this research, however, in addition a potential influence by chemicals, drugs etc. released to the closed environment must be considered. On this basis ecotoxicological data become more and more important for CELSS (Closed Ecological Life Support System) development and performance. The experiences gained during the last years in our research group lead to the development of an aquatic habitat, called AquaHab (formerly CBRU), which is a closed, self-sustaining system with a total water volume of 9 liters. In the frame program of a R&D project funded by the state of Bremen and OHB System, AquaHab is under adaptation to become an ecotoxicological research unit containing for example Japanese Medaka or Zebra Fish, amphipods, water snails and water plants. Test runs were standardized and analytical methods were developed. Beside general biological and water chemical parameters, activity measurements of biotransforming enzymes (G6PDH, CytP450-Oxidase, Peroxidase) and cell viability tests as well as residual analysis of the applied substance and respective metabolites were selected as evaluation criteria. In a first series of tests low doses effects of TBT (Tributyltin, 0.1 to 20 μgTBT/l nominal concentration) were analyzed. The AquaHab and data obtained for applied environmental risk assessment will be presented at the assembly.

  20. The development of a classification system for inland aquatic ...

    African Journals Online (AJOL)

    2015-10-05

    Oct 5, 2015 ... 6Department of Plant Sciences, University of the Free State, Qwaqwa Campus, Private .... classification systems for wetlands and other inland aquatic ... of vegetation, soil, inundation and landform features that are ... nised as the fundamental drivers that determine the existence ...... Earth Obs. Remote Sens.

  1. Sublethal effects of tritium on aquatic systems

    International Nuclear Information System (INIS)

    Strand, J.A.; Poston, T.M.

    1982-01-01

    It is the purpose of this continuing study to determine the relative biological effectiveness (RBE) of 3 H-beta irradiation when compared to 60 Co-gamma irradiation applying the relatively radiosensitive immune process of the rainbow trout, Salmo gairdneri. This study is also designed to investigate the nature of latent expression of immune incompetence in trout exposed to 3 H-irradiation during embryogenesis

  2. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  3. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

  4. Utilization of emergent aquatic plants for biomass-energy-systems development

    Energy Technology Data Exchange (ETDEWEB)

    Kresovich, S.; Wagner, C.K.; Scantland, D.A.; Groet, S.S.; Lawhon, W.T.

    1982-02-01

    A review was conducted of the available literature pertaining to the following aspects of emergent aquatic biomass: identification of prospective emergent plant species for management; evaluation of prospects for genetic manipulation; evaluation of biological and environmental tolerances; examination of current production technologies; determination of availability of seeds and/or other propagules, and projections for probable end-uses and products. Species identified as potential candidates for production in biomass systems include Arundo donax, Cyperus papyrus, Phragmites communis, Saccharum spontaneum, Spartina alterniflora, and Typha latifolia. If these species are to be viable candidates in biomass systems, a number of research areas must be further investigated. Points such as development of baseline yield data for managed systems, harvesting conceptualization, genetic (crop) improvement, and identification of secondary plant products require refinement. However, the potential pay-off for developing emergent aquatic systems will be significant if development is successful.

  5. Endocrine Disrupting Chemical Impacts on Aquatic Systems

    Science.gov (United States)

    Jobling, Susan

    2014-07-01

    We often talk about the importance of water, but one area that's often overlooked is the safety of our water supply. How many people actually think about the purity of their water when they turn on the tap? We may have real reason to be concerned because our water delivery systems and treatment technology seem to be stuck in the past, relying on old water treatment and water delivery systems. While these systems still do a great job filtering out particles, parasites and bacteria, they usually fail to remove 21st century contaminants like pesticides, industrial chemicals, lead, pharmaceuticals and arsenic. Indeed our water contains already a whole plethora of things in daily commerce and pharmaceuticals are increasingly showing up in the water supply, including antibiotics, anti-convulsants, mood altering medications and sex hormones. As the world's dependence on chemicals grows, our water supplies will continue to feel the effects, which inevitably will touch every person on this planet...

  6. Are Aquatic Viruses a Biological Archive of Genetic Information from Universe?

    Science.gov (United States)

    Toparceanu, F.; Negoita, Gh. T.; Nita, I. I.; Sava, D.

    2009-04-01

    After 1990, when the viruses were admited as the most abundant lifeforms from aquatic environments, it became obvious that viral lysis had an essential role on release and recycling of nutrients. Studies on cellular cultures and modeling suggest that this is an important quantitative process. The viruses from oceans represent the widest source of genetic diversity on the Earth, uncharacterized yet. The ancient lifeforms records stretching back a million years are locked in ice caps. The trend of glaciers melting as effect of actual climate change will promote the release of ancient viruses from ice caps. The increasing of the freshwater layer led to the replace of some algae species by others. Law-Racovitza Station (69o23'S 76o23'E) from East Antarctica (Larsemann Hills Oasis) offers opportunities to study the Antarctic marine ecosystem, as well as archaic aquatic ecosystems from this area ( 150 lakes and waterways resulted from ice and snow melting during the austral summer). According to Law-Racovitza Station Scientific Program, we are performing studies regarding the effect of climate changes on virus-algae host relationship in these aquatic ecosystems. Phycodnaviruses, that infect the eukaryote algae, are comprised of ancient genes and they are considered a "peek" of genetic diversity useful in biological studies and exobiology regarding the evolution of genetic sequencing. The latest discoveries of the giant aquatic viruses open the unexpected perspectives for understanding the role of viral infection in global ecosystem; beyond the old concept which considered that the viruses were only etiological agents of human, animals and plants illnesses. The aquatic viruses which infect microalgae contain similar genes of other viruses, bacteria, arhebacteria and eukaryotes, all of them being on the same genome. Which is the signification of enormous abundance of viruses and excessive diversity of genetic information encoded by viruses? There is the possibility that

  7. Systems biology at work

    NARCIS (Netherlands)

    Martins Dos Santos, V.A.P.; Damborsky, J.

    2010-01-01

    In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

  8. Plant Systems Biology (editorial)

    Science.gov (United States)

    In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

  9. Formation of organizational and economic mechanism of rational use of aquatic biological resources

    Directory of Open Access Journals (Sweden)

    Stolbov A. G.

    2017-09-01

    Full Text Available The state of fisheries has been researched based on a systematic approach and comprehensive analysis of statistical data, the following issues have been characterized: the catch of aquatic biological resources (ABR, consumption of fish products, problems in the development of the fishing industry (fleet aging, lack of innovative technologies, the proliferation of IUU fishing4 , the high level of retail prices for fish, low degree of processing export products, overshoot "improper objects" of fishing, the gap in aquaculture development, low economic efficiency. To improve the quality of fishery management it has been proposed to form the organizational and economic mechanism of ABR rational use, which should include effective tools for the implementation of management decisions. Instead of the so-called "historical" principle it has been suggested to use the investment principle of quota allocation and rental payments. The basis for management of fishing industry should be scientifically based on the bioeconomic concept of ABR rational use, the essence of which is to preserve the ABR and at the same time to obtain the maximum output of finished products with high added value. To form the organizational and economic mechanism it is necessary to develop a programme of innovative development of the fisheries sector, a calendar programme of upgrading of fishing fleet, wellreasoned differential rates of rent payments for the ABR use, scenarios and graphic organization of work of fishing vessels in specific fishing areas, to form regional financial and industrial clusters, to expand the authority of the Fisheries Agency, to improve corporate social responsibility of the fishing business communities. Modernization of management system for ABR rational use can significantly reduce environmental pollution, ensure the effective delivery of catch to shore, their high-quality processing and the needs of the population in fish products.

  10. Governance of Aquatic Agricultural Systems: Analyzing Representation, Power, and Accountability

    Directory of Open Access Journals (Sweden)

    Blake D. Ratner

    2013-12-01

    Full Text Available Aquatic agricultural systems in developing countries face increasing competition from multiple stakeholders over rights to access and use natural resources, land, water, wetlands, and fisheries, essential to rural livelihoods. A key implication is the need to strengthen governance to enable equitable decision making amidst competition that spans sectors and scales, building capacities for resilience, and for transformations in institutions that perpetuate poverty. In this paper we provide a simple framework to analyze the governance context for aquatic agricultural system development focused on three dimensions: stakeholder representation, distribution of power, and mechanisms of accountability. Case studies from Cambodia, Bangladesh, Malawi/Mozambique, and Solomon Islands illustrate the application of these concepts to fisheries and aquaculture livelihoods in the broader context of intersectoral and cross-scale governance interactions. Comparing these cases, we demonstrate how assessing governance dimensions yields practical insights into opportunities for transforming the institutions that constrain resilience in local livelihoods.

  11. Biophysics and systems biology.

    Science.gov (United States)

    Noble, Denis

    2010-03-13

    Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

  12. Impact of power plants on aquatic systems: a social perspective

    International Nuclear Information System (INIS)

    Coutant, C.C.

    1975-01-01

    Topics discussed are: aquatic effects of thermal electric power stations; legal aspects of water pollution; EPA provisions for levels of thermal discharges to assure protection and propagation of a balanced, indigenous population of shellfish, fish, and wildlife in a body of water; cost benefit analysis of steam electric power effluents; cooling systems and siting of power plants; simulation modeling of population dynamics; and sociological aspects of water pollution

  13. Weed risk assessment for aquatic plants: modification of a New Zealand system for the United States.

    Directory of Open Access Journals (Sweden)

    Doria R Gordon

    Full Text Available We tested the accuracy of an invasive aquatic plant risk assessment system in the United States that we modified from a system originally developed by New Zealand's Biosecurity Program. The US system is comprised of 38 questions that address biological, historical, and environmental tolerance traits. Values associated with each response are summed to produce a total score for each species that indicates its risk of invasion. To calibrate and test this risk assessment, we identified 39 aquatic plant species that are major invaders in the continental US, 31 species that have naturalized but have no documented impacts (minor invaders, and 60 that have been introduced but have not established. These species represent 55 families and span all aquatic plant growth forms. We found sufficient information to assess all but three of these species. When the results are compared to the known invasiveness of the species, major invaders are distinguished from minor and non-invaders with 91% accuracy. Using this approach, the US aquatic weed risk assessment correctly identifies major invaders 85%, and non-invaders 98%, of the time. Model validation using an additional 10 non-invaders and 10 invaders resulted in 100% accuracy for the former, and 80% accuracy for the latter group. Accuracy was further improved to an average of 91% for all groups when the 17% of species with scores of 31-39 required further evaluation prior to risk classification. The high accuracy with which we can distinguish non-invaders from harmful invaders suggests that this tool provides a feasible, pro-active system for pre-import screening of aquatic plants in the US, and may have additional utility for prioritizing management efforts of established species.

  14. Resource Assessment for Microalgal/Emergent Aquatic Biomass Systems in the Arid Southwest: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Vigon, B. W.; Arthur, M. F.; Taft, L. G.; Wagner, C. K.; Lipinsky, E. S.; Litchfield, J. H.; McCandlish, C. D.; Clark, R.

    1982-12-23

    This research project has been designed to facilitate the eventual selection of biomass production systems using aquatic species (microalgal and emergent aquatic plant species (MEAP) which effectively exploit the potentially available resources of the Southwest.

  15. Presence of pesticide residues in water, sediment and biological samples taken from aquatic environments in Honduras

    International Nuclear Information System (INIS)

    Meyer, D.E.

    1999-01-01

    The objective of this study was to detect the presence of persistent pesticides in water, sediment and biological samples taken from aquatic environments in Honduras during the period 1995-98. Additionally, the LC 50 for 2 fungicides and 2 insecticides on post-larval Penaeus vannamei was determined in static water bioassays. A total of 80 water samples, 16 sediment samples and 7 biological samples (fish muscle tissue) were analyzed for detection of organochlorine and organophosphate pesticide residues. The results of sample analyses indicate a widespread contamination of Honduran continental and coastal waters with organochlorine pesticides. Most detections were of low ( 50 values and were therefore found to be much more toxic to the post-larval shrimp than the fungicides tridemorph and propiconazole. (author)

  16. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  17. Integrated monitoring and information systems for managing aquatic invasive species in a changing climate

    Science.gov (United States)

    Lee, Henry; Reusser, Deborah A.; Olden, Julian D.; Smith, Scott S.; Graham, Jim; Burkett, Virginia; Dukes, Jeffrey S.; Piorkowski, Robert J.; Mcphedran, John

    2008-01-01

    Changes in temperature, precipitation, and other climatic drivers and sea-level rise will affect populations of existing native and non-native aquatic species and the vulnerability of aquatic environments to new invasions. Monitoring surveys provide the foundation for assessing the combined effects of climate change and invasions by providing baseline biotic and environmental conditions, although the utility of a survey depends on whether the results are quantitative or qualitative, and other design considerations. The results from a variety of monitoring programs in the United States are available in integrated biological information systems, although many include only non-native species, not native species. Besides including natives, we suggest these systems could be improved through the development of standardized methods that capture habitat and physiological requirements and link regional and national biological databases into distributed Web portals that allow drawing information from multiple sources. Combining the outputs from these biological information systems with environmental data would allow the development of ecological-niche models that predict the potential distribution or abundance of native and non-native species on the basis of current environmental conditions. Environmental projections from climate models can be used in these niche models to project changes in species distributions or abundances under altered climatic conditions and to identify potential high-risk invaders. There are, however, a number of challenges, such as uncertainties associated with projections from climate and niche models and difficulty in integrating data with different temporal and spatial granularity. Even with these uncertainties, integration of biological and environmental information systems, niche models, and climate projections would improve management of aquatic ecosystems under the dual threats of biotic invasions and climate change

  18. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    Unger, Kristian

    2014-01-01

    Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

  19. Optimization of analytical techniques to characterize antibiotics in aquatic systems

    International Nuclear Information System (INIS)

    Al Mokh, S.

    2013-01-01

    Antibiotics are considered as pollutants when they are present in aquatic ecosystems, ultimate receptacles of anthropogenic substances. These compounds are studied as their persistence in the environment or their effects on natural organisms. Numerous efforts have been made worldwide to assess the environmental quality of different water resources for the survival of aquatic species, but also for human consumption and health risk related. Towards goal, the optimization of analytical techniques for these compounds in aquatic systems remains a necessity. Our objective is to develop extraction and detection methods for 12 molecules of aminoglycosides and colistin in sewage treatment plants and hospitals waters. The lack of analytical methods for analysis of these compounds and the deficiency of studies for their detection in water is the reason for their study. Solid Phase Extraction (SPE) in classic mode (offline) or online followed by Liquid Chromatography analysis coupled with Mass Spectrometry (LC/MS/MS) is the most method commonly used for this type of analysis. The parameters are optimized and validated to ensure the best conditions for the environmental analysis. This technique was applied to real samples of wastewater treatment plants in Bordeaux and Lebanon. (author)

  20. Biological Diversity, Ecological Health and Condition of Aquatic Assemblages at National Wildlife Refuges in Southern Indiana, USA

    Directory of Open Access Journals (Sweden)

    Thomas Simon

    2015-01-01

    Full Text Available The National Wildlife Refuge system is a vital resource for the protection and conservation of biodiversity and biological integrity in the United States. Surveys were conducted to determine the spatial and temporal patterns of fish, macroinvertebrate, and crayfish populations in two watersheds that encompass three refuges in southern Indiana. The Patoka River National Wildlife Refuge had the highest number of aquatic species with 355 macroinvertebrate taxa, six crayfish species, and 82 fish species, while the Big Oaks National Wildlife Refuge had 163 macroinvertebrate taxa, seven crayfish species, and 37 fish species. The Muscatatuck National Wildlife Refuge had the lowest diversity of macroinvertebrates with 96 taxa and six crayfish species, while possessing the second highest fish species richness with 51 species. Habitat quality was highest in the Muscatatuck River drainage with increased amounts of forested habitats compared to the Patoka River drainage. Biological integrity of the three refuges ranked the Patoka NWR as the lowest biological integrity (mean IBI reach scores = 35 IBI points, while Big Oaks had the highest biological integrity (mean IBI reach score = 41 IBI points. The Muscatatuck NWR had a mean IBI reach score of 31 during June, which seasonally increased to a mean of 40 IBI points during summer. Watershed IBI scores and habitat condition were highest in the Big Oaks NWR.

  1. Biological Diversity, Ecological Health and Condition of Aquatic Assemblages at National Wildlife Refuges in Southern Indiana, USA

    Science.gov (United States)

    Morris, Charles C.; Robb, Joseph R.; McCoy, William

    2015-01-01

    Abstract The National Wildlife Refuge system is a vital resource for the protection and conservation of biodiversity and biological integrity in the United States. Surveys were conducted to determine the spatial and temporal patterns of fish, macroinvertebrate, and crayfish populations in two watersheds that encompass three refuges in southern Indiana. The Patoka River National Wildlife Refuge had the highest number of aquatic species with 355 macroinvertebrate taxa, six crayfish species, and 82 fish species, while the Big Oaks National Wildlife Refuge had 163 macroinvertebrate taxa, seven crayfish species, and 37 fish species. The Muscatatuck National Wildlife Refuge had the lowest diversity of macroinvertebrates with 96 taxa and six crayfish species, while possessing the second highest fish species richness with 51 species. Habitat quality was highest in the Muscatatuck River drainage with increased amounts of forested habitats compared to the Patoka River drainage. Biological integrity of the three refuges ranked the Patoka NWR as the lowest biological integrity (mean IBI reach scores = 35 IBI points), while Big Oaks had the highest biological integrity (mean IBI reach score = 41 IBI points). The Muscatatuck NWR had a mean IBI reach score of 31 during June, which seasonally increased to a mean of 40 IBI points during summer. Watershed IBI scores and habitat condition were highest in the Big Oaks NWR. PMID:25632261

  2. Logical analysis of biological systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian

    2005-01-01

    R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

  3. Biological assessment of aquatic pollution: a review, with emphasis on plants as biomonitors.

    Science.gov (United States)

    Doust, J L; Schmidt, M; Doust, L L

    1994-05-01

    In a number of disciplines including ecology, ecotoxicology, water quality management, water resource management, fishery biology etc., there is significant interest in the testing of new materials, environmental samples (of water or sediments) and specific sites, in terms of their effects on biota. In the first instance, we consider various sources of aquatic pollution, sources typically associated with developed areas of the world. Historically, much water quality assessment has been performed by researchers with a background in chemistry or engineering, thus chemical analysis was a dominant form of assessment. However, chemical analyses, particularly of such materials as organochlorines and polyaromatic hydrocarbons can be expensive, and local environmental factors may cause the actual exposure of an organism to be little correlated with chemical concentrations in the surrounding water or sediments. To a large extent toxicity testing has proceeded independently of environmental quality assessment in situ, and the work has been done by different, and differently-trained researchers. Here we attempt to bring together the various forms of biological assessment of aquatic pollution, because in our opinion it is worth developing a coherent framework for the application of this powerful tool. Biotic assessment in its most primitive form involves the simple tracking of mortality in exposed organisms. However, in most natural environments it is extended, chronic exposure to contaminants that has the most wide-ranging and irreversible repercussions--thus measures of sub-lethal impairment are favoured. From an ecological standpoint, it is most valuable to assess ecological effects by direct study of in situ contaminant body burdens and impairment of growth and reproduction compared with 'clean' sites. A distinction is made here between bioindication and biomonitoring, and a case is made for including aquatic macrophytes (angiosperms) in studies of contaminant levels and

  4. Topical report on sources and systems for aquatic plant biomass as an energy resource

    Energy Technology Data Exchange (ETDEWEB)

    Goldman, J.C.; Ryther, J.H.; Waaland, R.; Wilson, E.H.

    1977-10-21

    Background information is documented on the mass cultivation of aquatic plants and systems design that is available from the literature and through consultation with active research scientists and engineers. The biology of microalgae, macroalgae, and aquatic angiosperms is discussed in terms of morphology, life history, mode of existence, and ecological significance, as they relate to cultivation. The requirements for growth of these plants, which are outlined in the test, suggest that productivity rates are dependent primarily on the availability of light and nutrients. It is concluded that the systems should be run with an excess of nutrients and with light as the limiting factor. A historical review of the mass cultivation of aquatic plants describes the techniques used in commercial large-scale operations throughout the world and recent small-scale research efforts. This review presents information on the biomass yields that have been attained to date in various geographical locations with different plant species and culture conditions, emphasizing the contrast between high yields in small-scale operations and lower yields in large-scale operations.

  5. Geographic information system in marine biology: Way for sustainable utilization of living resources

    Digital Repository Service at National Institute of Oceanography (India)

    Chavan, V.S.; Sreepada, R.A.

    Sustainable utilization of aquatic living resources needs accurate assessment. This stress the need for use of Geographic Information System (GIS). In the recent past interest has been generated for use of GIS in various areas of biological...

  6. Polyvinylpyrrolidone and arsenic-induced changes in biological responses of model aquatic organisms exposed to iron-based nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Llaneza, Verónica [University of Florida, Engineering School of Sustainable Infrastructure and Environment, Department of Environmental Engineering Sciences (United States); Rodea-Palomares, Ismael [Univ. Autonoma de Madrid, Dept. de Biologia, Facultad de Ciencias (Spain); Zhou, Zuo [University of Florida, Engineering School of Sustainable Infrastructure and Environment, Department of Environmental Engineering Sciences (United States); Rosal, Roberto [Univ. de Alcalá, Dept. de Ingeniería Química (Spain); Fernández-Pina, Francisca [Univ. Autonoma de Madrid, Dept. de Biologia, Facultad de Ciencias (Spain); Bonzongo, Jean-Claude J., E-mail: bonzongo@ufl.edu [University of Florida, Engineering School of Sustainable Infrastructure and Environment, Department of Environmental Engineering Sciences (United States)

    2016-08-15

    The efficiency of zero-valent iron particles used in the remediation of contaminated groundwater has, with the emergence of nanotechnology, stimulated interest on the use of nano-size particles to take advantage of high-specific surface area and reactivity characteristics of nanoparticles (NPs). Accordingly, engineered iron-NPs are among the most widely used nanomaterials for in situ remediation. However, while several ecotoxicity studies have been conducted to investigate the adverse impacts of these NPs on aquatic organisms, research on the implications of spent iron-based NPs is lacking. In this study, a comparative approach is used, in which the biological effects of three iron-based NPs (Fe{sub 3}O{sub 4} and γ-Fe{sub 2}O{sub 3} NPs with particle sizes ranging from 20 to 50 nm, and Fe{sup 0}-NPs with an average particle size of 40 nm) on Raphidocelis subcapitata (formely known as Pseudokirchneriella subcapitata) and Daphnia magna were investigated using both as-prepared and pollutant-doped Fe-based NPs. For the latter, arsenic (As) was used as example sorbed pollutant. The results show that improved degree of NP dispersion by use of polyvinylpyrrolidone overlapped with both increased arsenic adsorption capacity and toxicity to the tested organisms. For R. subcapitata, Fe-oxide NPs were more toxic than Fe{sup 0}-NPs, due primarily to differences in the degree of NPs aggregation and ability to produce reactive oxygen species. For the invertebrate D. magna, a similar trend of biological responses was observed, except that sorption of As to Fe{sup 0}-NPs significantly increased the toxic response when compared to R. subcapitata. Overall, these findings point to the need for research on downstream implications of NP-pollutant complexes generated during water treatment by injection of NPs into aquatic systems.

  7. Polyvinylpyrrolidone and arsenic-induced changes in biological responses of model aquatic organisms exposed to iron-based nanoparticles

    International Nuclear Information System (INIS)

    Llaneza, Verónica; Rodea-Palomares, Ismael; Zhou, Zuo; Rosal, Roberto; Fernández-Pina, Francisca; Bonzongo, Jean-Claude J.

    2016-01-01

    The efficiency of zero-valent iron particles used in the remediation of contaminated groundwater has, with the emergence of nanotechnology, stimulated interest on the use of nano-size particles to take advantage of high-specific surface area and reactivity characteristics of nanoparticles (NPs). Accordingly, engineered iron-NPs are among the most widely used nanomaterials for in situ remediation. However, while several ecotoxicity studies have been conducted to investigate the adverse impacts of these NPs on aquatic organisms, research on the implications of spent iron-based NPs is lacking. In this study, a comparative approach is used, in which the biological effects of three iron-based NPs (Fe_3O_4 and γ-Fe_2O_3 NPs with particle sizes ranging from 20 to 50 nm, and Fe"0-NPs with an average particle size of 40 nm) on Raphidocelis subcapitata (formely known as Pseudokirchneriella subcapitata) and Daphnia magna were investigated using both as-prepared and pollutant-doped Fe-based NPs. For the latter, arsenic (As) was used as example sorbed pollutant. The results show that improved degree of NP dispersion by use of polyvinylpyrrolidone overlapped with both increased arsenic adsorption capacity and toxicity to the tested organisms. For R. subcapitata, Fe-oxide NPs were more toxic than Fe"0-NPs, due primarily to differences in the degree of NPs aggregation and ability to produce reactive oxygen species. For the invertebrate D. magna, a similar trend of biological responses was observed, except that sorption of As to Fe"0-NPs significantly increased the toxic response when compared to R. subcapitata. Overall, these findings point to the need for research on downstream implications of NP-pollutant complexes generated during water treatment by injection of NPs into aquatic systems.

  8. Polyvinylpyrrolidone and arsenic-induced changes in biological responses of model aquatic organisms exposed to iron-based nanoparticles

    Science.gov (United States)

    Llaneza, Verónica; Rodea-Palomares, Ismael; Zhou, Zuo; Rosal, Roberto; Fernández-Pina, Francisca; Bonzongo, Jean-Claude J.

    2016-08-01

    The efficiency of zero-valent iron particles used in the remediation of contaminated groundwater has, with the emergence of nanotechnology, stimulated interest on the use of nano-size particles to take advantage of high-specific surface area and reactivity characteristics of nanoparticles (NPs). Accordingly, engineered iron-NPs are among the most widely used nanomaterials for in situ remediation. However, while several ecotoxicity studies have been conducted to investigate the adverse impacts of these NPs on aquatic organisms, research on the implications of spent iron-based NPs is lacking. In this study, a comparative approach is used, in which the biological effects of three iron-based NPs (Fe3O4 and γ-Fe2O3 NPs with particle sizes ranging from 20 to 50 nm, and Fe0-NPs with an average particle size of 40 nm) on Raphidocelis subcapitata (formely known as Pseudokirchneriella subcapitata) and Daphnia magna were investigated using both as-prepared and pollutant-doped Fe-based NPs. For the latter, arsenic (As) was used as example sorbed pollutant. The results show that improved degree of NP dispersion by use of polyvinylpyrrolidone overlapped with both increased arsenic adsorption capacity and toxicity to the tested organisms. For R. subcapitata, Fe-oxide NPs were more toxic than Fe0-NPs, due primarily to differences in the degree of NPs aggregation and ability to produce reactive oxygen species. For the invertebrate D. magna, a similar trend of biological responses was observed, except that sorption of As to Fe0-NPs significantly increased the toxic response when compared to R. subcapitata. Overall, these findings point to the need for research on downstream implications of NP-pollutant complexes generated during water treatment by injection of NPs into aquatic systems.

  9. Monitoring of Aquatic Biota in Intensive Fish Farming System

    Directory of Open Access Journals (Sweden)

    Lukáš Mareš

    2017-01-01

    Full Text Available The aim of the study was to conduct a detailed research of aquatic invertebrates in the intensive breeding system of salmonid fish in order to determine the taxonomic composition of the community and its seasonal dynamics, and to identify those species that may be hosts of parasitic disease agents. To date, this issue has not been studied at all in the Czech Republic. Monitoring was conducted on the Danish type recirculation system near the municipality of Pravíkov in the Highlands of the Czech Republic from April till November 2015. A total of 9 series of samples were taken. Macrozoobenthos was evaluated in terms of taxonomic composition and abundance. Basic physicochemical properties of water (temperature, oxygen concentration, pH and conductivity were also measured. In total, 69 taxa of aquatic invertebrates were noted, with the wall being the richest with a mean abundance of 756 pcs/m2. Permanent groups predominated; the most numerous group was the subphylum Crustaceae, represented by a single species, Asellus aquticus.

  10. Aquarium Viromes: Viromes of Human-Managed Aquatic Systems

    Science.gov (United States)

    Kim, Yiseul; Van Bonn, William; Aw, Tiong G.; Rose, Joan B.

    2017-01-01

    An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment. PMID:28713358

  11. Aquarium Viromes: Viromes of Human-Managed Aquatic Systems

    Directory of Open Access Journals (Sweden)

    Yiseul Kim

    2017-06-01

    Full Text Available An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems. Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment.

  12. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  13. Bioaccumulation in aquatic systems: methodological approaches, monitoring and assessment

    DEFF Research Database (Denmark)

    Schäfer, Sabine; Buchmeier, Georgia; Claus, Evelyn

    2015-01-01

    , various scientific and regulatory aspects of bioaccumulation in aquatic systems and the relevant critical issues are discussed. Monitoring chemical concentrations in biota can be used for compliance checking with regulatory directives, for identification of chemical sources or event-related environmental...... temporal and geographical range. Bioaccumulation is also assessed for regulation of chemicals of environmental concern whereby mainly data from laboratory studies on fish bioaccumulation are used. Field data can, however, provide additional important information for regulators. Strategies...... for bioaccumulation assessment still need to be harmonised for different regulations and groups of chemicals. To create awareness for critical issues and to mutually benefit from technical expertise and scientific findings, communication between risk assessment and monitoring communities needs to be improved...

  14. Aquatic productivity: isotopic tracer aided studies of chemical-biological interactions

    International Nuclear Information System (INIS)

    1975-01-01

    Inland waters subject to the accumulation and effects of trace contaminants are discussed and a review of international research projects on this subject is given. The following aspects are specially discussed: aquatic nitrogen and agriculture; aquatic ecosystems in arid zones of developing countries; micronutrients in aquatic ecosystems; microbiological activity (''primary production''); enzymic methods in water quality determinations. Recommendations of the Joint FAO/IAEA Advisory Group for measures to be taken in order to protect water quality are also given

  15. Electromagnetic fields in biological systems

    National Research Council Canada - National Science Library

    Lin, James C

    2012-01-01

    "Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

  16. Partial coupling and differential regulation of biologically and photochemically labile dissolved organic carbon across boreal aquatic networks

    Science.gov (United States)

    Lapierre, J.-F.; del Giorgio, P. A.

    2014-10-01

    Despite the rapidly increasing volume of research on the biological and photochemical degradation of DOC (dissolved organic carbon) in aquatic environments, little is known of the large-scale patterns in biologically and photochemically degradable DOC (BDOC and PDOC, respectively) in continental watersheds, and on the links that exist between these two key properties that greatly influence the flow of carbon from continents to oceans. Here we explored the patterns in the concentrations and proportions of BDOC and PDOC across hundreds of boreal lakes, rivers and wetlands spanning a large range of system trophic status and terrestrial influence, and compared the drivers of these two reactive pools of DOC at the landscape level. Using standardized incubations of natural waters, we found that the concentrations of BDOC and PDOC covaried across all systems studied but were nevertheless related to different pools of dissolved organic matter (DOM; identified by fluorescence analyses) in ambient waters. Concentrations of nutrients and protein-like fluorescent DOM (FDOM) explained nearly half of the variation in BDOC, whereas PDOC was exclusively predicted by DOM optical properties, consistent with the photochemical degradability of specific FDOM pools that we experimentally determined. The concentrations of colored DOM (CDOM), which we use here as a proxy of terrestrial influence, almost entirely accounted for the observed relationship between FDOM and the concentrations of both BDOC and PDOC. The concentrations of CDOM and of the putative biolabile fluorescence component shifted from complete decoupling in clear-water environments to strong coupling in darker streams and wetlands. This suggests a baseline autochthonous BDOC pool fueled by internal production that is gradually overwhelmed by land-derived BDOC as terrestrial influence increases across landscape gradients. The importance of land as a major source of both biologically and photochemically degradable DOC for

  17. Partial coupling and differential regulation of biologically and photo-chemically labile dissolved organic carbon across boreal aquatic networks

    Science.gov (United States)

    Lapierre, J.-F.; del Giorgio, P. A.

    2014-05-01

    Despite the rapidly increasing volume of research on the biological and photochemical degradation of DOC in aquatic environments, little is known on the large-scale patterns in biologically and photo-chemically degradable DOC (Bd-DOC and Pd-DOC, respectively) in continental watersheds, and on the links that exist between these two key properties that greatly influence the flow of carbon from continents to oceans. Here we explore the patterns of Bd- and Pd-DOC across hundreds of boreal lakes, rivers and wetlands spanning a large range of system trophy and terrestrial influence, and compared the drivers of these two reactive pools of DOC at the landscape level. Using standardized incubations of natural waters, we found that the concentrations of Bd- and Pd-DOC co-varied across all systems studied but were nevertheless related to different pools of dissolved organic matter (DOM, identified by fluorescence analyses) in ambient waters. A combination of nutrients and protein-like DOM explained nearly half of the variation in Bd-DOC, whereas Pd-DOC was exclusively predicted by DOM optical properties, consistent with the photochemical degradability of specific fluorescent DOM (FDOM) pools that we experimentally determined. The concentrations of colored DOM (CDOM), a proxy of terrestrial influence, almost entirely accounted for the observed relationship between FDOM and the concentrations of both Bd- and Pd-DOC. The concentrations of CDOM and of the putative bio-labile fluorescence component shifted from complete decoupling in clear-water environments to strong coupling in browner streams and wetlands. This suggests a baseline autochthonous Bd-DOC pool fuelled by internal production that is gradually overwhelmed by land-derived Bd-DOC as terrestrial influence increases across landscape gradients. The importance of land as a major source of both biologically and photo-chemically degradable DOC for continental watersheds resulted in a partial coupling of those carbon pools in

  18. Excited states in biological systems

    International Nuclear Information System (INIS)

    Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

    1979-01-01

    Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

  19. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak

    2005-01-01

    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  20. Mapping biological systems to network systems

    CERN Document Server

    Rathore, Heena

    2016-01-01

    The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

  1. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

    2004-01-01

    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  2. Systems biology and medicine

    Indian Academy of Sciences (India)

    work could potentially provide us with ways to identify drug ... appropriately balance cause, effect, and context of a given clinical ... would not provide answers/solutions to multitude of tasks that were ... a major challenge of contemporary biology is to embark on an ... nificantly govern the life and responsiveness of cells.

  3. Environmental state of aquatic systems in the Selenga River basin

    Science.gov (United States)

    Shinkareva, Galina; Lychagin, Mikhail

    2013-04-01

    The transboundary river system of Selenga is the biggest tributary of Lake Baikal (about 50 % of the total inflow) which is the largest freshwater reservoir in the world. It originates in the mountainous part of Mongolia and then drains into Russia. There are numerous industries and agricultural activities within the Selenga drainage basin that affect the environmental state of the river aquatic system. The main source of industrial waste in the Republic of Buryatia (Russia) is mining and in Mongolia it is mainly gold mining. Our study aimed to determine the present pollutant levels and main features of their spatial distribution in water, suspended matter, bottom sediments and water plants in the Selenga basin. The results are based on materials of the 2011 (July-August) field campaign carried out both in Russian and Mongolian part of the basin. The study revealed rather high levels of dissolved Fe, Al, Mn, Zn, Cu and Mo in the Selenga River water which often are higher than maximum permissible concentrations for water fishery in Russia. In Russian part of the basin most contrast distribution is found for W and Mo, which is caused by mineral deposits in this area. The study showed that Mo and Zn migrate mainly in dissolved form, since more than 70% of Fe, Al, and Mn are bound to the suspended solids. Suspended sediments in general are enriched by As, Cd and Pb in relation to the lithosphere averages. Compared to the background values rather high contents of Mo, Cd, and Mn were found in suspended matter of Selenga lower Ulan-Ude town. Transboundary transport of heavy metals from Mongolia is going both in dissolved and suspended forms. From Mongolia in diluted form Selenga brings a significant amount of Al, Fe, Mn, Zn, Cu and Mo. Suspended solids are slightly enriched with Pb, Cu, and Mn, in higher concentration - Mo. The study of the Selenga River delta allowed determining biogeochemical specialization of the region: aquatic plants accumulate Mn, Fe, Cu, Cd, and to

  4. Quantum Effects in Biological Systems

    CERN Document Server

    2016-01-01

    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  5. Heuristic Strategies in Systems Biology

    Directory of Open Access Journals (Sweden)

    Fridolin Gross

    2016-06-01

    Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

  6. Freshwater Mussels as Biological Sensors and Cyclers of Aquatic Nitrogen Constituents: An Experimental Investigation

    Science.gov (United States)

    Kruger, A.; Just, C. L.; Mudumbai, R.; Dasgupta, S.; Newton, T. J.; Durst, J.; Boddicker, M. D.; Diken, M. B.; Bril, J.; Baidoo-Williams, H. E.

    2011-12-01

    One of the most extensive manifestations of anthropogenic mismanagement of nitrogen is eutrophication of the Gulf of Mexico. Leaching and runoff transport nitrate compounds-excess agricultural fertilizer and animal waste-via the Mississippi River to the Gulf of Mexico. Phytoplankton then multiplies exponentially, and consumes most of the dissolved oxygen. This hypoxia kills fish and other organisms, leading to so-called dead zones in the Gulf that can cover 6,000-7,000 square miles. Dead zone mitigation plans call for coupling management actions with enhanced monitoring, modeling, and research on nitrogen delivery to, as well as processing within, the Mississippi River. Our vision is to create a biosensor network of native freshwater mussels in a major river to monitor, comprehend, and ultimately model key components of the nitrogen cycle. Native freshwater mussels are a guild of long-lived, suspension feeding bivalves that perform important ecological functions in aquatic systems. Mussels can influence nutrient cycling by transferring nutrients from the water column to the riverbed. A major problem for environmental scientists is that relatively little is known about the diurnal behaviors of freshwater mussels or the impacts these behaviors may have on the aquatic nitrogen cycle. Our multidisciplinary team is performing a series of laboratory experiments exploring the feasibility of using freshwater mussels as sensors of and capacitors for nitrates. For sensing, we place Hall-effect sensors on mussels to monitor the rhythmic opening and closing of their valves (gape). One shortcoming of previous work is that mussels were monitored in artificial conditions: glued fast in laboratory flumes, or tethered in constrained settings. To overcome this shortcoming, our team has built a mussel microhabitat with a constant river water feed stock, solar simulator, and a variety of water chemistry sensor. A main thrust of our work is to develop the technology to monitor mussel

  7. Compartmental study of biological systems

    International Nuclear Information System (INIS)

    Moretti, J.L.

    1975-01-01

    The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

  8. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

  9. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

  10. Informing biological design by integration of systems and synthetic biology.

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Aquatic toxicology: past, present, and prospects.

    OpenAIRE

    Pritchard, J B

    1993-01-01

    Aquatic organisms have played important roles as early warning and monitoring systems for pollutant burdens in our environment. However, they have significant potential to do even more, just as they have in basic biology where preparations like the squid axon have been essential tools in establishing physiological and biochemical mechanisms. This review provides a brief summary of the history of aquatic toxicology, focusing on the nature of aquatic contaminants, the levels of contamination in...

  12. Development trend of radiation biology research-systems radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

    Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

  13. Next generation framework for aquatic modeling of the Earth System

    Science.gov (United States)

    Fekete, B. M.; Wollheim, W. M.; Wisser, D.; Vörösmarty, C. J.

    2009-03-01

    Earth System model development is becoming an increasingly complex task. As scientists attempt to represent the physical and bio-geochemical processes and various feedback mechanisms in unprecedented detail, the models themselves are becoming increasingly complex. At the same time, the complexity of the surrounding IT infrastructure is growing as well. Earth System models must manage a vast amount of data in heterogeneous computing environments. Numerous development efforts are on the way to ease that burden and offer model development platforms that reduce IT challenges and allow scientists to focus on their science. While these new modeling frameworks (e.g. FMS, ESMF, CCA, OpenMI) do provide solutions to many IT challenges (performing input/output, managing space and time, establishing model coupling, etc.), they are still considerably complex and often have steep learning curves. The Next generation Framework for Aquatic Modeling of the Earth System (NextFrAMES, a revised version of FrAMES) have numerous similarities to those developed by other teams, but represents a novel model development paradigm. NextFrAMES is built around a modeling XML that lets modelers to express the overall model structure and provides an API for dynamically linked plugins to represent the processes. The model XML is executed by the NextFrAMES run-time engine that parses the model definition, loads the module plugins, performs the model I/O and executes the model calculations. NextFrAMES has a minimalistic view representing spatial domains and treats every domain (regardless of its layout such as grid, network tree, individual points, polygons, etc.) as vector of objects. NextFrAMES performs computations on multiple domains and interactions between different spatial domains are carried out through couplers. NextFrAMES allows processes to operate at different frequencies by providing rudimentary aggregation and disaggregation facilities. NextFrAMES was designed primarily for

  14. Visualizing Terrestrial and Aquatic Systems in 3D - in IEEE VisWeek 2014

    Science.gov (United States)

    The need for better visualization tools for environmental science is well documented, and the Visualization for Terrestrial and Aquatic Systems project (VISTAS) aims to both help scientists produce effective environmental science visualizations and to determine which visualizatio...

  15. Dynamic speciation analysis and bioavailability of metals in aquatic systems

    NARCIS (Netherlands)

    Leeuwen, van H.P.; Town, R.M.; Buffle, J.; Cleven, R.F.M.J.; Davison, W.; Puy, J.; Riemsdijk, van W.H.; Sigg, L.

    2005-01-01

    Dynamic metal speciation analysis in aquatic ecosystems is emerging as a powerful basis for development of predictions of bioavailability and reliable risk assessment strategies. A given speciation sensor is characterized by an effective time scale or kinetic window that defines the measurable metal

  16. From systems biology to systems biomedicine.

    Science.gov (United States)

    Antony, Paul M A; Balling, Rudi; Vlassis, Nikos

    2012-08-01

    Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Inverse problems in systems biology

    International Nuclear Information System (INIS)

    Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

    2009-01-01

    Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

  18. Nanoscale technology in biological systems

    CERN Document Server

    Greco, Ralph S; Smith, R Lane

    2004-01-01

    Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

  19. Molecular ecology of aquatic microbes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    Abstracts of reports are presented from a meeting on Molecular Ecology of Aquatic Microbes. Topics included: opportunities offered to aquatic ecology by molecular biology; the role of aquatic microbes in biogeochemical cycles; characterization of the microbial community; the effect of the environment on aquatic microbes; and the targeting of specific biological processes.

  20. Workshop Introduction: Systems Biology and Biological Models

    Science.gov (United States)

    As we consider the future of toxicity testing, the importance of applying biological models to this problem is clear. Modeling efforts exist along a continuum with respect to the level of organization (e.g. cell, tissue, organism) linked to the resolution of the model. Generally,...

  1. Abiotic variability among different aquatic systems of the central Amazon floodplain during drought and flood events.

    Science.gov (United States)

    Affonso, A G; Queiroz, H L; Novo, E M L M

    2015-11-01

    This paper examines water properties from lakes, (depression lakes, sensu Junk et al., 2012), channels (scroll lakes with high connectivity, sensu Junk et al., 2012) and paleo-channels (scroll lakes with low connectivity-sensu Junk et al., 2012, locally called ressacas) located in Mamirauá Sustainable Development Reserve, in Central Amazon floodplain, Amazonas, Brazil. We analysed surface temperature, conductivity, pH, dissolved oxygen, turbidity, transparency, suspended inorganic and organic matter, chlorophyll-a, pheophytin, total nitrogen, total phosphorus, organic and inorganic carbon in 2009 high water phase, 2009 and 2010 low water phases. Multivariate statistical analyses of 24 aquatic systems (6 ressacas, 12 lakes and 6 channels, 142 samples) were applied to the variables in order to: 1) quantify differences among aquatic system types; 2) assess how those differences are affected in the different phases of the hydrological year. First, we analysed the entire set of variables to test for differences among phases of the hydrological year and types of aquatic systems using a PERMANOVA two-way crossed design. The results showed that the all measured limnological variables are distinct regarding both factors: types of aquatic systems and hydrological phases. In general, the magnitude and amplitude of all variables were higher in the low water phase than in the high water phase, except for water transparency in all aquatic system's types. PERMANOVA showed that the differences between aquatic system's types and hydrological phases of all variables were highly significant for both main factors (type and phase) and for the type x phase interaction. Limnological patterns of Amazon floodplain aquatic systems are highly dynamic, dependent on the surrounding environment, flood pulse, main river input and system type. These patterns show how undisturbed systems respond to natural variability in such a diverse environment, and how distinct are those aquatic systems

  2. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  3. Systems biology: the reincarnation of systems theory applied in biology?

    Science.gov (United States)

    Wolkenhauer, O

    2001-09-01

    With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

  4. Abiotic variability among different aquatic systems of the central Amazon floodplain during drought and flood events

    Directory of Open Access Journals (Sweden)

    A. G. Affonso

    Full Text Available Abstract This paper examines water properties from lakes, (depression lakes, sensu Junk et al., 2012, channels (scroll lakes with high connectivity, sensu Junk et al., 2012 and paleo-channels (scroll lakes with low connectivity-sensu Junk et al., 2012, locally called ressacas located in Mamirauá Sustainable Development Reserve, in Central Amazon floodplain, Amazonas, Brazil. We analysed surface temperature, conductivity, pH, dissolved oxygen, turbidity, transparency, suspended inorganic and organic matter, chlorophyll-a, pheophytin, total nitrogen, total phosphorus, organic and inorganic carbon in 2009 high water phase, 2009 and 2010 low water phases. Multivariate statistical analyses of 24 aquatic systems (6 ressacas, 12 lakes and 6 channels, 142 samples were applied to the variables in order to: 1 quantify differences among aquatic system types; 2 assess how those differences are affected in the different phases of the hydrological year. First, we analysed the entire set of variables to test for differences among phases of the hydrological year and types of aquatic systems using a PERMANOVA two-way crossed design. The results showed that the all measured limnological variables are distinct regarding both factors: types of aquatic systems and hydrological phases. In general, the magnitude and amplitude of all variables were higher in the low water phase than in the high water phase, except for water transparency in all aquatic system’s types. PERMANOVA showed that the differences between aquatic system’s types and hydrological phases of all variables were highly significant for both main factors (type and phase and for the type x phase interaction. Limnological patterns of Amazon floodplain aquatic systems are highly dynamic, dependent on the surrounding environment, flood pulse, main river input and system type. These patterns show how undisturbed systems respond to natural variability in such a diverse environment, and how distinct are

  5. Tunable promoters in systems biology

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

    2005-01-01

    The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

  6. Systems Biology of Industrial Microorganisms

    Science.gov (United States)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  7. Radioactivity in the Canadian aquatic environment

    International Nuclear Information System (INIS)

    1983-01-01

    Sources of radionuclides arising from natural anthropogenic processes as well as technologically enhanced natural radiation are discussed. Transport, distribution and behaviour of these radionuclides in aquatic systems are influenced by physical, chemical, biological and geological processes and conditions in freshwater and marine environments. Dosimetry of aquatic organisms, as well as various methods of measuring dose rate are presented. Effects of ionizing radiation (acute and chronic exposure) on aquatic organisms, populations and ecosystems are reviewed. This review covers the entire spectrum of the aquatic environment. Results of many studies are summarized. 300+ refs

  8. Systems Biology-an interdisciplinary approach.

    Science.gov (United States)

    Friboulet, Alain; Thomas, Daniel

    2005-06-15

    System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

  9. Mathematical methods in systems biology.

    Science.gov (United States)

    Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

    2016-12-01

    The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

  10. Sources and remediation for mercury contamination in aquatic systems--a literature review

    International Nuclear Information System (INIS)

    Wang, Qianrui; Kim, Daekeun; Dionysiou, Dionysios D.; Sorial, George A.; Timberlake, Dennis

    2004-01-01

    Sources of mercury contamination in aquatic systems were studied in a comprehensive literature review. The results show that the most important anthropogenic sources of mercury pollution in aquatic systems are: (1) atmospheric deposition, (2) erosion, (3) urban discharges, (4) agricultural materials, (5) mining, and (6) combustion and industrial discharges. Capping and dredging are two possible remedial approaches to mercury contamination in aquatic systems, and natural attenuation is a passive decontamination alternative. Capping seems to be an economical and effective remedial approach to mercury-contaminated aquatic systems. Dredging is an expensive remedial approach. However, for heavily polluted systems, dredging may be more effective. Natural attenuation, involving little or no cost, is a possible and very economical choice for less contaminated sites. Proper risk assessment is necessary to evaluate the effectiveness of remedial and passive decontamination methods as well as their potential adverse environmental effects. Modeling tools have a bright future in the remediation and passive decontamination of mercury contamination in aquatic systems. Existing mercury transport and transformation models were reviewed and compared

  11. Aquatic studies

    International Nuclear Information System (INIS)

    Anon.

    1980-01-01

    Thermal stress to microorganisms was measured by the production of dissolved organic matter by algal communities and the mineralization of glucose by heterotrophic populations. Mutagenic activity as measured by the Ames/Salmonella/microsome assay indicate that such activity does not occur in Par Pond, although limited mutagenic activity does occur in a nearby canal system due to chlorination of cooling water. Sodium hypochlorite, used as an algicide in the reactor fuel storage basins, caused increased pitting corrosion to reactor fuel targets. Five other compounds selected for testing proved to be superior to sodium hypochlorite. Legionella pneumophila, the pathogen which causes Legionnaire's disease, was found to be a natural part of aquatic ecosystems. It occurs over a wide range of environments and is able to utilize nutrients provided by primary producers. Phytoplankton size classes of less than 3 μm (less than 5% of the total phytoplankton biomass) accounted for 15 to 40% of the total primary productivity in Par Pond, Pond C, and Clark Hill Reservoir. Three major biological data sets were compiled and are available in the SRL computer system for analysis: the SRP deer herd data; 20 years of Par Pond data; and 25 years of biological data on the Savannah River. Results of marine studies indicated that nearly all plutonium in the Savannah River and its estuary resulted from nuclear weapons fallout. The plutonium concentration in the Savannah River is about one fourth the concentration in the Newport River which has no nuclear operations associated with it

  12. Wetland Biomass Production: emergent aquatic management options and evaluations. A final subcontract report. [Includes a bibliography containing 686 references on Typha from biological abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Pratt, D.C.; Dubbe, D.R.; Garver, E.G.; Linton, P.J.

    1984-07-01

    The high yield potential and attractive chemical composition of Typha make it a particularly viable energy crop. The Minnesota research effort has demonstrated that total annual biomass yields equivalent to 30 dry tonnes/ha (13 tons/acre) are possible in planted stands. This compares with yields of total plant material between 9 and 16 dry tonnes/ha (4 to 7 tons/acre) in a typical Minnesota corn field. At least 50% of the Typha plant is comprised of a belowground rhizome system containing 40% starch and sugar. This high level of easily fermentable carbohydrate makes rhizomes an attractive feedstock for alcohol production. The aboveground portion of the plant is largely cellulose, and although it is not easily fermentable, it can be gasified or burned. This report is organized in a manner that focuses on the evaluation of the management options task. Results from stand management research performed at the University of Minnesota during 1982 and 1983 are integrated with findings from an extensive survey of relevant emergent aquatic plant research and utilization. These results and findings are then arranged in sections dealing with key steps and issues that need to be dealt with in the development of a managed emergent aquatic bio-energy system. A brief section evaluating the current status of rhizome harvesting is also included along with an indexed bibliography of the biology, ecology, and utilization of Typha which was completed with support from this SERI subcontract. 686 references, 11 figures, 17 tables.

  13. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  14. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  15. Microbiological monitoring of acid mine drainage treatment systems and aquatic surroundings using real-time PCR.

    Science.gov (United States)

    Han, J S; Kim, C G

    2009-01-01

    In general, acid mine drainage (AMD) causes low pH and high metal concentrations in mining areas and surroundings. The aim of this research was to achieve microbiological monitoring for AMD and to assess whether mine water outflows have any ecological effects on the aqueous ecosystem receiving effluents from different types of treatment system. The water quality of aquatic sample was analyzed and the molecular biological diversity of the samples was assessed using 16S rRNA methods, which were implemented to determine which bacteria existed throughout various unit processes for different AMD treatment systems and their receiving water environments. Acidiphilium cryptum, a heterotrophic acidophile, was found at the AMD sites, and Rhodoferax ferrireducens, which can reduce iron using insoluble Fe(III) as an electron acceptor, was detected at many AMD treatment facilities and downstream of the treatment processes. Subsequently, quantitative real-time PCR was conducted on specific genes of selected bacteria. Surprisingly, obvious trends were observed in the relative abundance of the various bacteria that corresponded to the water quality analytical results. The copy number of Desulfosporosinus orientus, a sulfate reducing bacteria, was also observed to decrease in response to decreases in metals according to the downstream flow of the AMD treatment system.

  16. Predicting the resilience and recovery of aquatic systems: a framework for model evolution within environmental observatories

    Science.gov (United States)

    Hipsey, Matthew R.; Hamilton, David P.; Hanson, Paul C.; Carey, Cayelan C.; Coletti, Janaine Z; Read, Jordan S.; Ibelings, Bas W; Valensini, Fiona J; Brookes, Justin D

    2015-01-01

    Maintaining the health of aquatic systems is an essential component of sustainable catchmentmanagement, however, degradation of water quality and aquatic habitat continues to challenge scientistsand policy-makers. To support management and restoration efforts aquatic system models are requiredthat are able to capture the often complex trajectories that these systems display in response to multiplestressors. This paper explores the abilities and limitations of current model approaches in meeting this chal-lenge, and outlines a strategy based on integration of flexible model libraries and data from observationnetworks, within a learning framework, as a means to improve the accuracy and scope of model predictions.The framework is comprised of a data assimilation component that utilizes diverse data streams from sensornetworks, and a second component whereby model structural evolution can occur once the model isassessed against theoretically relevant metrics of system function. Given the scale and transdisciplinarynature of the prediction challenge, network science initiatives are identified as a means to develop and inte-grate diverse model libraries and workflows, and to obtain consensus on diagnostic approaches to modelassessment that can guide model adaptation. We outline how such a framework can help us explore thetheory of how aquatic systems respond to change by bridging bottom-up and top-down lines of enquiry,and, in doing so, also advance the role of prediction in aquatic ecosystem management.

  17. Systems Biology of the Fluxome

    Directory of Open Access Journals (Sweden)

    Miguel A. Aon

    2015-07-01

    Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

  18. Design and performance of the Georgia Tech Aquatic Center photovoltaic system. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Rohatgi, A.; Begovic, M.; Long, R.; Ropp, M.; Pregelj, A.

    1996-12-31

    A building-integrated DC PV array has been constructed on the Georgia Tech campus. The array is mounted on the roof of the Georgia Tech Aquatic Center (GTAC), site of the aquatic events during the 1996 Paralympic and Olympic Games in Atlanta. At the time of its construction, it was the world`s largest roof-mounted photovoltaic array, comprised of 2,856 modules and rates at 342 kW. This section describes the electrical and physical layout of the PV system, and the associated data acquisition system (DAS) which monitors the performance of the system and collects measurements of several important meteorological parameters.

  19. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  20. Quantitative evaluation of environmental factors influencing the dynamics of mercury in the aquatic systems. Highlights and achievements

    International Nuclear Information System (INIS)

    Akagi, Hirokatsu

    2002-01-01

    The development of a combined mercury extraction - speciation technique for total mercury and methylinercury determination in various biological and environmental media have been established to study and evaluate environmental factors influencing the dynamics of mercury in aquatic systems. Comparability studies of the results from the conventional and radiochemical techniques were planned for the 1st year of the CRP. Validation of the radiochemical method will be undertaken during the current CRP because of constraints in obtaining the appropriate radiotracers. The use of radiotracer techniques will be undertaken to investigate the generation and distribution of methylmercury in the river water - sediment systems using 203 Hg. The improved conventional analytical procedure uses the cold vapor atomic absorption spectrometry for the determination of total mercury in biological and environmental samples. For methylmercury determination, samples are analyzed using combined techniques of dithizone extraction and gas chromatograpy with electron capture detection

  1. Biological Potential in Serpentinizing Systems

    Science.gov (United States)

    Hoehler, Tori M.

    2016-01-01

    Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

  2. A microcosm system to evaluate the toxicity of the triazine herbicide simazine on aquatic macrophytes

    Energy Technology Data Exchange (ETDEWEB)

    Vervliet-Scheebaum, Marco, E-mail: marco.vervliet@biologie.uni-freiburg.d [Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg (Germany); Straus, Alain [Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg (Germany); Tremp, Horst [Institute for Environmental Sciences, University Koblenz-Landau, Fortstr. 7, 76829 Landau (Germany); Hamer, Mick [Ecological Sciences, Syngenta Crop Protection AG, Jealott' s Hill International Research Centre, Bracknell, Berkshire RG42 6EY (United Kingdom); Maund, Stephen J. [Ecological Sciences, Syngenta Crop Protection AG, 4002 Basel (Switzerland); Wagner, Edgar [Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg (Germany); Schulz, Ralf [Institute for Environmental Sciences, University Koblenz-Landau, Fortstr. 7, 76829 Landau (Germany)

    2010-02-15

    This study evaluates the effects of the triazine herbicide simazine in an outdoor pond microcosm test system that contained two submerged rooted species (Myriophyllum spicatum and Elodea canadensis) and two emergent rooted species (Persicaria amphibia and Glyceria maxima) over a period of 84 days. Simazine was applied to the microcosms at nominal concentrations of 0.05, 0.5 and 5 mg/L. General biological endpoints and physiological endpoints were used to evaluate herbicide toxicity on macrophytes and the algae developing naturally in the system. Concentration-related responses of macrophytes and algae were obtained for the endpoints selected, resulting in a no observed ecologically adverse effect concentration (NOEAEC) at simazine concentrations of 0.05 mg active ingredient/L after 84 days. E. canadensis was the most negatively affected species based on length increase, which was consistently a very sensitive parameter for all macrophytes. The experimental design presented might constitute a suitable alternative to conventional laboratory single-species testing. - Simazine at concentrations of 0.05 mg/L does not cause long-term negative effects to aquatic macrophytes or algae.

  3. A microcosm system to evaluate the toxicity of the triazine herbicide simazine on aquatic macrophytes

    International Nuclear Information System (INIS)

    Vervliet-Scheebaum, Marco; Straus, Alain; Tremp, Horst; Hamer, Mick; Maund, Stephen J.; Wagner, Edgar; Schulz, Ralf

    2010-01-01

    This study evaluates the effects of the triazine herbicide simazine in an outdoor pond microcosm test system that contained two submerged rooted species (Myriophyllum spicatum and Elodea canadensis) and two emergent rooted species (Persicaria amphibia and Glyceria maxima) over a period of 84 days. Simazine was applied to the microcosms at nominal concentrations of 0.05, 0.5 and 5 mg/L. General biological endpoints and physiological endpoints were used to evaluate herbicide toxicity on macrophytes and the algae developing naturally in the system. Concentration-related responses of macrophytes and algae were obtained for the endpoints selected, resulting in a no observed ecologically adverse effect concentration (NOEAEC) at simazine concentrations of 0.05 mg active ingredient/L after 84 days. E. canadensis was the most negatively affected species based on length increase, which was consistently a very sensitive parameter for all macrophytes. The experimental design presented might constitute a suitable alternative to conventional laboratory single-species testing. - Simazine at concentrations of 0.05 mg/L does not cause long-term negative effects to aquatic macrophytes or algae.

  4. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  5. Anion binding in biological systems

    International Nuclear Information System (INIS)

    Feiters, Martin C; Meyer-Klaucke, Wolfram; Kostenko, Alexander V; Soldatov, Alexander V; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Kuepper, Frithjof C; Hollenstein, Kaspar; Locher, Kaspar P; Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R

    2009-01-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L 3 (2p 3/2 ) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  6. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  7. Source contributions and mass loadings for chemicals of emerging concern: Chemometric application of pharmaco-signature in different aquatic systems

    International Nuclear Information System (INIS)

    Jiang, Jheng-Jie; Lee, Chon-Lin; Brimblecombe, Peter; Vydrova, Lucie; Fang, Meng-Der

    2016-01-01

    To characterize the source contributions of chemicals of emerging concern (CECs) from different aquatic environments of Taiwan, we collected water samples from different aquatic systems, which were screened for 30 pharmaceuticals and illicit drugs. The total estimated mass loadings of CECs were 23.1 g/d in southern aquatic systems and 133 g/d in central aquatic systems. We developed an analytical framework combining pollutant fingerprinting, hierarchical cluster analysis (HCA), and principal component analysis with multiple linear regression (PCA-MLR) to infer the pharmaco-signature and source contributions of CECs. Based on this approach, we estimate source contributions of 62.2% for domestic inputs, 16.9% for antibiotics application, and 20.9% for drug abuse/medication in southern aquatic system, compared with 47.3% domestic, 35.1% antibiotic, and 17.6% drug abuse/medication inputs to central aquatic systems. The proposed pharmaco-signature method provides initial insights into the profile and source apportionment of CECs in complex aquatic systems, which are of importance for environmental management. - Highlights: • Pharmaco-signature provides first insights into the profile and source apportionment of CECs. • Performing HCA and PCA-MLR can discern the potential source of CECs in different aquatic systems. • Chemometric results resolved 3 factors: domestic inputs, antibiotic application and drug abuse. - The proposed pharmaco-signature method provides initial insights into the profile and source apportionment of CECs in complex aquatic systems.

  8. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  9. Novel laboratory approaches to multi-purpose aquatic bioregenerative closed-loop food production systems

    Science.gov (United States)

    Blüm, V.; Andriske, M.; Kreuzberg, K.; Paassen, U.; Schreibman, M. P.; Voeste, D.

    Based on the construction principle of the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) two novel combined animal-plant production systems were developed in laboratory scale the first of which is dedicated to mid-term operation in closed state up to two years. In principle both consist of the "classic" C.E.B.A.S. subcomponents: animal tank (Zoological Component), plant cultivators (Botanical Component), ammonia converting bacteria filter (Microbial Component) and data acquisition/control unit (Electronical Component). The innovative approach in the first system is the utilization of minimally three aquatic plant cultivators for different species. In this one the animal tank has a volume of about 160 liters and is constructed as an "endless-way system" surronding a central unit containing the heat exchanger and the bacteria filter with volumes of about 1.5 liters each. A suspension plant cultivator (1 liter) for the edible duckweed Wolffia arrhiza is externally connected. The second plant cultivator is a meandric microalgal bioreactor for filamentous green algae. The third plant growth facilitiy is a chamber with about 2.5 liters volume for cultivation of the "traditional" C.E.B.A.S. plant species, the rootless buoyant Ceratophyllum demersum. Both latter units are illuminated with 9 W fluorescent lamps. In the current experiment the animal tank contains the live-bearing teleost fish Xiphophorus helleri and the small pulmonate water snail Biomphalaria glabrata because their physiological adaptation to the closed system conditions is well known from many previous C.E.B.A.S. experiments. The water temperature is maintained at 25 °C and the oxygen level is regulated between 4 and 7 mg/1 by switching on and off the plant cultivator illuminations according to a suitable pattern thus utilizing solely the oxygen produced by photosynthesis. The animals and the micoorganisms of filter and bioflim provide the plants with a sufficient amount of carbon dioxide

  10. Seed reproductive biology of the rare aquatic carnivorous plant Aldrovanda vesiculosa L. (Droseraceae)

    Czech Academy of Sciences Publication Activity Database

    Cross, A. T.; Adamec, Lubomír; Turner, S. R.; Dixon, K. W.; Merritt, D. J.

    2016-01-01

    Roč. 180, č. 4 (2016), s. 515-529 ISSN 0024-4074 Institutional support: RVO:67985939 Keywords : flowering ecology * freshwater wetlands * germination biology Subject RIV: EF - Botanics Impact factor: 2.277, year: 2016

  11. [Network structures in biological systems].

    Science.gov (United States)

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  12. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-04-11

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

  13. The biology and in vitro propagation of the ornamental aquatic plant, Aponogeton ulvaceus.

    Science.gov (United States)

    Kam, Melissa Yit Yee; Chai, Li Chin; Chin, Chiew Foan

    2016-01-01

    Aponogeton ulvaceus Baker (Aponogetonaceae) is a commercially important ornamental aquatic plant species with traditional medicinal uses. Due to the low survival rate of seedlings, propagation by conventional means has been met with many difficulties. In this study, botanical aspects of A. ulvaceus were examined with regards to the morphology, anatomy and physiology of the plant and an efficient protocol for its in vitro propagation using immature tuber explants has been established. The existence of glandular trichomes on the leaves was discovered and the occurrence of circumnutation in A. ulvaceus has been demonstrated. Immature tuber segments with meristems were cultured on MS medium supplemented with various combinations (0, 1, 2, and 3 mg/L) of BAP and NAA for callus induction. The highest percentage of callus production (100 %) was obtained in two different treatments: 1 mg/L BAP and 3 mg/L NAA, and 2 mg/L BAP and 3 mg/L NAA. For shoot and root organogenesis, the combination of 1 mg/L BAP and 1 mg/L NAA was shown to be significant for A. ulvaceus regeneration when compared to control, which yields a mean shoot and root number of 22.50 and 29.50 respectively. The current protocol is the first reported successful establishment of in vitro clonal propagation of A. ulvaceus .

  14. Modeling of radiocesium transport kinetics in system water-aquatic plants

    International Nuclear Information System (INIS)

    Svadlenkova, M.

    1988-01-01

    Compartment models were used to describe the kinetics of the transport of radionuclides in the system water-biomass of aquatic plants. Briefly described are linear models and models with time variable parameters. The model was tested using data from a locality in the environs of the Bohunice nuclear power plant. Cladophora glomerata algae were the monitored plants, 137 Cs the monitored radionuclide. The models may be used when aquatic plants serve as bioindicators of the radioactive contamination of surface waters, for monitoring the transport of radionuclides in food chains. (M.D.). 10 refs

  15. Systems biology and biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  16. Radical production in biological systems

    International Nuclear Information System (INIS)

    Johnson, J.R.; Akabani, G.

    1994-10-01

    This paper describes our effort to develop a metric for radiation exposure that is more fundamental than adsorbed dose and upon which a metric for exposure to chemicals could be based. This metric is based on the production of radicals by the two agents. Radicals produced by radiation in biological systems commonly assumed to be the same as those produced in water despite the presence of a variety of complex molecules. This may explain why the extensive efforts to describe the relationship between energy deposition (track structure) and molecular damage to DNA, based on the spectrum of radicals produced, have not been successful in explaining simple biological effects such as cell killing. Current models assume that DNA and its basic elements are immersed in water-like media and only model the production and diffusion of water-based radicals and their interaction with DNA structures; these models lack the cross sections associated with each macro-component of DNA and only treat water-based radicals. It has been found that such models are not realistic because DNA is not immersed in pure water. A computer code capable of simulating electron tracks, low-energy electrons, energy deposition in small molecules, and radical production and diffusion in water like media has been developed. This code is still in at a primitive stage and development is continuing. It is being used to study radical production by radiation, and radical diffusion and interactions in simple molecular systems following their production. We are extending the code to radical production by chemicals to complement our PBPK modeling efforts. It therefore has been developed primarily for use with radionuclides that are in biological materials, and not for radiation fields

  17. MOIRA models and methodologies for assessing the effectiveness of countermeasures in complex aquatic systems contaminated by radionuclides

    International Nuclear Information System (INIS)

    Monte, L.; Haakanson, L.; Gallego Diaz, E.

    1999-01-01

    The present report is composed of a set of articles written by the partners of the MOIRA project (a model-based computerized system for management support to identify optimal remedial strategies for restoring radionuclide contaminated aquatic ecosystems and drainage areas). The report describes models for predicting the behaviour of radionuclides in complex aquatic systems and the effects of countermeasures for their restoration [it

  18. Integrating phosphoproteomics in systems biology

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-07-01

    Full Text Available Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.

  19. Systems biology of fungal infection

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2012-04-01

    Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

  20. Seed dynamics and control of Pistia stratiotes in two aquatic systems ...

    African Journals Online (AJOL)

    The fruiting and seed dynamics of the alien invasive aquatic species Pistia stratiotes L. (water lettuce; Araceae) was investigated in the seasonally flooded Selinda Canal and Zibadianja Lake of the Kwando–Linyanti River system and in the perennial Chobe River, Botswana, in 1999–2003. The mean number of 30.3 seeds ...

  1. Consequences of the release of chemical pollutants on the transfers of radiioactive products in aquatic systems

    International Nuclear Information System (INIS)

    Bittel, R.

    1975-01-01

    With the increasing rate of industrial activities, aquatic systems undergo, more and more frequently, the accumulation of chemical and radioactive wastes released separatly or associated in the same discharge. An attempt is made to evaluate the consequence of the association of pollutants on the transfers of neutron activation radionuclides. Emphasis is given to heavy metal pollution and complexing agents [fr

  2. Effects of linuron on a rooted aquatic macrophyte in sediment-dosed test systems

    NARCIS (Netherlands)

    Buresova, H.; Crum, S.J.H.; Belgers, J.D.M.; Adriaanse, P.I.; Arts, G.H.P.

    2013-01-01

    Effects of linuron on the sediment-rooted aquatic macrophyte Myriophyllum spicatum L. were studied in sediment-dosed test systems following a proposed guideline with extended test duration. Sediment, pore water, overlying water and macrophyte shoots were sampled weekly for chemical analyses. Linuron

  3. BIOACCUMULATION AND AQUATIC SYSTEM SIMULATOR (BASS) USER'S MANUAL BETA TEST VERSION 2.1

    Science.gov (United States)

    BASS (Bioaccumulation and Aquatic System Simulator) is a Fortran 95 simulation program that predicts the population and bioaccumulation dynamics of age-structured fish assemblages that are exposed to hydrophobic organic pollutants and class B and borderline metals that complex wi...

  4. Quantitative evaluation of environmental factors influencing the dynamics of mercury in the aquatic systems

    International Nuclear Information System (INIS)

    Akagi, H.; Sakamoto, M.; Ikingura, Justinian R.

    2002-01-01

    Highly sensitive and systematic methods for determining total mercury and methylmercury in various biological and environmental materials have been established to study and evaluate the environmental factors influencing the dynamics of mercury in aquatic system. For the analysis of total mercury, a biological or sediment sample is digested in a 50ml thick walled digestion flask using HNO 3 -HClO 4 --H 2 SO 4 (1:1:5) mixture by heating at 200±5 deg. C on a hot plate for 30 minutes. In the analysis of water, the sample is treated first with KMnO 4 and H 2 SO 4 and then extracted with dithizone in toluene. The extract is evaporated to dryness and digested in the same manner as described above. After cooling, the digested sample is filled up to the 50 ml mark with mercury-free water. The analysis of mercury in the sample solution is done by cold-vapor atomic absorption spectrometry using a semi-automated system recently developed in our laboratory. With this system, sensitivity and accuracy are substantially improved and the determination of the sample is completed within one minute. The detection limit for this method is 05 ng Hg in the sample solution. Analytical procedure for methylmercury in biological samples consists of (1) alkaline digestion with 1N KOH in ethanol (2) washing out fatty materials with hexane after slightly acidified with 1N HCl. (3) extraction with dithizone in toluene (4) clean-up with Na 2 S (5) re-extraction with dithizone in toluene; and 6) measurement methylmercury by ECD-gas chromatography. For methylmercury in sediment or water samples, the sediment is treated with 1N KOH in ethanol, whereas the water sample is treated with KMnO 4 and H 2 SO 4 . After these pre-treatments, methylmercury is extracted with dithizone in toluene and then followed by clean-up with Na 2 S, re-extraction with dithizone in toluene and measurement of methylmercury in the same way as described above. The detection limit of these procedures is around 5ng/g in a 0

  5. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  6. Radionuclide biological half-life values for terrestrial and aquatic wildlife

    International Nuclear Information System (INIS)

    Beresford, N.A.; Beaugelin-Seiller, K.; Burgos, J.; Cujic, M.; Fesenko, S.; Kryshev, A.; Pachal, N.; Real, A.; Su, B.S.; Tagami, K.; Vives i Batlle, J.; Vives-Lynch, S.; Wells, C.; Wood, M.D.

    2015-01-01

    The equilibrium concentration ratio is typically the parameter used to estimate organism activity concentrations within wildlife dose assessment tools. Whilst this is assumed to be fit for purpose, there are scenarios such as accidental or irregular, fluctuating, releases from licensed facilities when this might not be the case. In such circumstances, the concentration ratio approach may under- or over-estimate radiation exposure depending upon the time since the release. To carrying out assessments for such releases, a dynamic approach is needed. The simplest and most practical option is representing the uptake and turnover processes by first-order kinetics, for which organism- and element-specific biological half-life data are required. In this paper we describe the development of a freely available international database of radionuclide biological half-life values. The database includes 1907 entries for terrestrial, freshwater, riparian and marine organisms. Biological half-life values are reported for 52 elements across a range of wildlife groups (marine = 9, freshwater = 10, terrestrial = 7 and riparian = 3 groups). Potential applications and limitations of the database are discussed. - Highlights: • 1907 biological half-life values have been collated for wildlife species. • Data cover 52 elements. • 27 marine, freshwater, riparian and terrestrial organisms are included.

  7. Institute for Genomics and Systems Biology

    Science.gov (United States)

    Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

  8. Daphnia as a model organism in limnology and aquatic biology: some aspects of its reproduction and development

    Directory of Open Access Journals (Sweden)

    Adam Petrusek

    2011-08-01

    Full Text Available Invertebrates comprise the overwhelming majority of all animal species - around 95% of described species, not including substantial cryptic variation. As it is an extremely diverse and heterogeneous group, research on various invertebrate taxa often follows parallel trajectories, with little interaction among experts on different groups. To promote sharing of knowledge within as well as across taxa, the International Society of Invertebrate Reproduction and Development (ISIRD was established in 1975 in Calicut, India. Since that time, the ISIRD has organised international conferences at three-year intervals where various aspects of invertebrate biology are presented and discussed, naturally with the focus on reproduction and development. Traditionally, marine invertebrate groups have been well represented at all ISIRD congresses, but freshwater invertebrates have often been relatively overlooked at these meetings. The 12th ISIRD congress took place between August 16 and 20, 2010 in Prague, the Czech Republic. Several different Czech institutions collaborated on the organisation of this meeting. As aquatic invertebrate research has a long tradition in the country, we decided to include a section dedicated to popular model organisms in aquatic ecology and evolutionary biology, the "water fleas", cladocerans of the genus Daphnia. The section entitled "Daphnia and other cladocerans as model organisms" was open to any aspects of cladoceran biology directly or indirectly related to their reproduction or development. Unfortunately, the timing of the Prague congress completely overlapped the triennial congress of the International Society of Theoretical and Applied Limnology (SIL in Cape Town, South Africa. This large meeting in a very attractive setting attracted many cladocerologists from all over the world, including Europe. Therefore, the Daphnia section of the Prague ISIRD meeting remained moderate in size, attracting 13 contributions (eight talks

  9. Answering biological questions: Querying a systems biology database for nutrigenomics

    NARCIS (Netherlands)

    Evelo, C.T.; Bochove, K. van; Saito, J.T.

    2011-01-01

    The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

  10. Habitat mosaics and path analysis can improve biological conservation of aquatic biodiversity in ecosystems with low-head dams.

    Science.gov (United States)

    Hitchman, Sean M; Mather, Martha E; Smith, Joseph M; Fencl, Jane S

    2018-04-01

    . As we show here, mosaic habitat sampling and path analysis can help conservation practitioners improve science-based management plans for disturbed aquatic systems worldwide. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Habitat mosaics and path analysis can improve biological conservation of aquatic biodiversity in ecosystems with low-head dams

    Science.gov (United States)

    Hitchman, Sean M.; Mather, Martha E.; Smith, Joseph M.; Fencl, Jane S.

    2018-01-01

    richness. As we show here, mosaic habitat sampling and path analysis can help conservation practitioners improve science-based management plans for disturbed aquatic systems worldwide.

  12. Aquatic food production modules in bioregenerative life support systems based on higher plants

    Science.gov (United States)

    Bluem, V.; Paris, F.

    Most bioregenerative life support systems (BLSS) are based on gravitropic higher plants which exhibit growth and seed generation disturbances in microgravity. Even when used for a lunar or martian base the reduced gravity may induce a decreased productivity in comparison to Earth. Therefore, the implementation of aquatic biomass production modules in higher plant and/or hybrid BLSS may compensate for this and offer, in addition, the possibility to produce animal protein for human nutrition. It was shown on the SLS-89 and SLS-90 space shuttle missions with the C.E.B.A.S.-MINI MODULE that the edible non gravitropic rootless higher aquatic plant Ceratophyllum demeresum exhibits an undisturbed high biomass production rate in space and that the teleost fish species, Xiphophorus helleri, adapts rapidly to space conditions without loss of its normal reproductive functions. Based on these findings a series of ground-based aquatic food production systems were developed which are disposed for utilization in space. These are plant production bioreactors for the species mentioned above and another suitable candidate, the lemnacean (duckweed) species, Wolffia arrhiza. Moreover, combined intensive aquaculture systems with a closed food loop between herbivorous fishes and aquatic and land plants are being developed which may be suitable for integration into a BLSS of higher complexity.

  13. Effects of fishing technique on assessing species composition in aquatic systems in semi-arid Brazil

    Directory of Open Access Journals (Sweden)

    ESF Medeiros

    Full Text Available In most ecological field research, appropriate sampling is critical for the understanding of processes underlying fish populations and communities, and is even more important in heterogeneous environments such as the aquatic systems of the semi-arid region of Brazil. This study intends to make a contribution to the development of sampling programs and gear selection in aquatic systems of semi-arid Brazil by evaluating the effects of different fishing techniques on the assessment of richness and composition of the fish fauna in selected aquatic environments. Six sites were selected to represent typical artificial (reservoirs and natural (intermittent streams environments and four different types of sampling gear were applied to each site during four occasions. The present study shows that when selecting sampling techniques to be used in aquatic systems in semi-arid Brazil, one must consider the objectives of the study, e.g. ecological or taxonomic, in order to decide on inclusion of rare species in the sampling population. Also, the effect of the sampling gear on natural abundances of fish must be considered given that some sampling techniques are highly detrimental to fish population numbers.

  14. Fostering synergy between cell biology and systems biology.

    Science.gov (United States)

    Eddy, James A; Funk, Cory C; Price, Nathan D

    2015-08-01

    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  15. Using Stable Isotopes to Detect Land Use Change and Nitrogen Sources in Aquatic Systems

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, K. M. [National Isotope Center, GNS Science, Lower Hutt (New Zealand)

    2013-05-15

    Changing land use is one of the primary causes of increased sedimentation and nutrient levels in aquatic systems, resulting in contamination and reduction of biodiversity. Detecting and quantifying these inputs is the first step towards remediation, and enabling targeted reductions of transport processes into waterways from human impacted land surfaces. More recently, stable isotope analyses are being used as detection and quantification tools in aquatic environments. Carbon ({delta}{sup 13}C) and nitrogen ({delta}{sup 15}N) isotopes of sediments, as well as algae and invertebrates from aquatic systems can be used as proxies to record both short and long term environmental change. Excess nitrogen (or nitrogen-compounds) derived from urbanization, industry, forestry, farming and agriculture, increase the bioavailability of nitrogen to aquatic organisms, changing their natural {delta}15N isotopic signatures. Allochthonous (terrestrial) input from soil destabilization and human activity in surrounding catchments changes {delta}{sup 13}C isotopic compositions and increases the C:N ratio of sediments. Heavy metal and other organic pollutants can also be used to indicate urbanization and industrial contamination. The combined use of carbon and nitrogen isotopes, C:N ratios and heavy metals are powerful environmental monitoring tools, which are useful indicators of source and transport pathways of terrestrial derived material and anthropogenic pollutants into streams, rivers and estuaries. (author)

  16. Quantum Dynamics in Biological Systems

    Science.gov (United States)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  17. Editorial overview : Systems biology for biotechnology

    NARCIS (Netherlands)

    Heinemann, Matthias; Pilpel, Yitzhak

    About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

  18. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  19. Sublethal effects of tritium on aquatic systems. Ecological effects of lithium and beryllium on important aquatic organisms and associted communities. Teratogenic effects of low-level magnetic fields

    International Nuclear Information System (INIS)

    Strand, J.A.; Emery, R.M.

    1980-01-01

    Continuing studies of the sublethal effects of tritium on freshwater species emphasize the potential for genetic transmission of suppressed immune competence in offspring of parental rainbow trout (Salmo gairdneri) exposed to tritium (0, 0.04, 0.4, 40.0 rads) during embryogenesis. We plan to determine the relative biological effectiveness of tritium beta irradiation when compared to 60 Co gamma irradiation using the relatively radiosensitive immune process of rainbow trout. During FY 1979, we concluded genetic effects studies and prepared a manuscript for open literature publication summarizing FY 1977 and FY 1978 studies on the permanence of suppression of the primary immune response in rainbow trout sublethally irradiated during embryogenesis. We are also studying the potential effects of beryllium and lithium on aquatic systems. Because of mining and refining subsequent to the use of these metals in the construction of fusion reactors, increased levels of each are likely to be encountered in surface waters. Studies included an evaluation of potential toxicity of lithium on embryological life stages of rainbow trout and an assessment of fate and effects in artificial stream habitats. Levels of lithium necessary to cause an observed effect would have to be at least three orders of magnitude above observed background. Studies initiated in FY 1978 include evaluation of effects of low-level magnetic fields on embryologic development of rainbow trout. The objective of these studies to provide data useful in assessing potentially harmful effects of low-level magnetic fields encountered by attendant personnel working in the transport and hot cell areas of fusion reactors. This approach is less costly than using mammalian systems, provides large numbers of experimental organisms for meaningful statistical analysis and permits examination of potential latent effects in a representative vertebrate

  20. Magnetic Actuation of Biological Systems

    Science.gov (United States)

    Lauback, Stephanie D.

    Central to the advancement of many biomedical and nanotechnology capabilities is the capacity to precisely control the motion of micro and nanostructures. These applications range from single molecule experiments to cell isolation and separation, to drug delivery and nanomachine manipulation. This dissertation focuses on actuation of biological micro- and nano-entities through the use of weak external magnetic fields, superparamagnetic beads, and ferromagnetic thin films. The magnetic platform presents an excellent method for actuation of biological systems due to its ability to directly control the motion of an array of micro and nanostructures in real-time with calibrated picoNewton forces. The energy landscape of two ferromagnetic thin film patterns (disks and zigzag wires) is experimentally explored and compared to corresponding theoretical models to quantify the applied forces and trajectories of superparamagnetic beads due to the magnetic traps. A magnetic method to directly actuate DNA nanomachines in real-time with nanometer resolution and sub-second response times using micromagnetic control was implemented through the use of stiff DNA micro-levers which bridged the large length scale mismatch between the micro-actuator and the nanomachine. Compared to current alternative methods which are limited in the actuation speeds and the number of reconfiguration states of DNA constructs, this magnetic approach enables fast actuation (˜ milliseconds) and reconfigurable conformations achieved through a continuous range of finely tuned steps. The system was initially tested through actuation of the stiff arm tethered to the surface, and two prototype DNA nanomachines (rotor and hinge) were successfully actuated using the stiff mechanical lever. These results open new possibilities in the development of functional robotic systems at the molecular scale. In exploiting the use of DNA stiff levers, a new technique was also developed to investigate the emergence of the

  1. Applications of biological tools or biomarkers in aquatic biota: A case study of the Tamar estuary, South West England.

    Science.gov (United States)

    Dallas, Lorna J; Jha, Awadhesh N

    2015-06-30

    Biological systems are the ultimate recipients of pollutant-induced damage. Consequently, our traditional reliance on analytical tools is not enough to assess ecosystem health. Biological responses or biomarkers are therefore also considered to be important tools for environmental hazard and risk assessments. Due to historical mining, other anthropogenic activities, and its conservational importance (e.g. NATURA sites, SACs), the Tamar estuary in South West England is an ideal environment in which to examine applications of such biological tools. This review presents a thorough and critical evaluation of the different biological tools used in the Tamar estuary thus far, while also discussing future perspectives for biomarker studies from a global perspective. In particular, we focus on the challenges which hinder applications of biological tools from being more readily incorporated into regulatory frameworks, with the aim of enabling both policymakers and primary stakeholders to maximise the environmental relevance and regulatory usefulness of such tools. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Aquatic Insect from Iran for Possible Use of Biological Control of Main Vector-Borne Disease of Malaria and Water Indicator of Contamination

    Directory of Open Access Journals (Sweden)

    Zahra Saeidi

    2018-03-01

    Full Text Available Iran has a wide variety of zoogeographical regions and different seasons. Here are some important mosquito-borne diseases. Mosquitoes normally live in waters. Its aquatic insect fauna is highly unexplored. To being resolved this faunal gap, a variety of literature records from previous century in different parts of Iran was reviewed. In some southern and southeastern foci in Iran, Malaria is still a main endemic disease which is unstable with two seasonal spring and autumn peaks even though Iran is lunching Malaria elimination. This review article showed the wide variety of aquatic insects throughout the country. Researchers can discuss water pollutant and its quality by using aquatic insect fauna as well as biological control for vectors. Types of aquatic in­sects and macroinvertebrates sampling can be useful for water quality monitoring as indicators. Looking at aquatic insects’ life in water could be one of the most cost-effective and the easiest method to assess the water contaminations by different pollutants and will provide a guideline for scientific communities and environmental agencies for decision making.

  3. Abstracts of the 31. annual aquatic toxicity workshop

    International Nuclear Information System (INIS)

    Burridge, L.E.; Haya, K.; Niimi, A.J.

    2004-01-01

    This conference provided an opportunity for an informal exchange of recent research information and knowledge on aquatic and environmental toxicology. Topics ranged from basic aquatic toxicology to applications in environmental monitoring, setting regulations and developing criteria for sediment and water quality. The workshops were attended by representatives from industry, governments and universities. The current challenges and approaches to deal with aquatic toxicology and their biological effect on aquatic biota were discussed. The sessions were entitled as follows: environmental effects monitoring; pesticides; ecological risk assessment; sediment disposal at sea; oil and gas; pharmaceuticals; artifactual toxicity in municipal waste water; sediment and soil toxicity; contaminants in aquatic systems; biological effects; and discoveries in aquatic sciences. The conference included 4 plenary sessions and 119 platform papers, of which 24 papers have been indexed separately for inclusion in this database. refs., tabs., figs

  4. Application of portable in situ UV fluorescence sensors in natural and engineered aquatic systems.

    Science.gov (United States)

    Fox, Bethany; Rushworth, Cathy; Atrridge, John

    2016-04-01

    Natural organic matter (NOM) is ubiquitous throughout aquatic systems. This heterogeneous mixture of organic matter is central for aquatic ecosystems and, both local and global, biogeochemical cycling. Improvements in technology and data analysis has allowed for advances in the understanding and characterisation of aquatic organic matter. However, much of the technological expansions have focussed on benchtop instruments. In recent years, there has been interest in the continued development of portable in situ sensors for monitoring NOM characteristics within a wide range of applications, spanning both natural and engineered systems. The UviLux (Chelsea Technologies Group Ltd., UK) is an in situ portable UV fluorescence sensor that can be configured to monitor a range of NOM in aquatic systems, as well as anthropogenic inputs such as polycyclic aromatic hydrocarbons (PAH) and optical brighteners. Here we will focus on the use of the Tryptophan and CDOM UviLux sensors across a variety of applications in both natural systems, such as rivers and leachate into groundwater, and engineered systems, including drinking water and waste water treatment. Recent work has focused on standardising the fluorescence output across the UviLux range of sensors, reporting data in quinine sulphate units (QSU), which enables the output from two different fluorometers to be directly compared both to each other, and to bench-top data. A key advantage of deploying multiple sensors is the ability to fingerprint the fluorescence, by providing, for example, a Tryptophan/CDOM ratio. From the data collected, the ratio of the different fluorescence regions has been shown to provide more robust in situ data and help identify true temporal variations and patterns across multiple applications and sampling locations.

  5. Radiogenic isotope geochemistry of sedimentary and aquatic systems

    International Nuclear Information System (INIS)

    Stille, P.; Shields, G.

    1997-01-01

    The following topics are discussed: Basic principles of isotopic geochemistry; weathering; isotopic geochemistry of river water; isotopic geochemistry in the environment; isotopic composition of seawater past and present (Sr, Nd, Pb, Os, Ce); isotope geochemistry of detrital and authigenic clay minerals in marine sediemnts (Rb-Sr, K-Ar, O); the Sm-N isotope system in detrital and authigenic argillaceous sediments. (SR), provided they are of exceptional interest and focused on a single topic. (orig./SR)

  6. Radiogenic isotope geochemistry of sedimentary and aquatic systems

    Energy Technology Data Exchange (ETDEWEB)

    Stille, P.; Shields, G. [Centre National de la Recherche Scientifique (CNRS), 67 - Strasbourg (France). Centre de Sedimentologie et Geochimie de la Surface

    1997-12-31

    The following topics are discussed: Basic principles of isotopic geochemistry; weathering; isotopic geochemistry of river water; isotopic geochemistry in the environment; isotopic composition of seawater past and present (Sr, Nd, Pb, Os, Ce); isotope geochemistry of detrital and authigenic clay minerals in marine sediemnts (Rb-Sr, K-Ar, O); the Sm-N isotope system in detrital and authigenic argillaceous sediments. (SR), provided they are of exceptional interest and focused on a single topic. (orig./SR)

  7. The energetic contributions of aquatic primary producers to terrestrial food webs in a mid-size river system.

    Science.gov (United States)

    Kautza, Adam; Mazeika, S; Sullivan, P

    2016-03-01

    Rivers are increasingly recognized as providing nutritional subsidies (i.e., energy and nutrients) to adjacent terrestrial food webs via depredation of aquatic organisms (e.g., emergent aquatic insects, crayfish, fish) by terrestrial consumers. However, because these prey organisms assimilate energy from both aquatic (e.g., benthic algae, phytoplankton, aquatic macrophytes) and terrestrial (e.g., riparian leaf detritus) primary producers, river subsidies to terrestrial consumers represent a combination of aquatically and terrestrially derived energy. To date, the explicit contribution of energy derived from aquatic primary producers to terrestrial consumers has not been fully explored yet might be expected to be quantitatively important to terrestrial food webs. At 12 reaches along a 185-km segment of the sixth-order Scioto River system (Ohio, USA), we quantified the relative contribution of energy derived from aquatic primary producers to a suite of terrestrial riparian consumers that integrate the adjacent landscape across multiple spatial scales through their foraging activities (tetragnathid spiders, rove beetles, adult coenagrionid damselflies, riparian swallows, and raccoons). We used naturally abundant stable isotopes (13C and 15N) of periphyton, phytoplankton, macrophytes, and terrestrial vegetation to evaluate the energetic contribution of aquatic primary producers to terrestrial food webs. Shoreline tetragnathid spiders were most reliant on aquatic primary producers (50%), followed by wider-ranging raccoons (48%), damselflies (44%), and riparian swallows (41%). Of the primary producers, phytoplankton (19%) provisioned the greatest nutritional contribution to terrestrial consumers (considered collectively), followed by periphyton (14%) and macrophytes (11%). Our findings provide empirical evidence that aquatic primary producers of large streams and rivers can be a critical nutritional resource for terrestrial food webs. We also show that aquatically

  8. Applicability of Computational Systems Biology in Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

    2014-01-01

    be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method......Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources...... and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search...

  9. International Symposium on the Biology and Management of Aquatic Plants. Volume 31

    Science.gov (United States)

    1993-01-01

    Yang. 1991. Lipid peroxidation and antioxidative transgenic plants overexpressing peroxidase. Plant Physiol 96:577- defense systems in early leaf...Factors 3. Chandrasena, J. P. N. R. and W. H. T. Dhammika. 1988. Studies on limiting the distribution of cogongrass, Imperata cylindrica, and torpe

  10. Biogeochemistry of iodine in aquatic and terrestrial systems

    International Nuclear Information System (INIS)

    Behrens, H.

    2006-01-01

    Full text: It was found that in surface water (rivers, lakes) iodide becomes to a large extent bound onto organic materials (mainly humic substances), the reaction being mediated by extracellular enzymes (peroxidases) which are provided by microbial activity. In soils and sediments also fixation of iodine on solid organic materials occurs by the same process. The reaction appears as a continuing iodination and simultaneous deiodination only in aerobic systems. When switching to anaerobic conditions, only the deiodination resumes resulting in a complete release of the organoiodine into dissolved iodide. (author)

  11. Metabolomics: Definitions and Significance in Systems Biology.

    Science.gov (United States)

    Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

    2017-01-01

    Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

  12. Evaluation of a new method for assessing resilience in urban aquatic social-ecological systems

    Directory of Open Access Journals (Sweden)

    Jonathan P. Moores

    2017-12-01

    Full Text Available Urban aquatic social-ecological systems (SESs comprise socio-technical elements, the built environment and its management, and natural elements (water bodies that provide ecosystem services. Changed hydrology, poor stormwater quality, and the modification of water bodies associated with urban development brings challenges for maintaining ecosystem services provision in an urban aquatic SES. Water sensitive urban design (WSUD has emerged as a form of development that aims to better support the provision of ecosystem services. Resilience concepts provide a basis for discriminating between WSUD and conventional development approaches. Building on an existing decision support system, a new, preliminary method for assessing resilience based on the combination of the socio-technical capacity (STC and natural capacity (NC of urban aquatic SESs has been developed. The STC score reflects a multicriteria assessment of the characteristics of stormwater infrastructure and management. The NC score reflects an assessment of the state and trajectory of biophysical attributes of the system associated with the provision of ecosystem services. By modeling a series of future urban development scenarios in Auckland, New Zealand, the method has been shown to discriminate between scenario outcomes within constraints associated with the biophysical and built characteristics modeled. Results are consistent with key concepts of resilience theory: outcomes are grouped in regimes and exhibit hysteresis, with the ability of WSUD to improve the state of the system strongly influenced by the presence of legacy effects. The method provides a source of additional, valuable information that complements other indicators by providing a snapshot of the interaction of catchment management effort and outcomes and indicating the likely future state of the SES. Recognizing that the method is limited to providing a relative assessment of resilience and adopts certain simplistic

  13. The aquatic systems of Doñana (SW Spain): watersheds and frontiers

    OpenAIRE

    Serrano Martín, Laura; Reina Vázquez, Marta María; Martín Farfán, Gonzalo; Reyes Bárbara, Isabel; Arechederra, Arantza; León, D.; Toja Santillana, Julia

    2006-01-01

    Doñana includes an extraordinary variety of aquatic systems. They are broadly classified according to their location (on either aeolian sands or marshland) as their hydrology largely depends on the geomorphology of their basins. Their chemical composition is mainly influenced by rainfall, evaporative concentration, groundwater discharge, biogeochemical interactions at the sediment-water interface, and the quality composition of their watersheds. The influence of the watershed can be studie...

  14. The potential of the fresh-water fern Azolla in aquatic farming systems

    Science.gov (United States)

    Bijl, Peter K.; Werf, vd, Adrie; Schluepmann, Henriette; Reichart, Gert-Jan; Brouwer, Paul; Nierop, Klaas G. J.; Hellgardt, Klaus; Brinkhuis, Henk

    2014-05-01

    With aquatic farming systems a new avenue in agriculture is explored, in which the competition with conventional arable land is avoided. The aquatic, ubiquitous, floating fern Azolla is not yet widely explored as potential crop in such farming systems, despite its high potential because it grows in many natural systems under low-light intensities, has an enormous annual yield, and has special biomass qualities for applications in food, feed and specialty chemical industries. But, what makes Azolla particularly interesting as cost-effective crop is its capability to take up atmospheric nitrogen through symbiosis with nitrogen-fixing bacteria Anabaena azollae. This makes Azolla independent of nitrogen fertilization. In order to explore the potential of Azolla as a crop for a suite of applications, we have assembled a team of expertise: AZOFAST, consisting of agricultural engineers, plant physiologists, chemical engineers and organic chemists. Our growth experiments reveal high annual production yields with constant harvest. We are developing a germination and spore collecting/preservation protocol as a first step to domestication. Finally we have explored the biomass quality of different species of extant Azolla. We performed organic chemical analyses on lipid and tannin extracts, and quantified yields of specific compounds within these fractions. In our presentation we will present some of our results to show the potential of Azolla as a new, sustainable aquatic crop serving all kinds of industrial streams from protein feed to platform chemicals.

  15. Systems biology of personalized nutrition

    NARCIS (Netherlands)

    Ommen, B. van; Broek, T. van den; Hoogh, I. de; Erk, M. van; Someren, E. van; Rouhani-Rankouhi, T.; Anthony, J.C.; Hogenelst, K.; Pasman, W.; Boorsma, A.; Wopereis, S.

    2017-01-01

    Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the

  16. Microbial plant litter decomposition in aquatic and terrestrial boreal systems along a natural fertility gradient

    Science.gov (United States)

    Soares, A. Margarida P. M.; Kritzberg, Emma S.; Rousk, Johannes

    2017-04-01

    Plant litter decomposition is a global ecosystem process, with a crucial role in carbon and nutrient cycling. The majority of litter processing occurs in terrestrial systems, but an important fraction also takes place in inland waters. Among environmental factors, pH impacts the litter decomposition through its selective influence on microbial decomposers. Fungal communities are less affected by pH than bacteria, possibly owing to a wider pH tolerance by this group. On the other hand, bacterial pH optima are constrained to a narrower range of pH values. The microbial decomposition of litter is universally nutrient limited; but few comparisons exist between terrestrial and aquatic systems. We investigated the microbial colonisation and decomposition of plant litter along a fertility gradient, which varied in both pH and N availability in both soil and adjacent water. To do this we installed litterbags with birch (Betula pendula) in streams and corresponding soils in adjacent riparian areas in a boreal system, in Krycklan, Sweden. During the four months covering the ice-free growth season we monitored the successional dynamics of fungal (acetate incorporation into ergosterol) and bacterial growth (thymidine incorporation), microbial respiration in leaf litter, and quantitative and qualitative changes in litter over time. We observed that bacterial growth rates were initially higher in litter decomposing in streams than those in soils, but differences between terrestrial and aquatic bacterial production converged towards the end of the experiment. In litter bags installed in soils, bacterial growth was lower at sites with more acidic pH and lower N availability, while aquatic bacteria were relatively unaffected by the fertility level. Fungal growth rates were two-fold higher for litter decomposing in streams than in soils. In aquatic systems, fungal growth was initially lower in low fertility sites, but differences gradually disappeared over the time course. Fungal

  17. Philosophy of Systems and Synthetic Biology

    DEFF Research Database (Denmark)

    Green, Sara

    2017-01-01

    This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

  18. Prescribed-fire effects on an aquatic community of a southwest montane grassland system

    Science.gov (United States)

    Caldwell, Colleen A.; Jacobi, Gerald Z.; Anderson, Michael C.; Parmenter, Robert R.; McGann, Jeanine; Gould, William R.; DuBey, Robert; Jacobi, M. Donna

    2013-01-01

    The use of prescription fire has long been recognized as a reliable management tool to suppress vegetative succession processes and to reduce fuel loading to prevent catastrophic wildfires, but very little attention has been paid to the effects on aquatic systems. A late-fall prescribed burn was implemented to characterize effects on an aquatic community within a montane grassland system in north-central New Mexico. The fire treatment was consistent with protocols of a managed burn except that the fire was allowed to burn through the riparian area to the treatment stream to replicate natural fire behavior. In addition to summer and fall preburn assessment of the treatment and reference stream, we characterized immediate postfire effects (within a week for macroinvertebrates and within 6 months for fish) and seasonal effects over a 2-year period. Responses within the treatment stream were compared with an unburned reference stream adjacent to the prescription burn. During the burn, the diel range in air temperature increased by 5°C while diel range in water temperature did not change. Carbon–nitrogen ratios did not differ between treatment and reference streams, indicating the contribution of ash from the surrounding grassland was negligible. Although total taxa and species richness of aquatic macroinvertebrates were not altered, qualitative indices revealed departure from preburn condition due to loss of sensitive taxa (mayflies [order Ephemeroptera] and stoneflies [order Plecoptera]) and an increase in tolerant taxa (midges [order Chironomidae]) following the burn. Within 1 year of the burn, these attributes returned to preburn conditions. The density and recruitment of adult Brown Trout Salmo trutta did not differ between pre- and postburn collections, nor did fish condition differ. Fire is rarely truly replicated within a given study. Although our study represents one replication, the results will inform managers about the importance in timing (seasonality

  19. Micro-separation toward systems biology.

    Science.gov (United States)

    Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

    2006-02-17

    Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

  20. Biological Systems Thinking for Control Engineering Design

    Directory of Open Access Journals (Sweden)

    D. J. Murray-Smith

    2004-01-01

    Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

  1. Impact of Thermodynamic Principles in Systems Biology

    NARCIS (Netherlands)

    Heijnen, J.J.

    2010-01-01

    It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

  2. Aspergilli: Systems biology and industrial applications

    DEFF Research Database (Denmark)

    Knuf, Christoph; Nielsen, Jens

    2012-01-01

    possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

  3. Aquatic modules for bioregenerative life support systems based on the C.E.B.A.S. biotechnology

    Science.gov (United States)

    Bluem, Volker; Paris, Frank

    2001-03-01

    Most concepts for bioregenerative life support systems are based on edible higher land plants which create some problems with growth and seed generation under space conditions. Animal protein production is mostly neglected because of the tremendous waste management problems with tetrapods under reduced weightlessness. Therefore, the "Closed Equilibrated Biological Aquatic System" (C.E.B.A.S.) was developed which represents an artificial aquatic ecosystem containing aquatic organisms which are adpated at all to "near weightlessness conditions" (fishes Xiphophorus helleri, water snails Biomphalaria glabrata, ammonia oxidizing bacteria and the rootless non-gravitropic edible water plant Ceratophyllum demersum). Basically the C.E.B.A.S. consists of 4 subsystems: a ZOOLOGICASL COMPONENT (animal aquarium), a BOTANICAL COMPONENT (aquatic plant bioreactor), a MICROBIAL COMPONENT (bacteria filter) and an ELECTRONICAL COMPONENT (data acquisition and control unit). Superficially, the function principle appears simple: the plants convert light energy into chemical energy via photosynthesis thus producing biomass and oxygen. The animals and microorganisms use the oxygen for respiration and produce the carbon dioxide which is essential for plant photosynthesis. The ammonia ions excreted by the animals are converted by the bacteria to nitrite and then to nitrate ions which serve as a nitrogen source for the plants. Other essential ions derive from biological degradation of animal waste products and dead organic matter. The C.E.B.A.S. exists in 2 basic versions: the original C.E.B.A.S. with a volume of 150 liters and a self-sustaining standing time of more than 13 month and the so-called C.E.B.A.S. MINI MODULE with a volume of about 8.5 liters. In the latter there is no closed food loop by reasons of available space so that animal food has to be provided via an automated feeder. This device was flown already successfully on the STS-89 and STS-90 spaceshuttle missions and the

  4. Systems biology in critical-care nursing.

    Science.gov (United States)

    Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

    2011-01-01

    Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

  5. Marine biological data and information management system

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.

    Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

  6. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  7. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  8. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  9. Relationships between aquatic invertebrates, water quality and vegetation in an Andean peatland system

    Directory of Open Access Journals (Sweden)

    E. Oyague Passuni

    2015-12-01

    Full Text Available Peatlands (known as bofedales in the Peruvian Andes provide important social and environmental services in the Peruvian Puna ecoregion, especially as sources of water and forage for domestic livestock. In biological terms, these peatlands are key habitats with their own community structure, dynamics and interactions; and they serve as biodiversity hotspots within the High Andes. In this article we assess the relationships between: (i physical structure, (ii water quality, (iii plant communities and (iv the assemblages of aquatic invertebrates (benthic macroinvertebrates in three peatlands located in Cuzco Region, southern Peru. The results suggest that the benthic macroinvertebrate assemblage is a good indicator of the trophic status of the small pools that are typically present in bofedales. Trophic status is, in turn, primarily related to spatial and seasonal water availability and the types of plant communities present in each peatland.

  10. An engineering design approach to systems biology.

    Science.gov (United States)

    Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

    2017-07-17

    Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

  11. Physico-chemical and hydraulic mechanisms of radionuclide mobilization in aquatic systems

    International Nuclear Information System (INIS)

    Konoplev, A.V.; Bulgakov, A.A.; Comans, R.N.J.; Hilton, J.; Smith, J.; Madruga, M.J.; Voitsekhovich, O.V.; Sansone, U.; Kudelsky, A.V.

    1996-01-01

    This paper presents main results of joint studies carried out in frame of EC-coordinated ECP-3 Project 'Modelling and study of the mechanisms of the transfer of radioactive material from the terrestrial ecosystem to and in water bodies around Chernobyl' in part of geochemical pathways. Physico-chemical models of specific migration processes are developed and recommended for application as sub models for inclusion in the decision support system (JSP-1). Main parameters, determining the behaviour of radionuclides in aquatic ecosystems are identified and methods for their estimation in |emergency situations are proposed

  12. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  13. Biological Monitoring Using Macroinvertebrates as Bioindicators of Water Quality of Maroaga Stream in the Maroaga Cave System, Presidente Figueiredo, Amazon, Brazil

    Directory of Open Access Journals (Sweden)

    Christiane Brito Uherek

    2014-01-01

    Full Text Available Aquatic environments are being modified by anthropogenic activities regarding their biological, physical, and chemical conditions; even pristine aquatic ecosystems can be threatened. This study focused on the biological monitoring of Maroaga Stream—a first order stream located in an Environmental Protection Area in the Amazon using the Biological Monitoring Working Party (BMWP Score System. The BMWP Score System revealed that the Maroaga Stream was a Class I stream (score of 138 points, indicating clean or not significantly altered water quality. The results suggest the adequate environmental conditions and ecological responses of the Maroaga Stream.

  14. Gulf-Wide Information System, Environmental Sensitivity Index Semi-aquatic, Fur-bearing Mammal Database, Geographic NAD83, LDWF (2001) [esi_s_mammal_LDWF_2001

    Data.gov (United States)

    Louisiana Geographic Information Center — This data set contains sensitive biological resource data for small semi-aquatic, fur-bearing mammals in coastal Louisiana. Vector polygons represent areas of...

  15. Aquatic Plant Control Research Program. Biological Control of Pistia stratiotes L. (Waterlettuce) Using Neohydronomus affinis Hustache (Coleoptera: Curculionidae).

    Science.gov (United States)

    1992-07-01

    plant must also be examined for herbivores attacking the weed. This ensures that time and money are not wasted by importing insects already present in...Agricultural Research Service Aquatic Weed Research Laboratory in Fort Lauder - dale, FL, from quarantine tacilities in Gainesville, FL, on 11 February

  16. Evaluating Aquatic invertebrate vulnerability to insecticides based on intrinsic sensitivuty, biological traits, and toxic mode of action

    NARCIS (Netherlands)

    Rico, A.; Brink, van den P.J.

    2015-01-01

    In the present study, the authors evaluated the vulnerability of aquatic invertebrates to insecticides based on their intrinsic sensitivity and their population-level recovery potential. The relative sensitivity of invertebrates to 5 different classes of insecticides was calculated at the genus,

  17. Biological Nutrient Removal in Compact Biofilm Systems

    OpenAIRE

    Bassin, J.P.

    2012-01-01

    The removal of nutrients such as nitrogen and phosphorus from both domestic and industrial wastewaters is imperative since they potentially harm the environment. One of the main consequences of excessive availability of nitrogen and phosphorus in aquatic ecosystems (freshwater, marine and estuarine) is the overgrowth of algae and other aquatic plants, a phenomenon designated as eutrophication. Algae and aquatic plants induce depletion of oxygen in water basins, resulting in massive death of e...

  18. Accumulation of selenium in aquatic systems downstream of a uranium mining operation in northern Saskatchewan, Canada

    International Nuclear Information System (INIS)

    Muscatello, J.R.; Belknap, A.M.; Janz, D.M.

    2008-01-01

    The objective of this study was to investigate the accumulation of selenium in lakes downstream of a uranium mine operation in northern Saskatchewan, Canada. Selenium concentrations in sediment and biota were elevated in exposure areas even though water concentrations were low (<5 μg/L). The pattern (from smallest to largest) of selenium accumulation was: periphyton < plankton and filterer invertebrates < detritivore and predator invertebrates < small bodied (forage) fish and predatory fish. Biomagnification of selenium resulted in an approximately 1.5-6 fold increase in the selenium content between plankton, invertebrates and forage fish. However, no biomagnification was observed between forage fish and predatory fish. Selenium content in organisms from exposure areas exceeded the proposed 3-11 μg/g (dry weight) dietary toxicity threshold for fish, suggesting that the selenium released into these aquatic systems has the potential to bioaccumulate and reach levels that could impair fish reproduction. - Selenium bioaccumulation patterns in a north temperate, cold water aquatic ecosystem were similar to those reported from warm water systems

  19. Chemical cocktails in aquatic systems: Pesticide effects on the response and recovery of >20 animal taxa

    International Nuclear Information System (INIS)

    Hua, Jessica; Relyea, Rick

    2014-01-01

    Natural systems are often exposed to individual insecticides or combinations of multiple insecticides. Using an additive and substitutive design, we examined how populations and communities containing >20 animal taxa are affected by four insecticides applied individually and as a mixture for 18 wks in aquatic mesocosms. The four insecticides had distinct lethal effects on the response and recovery of cladocerans, copepods, amphipods, isopods, and amphibians but not snails. The lethal effect on cladocerans and copepods induced trophic cascades that facilitated algal blooms and abiotic changes (higher pH and dissolved oxygen, but lower light transmission). Exposure to endosulfan resulted in a lag effect reducing cladocerans and spring-breeding amphibian abundance. The reduction in spring-breeding amphibian abundance led to cascading indirect effects on summer-breeding amphibians. Finally, the mixture treatment had lethal effects throughout the community that led to long-term effects on amphibian mass and unique indirect consequences on phytoplankton and abiotic variables. - Highlights: • Insecticides had unique direct and indirect effects on response and recovery. • Due to lag effects, endosulfan was more toxic than expected based on 4d tests. • Variation in oviposition phenology led to positive effects on amphibians. • Lethal direct effects of mixtures were pervasive and led to unique indirect effects. - Insecticides applied individually and in a mixture have complex direct and indirect consequences on aquatic system response and recovery

  20. Development of a definitive method for iodine speciation in aquatic systems

    International Nuclear Information System (INIS)

    Reifenhaeuser, C.; Heumann, K.G.

    1990-01-01

    A definitive method of isotope dilution mass spectrometry (IDMS) was developed to determine four different iodine species in aquatic systems (iodide, iodate and two organoiodine compounds: one of the organic species is chromatographically elutable from a column filled with an anion exchanger resin, the other one is not). The iodine species were analysed after the isotope dilution step with an enriched 129 I spike and after their chromatographic separation. The total iodine concentration was measured after decomposition of organic compounds in the aquatic system by UV irradiation. Different types of natural water samples (river water, water of a pond, moorland lake water) were analysed and important water parameters like pH-value, redox potential, oxygen content and dissolved organic carbon were measured for each of these samples. The total iodine concentration in the different samples differed only slightly in the range of 2-7 μg/l. In most of the moorland lake water samples only the two organoiodine species could be detected. In these samples the concentration of iodide and iodate was less than the detection limit of 0.5 μg/l and 0.1 μg/l, respectively. On the other hand, all four iodine species could be determined in most of the river water samples. Positive correlations were found for the oxygen content of the water samples and the iodate concentration as well as for the redox potential and the anionic organoiodine compound. (orig.)

  1. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  2. Decision Making in Biological Systems

    DEFF Research Database (Denmark)

    Tian, Chengzhe

    This thesis consists of five projects in three topics with a shared theme of understanding cellular decision-making processes with mathematical modeling. In the first topic, we address the possible interaction between bacterial Toxin-Antitoxin (TA) systems and stringent response alarmone guanosin...

  3. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  4. Biodegradability of dissolved organic carbon in permafrost soils and aquatic systems: a meta-analysis

    Science.gov (United States)

    Vonk, J. E.; Tank, S. E.; Mann, P. J.; Spencer, R. G. M.; Treat, C. C.; Striegl, R. G.; Abbott, B. W.; Wickland, K. P.

    2015-12-01

    As Arctic regions warm and frozen soils thaw, the large organic carbon pool stored in permafrost becomes increasingly vulnerable to decomposition or transport. The transfer of newly mobilized carbon to the atmosphere and its potential influence upon climate change will largely depend on the degradability of carbon delivered to aquatic ecosystems. Dissolved organic carbon (DOC) is a key regulator of aquatic metabolism, yet knowledge of the mechanistic controls on DOC biodegradability is currently poor due to a scarcity of long-term data sets, limited spatial coverage of available data, and methodological diversity. Here, we performed parallel biodegradable DOC (BDOC) experiments at six Arctic sites (16 experiments) using a standardized incubation protocol to examine the effect of methodological differences commonly used in the literature. We also synthesized results from 14 aquatic and soil leachate BDOC studies from across the circum-arctic permafrost region to examine pan-arctic trends in BDOC. An increasing extent of permafrost across the landscape resulted in higher DOC losses in both soil and aquatic systems. We hypothesize that the unique composition of (yedoma) permafrost-derived DOC combined with limited prior microbial processing due to low soil temperature and relatively short flow path lengths and transport times, contributed to a higher overall terrestrial and freshwater DOC loss. Additionally, we found that the fraction of BDOC decreased moving down the fluvial network in continuous permafrost regions, i.e. from streams to large rivers, suggesting that highly biodegradable DOC is lost in headwater streams. We also observed a seasonal (January-December) decrease in BDOC in large streams and rivers, but saw no apparent change in smaller streams or soil leachates. We attribute this seasonal change to a combination of factors including shifts in carbon source, changing DOC residence time related to increasing thaw-depth, increasing water temperatures later

  5. Neonicotinoids in the Canadian aquatic environment: a literature review on current use products with a focus on fate, exposure, and biological effects.

    Science.gov (United States)

    Anderson, J C; Dubetz, C; Palace, V P

    2015-02-01

    Developed to replace organophosphate and carbamate insecticides, neonicotinoids are structurally similar to nicotine. The three main neonicotinoid insecticides, imidacloprid, clothianidin, and thiamethoxam, are being re-evaluated by Health Canada's Pest Management Regulatory Agency (PMRA). An important aspect of the re-evaluation is the potential for effects in non-target organisms, including aquatic organisms. Leaching into surface waters is one of the major concerns surrounding extensive use of neonicotinoids, especially in close proximity to water bodies. The PMRA has classified IMI as 'persistent' with a 'high' leaching potential. Globally, neonicotinoids have been detected in a variety of water bodies, typically at concentrations in the low μg/L range. While IMI has been included in some monitoring exercises, there are currently very few published data for the presence of CLO and THM in Canadian water bodies. The majority of neonicotinoid toxicity studies have been conducted with IMI due to its longer presence on the market and high prevalence of use. Aquatic insects are particularly vulnerable to neonicotinoids and chronic toxicity has been observed at concentrations of IMI below 1 μg/L. Acute toxicity has been reported at concentrations below 20 μg/L for the most sensitive species, including Hyalella azteca, ostracods, and Chironomus riparius. Fish, algae, amphibians, and molluscs are relatively insensitive to IMI. However, the biological effects of THM and CLO have not been as well explored. The Canadian interim water quality guideline for IMI is 0.23 μg/L, but there is currently insufficient use, fate, and toxicological information available to establish guidelines for CLO and THM. Based on concentrations of neonicotinoids reported in surface waters in Canada and globally, there is potential for aquatic invertebrates to be negatively impacted by neonicotinoids. Therefore, it is necessary to address knowledge gaps to inform decisions around guidelines

  6. Expanding Aquatic Observations through Recreation

    Directory of Open Access Journals (Sweden)

    Robert J. W. Brewin

    2017-11-01

    Full Text Available Accurate observations of the Earth system are required to understand how our planet is changing and to help manage its resources. The aquatic environment—including lakes, rivers, wetlands, estuaries, coastal and open oceans—is a fundamental component of the Earth system controlling key physical, biological, and chemical processes that allow life to flourish. Yet, this environment is critically undersampled in both time and space. New and cost-effective sampling solutions are urgently needed. Here, we highlight the potential to improve aquatic sampling by tapping into recreation. We draw attention to the vast number of participants that engage in aquatic recreational activities and argue, based on current technological developments and recent research, that the time is right to employ recreational citizens to improve large-scale aquatic sampling efforts. We discuss the challenges that need to be addressed for this strategy to be successful (e.g., sensor integration, data quality, and citizen motivation, the steps needed to realize its potential, and additional societal benefits that arise when engaging citizens in scientific sampling.

  7. Systems Biology and Stem Cell Pluripotency

    DEFF Research Database (Denmark)

    Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

    2016-01-01

    Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

  8. Laser-induced photoacoustic spectroscopy for the speciation of transuranic elements in natural aquatic systems

    International Nuclear Information System (INIS)

    Kim, J.I.; Stumpe, R.; Klenze, R.

    1991-01-01

    Laser-induced photoacoustic spectroscopy (LPAS) is a new elegant instrumentation for the chemical speciation of aquatic transuranium (TRU) ions in very dilute concentrations (>10 -8 mol L -1 ). The paper describes the principle of LPAS and its application to the study of the chemical behaviour of TRU ions in natural aquatic systems, the knowledge of which has become increasingly in demand in connection with the safety analysis of nuclear waste disposal in the geosphere. The first part of the paper describes the principle, instrumentation and characteristics of LPAS in aqueous solution, taking particular examples from our own experience. The theoretical estimation of the speciation sensitivity is demonstrated and the result is compared with experiment. The second part deals with the spectral work in aqueous solution and then with the application of LPAS for the speciation of TRU ions in groundwater. Some examples demonstrated are hydrolysis reaction, complexation and colloid generation of the Am 3+ ion. Speciation sensitivities of U, Np, Pu and Am of different oxidation states in a variety of aqueous solutions are summarized. The application is of course open to a broad field of microchemistry in which the conventional spectrophotometric method has difficulty with sensitivity

  9. Modelling approaches to thermal pollution in inland aquatic systems and issues related to its environmental impacts

    International Nuclear Information System (INIS)

    Mahadevan, T.N.; Nair, R.N.; Sadasivan, S.

    2002-01-01

    Guidelines for the safe discharge of thermal effluents in aquatic environmental systems both surface water and marine coastal out falls has become very relevant to Indian environmental conditions with its rich biodiversity. While aquatic ecology may form the basis for such guidelines, the need for regulatory approach to the related issues has become the prime mover in thermal discharge problems. This is more so since the impacts considered are under short term and long term exposure conditions where the bio acclimatization and thermal stress factors may come to cross roads. Constant temperatures and cyclic temperature elevations also causes differential thermal stress which could be site specific. The recent notification by the Ministry of Environment and Forest (MoEF) revising the temperature limit for discharge of condenser cooling water from thermal power plants into coastal areas using sea water from 5 deg to 7 degC over and above the ambient temperature of the receiving water bodies. Discussions on whether the limiting temperature is to be achieved at the point of discharge or within a specified zone of the thermal plume is currently being debated. The act also stipulates installation of cooling towers using water from rivers, lakes and reservoirs irrespective of the plant location and capacity. For existing thermal plants the rise in temperature of the condenser cooling water from inlet to the let of the condenser shall not be more than 10 degC. (author)

  10. MOIRA models and methodologies for assessing the effectiveness of countermeasures in complex aquatic systems contaminated by radionuclides

    Energy Technology Data Exchange (ETDEWEB)

    Monte, L. [ENEA, Centro Ricerche Casaccia, Rome (Italy). Dipt. Ambiente; Brittain, J.E. [Oslo Univ., Oslo (Norway); Zoological Museum, Oslo (Norway); Haakanson, L. [Uppsala Univ., Uppsala (Sweden). Inst. of Earth Science; Gallego Diaz, E. [Madrid Univ. Politecnica, Madrid (Spain). Dept. de Ingenieria Nuclear

    1999-07-01

    The present report is composed of a set of articles written by the partners of the MOIRA project (a model-based computerized system for management support to identify optimal remedial strategies for restoring radionuclide contaminated aquatic ecosystems and drainage areas). The report describes models for predicting the behaviour of radionuclides in complex aquatic systems and the effects of countermeasures for their restoration. [Italian] Il rapporto contiene articoli preparati nell'ambito del progetto MOIRA (a model-based computerized system for management support to identify optimal remedial strategies for restoring radionuclide contaminated aquatic ecosystems and drainage areas), che descrive alcuni modelli per la previsione del comportamento di radionuclidi in sistemi acquatici complessi e per la valutazione dell'effetto delle contromisure per il loro recupero.

  11. MOIRA models and methodologies for assessing the effectiveness of countermeasures in complex aquatic systems contaminated by radionuclides

    Energy Technology Data Exchange (ETDEWEB)

    Monte, L [ENEA, Centro Ricerche Casaccia, Rome (Italy). Dipt. Ambiente; Brittain, J E [Oslo Univ., Oslo (Norway); Zoological Museum, Oslo [Norway; Haakanson, L [Uppsala Univ., Uppsala (Sweden). Inst. of Earth Science; Gallego Diaz, E [Madrid Univ. Politecnica, Madrid (Spain). Dept. de Ingenieria Nuclear

    1999-07-01

    The present report is composed of a set of articles written by the partners of the MOIRA project (a model-based computerized system for management support to identify optimal remedial strategies for restoring radionuclide contaminated aquatic ecosystems and drainage areas). The report describes models for predicting the behaviour of radionuclides in complex aquatic systems and the effects of countermeasures for their restoration. [Italian] Il rapporto contiene articoli preparati nell'ambito del progetto MOIRA (a model-based computerized system for management support to identify optimal remedial strategies for restoring radionuclide contaminated aquatic ecosystems and drainage areas), che descrive alcuni modelli per la previsione del comportamento di radionuclidi in sistemi acquatici complessi e per la valutazione dell'effetto delle contromisure per il loro recupero.

  12. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

  13. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  14. Temporal Changes in Photochemically Labile DOM and Implications for Carbon Budgets in Peatland Aquatic Systems

    Science.gov (United States)

    Pickard, A.

    2015-12-01

    Aquatic systems in peatland catchments are subject to high loading of dissolved organic matter (DOM) from surrounding terrestrial environments. However the significance of photochemical transformation of DOM in peatland carbon budgets remains poorly constrained. In this study UV irradiation experiments were conducted on water samples collected over one year from two contrasting systems in Scotland: a stream draining a peatland with high levels of DOM and a reservoir draining a peat catchment with low levels of DOM. Further samples were collected from the high DOM system during two storm events. After experimental exposure, optical and chemical analyses were employed to determine photochemical lability of the DOM pool. At both sites irradiation-induced decreases in dissolved organic carbon (DOC) as a percentage of the total carbon pool were greatest in winter, suggesting that DOM was depleted in photo-reactive molecules in summer. Seasonal variability in DOC was high at the stream site and was positively correlated with CO₂ and CO photoproduction (r2 = 0.81 and 0.83, respectively; pLignin phenol analyses indicate considerable contribution of peat to the DOM pool at the stream site, particularly during summer. Whilst DOC concentrations did not vary greatly during storm events, UV-Vis absorbance indicators did, signifying changing DOM source material from activation of different hydrological pathways. The most photo-reactive DOM occurred 5-10 hours after peak discharge, suggesting that storms replenish photochemically labile DOM in headwater streams. Conservative estimates using data from this study suggest that up to 7% of the DOM pool of peatland streams can be lost (primarily as CO₂ and CO) upon exposure to 8 hours of environmentally representative UV irradiation. Further investigation in field campaigns under natural UV exposure are underway to assess the importance of photodegradation of DOM as a loss pathway of carbon based gases from aquatic systems.

  15. Systems biology solutions for biochemical production challenges

    DEFF Research Database (Denmark)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

    2017-01-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

  16. Systems biology solutions for biochemical production challenges.

    Science.gov (United States)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

    2017-06-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. Radioecology of the aquatic environment

    International Nuclear Information System (INIS)

    Amiard-Triquet, C.; Amiard, J.C.

    1980-01-01

    This book is divided into nine parts as follows: origin of radionuclides in the aquatic environment; assessment of radioactive contamination of the aquatic environment; evolution of radionuclides in waters; behaviour of radionuclides in sediments; quantitative data on accumulation, distribution and biological release of radioactive pollutants; mechanisms of the biological accumulation; influence of ecological factors on radioactive contamination of ecosystems; effects of irradiation on aquatic organisms. The last part is devoted to general conclusions on sanitary and ecological consequences of radioactive pollution of the aquatic environment [fr

  18. Plant-microbe interaction in aquatic system and their role in the management of water quality: a review

    Science.gov (United States)

    Srivastava, Jatin K.; Chandra, Harish; Kalra, Swinder J. S.; Mishra, Pratibha; Khan, Hena; Yadav, Poonam

    2017-06-01

    Microbial assemblage as biofilm around the aquatic plant forms a firm association that largely depends upon the mutual supplies of nutrients, e.g., microbes interact with plants in an aquatic system most likely for organic carbon and oxygen, whereas plants receive defensive immunity and mineral exchange. Apart from the mutual benefits, plant-microbe interactions also influence the water quality especially at rhizosphere providing inherent ability to the aquatic system for the mitigation of pollution from the water column. The review presents and in-depth information along with certain research advancements made in the field of ecological and bio/chemical aspects of plant-microbe interactions and the underlying potential to improve water quality.

  19. GigaUnit Transplant System: A New Mechanical Tool for Transplanting Submerged Aquatic Vegetation

    National Research Council Canada - National Science Library

    Shafer, Deborah J

    2008-01-01

    Submerged aquatic vegetation (SAV) performs many important ecosystem functions, including wave attenuation and sediment stabilization, water quality improvement, primary production, food web support for secondary consumers...

  20. Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

    OpenAIRE

    Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  1. Medically-derived I-131: a potential tool for understanding the fate of wastewater nitrogen in aquatic systems

    Science.gov (United States)

    Rose, P. S.; Smith, J. P.; Aller, R. C.; Cochran, J. K.; Swanson, R. L.; Murthy, S. N.; Coffin, R. B.

    2010-12-01

    Iodine-131(t1/2 = 8 days) has been measured in Potomac River water and sediments in the vicinity of the Blue Plains Water Pollution Control Plant (WPCP), Washington, DC. The source of I-131 is medical, where it is commonly used to treat thyroid cancer and hyperthyroidism. Iodine is metabolized by patients and eliminated primarily in urine. While other medical radioisotopes may enter the environment via sewage effluent, the nature and quantity of treatments using I-131 cause it to account for much of the radioactivity in sewage effluent. Natural iodine in aquatic systems is biologically cycled similar to other nutrients, such as nitrogen. Iodine-131 concentrations measured in sewage effluent from Blue Plains WPCP and in the Potomac River suggest a relatively continuous discharge of this isotope. Dissolved I-131 shows a strong, positive correlation with δ15N values of nitrate in the river. The range of I-131 concentrations detected in surface waters is 0.18 ± 0.01 to 0.68 ± 0.02 Bq/L. Surface water δ15NO3 values ranged from 8.7 ± 0.3 to 33.4 ± 7.3 ‰ with NO3+NO2 concentrations between 0.38 ± 0.02 and 2.79 ± 0.13 mgN/L. Sediment profiles of particulate I-131 and δ15N indicate rapid mixing or sedimentation and in many cases remineralization of a heavy nitrogen source consistent with wastewater nitrogen. Iodine-131 concentrations in sediments ranged from 1.31 ± 0.8 to 117 ± 2 Bq/kg dry weight. Values of δ15N in sediments ranged from 4.7 ± 0.1 ‰ to 9.3 ± 0.1 ‰. We propose that I-131 coupled with δ15N can be an excellent tracer for the short-term fate of wastewater nitrogen in this system. However, the utility of I-131 as a tracer is not limited to use in the Potomac River. Other studies have documented the presence of I-131 in several aquatic systems and continuous discharges of this radioisotope in sewage effluent are likely to be widespread in urban environments.

  2. Systems Biology — the Broader Perspective

    Directory of Open Access Journals (Sweden)

    Jonathan Bard

    2013-06-01

    Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

  3. Quantitative evaluation of environmental factors influencing the dynamics of mercury in the aquatic systems

    International Nuclear Information System (INIS)

    Akagi, H.; Sakamoto, M.

    2001-01-01

    A highly sensitive radiochemical technique for evaluating the transformation and distribution of mercury has been developed to facilitate studies on the kinetics of mercury in the aquatic systems. Sediment, water, or biota, previously spiked with 203-mercuric compounds and incubated for a few or several weeks, are extracted with 0.1% dithizone-benzene(Dz-Bz) after an appropriate pretreatment to dissolve the incorporated mercury compounds. The quantitative separation of inorganic mercury and methylmercury in the Dz-Bz extract is done by thin-layer chromatography, before the mercury species are analyzed radiometrically using a gamma counter. The technique is applicable to a wide range of environmental materials contaminated with mercury down to very low background concentrations. (author)

  4. Characterisation and quantification of organic phosphorus and organic nitrogen components in aquatic systems: A Review

    Energy Technology Data Exchange (ETDEWEB)

    Worsfold, Paul J. [School of Earth, Ocean and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL48AA (United Kingdom)], E-mail: pworsfold@plymouth.ac.uk; Monbet, Philippe [School of Earth, Ocean and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL48AA (United Kingdom); Water Studies Centre, School of Chemistry, Monash University, Clayton 3800, Victoria (Australia); Tappin, Alan D.; Fitzsimons, Mark F.; Stiles, David A. [School of Earth, Ocean and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL48AA (United Kingdom); McKelvie, Ian D. [Water Studies Centre, School of Chemistry, Monash University, Clayton 3800, Victoria (Australia)

    2008-08-22

    This review provides a critical assessment of knowledge regarding the determination of organic phosphorus (OP) and organic nitrogen (ON) in aquatic systems, with an emphasis on biogeochemical considerations and analytical challenges. A general background on organic phosphorus and organic nitrogen precedes a discussion of sample collection, extraction, treatment/conditioning and preconcentration of organic phosphorus/nitrogen from sediments, including suspended particulate matter, and waters, including sediment porewaters. This is followed by sections on the determination of organic phosphorus/nitrogen components. Key techniques covered for organic phosphorus components are molecular spectrometry, atomic spectrometry and enzymatic methods. For nitrogen the focus is on the measurement of total organic nitrogen concentrations by carbon hydrogen nitrogen analysis and high temperature combustion, and organic nitrogen components by gas chromatography, high-performance liquid chromatography, gel electrophoresis, mass spectrometry, nuclear magnetic resonance spectrometry, X-ray techniques and enzymatic methods. Finally future trends and needs are discussed and recommendations made.

  5. Using a holistic approach to assess the impact of engineered nanomaterials inducing toxicity in aquatic systems.

    Science.gov (United States)

    He, Xiaojia; Aker, Winfred G; Leszczynski, Jerzy; Hwang, Huey-Min

    2014-03-01

    In this report, we critically reviewed selected intrinsic physicochemical properties of engineered nanomaterials (ENMs) and their role in the interaction of the ENMs with the immediate surroundings in representative aquatic environments. The behavior of ENMs with respect to dynamic microenvironments at the nano-bio-eco interface level, and the resulting impact on their toxicity, fate, and exposure potential are elaborated. Based on this literature review, we conclude that a holistic approach is urgently needed to fulfill our knowledge gap regarding the safety of discharged ENMs. This comparative approach affords the capability to recognize and understand the potential hazards of ENMs and their toxicity mechanisms, and ultimately to establish a quantitative and reliable system to predict such outcomes. Copyright © 2014. Published by Elsevier B.V.

  6. Virus-Bacterium Interactions in Water and Sediment of West African Inland Aquatic Systems

    Science.gov (United States)

    Bettarel, Yvan; Bouvy, Marc; Dumont, Claire; Sime-Ngando, Télesphore

    2006-01-01

    The ecology of virioplankton in tropical aquatic ecosystems is poorly documented, and in particular, there are no references concerning African continental waters in the literature. In this study, we examined virus-bacterium interactions in the pelagic and benthic zones of seven contrasting shallow inland waters in Senegal, including one hypersaline lake. SYBR Gold-stained samples revealed that in the surface layers of the sites, the numbers of viruses were in the same range as the numbers of viruses reported previously for productive temperate systems. Despite high bacterial production rates, the percentages of visibly infected cells (as determined by transmission electron microscopy) were similar to the lowest percentages (range, 0.3 to 1.1%; mean, 0.5%) found previously at pelagic freshwater or marine sites, presumably because of the local environmental and climatic conditions. Since the percentages of lysogenic bacteria were consistently less than 8% for pelagic and benthic samples, lysogeny did not appear to be a dominant strategy for virus propagation at these sites. In the benthic samples, viruses were highly concentrated, but paradoxically, no bacteria were visibly infected. This suggests that sediment provides good conditions for virus preservation but ironically is an unfavorable environment for proliferation. In addition, given the comparable size distributions of viruses in the water and sediment samples, our results support the paradigm that aquatic viruses are ubiquitous and may have moved between the two compartments of the shallow systems examined. Overall, this study provides additional information about the relevance of viruses in tropical areas and indicates that the intensity of virus-bacterium interactions in benthic habitats may lower than the intensity in the adjacent bodies of water. PMID:16885276

  7. Persistence of organophosphorus pesticides in aquatic environments. Coordinated programme on isotope-tracer-aided research and monitoring on agricultural residue - biological interactions in aquatic environment

    International Nuclear Information System (INIS)

    Horvath, L.

    1982-08-01

    A radiometric enzymic assay method was developed for quick measuring of organophosphorous insecticides in water samples. All steps of the assay procedure were carried out in scintillation vials. 50 μl enzyme solution (acetylcholinesterase of electric eel) and 50 μl buffer pH 7 were pipetted into the vial followed by 100 μl of water sample or aqueous solution of the insecticide and the mixture was incubated for 60 minutes. 50 μl 3 H-acetylcholine were added to the vial and the enzymic reaction stopped after 10 minutes by adding 200 μl buffer solution pH 2.5. 10 ml scintillation cocktail were then added and after shaking and 30 minutes standing the radioactivity was determined in a liquid scintillation spectrometer. Acetylcholine remained in the water phase while 3 H-acetic acid released in enzymic hydrolysis may be extracted by an organic solvent. By this method, not only the parent compound but also some of its degradation products, which possess some anticholinesteratic activity can be measured. The method is suitable for combination with thin-layer chromatography for identification purposes. Using this method, we studied the degradation of the organophosphorous insecticides malathion, parathion, DDVP and imidan. The degradation in distilled water and natural water was compared. For example, the half-time of malathion in distilled water at room temperature was 6 days while in natural water (Danube river) it was 4 hours. The degradation processes were also studied in model systems containing sediment and water. Degradation was faster in models containing solid particles than in filtered water. The radiometric enzymic method was tested as analytical procedure for residue monitoring. Since 1978 a residue monitoring programme was in progress in the Danube river near Budapest. Occasionally high residue levels were detected in spring and early summer. The radiometric enzymic method has proved to be a useful analytical method for anticholinesterase pesticides in

  8. Systems Biology for Organotypic Cell Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

    2016-08-04

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

  9. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-01-01

    This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the…

  10. Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2010-10-01

    Introduction Duchenne muscular dystrophy (DMD) is the most common and incurable muscular dystrophy of childhood. Muscle regeneration fails with...SUBJECT TERMS Duchenne Muscular dystrophy , Glucocorticoids, Systems biology, Drug mechanism 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION...better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant proposal is led by Dr. Eric Hoffman, and it

  11. Modular microfluidic system for biological sample preparation

    Science.gov (United States)

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  12. Radiological/biological/aerosol removal system

    Science.gov (United States)

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  13. Notions of radiation chemistry in biological systems

    International Nuclear Information System (INIS)

    Mastro, N.L. del.

    1989-10-01

    The present paper examines some aspects of the direct and indirect biological radiation effects: pair formation, free radicals, superoxide ion, hydrogen peroxide, hydroxyl radical, oxygen singlet together with the endogen radioprotector mechanisms of organisms and the ways in which an improved radioresistance of biochemical systems can be achieved. (author) [pt

  14. Amoxicillin in a biological water recovery system

    International Nuclear Information System (INIS)

    Morse, A.; Jackson, A.; Rainwater, K.; Pickering, K.

    2002-01-01

    Pharmaceuticals are new contaminants of concern in the aquatic environment, having been identified in groundwater, surface water, and residential tap water. Possible sources of pharmaceuticals include household wastewaters, runoff from feedlots, or waste discharges from pharmaceutical manufacturing plants. When surface water or groundwater supplies impacted by pharmaceuticals are used in drinking water production, the contaminants may reduce drinking water quality. Many pharmaceuticals, such as amoxicillin, pass through the body largely unmetabolized and directly enter wastewater collection systems. Pharmaceuticals are designed to persist in the body long enough to have the desired therapeutic effect. Therefore, they may also have the ability to persist in the environment (Seiler et al, 1999). The purpose of this work is to determine the overall transformation potential of a candidate pharmaceutical in wastewater treatment with specific emphasis on recycle systems. Amoxicillin is the selected pharmaceutical agent, an orally absorbed broad-spectrum antibiotic with a variety of clinical uses including ear, nose, and throat infections and lower respiratory tract infections. Experiments were conducted using an anaerobic reactor (with NO 3 - and NO 2 - as the e - acceptors) followed by a two-phase nitrifying tubular reactor. Influent composed of water, urine and surfactant was spiked with amoxicillin and fed into the wastewater recycle system. The concentration of amoxicillin in the feed and effluent was quantified using an HPLC. Results from this study include potential for long-term buildup in recycled systems, accumulation of breakdown products and possible transfer of antibiotic resistance to microorganisms in the system effluent. In addition, the results of this study may provide information on contamination potential for communities that are considering supplementing drinking water supplies with recovered wastewater or for entities considering a closed loop

  15. Tritium and 14C background levels in pristine aquatic systems and their potential sources of variability

    International Nuclear Information System (INIS)

    Eyrolle-Boyer, Frédérique; Claval, David; Cossonnet, Catherine; Zebracki, Mathilde; Gairoard, Stéphanie; Radakovitch, Olivier; Calmon, Philippe; Leclerc, Elisabeth

    2015-01-01

    Tritium and 14 C are currently the two main radionuclides discharged by nuclear industry. Tritium integrates into and closely follows the water cycle and, as shown recently the carbon cycle, as does 14 C (Eyrolle-Boyer et al., 2014a, b). As a result, these two elements persist in both terrestrial and aquatic environments according to the recycling rates of organic matter. Although on average the organically bound tritium (OBT) activity of sediments in pristine rivers does not significantly differ today (2007–2012) from the mean tritiated water (HTO) content on record for rainwater (2.4 ± 0.6 Bq/L and 1.6 ± 0.4 Bq/L, respectively), regional differences are expected depending on the biomass inventories affected by atmospheric global fallout from nuclear testing and the recycling rate of organic matter within watersheds. The results obtained between 2007 and 2012 for 14 C show that the levels varied between 94.5 ± 1.5 and 234 ± 2.7 Bq/kg of C for the sediments in French rivers and across a slightly higher range of 199 ± 1.3 to 238 ± 3.1 Bq/kg of C for fish. This variation is most probably due to preferential uptake of some organic carbon compounds by fish restraining 14 C dilution with refractory organic carbon and/or with old carbonates both depleted in 14 C. Overall, most of these ranges of values are below the mean baseline value for the terrestrial environment (232.0 ± 1.8 Bq/kg of C in 2012, Roussel-Debet, 2014a) in relation to dilution by the carbonates and/or fossil organic carbon present in aquatic systems. This emphasises yet again the value of establishing regional baseline value ranges for these two radionuclides in order to account for palaeoclimatic and lithological variations. Besides, our results obtained from sedimentary archive investigation have confirmed the delayed contamination of aquatic sediments by tritium from the past nuclear tests atmospheric fallout, as recently demonstrated from data chronicles (Eyrolle-Boyer et al., 2014a

  16. Caffeine and paraxanthine in aquatic systems: Global exposure distributions and probabilistic risk assessment.

    Science.gov (United States)

    Rodríguez-Gil, J L; Cáceres, N; Dafouz, R; Valcárcel, Y

    2018-01-15

    This study presents one of the most complete applications of probabilistic methodologies to the risk assessment of emerging contaminants. Perhaps the most data-rich of these compounds, caffeine, as well as its main metabolite (paraxanthine), were selected for this study. Information for a total of 29,132 individual caffeine and 7442 paraxanthine samples was compiled, including samples where the compounds were not detected. The inclusion of non-detect samples (as censored data) in the estimation of environmental exposure distributions (EEDs) allowed for a realistic characterization of the global presence of these compounds in aquatic systems. EEDs were compared to species sensitivity distributions (SSDs), when possible, in order to calculate joint probability curves (JPCs) to describe the risk to aquatic organisms. This way, it was determined that unacceptable environmental risk (defined as 5% of the species being potentially exposed to concentrations able to cause effects in>5% of the cases) could be expected from chronic exposure to caffeine from effluent (28.4% of the cases), surface water (6.7% of the cases) and estuary water (5.4% of the cases). Probability of exceedance of acute predicted no-effect concentrations (PNECs) for paraxanthine were higher than 5% for all assessed matrices except for drinking water and ground water, however no experimental effects data was available for paraxanthine, resulting in a precautionary deterministic hazard assessment for this compound. Given the chemical similarities between both compounds, real effect thresholds, and thus risk, for paraxanthine, would be expected to be close to those observed for caffeine. Negligible Human health risk from exposure to caffeine via drinking or groundwater is expected from the compiled data. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. A comparison of freshwater mussels and passive samplers as indicators of heavy metal pollution in aquatic systems

    DEFF Research Database (Denmark)

    Søberg, Laila C.; Vollertsen, Jes; Nielsen, Asbjørn Haaning

    2013-01-01

    under controlled conditions in order to determine whether either system was capable of functioning as a reliable source of data on aquatic pollution. The laboratory results indicated that mussels are useful in this context. However, passive samplers will require further development to be useful since...

  18. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...... of a system thereby suggesting new ways of thinking specific toxicological endpoints. Furthermore, computational methods can serve as valuable input for the hypothesis generating phase of the preparations of a research project....

  19. Physical data and biological data for algae, aquatic invertebrates, and fish from selected reaches on the Carson and Truckee rivers, Nevada and California, 1993-97

    Science.gov (United States)

    Lawrence, S.J.; Seiler, R.L.

    2002-01-01

    This report, a product of the National Water- Quality Assessment Program, is a compilation of physical data and biological data for algae, aquatic invertebrates, and fish collected in the Carson and Truckee River Basins, Nevada and California. Most of the data were collected between 1993 and 1996 at selected reaches on the Carson and Truckee Rivers. Algae and aquatic invertebrate samples were collected from cobble riffles, submerged woody-snag habitats, and from depositional areas such as pools. Between 1993 and 1996, fish and crayfish were collected from all wadeable habitats at each of seven basic-fixed sites using either electroshocking methods or seining. Additional fish and crayfish were collected at one site on the Truckee River in 1997. Fish were identified to species, measured for total and standard length, checked for anomalies, and weighed at the collection site. Fish were returned to the stream after measurements were taken. Measurements of water depth, stream velocity, determinations of substrate type and substrate embeddedness were made at each sampling site. Algae and aquatic invertebrate samples were sent to the U.S. Geological Survey National Water-Quality Laboratory for identification and enumeration. A total of 103 semi-quantitative and 55 qualitative algae samples were collected at 20 river reaches on the Carson and Truckee Rivers between 1993 and 1996. These samples represent algae in cobble riffles, on submerged woody snags, and on sediment surfaces in depositional areas. In those 158 samples, 514 algal species, varieties, or forms were identified. Of the 8 algal phyla represented, the diatoms (Phylum Bacillariophyta) were the most abundant with 351 species, varieties, or forms. The green algae (Phylum Chlorophyta) were next in abundance with 108 species, varieties, or forms followed by the blue-green algae (Phylum Cyanophyta) with 41 species, varieties, or forms. A total of 49 semi-quantitative aquatic invertebrate samples were collected at 27

  20. In-situ non-invasive device for early detection of fouling in aquatic systems

    KAUST Repository

    Fortunato, Luca

    2017-01-05

    An in-situ, non-destructive sensor device, system and method are provided to detect or assess fouling at a very early stage of development. They can be used to detect or assess fouling on a surface of an aquatic system. They can be used to obtain a depth profile of the fouling. Data concerning the depth profile can be extracted and used to assess the fouling on the surface, in one or more aspects, the method can include providing an optical tomography spectrometer; optically positioning the optical tomography spectrometer in association with a surface of an area to be assessed for fouling in an aqueous system; irradiating the surface; acquiring, from irradiating the surface, a plurality of signals as a function of a distance from the surface at different times; extracting data from the signals as a function of the distance to obtain a depth profile of the surface at the different times; and determining a change in the depth profile between the different times to assess fouling on the surface.

  1. Laser-induced photoacoustic spectroscopy for the specification of actinides in natural aquatic systems

    International Nuclear Information System (INIS)

    Stumpe, R.; Kim, J.I.

    1986-06-01

    A laser-induced photoacoustic spectroscopy is developed for the direct speciation of transuranic elements in natural aquatic systems. Speciation sensitivities are attained to the sub-μmol range, e.g., the Am 3+ ion with its molar absorption coefficient of 378 L -1 cm -1 can be detected up to 10 -8 mol L -1 . The first part of this monograph deals with the construction of spectrometer, the spectroscopic characterization and the sensitivity determination for transuranic elements of different oxidation states. With an introduction of differential detection system, the compensation of background effects is realized. The spectral work is automated by a special operating system including analog-digital data processing. The second part includes applications of the spectroscopy to the speciation of transuranic ions at concentrations -6 mol L -1 for their oxidation states, hydrolysis reactions, complexation, redox behaviour and colloid generation in various solutions. The third part comprises the systematic investigation of the chemical behaviour of transuranic elements in selected groundwaters in which multicomponent concurrent reactions are involved. (orig.) [de

  2. Data report: an assessment of the occurrence of human viruses in Long Island aquatic systems

    Energy Technology Data Exchange (ETDEWEB)

    Vaughn, J.M.; Landry, E.F.

    1977-12-01

    A virus survey was conducted in Nassau and Suffolk Counties under the auspices of the federally-funded ''208'' program from June 1976 to June 1977. The survey involved the concentration, enumeration, and identification of human enteroviruses from selected aquatic systems on Long Island including embayments, lakes, creeks, public drinking water supplies, groundwater influenced by wastewater recharge, sanitary landfills, and stormwater recharge basins; and the effluents from secondary and tertiary sewage treatment plants. Enteroviruses were isolated from all systems studied except the public water supply wells. As expected, viruses were most often encountered in the chlorinated effluents of sewage treatment plants. On two separate occasions, wild type Poliovirus was isolated from one of these plants. The limited sampling conducted at each site (1 per month) obviated any extensive interpretation of the data for the purpose of identifying the precise hazard posed by enteric viruses in Long Island waters. Among tentative conclusions were: support for the continued study of recharge of groundwater aquifers via the application of properly treated domestic wastewater to recharge basins; caution regarding placement of private septic systems in saturated zones near surface water bodies; the discharge of sewage effluents into embayments; and the identification of those areas requiring further virological study.

  3. The Dnieper River Aquatic System Radioactive Contamination; Long-tern Natural Attenuation And Remediation History

    Science.gov (United States)

    Voitsekhovych, Oleg; Laptev, Genadiy; Kanivets, Vladimir; Konoplev, Alexey

    2013-04-01

    Near 27 year passed after the Chernobyl Accident, and the experience gained to study radionuclide behavior in the aquatic systems and to mitigate water contamination are still pose of interest for scientists, society and regulatory austerities. There are different aspects of radionuclide transport in the environment were studied since the Chernobyl fallout in 1986 covered the river catchments, wetlands, river, lakes/reservoirs and reached the Black Sea. The monitoring time series data set and also data on the radionuclides behavior studies in the water bodies (river, lakes and the Black Sea) are available now in Ukraine and other affected countries. Its causation analyses, considering the main geochemical, physical and chemical and hydrological process, governing by radionuclide mobility and transport on the way from the initially contaminated catchments, through the river-reservoir hydrological system to the Black Sea can help in better understanding of the main factors governing be the radionuclide behavior in the environment. Radionuclide washout and its hydrological transport are determined speciation of radionuclides as well as soil types and hydrological mode and also geochemistry and landscape conditions at the affected areas. Mobility and bioavailability of radionuclides are determined by ratio of radionuclide chemical forms in fallout and site-specific environmental characteristics determining rates of leaching, fixation/remobilization as well as sorption-desorption of mobile fraction (its solid-liquid distribution). In many cases the natural attenuation processes governing by the above mentioned processes supported by water flow transportation and sedimentation played the key role in self-rehabilitation of the aquatic ecosystems. The models developed during post-Chernobyl decade and process parameters studies can help in monitoring and remediation programs planed for Fukusima Daichi affected watersheds areas as well. Some most important monitoring data

  4. Remaining Sites Verification Package for the 100-F-52, 146-FR Radioecology and Aquatic Biology Laboratory Soil. Attachment to Waste Site Reclassification Form 2008-022

    International Nuclear Information System (INIS)

    Capron, J.M.

    2008-01-01

    The 100-F-52 waste site consisted of the soil under and around the former 146-FR Radioecology and Aquatic Biology Laboratory. The laboratory was used for studies of the effects of pre-reactor and post-reactor process water on fish eggs, young fish, and other small river creatures of interest. In accordance with this evaluation, the confirmatory sampling results support a reclassification of this site to No Action. The current site conditions achieve the remedial action objectives and the corresponding remedial action goals established in the Remaining Sites ROD. The results of confirmatory sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River

  5. Remaining Sites Verification Package for the 100-F-52, 146-FR Radioecology and Aquatic Biology Laboratory Soil, Waste Site Reclassification Form 2008-022

    Energy Technology Data Exchange (ETDEWEB)

    J. M. Capron

    2008-06-27

    The 100-F-52 waste site consisted of the soil under and around the former 146-FR Radioecology and Aquatic Biology Laboratory. The laboratory was used for studies of the effects of pre-reactor and post-reactor process water on fish eggs, young fish, and other small river creatures of interest. In accordance with this evaluation, the confirmatory sampling results support a reclassification of this site to No Action. The current site conditions achieve the remedial action objectives and the corresponding remedial action goals established in the Remaining Sites ROD. The results of confirmatory sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

  6. Internal nitrogen removal from sediments by the hybrid system of microbial fuel cells and submerged aquatic plants.

    Directory of Open Access Journals (Sweden)

    Peng Xu

    Full Text Available Sediment internal nitrogen release is a significant pollution source in the overlying water of aquatic ecosystems. This study aims to remove internal nitrogen in sediment-water microcosms by coupling sediment microbial fuel cells (SMFCs with submerged aquatic plants. Twelve tanks including four treatments in triplicates were designed: open-circuit (SMFC-o, closed-circuit (SMFC-c, aquatic plants with open-circuit (P-SMFC-o and aquatic plants with closed-circuit (P-SMFC-c. The changes in the bio-electrochemical characteristics of the nitrogen levels in overlying water, pore water, sediments, and aquatic plants were documented to explain the migration and transformation pathways of internal nitrogen. The results showed that both electrogenesis and aquatic plants could facilitate the mineralization of organic nitrogen in sediments. In SMFC, electrogenesis promoted the release of ammonium from the pore water, followed by the accumulation of ammonium and nitrate in the overlying water. The increased redox potential of sediments due to electrogenesis also contributed to higher levels of nitrate in overlying water when nitrification in pore water was facilitated and denitrification at the sediment-water interface was inhibited. When the aquatic plants were introduced into the closed-circuit SMFC, the internal ammonium assimilation by aquatic plants was advanced by electrogenesis; nitrification in pore water and denitrification in sediments were also promoted. These processes might result in the maximum decrease of internal nitrogen with low nitrogen levels in the overlying water despite the lower power production. The P-SMFC-c reduced 8.1%, 16.2%, 24.7%, and 25.3% of internal total nitrogen compared to SMFC-o on the 55th, 82th, 136th, and 190th days, respectively. The smaller number of Nitrospira and the larger number of Bacillus and Pseudomonas on the anodes via high throughput sequencing may account for strong mineralization and denitrification in the

  7. Set membership experimental design for biological systems

    Directory of Open Access Journals (Sweden)

    Marvel Skylar W

    2012-03-01

    Full Text Available Abstract Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This

  8. Optoelectronic system and apparatus for connection to biological systems

    Science.gov (United States)

    Okandan, Murat; Nielson, Gregory N.

    2018-03-06

    The present invention relates to a biological probe structure, as well as apparatuses, systems, and methods employing this structure. In particular embodiments, the structure includes a hermetically sealed unit configured to receive and transmit one or more optical signals. Furthermore, the structure can be implanted subcutaneously and interrogated externally. In this manner, a minimally invasive method can be employed to detect, treat, and/or assess the biological target. Additional methods and systems are also provided.

  9. A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

    Science.gov (United States)

    Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

  10. Hydrolytic Activation Kinetics of the Herbicide Benzobicyclon in Simulated Aquatic Systems.

    Science.gov (United States)

    Williams, Katryn L; Tjeerdema, Ronald S

    2016-06-22

    Herbicide resistance is a growing concern for weeds in California rice fields. Benzobicyclon (BZB; 3-(2-chloro-4-(methylsulfonyl)benzoyl)-2-phenylthiobicyclo[3.2.1]oct-2-en-4-one) has proven successful against resistant rice field weeds in Asia. A pro-herbicide, BZB forms the active agent, benzobicyclon hydrolysate (BH), in water; however, the transformation kinetics are not understood for aquatic systems, particularly flooded California rice fields. A quantitative experiment was performed to assess the primary mechanism and kinetics of BZB hydrolysis to BH. Complete conversion to BH was observed for all treatments. Basic conditions (pH 9) enhanced the reaction, with half-lives ranging from 5 to 28 h. Dissolved organic carbon (DOC) hindered transformation, which is consistent with other base-catalyzed hydrolysis reactions. BH was relatively hydrolytically stable, with 18% maximum loss after 5 days. Results indicate BZB is an efficient pro-herbicide under aqueous conditions such as those of a California rice field, although application may be best suited for fields with recirculating tailwater systems.

  11. Pressure, O2, and CO2, in aquatic Closed Ecological Systems

    Science.gov (United States)

    Taub, Frieda B.; McLaskey, Anna K.

    2013-03-01

    Pressure increased during net photosynthetic O2 production in the light and decreased during respiratory O2 uptake during the dark in aquatic Closed Ecological Systems (CESs) with small head gas volumes. Because most CO2 will be in the liquid phase as bicarbonate and carbonate anions, and CO2 is more soluble than O2, volumes of gaseous CO2 and gaseous O2 will not change in a compensatory manner, leading to the development of pressure. Pressure increases were greatest with nutrient rich medium with NaHCO3 as the carbon source. With more dilute media, pressure was greatest with NaHCO3, and less with cellulose or no-added carbon. Without adequate turbulence, pressure measurements lagged dissolved O2 concentrations by several hours and dark respiration would have been especially underestimated in our systems (250-1000 ml). With adequate turbulence (rotary shaker), pressure measurements and dissolved O2 concentrations generally agreed during lights on/off cycles, but O2 measurements provided more detail. At 20 °C, 29.9 times as much O2 will distribute into the gas phase as in the liquid, per unit volume, as a result of the limited solubility of O2 in water and according to Henry's Law. Thus even a small head gas volume can contain more O2 than a larger volume of water. When both dissolved and gaseous O2 and CO2 are summed, the changes in Total O2 and CO2 are in relatively close agreement when NaHCO3 is the carbon source. These findings disprove an assumption made in some of Taub's earlier research that aquatic CESs would remain at approximately atmospheric pressure because approximately equal molar quantities of O2 and CO2 would exchange during photosynthesis and respiration; this assumption neglected the distribution of O2 between water and gas phases. High pressures can occur when NaHCO3 is the carbon source in nutrient rich media and if head-gas volumes are small relative to the liquid volume; e.g., one "worse case" condition developed 800 mm Hg above atmospheric

  12. Aquatic plants

    DEFF Research Database (Denmark)

    Madsen, T. V.; Sand-Jensen, K.

    2006-01-01

    Aquatic fl owering plants form a relatively young plant group on an evolutionary timescale. The group has developed over the past 80 million years from terrestrial fl owering plants that re-colonised the aquatic environment after 60-100 million years on land. The exchange of species between terre...... terrestrial and aquatic environments continues today and is very intensive along stream banks. In this chapter we describe the physical and chemical barriers to the exchange of plants between land and water.......Aquatic fl owering plants form a relatively young plant group on an evolutionary timescale. The group has developed over the past 80 million years from terrestrial fl owering plants that re-colonised the aquatic environment after 60-100 million years on land. The exchange of species between...

  13. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

  14. Complex biological and bio-inspired systems

    Energy Technology Data Exchange (ETDEWEB)

    Ecke, Robert E [Los Alamos National Laboratory

    2009-01-01

    The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

  15. Aquatic biota as potential biological indicators of the contamination, bioaccumulation and health risks caused by organochlorine pesticides in a large, shallow Chinese lake (Lake Chaohu)

    DEFF Research Database (Denmark)

    Liu, Wen-Xiu; Wang, Yan; He, Wei

    2016-01-01

    Aquatic biota have long been recognized as bioindicators of the contamination caused by hydrophobic organic contaminants (HOCs) in aquatic environments. The primary purpose of the present study is to identify which species of aquatic biota are the most sensitive to organochlorine pesticides (OCPs...

  16. Life: An Introduction to Complex Systems Biology

    CERN Document Server

    Kaneko, Kunihiko

    2006-01-01

    What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

  17. Tritium and 14C background levels in pristine aquatic systems and their potential sources of variability.

    Science.gov (United States)

    Eyrolle-Boyer, Frédérique; Claval, David; Cossonnet, Catherine; Zebracki, Mathilde; Gairoard, Stéphanie; Radakovitch, Olivier; Calmon, Philippe; Leclerc, Elisabeth

    2015-01-01

    Tritium and (14)C are currently the two main radionuclides discharged by nuclear industry. Tritium integrates into and closely follows the water cycle and, as shown recently the carbon cycle, as does (14)C (Eyrolle-Boyer et al., 2014a, b). As a result, these two elements persist in both terrestrial and aquatic environments according to the recycling rates of organic matter. Although on average the organically bound tritium (OBT) activity of sediments in pristine rivers does not significantly differ today (2007-2012) from the mean tritiated water (HTO) content on record for rainwater (2.4 ± 0.6 Bq/L and 1.6 ± 0.4 Bq/L, respectively), regional differences are expected depending on the biomass inventories affected by atmospheric global fallout from nuclear testing and the recycling rate of organic matter within watersheds. The results obtained between 2007 and 2012 for (14)C show that the levels varied between 94.5 ± 1.5 and 234 ± 2.7 Bq/kg of C for the sediments in French rivers and across a slightly higher range of 199 ± 1.3 to 238 ± 3.1 Bq/kg of C for fish. This variation is most probably due to preferential uptake of some organic carbon compounds by fish restraining (14)C dilution with refractory organic carbon and/or with old carbonates both depleted in (14)C. Overall, most of these ranges of values are below the mean baseline value for the terrestrial environment (232.0 ± 1.8 Bq/kg of C in 2012, Roussel-Debet, 2014a) in relation to dilution by the carbonates and/or fossil organic carbon present in aquatic systems. This emphasises yet again the value of establishing regional baseline value ranges for these two radionuclides in order to account for palaeoclimatic and lithological variations. Besides, our results obtained from sedimentary archive investigation have confirmed the delayed contamination of aquatic sediments by tritium from the past nuclear tests atmospheric fallout, as recently demonstrated from data chronicles (Eyrolle

  18. Laser-induced photoacoustic spectroscopy for the speciation of transuranic elements in natural aquatic systems

    International Nuclear Information System (INIS)

    Kim, J.I.; Stumpe, R.; Klenze, R.

    1990-08-01

    Laser-induced Photoacoustic Spectroscopy (LPAS) is a new elegant instrumentation for the chemical speciation of acoustic transuranium (TRU) ions in very dilute concentrations (> 10 -8 mol L -1 ). The paper describes the principle of LPAS and its application to the study of the chemical behaviour of TRU ions in natural aquatic systems, the knowledge of which has become increasingly in demand in connection with the safety analysis of nuclear waste disposal in the geosphere. The first part of the paper describes the principle, instrumentation and characteristics of LPAS in aqueous solution, taking particular examples from our own experience. The theoretical estimation of the speciation sensitivity is demonstrated and the result is compared with experiment. The second part deals with the spectral work in aqueous solution and then with the aplication of LPAS for the speciation of TRU ions in groundwater. Some examples demonstrated are hydrolysis reaction, complexation and colloid generation of the Am 3+ ion. Speciation sensitivities of U, Np, Pu and Am of different oxidation states in a variety of aqueous solutions are summarized. The application is of course open to a broad field of microchemistry in which the conventional spectrophotometric method has difficulty with sensitivity. (orig.)

  19. Aquatic macrophytes as indicators of heavy metal pollution of water in DTD canal system

    Directory of Open Access Journals (Sweden)

    Pajević Slobodanka P.

    2003-01-01

    Full Text Available The aim of this investigation was to establish the presence or absence of chemical contamination of water and the littoral zone (banks of Danube-Tisza-Danube (DTD canal system. The investigation covered the canal section from Bezdan to Prigrevica. By analyzing the chemical composition of dominant aquatic species in four locations of the section, we defined the species with the highest capacity to accumulate nutrients and heavy metals. Concentrations of P and K as well as of a beneficial element Na in the tissues of the analyzed macrophytes were both species- and site-dependent. The highest accumulation was registered for Ceratophyllum demersum while the species Elodea canadensis showed increased P and K accumulation values in the location Sombor. The lowest concentrations of almost all heavy metals were recorded near Sombor, indicating that this section suffered the lowest chemical pollution. Highest concentrations of all of the analyzed heavy metals were recorded in the tissue of Ceratophyllum demersum from the location Prigrevica, possibly due to the influx of polluted drainage waters from surrounding agricultural areas as well as industrial wastewaters. The obtained results showed that the enforcement of biomonitoring and analyses of other parameters indicative of ecosystem conditions might be useful for improved protection of areas experiencing a strong human impact.

  20. System biology and the project Encode

    Directory of Open Access Journals (Sweden)

    M. Yu. Obolenskaya

    2014-08-01

    Full Text Available The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

  1. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

  2. Biological Therapy in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Mariana Postal

    2012-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototypic inflammatory autoimmune disorder characterized by multisystem involvement and fluctuating disease activity. Symptoms range from rather mild manifestations such as rash or arthritis to life-threatening end-organ manifestations. Despite new and improved therapy having positively impacted the prognosis of SLE, a subgroup of patients do not respond to conventional therapy. Moreover, the risk of fatal outcomes and the damaging side effects of immunosuppressive therapies in SLE call for an improvement in the current therapeutic management. New therapeutic approaches are focused on B-cell targets, T-cell downregulation and costimulatory blockade, cytokine inhibition, and the modulation of complement. Several biological agents have been developed, but this encouraging news is associated with several disappointments in trials and provide a timely moment to reflect on biologic therapy in SLE.

  3. Aquatic modules for bioregenerative life support systems: Developmental aspects based on the space flight results of the C.E.B.A.S. mini-module

    Science.gov (United States)

    Blüm, V.

    The Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) is an artificial aquatic ecosystem which contains teleost fishes, water snails, ammonia oxidizing bacteria and edible non-gravitropic water plants. It serves as a model for aquatic food production modules which are not seriously affected by microgravity and other space conditions. Its space flight version, the so-called C.E.B.A.S. MINI-MODULE was already successfidly tested in the STS-89 and STS-90 (NEUROLAB) missions. It will be flown a third time in space with the STS-107 mission in January 2003. All results obtained so far in space indicate that the basic concept of the system is more than suitable to drive forward its development. The C.E.B.A.S. MINI-MODULE is located within a middeck locker with limited space for additional components. These technical limitations allow only some modifications which lead to a maximum experiment time span of 120 days which is not long enough for scientifically essential multi-generation-experiments. The first necessary step is the development of "harvesting devices" for the different organisms. In the limited space of the plant bioreactor a high biomass production leads to self-shadowing effects which results in an uncontrolled degradation and increased oxygen consumption by microorganisms which will endanger the fishes and snails. It was shown already that the latter reproduce excellently in space and that the reproductive functions of the fish species are not affected. Although the parent-offspring-cannibalism of the ovoviviparous fish species ( Xiphophorus helleri) serves as a regulating factor in population dynamics an uncontrolled snail reproduction will also induce an increased oxygen consumption per se and a high ammonia concentration in the water. If harvesting locks can be handled by astronauts in, e. g., 4-week intervals their construction is not very difficult and basic technical solutions are already developed. The second problem is the feeding of the

  4. Aquatic modules for bioregenerative life support systems: Developmental aspects based on the space flight results of the C.E.B.A. Mini Module

    Science.gov (United States)

    Bluem, S. V.

    The Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) is an artificial aquatic ecosystem which contains teleost fishes, water snails, ammonia oxidizing bacteria and edible non-gravitropic water plants. It serves as a model for aquatic food production modules which are not seriously affected by microgravity and other space conditions. Its space flight version, the so-called C.E.B.AS. MINI-MODULE was already successfully tested in the STS-89 and STS 90 (NEUROLAB) missions.- I will be flown a third time in space with the STS 107 mission in July 2002. All- results obtained so far in space indicate that the basic concept of the system is more than suitable to drive forward its development. The C.E.B.A.S. MINI-MODULE is located within a middeck locker whith limited the space for additional components. These technical limitations allow only some modifications which lead to a maximum experiment time span of 120 days which is not long enough for the demanded scientifically essential multi-generation-experiments. This first necessary step is the development of "harvesting devices" for the different organisms. In the limited space of the plant bioreactor a high biomass production leads to self- shadowing effects which results in an uncontrolled degradation and increased oxygen consum ption by microorganisms which will endanger the fishes and snails. It was shown already that the latter reproduce excellently in space and that the reproductive functions of the fishes are not affected. Although the parent - offspring- cannibalism of the used ovoviviparous fish species (Xiphophorus helleri) serves as a regulating factor in population dynamics an uncontrolled snail reproduction will also induce an increased ox gen consumption per se and a high ammonia concentrationy in the water. If harvesting locks can be handled by astronauts in, e. g., 4w e e k- intervals their construction is not very difficult and basic technical solutions are already developed. The second problem is

  5. Solar ultraviolet radiation effects on biological systems

    International Nuclear Information System (INIS)

    Diffey, B.L.

    1991-01-01

    This extensive review discusses the topic under the following headings: ultraviolet climatology, molecular and cellular ultraviolet photobiology (absorption, photoproducts, repair), effects of solar UVR on aquatic life (phyto and zooplankton), plants and humans. The section on human effects includes tanning, photo-aging, non-melanoma and melanoma skin cancers and the effects of solar UVR on the eye. (UK)

  6. Solar ultraviolet radiation effects on biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Diffey, B.L. (Dryburn Hospital, Durham (UK). Regional Medical Physics Dept.)

    1991-03-01

    This extensive review discusses the topic under the following headings: ultraviolet climatology, molecular and cellular ultraviolet photobiology (absorption, photoproducts, repair), effects of solar UVR on aquatic life (phyto and zooplankton), plants and humans. The section on human effects includes tanning, photo-aging, non-melanoma and melanoma skin cancers and the effects of solar UVR on the eye. (UK).

  7. Biological Nutrient Removal in Compact Biofilm Systems

    NARCIS (Netherlands)

    Bassin, J.P.

    2012-01-01

    The removal of nutrients such as nitrogen and phosphorus from both domestic and industrial wastewaters is imperative since they potentially harm the environment. One of the main consequences of excessive availability of nitrogen and phosphorus in aquatic ecosystems (freshwater, marine and estuarine)

  8. Adaptable data management for systems biology investigations

    Directory of Open Access Journals (Sweden)

    Burdick David

    2009-03-01

    Full Text Available Abstract Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry. We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

  9. It's the System, Stupid: How Systems Biology Is Transforming.

    Science.gov (United States)

    2010-01-01

    So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient.

  10. Systems Biology: Impressions from a Newcomer Graduate Student in 2016

    Science.gov (United States)

    Simpson, Melanie Rae

    2016-01-01

    As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

  11. The Feasibility of Systems Thinking in Biology Education

    Science.gov (United States)

    Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

    2011-01-01

    Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

  12. Biological diversity in the patent system.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI established by the Global Biodiversity Information Facility (GBIF and Encyclopedia of Life (EOL. We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on

  13. Nuclear magnetic resonance applications in biological systems

    International Nuclear Information System (INIS)

    Jiang Ling; Liu Maili

    2011-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a state-of-the-art technology which has been widely applied in biological systems over the past decades. It is a powerful tool for macromolecular structure determination in solution, and has the unique advantage of being capable of elucidating the structure and dynamic behavior of proteins during vital biomedical processes. In this review, we introduce the recent progress in NMR techniques for studying the structure, interaction and dynamics of proteins. The methods for NMR based drug discovery and metabonomics are also briefly introduced. (authors)

  14. System for determining sizes of biological macromolecules

    International Nuclear Information System (INIS)

    Nelson, R.M.; Danby, P.C.

    1987-01-01

    An electrophoresis system for determining the sizes of radiolabelled biological macromolecules is described. It comprises a cell containing an electrophoresis gel and having at least one lane, a voltage source connected across the gel for effecting the movement of macromolecules in the lane, a detector fixed relative to the moving molecules for generating electrical pulses responsive to signals emitted by the radiolabelled molecules; a pulse processor for counting the pulse rate, and a computational device for comparing the pulse rate to a predetermined value. (author)

  15. A Dynamic Information Framework (DIF): A Portal for the Changing Biogeochemistry of Aquatic Systems

    Science.gov (United States)

    Richey, J. E.; Fernandes, E. C. M.

    2014-12-01

    The ability of societies to adapt to climate and landuse change in aquatic systems is functionally and practically expressed by how regional stakeholders are able to address complex management issues. These targets represent a very complex set of intersecting issues of scale, cross-sector science and technology, education, politics, and economics. Implications transcend individual projects and ministries. An immediate challenge is to incorporate the realities of changing environmental conditions in these sectors into the policies and projects of the Ministries nominally responsible. Ideally this would be done on the basis of the absolute best understanding of the issues involved, and done in a way that optimizes a multi-stakeholder return. Central to a response is "actionable information-" the synthesis and "bringing to life" of the key information that integrates the end-to-end knowledge required to provide the high-level decision support to make the most informed decisions. But, in practice, the information necessary and even perspectives are virtually absent, in much of especially the developing world. To meet this challenge, we have been developing a Dynamic Information Framework (DIF), primarily through collaborations with the World Bank in Asia, Africa, and Brazil. The DIF is, essentially a decision support structure, built around "earth system" models. The environment is built on progressive information layers that are fed through hydrological and geospatial landscape models to produce outputs that address specific science questions related to water resources management of the region. Information layers from diverse sources are assembled, according to the principles of how the landscape is organized, and computer models are used to bring the information "to life." A fundamental aspect to a DIF is not only the convergence of multi-sector information, but how that information can be conveyed, in the most compelling, and visual, manner. Deployment of the

  16. Entrainment and impingement of aquatic fauna at cooling water system of Madras Atomic Power Station (MAPS)

    International Nuclear Information System (INIS)

    Barath Kumar, S.; Das, N.P.I.; Satpathy, K.K.

    2015-01-01

    Marine organisms get impinged to the intake screens of Madras Atomic Power Station (MAPS) due to the suction force of the cooling water system of the power plant. The present work has studied the loss of aquatic organism at MAPS due to impingement at cooling water screens. In total 67 species of marine faunas impinged on the water intake screens of MAPS during the study. The proportion of fish, shrimp, crab, jellyfish and others, with respect to the total biomass of impinged organisms are 1.59 % (33 species), 0.30% (9), 2.77 % (16), 95.10% (3) and 0.24% (4), respectively. Jellyfishes were observed to be the largest entrained group covering around 44.85% of individual and constituting almost 94.82 % of biomass recorded during the study period and sea nettle jelly (Chrysaora quinquecirrha) was impinged with highest frequency. The diel study shows higher impingement occurred during night time, on full moon day and at low tides in contrast to their counterparts. Fishes accounts for 14.84 % of individual count and mere 1.67 % of biomass. Totally 33 number of fish species were observed. The highest impinged species were pony fishes (Secutor ruconius, Secutor insidiator, Photopectoralis bindus, Alepes kleinii and Leiognathus equulus) (21% occurrence). These few entrained fishes are mostly very small in size and have less commercial value. The total loss of marine fauna by impingement during study period was estimated to be 4779 (or 463.46 kg). The present data when compared with the impingement data from other coastal power plants, shows that the impinged fish biomass at MAPS cooling water system is much less than the other temperate and tropical power plants. (author)

  17. Dielectric relaxation in biological systems physical principles, methods, and applications

    CERN Document Server

    Feldman, Yuri

    2015-01-01

    This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

  18. Redefining plant systems biology: from cell to ecosystem

    NARCIS (Netherlands)

    Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

    2011-01-01

    Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

  19. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    Johnson, A.R.; Caudill, J.G.; Giddings, R.F.; Rodriguez, J.M.; Roos, R.C.; Wilde, J.W.

    2010-01-01

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimate spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  20. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  1. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  2. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

    These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

  3. Model checking biological systems described using ambient calculus

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

    2005-01-01

    Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

  4. Calculating life? Duelling discourses in interdisciplinary systems biology.

    Science.gov (United States)

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  5. Microbial stress tolerance for biofuels. Systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zonglin Lewis (ed.) [National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL (United States)

    2012-07-01

    The development of sustainable and renewable biofuels is attracting growing interest. It is vital to develop robust microbial strains for biocatalysts that are able to function under multiple stress conditions. This Microbiology Monograph provides an overview of methods for studying microbial stress tolerance for biofuels applications using a systems biology approach. Topics covered range from mechanisms to methodology for yeast and bacteria, including the genomics of yeast tolerance and detoxification; genetics and regulation of glycogen and trehalose metabolism; programmed cell death; high gravity fermentations; ethanol tolerance; improving biomass sugar utilization by engineered Saccharomyces; the genomics on tolerance of Zymomonas mobilis; microbial solvent tolerance; control of stress tolerance in bacterial host organisms; metabolomics for ethanologenic yeast; automated proteomics work cell systems for strain improvement; and unification of gene expression data for comparable analyses under stress conditions. (orig.)

  6. Spatial Structures and Regulation in Biological Systems

    DEFF Research Database (Denmark)

    Yde, Pernille

    , and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

  7. Fish and aquatic habitat conservation in South America: a continental overview with emphasis on neotropical systems.

    Science.gov (United States)

    Barletta, M; Jaureguizar, A J; Baigun, C; Fontoura, N F; Agostinho, A A; Almeida-Val, V M F; Val, A L; Torres, R A; Jimenes-Segura, L F; Giarrizzo, T; Fabré, N N; Batista, V S; Lasso, C; Taphorn, D C; Costa, M F; Chaves, P T; Vieira, J P; Corrêa, M F M

    2010-06-01

    Fish conservation in South America is a pressing issue. The biodiversity of fishes, just as with all other groups of plants and animals, is far from fully known. Continuing habitat loss may result in biodiversity losses before full species diversity is known. In this review, the main river basins of South America (Magdalena, Orinoco, Amazon and Paraná-La Plata system), together with key aquatic habitats (mangrove-fringed estuaries of the tropical humid, tropical semi-arid and subtropical regions) are analysed in terms of their characteristics and main concerns. Habitat loss was the main concern identified for all South American ecosystems. It may be caused by damming of rivers, deforestation, water pollution, mining, poor agricultural practice or inadequate management practice. Habitat loss has a direct consequence, which is a decrease in the availability of living resources, a serious social and economic issue, especially for South American nations which are all developing countries. The introduction of exotic species and overfishing were also identified as widespread across the continent and its main freshwater, coastal and marine ecosystems. Finally, suggestions are made to find ways to overcome these problems. The main suggestion is a change of paradigm and a new design for conservation actions, starting with integrated research and aiming at the co-ordinated and harmonized management of the main transboundary waters of the continent. The actions would be focused on habitat conservation and social rescue of the less well-off populations of indigenous and non-indigenous peoples. Energy and freshwater demands will also have to be rescaled in order to control habitat loss.

  8. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  9. Global distribution of N2O emissions from aquatic systems : natural emissions and anthropogenic effects

    NARCIS (Netherlands)

    Seitzinger, S.P.; Styles, R.V.; Kroeze, C.

    2000-01-01

    Context Abstract: Atmospheric concentrations of nitrous oxide, a greenhouse gas, are increasing due to human activities. Our analysis suggests that a third of global anthropogenic N2O emission is from aquatic sources (rivers, estuaries, continental shelves) and the terrestrial sources comprise the

  10. On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

    Science.gov (United States)

    Gomez-Ramirez, Jaime; Sanz, Ricardo

    2013-09-01

    One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Is litter decomposition 'primed' by primary producer-release of labile carbon in terrestrial and aquatic experimental systems?

    Science.gov (United States)

    Soares, A. Margarida P. M.; Kritzberg, Emma S.; Rousk, Johannes

    2015-04-01

    It is possible that recalcitrant organic matter (ROM) can be 'activated' by inputs of labile organic matter (LOM) through the priming effect (PE). Investigating the PE is of major importance to fully understand the microbial use of ROM and its role on carbon (C) and nutrient cycling in both aquatic and terrestrial ecosystems. In aquatic ecosystems it is thought that the PE is triggered by periphytic algae release of LOM. Analogously, in terrestrial systems it is hypothesized that the LOM released in plant rhizospheres, or from the green crusts on the surface of agricultural soils, stimulate the activity and growth of ROM decomposers. Most previous studies on PE have utilised pulse additions of single substrates at high concentrations. However, to achieve an assessment of the true importance of the PE, it is important to simulate a realistic delivery of LOM. We investigated, in a series of 2-week laboratory experiments, how primary producer (PP)-release of LOM influence litter degradation in terrestrial and aquatic experimental systems. We used soil (terrestrial) and pond water (aquatic) microbial communities to which litter was added under light and dark conditions. In addition, glucose was added at PP delivery rates in dark treatments to test if the putative PE in light systems could be reproduced. We observed an initial peak of bacterial growth rate followed by an overall decrease over time with no treatment differences. In light treatments, periphytic algae growth and increased fungal production was stimulated when bacterial growth declined. In contrast, both fungal growth and algal production were negligible in dark treatments. This reveals a direct positive influence of photosynthesis on fungal growth. To investigate if PP LOM supplements, and the associated fungal growth, translate into a modulated litter decomposition, we are using stable isotopes to track the use of litter and algal-derived carbon by determining the δ13C in produced CO2. Fungi and bacteria

  12. Notions of similarity for systems biology models.

    Science.gov (United States)

    Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

    2018-01-01

    Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

  13. Hydrogen production from biomass by biological systems

    International Nuclear Information System (INIS)

    Sharifan, H.R.; Qader, S.

    2009-01-01

    Hydrogen gas is seen as a future energy carrier, not involved in 'greenhouse' gas and its released energy in combustion can be converted to electric power. Biological system with low energy can produce hydrogen compared to electrochemical hydrogen production via solar battery-based water splitting which requires the use of solar batteries with high energy requirements. The biological hydrogen production occurs in microalgae and cyanobacteria by photosynthesis. They consume biochemical energy to produce molecular hydrogen. Hydrogen in some algae is an anaerobic production in the absence of light. In cyanobacteria the hydrogen production simultaneously happens with nitrogen fixation, and also catalyzed by nitrogenase as a side reaction. Hydrogen production by photosynthetic bacteria is mediated by nitrogenase activity, although hydrogenases may be active for both hydrogen production and hydrogen uptake under some conditions. Genetic studies on photosynthetic microorganisms have markedly increased in recent times, relatively few genetic engineering studies have focused on altering the characteristics of these microorganisms, particularly with respect to enhancing the hydrogen-producing capabilities of photosynthetic bacteria and cyanobacteria. (author)

  14. Applicability of a bioelectronic cardiac monitoring system for the detection of biological effects of pollution in bioindicator species in the Gulf of Finland

    Science.gov (United States)

    Kholodkevich, Sergey V.; Kuznetsova, Tatiana V.; Sharov, Andrey N.; Kurakin, Anton S.; Lips, Urmas; Kolesova, Natalia; Lehtonen, Kari K.

    2017-07-01

    Field testing of an innovative technology based on a bioelectronic cardiac monitoring system was carried out in the Gulf of Finland (Baltic Sea). The study shows that the bioelectronic system is suitable for the selected bivalve mollusks Mytilus trossulus, Macoma balthica and Anodonta anatina. Specimens taken from reference sites demonstrated a heart rate recovery time of freshwater and brackish water areas. Development of methodological basis for the testing of adaptive capacities (health) of key aquatic organisms provides new knowledge of biological effects of anthropogenic chemical stress in aquatic organisms.

  15. 3S - Systematic, systemic, and systems biology and toxicology.

    Science.gov (United States)

    Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

    2018-01-01

    A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

  16. Computational Modeling of Biological Systems From Molecules to Pathways

    CERN Document Server

    2012-01-01

    Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

  17. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-01-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched

  18. Revisiting the concept of recalcitrance and organic matter persistence in soils and aquatic systems: Does environment trump chemistry?

    Science.gov (United States)

    Marin-Spiotta, E.

    2014-12-01

    Most ecological models of decomposition rely on plant litter chemistry. However, growing evidence suggests that the chemical composition of organic matter (OM) is not a good predictor of its eventual fate in terrestrial or aquatic environments. New data on variable decomposition rates of select organic compounds challenge concepts of chemical recalcitrance, i.e. the inherent ability of certain molecular structures to resist biodegradation. The role of environmental or "ecosystem" properties on influencing decomposition dates back to some of the earliest research on soil OM. Despite early recognition that the physical and aqueous matrices are critical in determining the fate of organic compounds, the prevailing paradigm hinges on intrinsic chemical properties as principal predictors of decay rate. Here I build upon recent reviews and discuss new findings that contribute to three major transformations in our understanding of OM persistence: (1) a shift away from an emphasis on chemical recalcitrance as a primary predictor of turnover, (2) new interpretations of radiocarbon ages which challenge predictions of reactivity, and (3) the recognition that most detrital OM accumulating in soils and in water has been microbially processed. Predictions of OM persistence due to aromaticity are challenged by high variability in lignin and black C turnover observed in terrestrial and aquatic environments. Contradictions in the behavior of lignin are, in part, influenced by inconsistent methodologies among research communities. Even black C, long considered to be one of the most recalcitrant components of OM, is susceptible to biodegradation, challenging predictions of the stability of aromatic structures. At the same time, revised interpretations of radiocarbon data suggest that organic compounds can acquire long mean residence times by various mechanisms independent of their molecular structure. Understanding interactions between environmental conditions and biological

  19. Hologenomics: Systems-Level Host Biology.

    Science.gov (United States)

    Theis, Kevin R

    2018-01-01

    The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

  20. Chemical composition and antimicrobial activity of Cymbopogon nardus citronella essential oil against systemic bacteria of aquatic animals

    Science.gov (United States)

    Wei, Lee Seong; Wee, Wendy

    2013-01-01

    Background & Objectives This paper describes chemical composition and antimicrobial activity of Cymbopogon nardus citronella essential oil against Edwardsiella spp. (n = 21), Vibrio spp. (n = 6), Aeromonas spp. (n = 2), Escherichia coli (n = 2), Salmonella spp. (n = 2), Flavobacterium spp. (n = 1), Pseudomonas spp. (n = 1) and Streptococcus spp. (n = 1) isolated from internal organs of aquatic animals. Due to the ban of antibiotics for aquaculture use, this study was carried out to evaluate the potential of citronella essential oil as alternative to commercial antibiotic use against systemic bacteria in cultured aquatic animals. Materials & Methods The essential oil of C. nardus was prepared by using the steam distillation method and the chemical composition of the essential oil was analyzed by gas chromatography–mass spectroscopy (GC–MS). Minimum inhibitory concentration (MIC) of the essential oil tested against bacterial isolates from various aquatic animals and ATCC type strains were determined using two-fold broth micro dilution method with kanamycin and eugenol as positive controls. Results A total of 22 chemical compounds were detected in C. nardus essential oil with 6-octenal, 3, 7-dimethyl- or citronellal representing the major compounds (29.6%). The MIC values of the citronella oil ranged from 0.244 µg/ml to 0.977 µg/ml when tested against the bacterial isolates. Conclusion The results of the present study revealed the potential of C. nardus essential oil as alternative to commercial antibiotics for aquaculture use. PMID:23825733

  1. Highway 61 Revisited: Finding Drivers for Hypoxia in Aquatic Systems in the Mississippi Alluvial Plain

    Science.gov (United States)

    Shields, F., Jr.; Murdock, J. N.; Lizotte, R. E., Jr.; Knight, S. S.; Locke, M. A.; Testa, S., III

    2011-12-01

    Streams and lakes in the intensively cultivated Mississippi River alluvial plain frequently experience periods of hypoxia that are evidence of ecological stress. Although hydrologic perturbations and sediments and nutrients derived from nonpoint sources are likely drivers of these conditions, the most efficient pathway for obtaining partial ecological recovery (e.g., N load reduction or P load reduction or flow augmentation or erosion control) is not clear. To gain deeper understanding of these systems, three similar ~20 km2 watersheds in northwestern Mississippi were selected for study and instrumented for collection of hydrologic and water quality data in 2011. Aquatic systems within each watershed consisted of shallow natural lakes embedded in networks of sporadically flowing ditches, natural channels and wetlands, with hydrology strongly impacted by irrigation withdrawals from groundwater and return flows to surface water bodies. Waters were usually turbid, with mean Secchi disk readings 10-15 cm and mean suspended solids concentrations 200-600 mg/L. Strong diurnal fluctuations in dissolved oxygen concentration (DO) occurred even in the wetter, cooler winter months, with up to 50% of daily means below state standards (5 mg/L). The average diurnal range (daily max-daily min) in DO varied from 0.9 to 2.5 mg/L for lakes and from 1.7 to 6.0 mg/L for channels. Attendant extreme diurnal variations in temperature and pH were also observed. Observations of chlorophyll a concentrations, water column phytoplankton, and attached algae indicate the importance of algal photosynthesis and respiration to DO levels, but these processes are limited by light availability and N and P concentrations in a complex fashion. Light levels are governed by channel width, water depth and turbidity, which is due to suspended sediment and algae. Preliminary nutrient limitation studies showed both N and P limit algal growth, and microbial production and respiration. N and N+P co

  2. Mass-Dependent and -Independent Fractionation of Mercury Isotopes in Aquatic Systems

    Science.gov (United States)

    Bergquist, B. A.; Joel, B. D.; Jude, D. J.

    2008-12-01

    Mercury is a globally distributed and highly toxic pollutant. Although Hg is a proven health risk, much of the natural cycle of Hg is not well understood and new approaches are needed to track Hg and the chemical transformations it undergoes in the environment. Recently, we demonstrated that Hg isotopes exhibit two types of isotope fractionation: (1) mass dependent fractionation (MDF) and (2) mass independent fractionation (MIF) of only the odd isotopes (Bergquist and Blum, 2007). The observation of large MIF of Hg isotopes (up to 5 permil) is exciting because only a few other isotopic systems have been documented to display large MIF, the most notable of which are oxygen and sulfur. In both cases, the application of MIF has proven very useful in a variety of fields including cosmochemistry, paleoclimatology, physical chemistry, atmospheric chemistry, and biogeochemistry. Both MDF and MIF isotopic signatures are observed in natural samples, and together they open the door to a new method for tracing Hg pollution and for investigating Hg behavior in the environment. For example, fish record MDF that appears to be related to size and age. Additionally, fish display MIF signatures that are consistent with the photo-reduction of methylmercury (Bergquist and Blum, 2007). If the MDF and MIF in ecosystems can be understood, the signatures in fish could inform us about the sources and processes transforming Hg and why there are differences in the bioaccumulation of Hg in differing ecosystems and populations of fish. This requires sampling of a variety of ecosystems, the sampling of many components of the ecosystems, and the use of other tracers such as carbon and nitrogen isotopes. We have expanded our studies of aquatic ecosystems to include several lakes in North America. Similar to other isotopic systems used to study food web dynamics and structure (i.e., C and N), the MDF of Hg in fish appears to be related to size and age. The MDF recorded in fish likely reflects

  3. Biomarkers of Nanoparticles Impact on Biological Systems

    Science.gov (United States)

    Mikhailenko, V.; Ieleiko, L.; Glavin, A.; Sorochinska, J.

    Studies of nanoscale mineral fibers have demonstrated that the toxic and carcinogenic effects are related to the surface area and surface activity of inhaled particles. Particle surface characteristics are considered to be key factors in the generation of free radicals and reactive oxygen species and are related to the development of apoptosis or cancer. Existing physico-chemical methods do not always allow estimation of the nanoparticles impact on organismal and cellular levels. The aim of this study was to develop marker system for evaluation the toxic and carcinogenic effects of nanoparticles on cells. The markers are designed with respect to important nanoparticles characteristics for specific and sensitive assessment of their impact on biological system. We have studied DNA damage, the activity of xanthine oxidoreductase influencing the level of free radicals, bioenergetic status, phospholipids profile and formation of 1H-NMR-visible mobile lipid domains in Ehrlich carcinoma cells. The efficiency of the proposed marker system was tested in vivo and in vitro with the use of C60 fullerene nanoparticles and multiwalled carbon nanotubes. Our data suggest that multiwalled carbon nanotubes and fullerene C60 may pose genotoxic effect, change energy metabolism and membrane structure, alter free radical level via xanthine oxidase activation and cause mobile lipid domains formation as determined in vivo and in vitro studies on Ehrlich carcinoma cells.

  4. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

  5. The design, construction, and monitoring of photovoltaic power system and solar thermal system on the Georgia Institute of Technology Aquatic Center. Volume 1

    Energy Technology Data Exchange (ETDEWEB)

    Long, R.C.

    1996-12-31

    This is a report on the feasibility study, design, and construction of a PV and solar thermal system for the Georgia Tech Aquatic Center. The topics of the report include a discussion of site selection and system selection, funding, design alternatives, PV module selection, final design, and project costs. Included are appendices describing the solar thermal system, the SAC entrance canopy PV mockup, and the PV feasibility study.

  6. A SYSTEMIC VISION OF BIOLOGY: OVERCOMING LINEARITY

    Directory of Open Access Journals (Sweden)

    M. Mayer

    2005-07-01

    Full Text Available Many  authors have proposed  that contextualization of reality  is necessary  to teach  Biology, empha- sizing students´ social and  economic realities.   However, contextualization means  more than  this;  it is related  to working with  different kinds of phenomena  and/or objects  which enable  the  expression of scientific concepts.  Thus,  contextualization allows the integration of different contents.  Under this perspective,  the  objectives  of this  work were to articulate different  biology concepts  in order  to de- velop a systemic vision of biology; to establish  relationships with other areas of knowledge and to make concrete the  cell molecular  structure and organization as well as their  implications  on living beings´ environment, using  contextualization.  The  methodology  adopted  in this  work  was based  on three aspects:  interdisciplinarity, contextualization and development of competences,  using energy:  its flux and transformations as a thematic axis and  an approach  which allowed the  interconnection between different situations involving  these  concepts.   The  activities developed  were:  1.   dialectic exercise, involving a movement around  micro and macroscopic aspects,  by using questions  and activities,  sup- ported  by the use of alternative material  (as springs, candles on the energy, its forms, transformations and  implications  in the  biological way (microscopic  concepts;  2, Construction of molecular  models, approaching the concepts of atom,  chemical bonds and bond energy in molecules; 3. Observations de- veloped in Manguezal¨(mangrove swamp  ecosystem (Itapissuma, PE  were used to work macroscopic concepts  (as  diversity  and  classification  of plants  and  animals,  concerning  to  energy  flow through food chains and webs. A photograph register of all activities  along the course plus texts

  7. Review and Synthesis of Evidence Regarding Environmental Risks Posed by Munitions Constituents (MC) in Aquatic Systems

    Science.gov (United States)

    2017-10-31

    the ingestion of contaminated sediment and food items that have accumulated MC in their tissues. Because MCs are poorly accumulated in fish and...explosives have been extensively used by the DoD. Contamination of terrestrial sites by MC has occurred largely due to (1) explosive manufacturing ...varied widely across a diversity of MC and species. For most aquatic sites, MC contamination in sediment and in the water- column presents low risk to

  8. Oxygen optodes as fast sensors for eddy correlation measurements in aquatic systems

    DEFF Research Database (Denmark)

    Chipman, Lindsay; Huettel, Markus; Berg, Peter

    2012-01-01

    The aquatic eddy-correlation technique can be used to noninvasively determine the oxygen exchange across the sediment-water interface by analyzing the covariance of vertical flow velocity and oxygen concentration in a small measuring volume above the sea bed. The method requires fast sensors...... that combine the advantages of noninvasive measurements and integration of fluxes over a large footprint area, using a relatively rugged and less expensive sensor....

  9. Ecological and biological systems under extreme conditions

    Energy Technology Data Exchange (ETDEWEB)

    Zlobin, V S; Nenishkiene, V B

    1989-01-01

    The behaviour of biological and ecological systems under extreme conditions (high and low temperatures, electromagnetic fields of different frequencies, ultraviolet. X-ray and gamma radiation) is analyzed. The ecosystems of macro- and microalgae living in salt, brackinsh and fresh waters are considered in the evolutional aspect basing on their chemical and biochemical composition taking into account the mechanism of radionuclide uptake by water plant cells, osmotic regulation, water and ice structures, combined water in a living organism. The problems of life-support in cosmic flights and of mastering the planets of the Solar system, for instance Mars and Venus, utilizing some microalgae and bacteria with high adaptive properties are discussed. Abnormal water points and their role in the metabolism of a water plant cell are estimated. The 'life niches' are determined at the temperatures exceeding 100 deg C and the possibility of existence for living organisms in high pressure and temperature is grounded. Attempts are made to change the metabolism of the plant and animal cell by subjecting it to the action of electromagnetic and thermal fields, heavy water, chemical and pharmocological substances changing the structure of bound water. 333 refs.; 79 tabs.

  10. Drawing inspiration from biological optical systems

    Science.gov (United States)

    Wolpert, H. D.

    2009-08-01

    Bio-Mimicking/Bio-Inspiration: How can we not be inspired by Nature? Life has evolved on earth over the last 3.5 to 4 billion years. Materials formed during this time were not toxic; they were created at low temperatures and low pressures unlike many of the materials developed today. The natural materials formed are self-assembled, multifunctional, nonlinear, complex, adaptive, self-repairing and biodegradable. The designs that failed are fossils. Those that survived are the success stories. Natural materials are mostly formed from organics, inorganic crystals and amorphous phases. The materials make economic sense by optimizing the design of the structures or systems to meet multiple needs. We constantly "see" many similar strategies in approaches, between man and nature, but we seldom look at the details of natures approaches. The power of image processing, in many of natures creatures, is a detail that is often overlooked. Seldon does the engineer interact with the biologist and learn what nature has to teach us. The variety and complexity of biological materials and the optical systems formed should inspire us.

  11. Complexity, Analysis and Control of Singular Biological Systems

    CERN Document Server

    Zhang, Qingling; Zhang, Xue

    2012-01-01

    Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

  12. Study of methylation sites and factors in contaminated aquatic systems in the Amazon using an optimized radiochemical technique - Brazil

    International Nuclear Information System (INIS)

    Davee Guimaraes, Jean Remy; Narvaez Mauro, Jane Beatriz; Roulet, Marc; Meili, Markus; Hylander, Lars

    2001-01-01

    In the last few years, some new data have brought light on the Hg cycle in the Amazon. Roulet et al (1998 and 1999) found high natural Hg contents in soils and showed that soil erosion, due to agriculture and other human activities, had increased the Hg burdens in aquatic systems. They also showed that, surprisingly, the activity of goldminers on many upstream affluents of the Tapajos river did not result in downstream gradients in dissolved or particulate Hg. Our own data (Malm et al, 1995, 1997) from long term surveys show little or no reduction in fish or human hair Hg levels in different water basins, despite a 3 to 10-fold decrease in goldmining activities since 1990. Regardless of the on-going debate on the relative magnitude of natural and man-made Hg sources in the Amazon, Hg is being transported and increasingly accumulated in productive lakes and floodplains in all the Amazon basin, leading riverine populations to unsafe Hg exposure levels. This Hg transport is done mainly in the particulate form, and the floating vegetation is a very efficient particle trap, besides providing support to an abundant periphyton, features that favor MeHg formation and bio-availability. A high Hg methylation potential in macrophytes is relevant for many reasons. This characteristic tropical aquatic vegetation produces highly bioavailable MeHg, because of its high standing stock (1 kg dw. m -2 , Sioli, 1986) in direct contact with the water column and very high relative area. Because the root zone of these floating aquatic plants is densely populated by a varied fauna of invertebrates and fish and represents an essential carbon source for aquatic food chains, it may constitute a major pathway of MeHg uptake into tropical aquatic food webs. In contrast, the production of MeHg in surface sediments is ∼30 times lower than in macrophyte roots, its bioavailability is probably limited, as well as the sediment-water flux of MeHg. Moreover, the role of floating meadows as important

  13. Environmental assessment of surfactant using aquatic microcosm system; Konuma no suiken seitaikei ni oyobosu kaimen kasseizai no microcosm system wo mochiita hyoka

    Energy Technology Data Exchange (ETDEWEB)

    Takamatsu, Y.; Matsumura, M. [University of Tsukuba, Tsukuba (Japan); Inamori, Y. [National Institute for Environmental Studies, Tsukuba (Japan); Sudo, R. [Tohoku University, Sendai (Japan). Faculty of Engineering

    1995-10-10

    Microcosm system was applied to assess effect of surfactants on aquatic ecosystem. Surfactants such as LAS and Soap were added to an aquatic flask-size microcosm consisting of four species of bacteria as decomposer, one species of ciliate protozoa (Cyclidium glaucoma), two rotifers (Philodina sp. and Lepadella sp.) and one aquatic oligochaete (Aeolosoma hemprichi) as predator, and a green alga (Chlorella sp.) and a filamentous blue-green alga (Tolypothrix sp.) as producer. In the system, NOEC (no observed effect concentration) of LAS was below 1.5mg{center_dot}l{sup -1}, whereas soap was below 30mg{center_dot}l{sup -1}. Microcosm test is a pertinent tool to assess the effect of surfactant on ecosystem because microcosm test makes it possible to evaluate the effect of surfactant from a viewpoint of the interaction of microorganisms, material cycle and energy flow. With these respects, microcosm test is useful environmental assessment method which can reflect aquatic ecosystem. 10 refs., 6 figs., 1 tab.

  14. Network Reconstruction of Dynamic Biological Systems

    OpenAIRE

    Asadi, Behrang

    2013-01-01

    Inference of network topology from experimental data is a central endeavor in biology, since knowledge of the underlying signaling mechanisms a requirement for understanding biological phenomena. As one of the most important tools in bioinformatics area, development of methods to reconstruct biological networks has attracted remarkable attention in the current decade. Integration of different data types can lead to remarkable improvements in our ability to identify the connectivity of differe...

  15. Aquatic conditions

    Science.gov (United States)

    Warren E. Heilman

    1999-01-01

    This publication provides citizens, private and public organizations, scientists, and others with information about the aquatic conditions in or near national forests in the Ozark-Ouachita Highlands: the Mark Twain in Missouri, the Ouachita in Arkansas and Oklahoma, and the Ozark-St. Francis National Forests in Arkansas. This report includes water quality analyses...

  16. Systems biology of microbial exopolysaccharides production

    Directory of Open Access Journals (Sweden)

    Ozlem eAtes

    2015-12-01

    Full Text Available Exopolysaccharides (EPS produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture and medicine. EPSs are mainly associated with high-value applications and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore a systems-based approach constitutes an important step towards understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan and dextran.

  17. Systems Biology of Microbial Exopolysaccharides Production.

    Science.gov (United States)

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

  18. Removal of Chromophoric Dissolved Organic Matter and Heavy Metals in a River-Sea System: Role of Aquatic Microgel Formation

    Science.gov (United States)

    Shiu, R. F.; Lee, C. L.

    2016-12-01

    Dissolved organic carbon (DOC) polymers are complex and poorly understood mixture of organic macromolecules in environment system. Portions of these polymers spontaneously form microgels that play key roles in many biogeochemical reactions, including mediating aggregation processes, element cycling, and pollutant mobility. However, the detailed interaction of microgels-heterogeneous materials in aquatic systems is still lacking. Insight into the interaction between surrounding materials and microgels from different types of aquatic DOC polymers are extremely important, as it is crucial in determining the fate and transport of these materials. Here, we use riverine and marine DOC polymers to examine their aggregation behavior, and to evaluate the roles of microgel formation in scavenging of chromophoric dissolved organic matter (CDOM) and heavy metals in a river-sea system. Our results indicate that riverine and marine microgels did not exhibit too much difference in size ( 3-5 μm) and self-assembly curve; however, the assembly effectiveness ([microgel]/DOC) of marine samples was much higher than riverine. Instead of concentration of DOC, other factors such as types and sources of DOC polymers may control the microgel abundance in aquatic environments. After filtering water samples (microgels removed), the CDOM and selected metals (Cu, Ni, Mn) in the filtrate were quantified. CDOM and metals were concurrently removed to an extent via DOC polymer re-aggregation, which also suggested that the microgels had the sequestering capability in CDOM and metals. This finding provides an alternative route for CDOM and heavy metals removal from the water column. As such the process of re-aggregation into microgels should then be considered besides traditional phase partitioning in the assessment of the ecological risk and fate of pollutant.

  19. Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

    Science.gov (United States)

    Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

    2017-07-05

    Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Quantifying electron transfer reactions in biological systems

    DEFF Research Database (Denmark)

    Sjulstok, Emil Sjulstok; Olsen, Jógvan Magnus Haugaard; Solov'yov, Ilia A

    2015-01-01

    which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between...

  1. Systems biology: properties of reconstructed networks

    National Research Council Canada - National Science Library

    Palsson, Bernhard

    2006-01-01

    ... between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, Palsson provides problem sets, projects, and PowerPoint slides in an associated web site and keeps the presentation in the book concrete with illustrat...

  2. Precision medicine driven by cancer systems biology.

    Science.gov (United States)

    Filipp, Fabian V

    2017-03-01

    Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors. Mutation hotspots, structural modeling, UV signature, and genomic as well as non-genomic mechanisms of disease initiation and progression are taken into consideration to identify resistance mutations and novel drug targets. A comprehensive precision medicine profile of a malignant melanoma patient illustrates future rational drug targeting strategies. Network analysis emphasizes an important role of epigenetic and metabolic master regulators in oncogenesis. Co-occurrence of driver mutations in signaling, metabolic, and epigenetic factors highlights how cumulative alterations of our genomes and epigenomes progressively lead to uncontrolled cell proliferation. Precision insights have the ability to identify independent molecular pathways suitable for drug targeting. Synergistic treatment combinations of orthogonal modalities including immunotherapy, mitogen-activated protein kinase inhibitors, epigenetic inhibitors, and metabolic inhibitors have the potential to overcome immune evasion, side effects, and drug resistance.

  3. Isotopic fractionation of tritium in biological systems.

    Science.gov (United States)

    Le Goff, Pierre; Fromm, Michel; Vichot, Laurent; Badot, Pierre-Marie; Guétat, Philippe

    2014-04-01

    Isotopic fractionation of tritium is a highly relevant issue in radiation protection and requires certain radioecological considerations. Sound evaluation of this factor is indeed necessary to determine whether environmental compartments are enriched/depleted in tritium or if tritium is, on the contrary, isotopically well-distributed in a given system. The ubiquity of tritium and the standard analytical methods used to assay it may induce biases in both the measurement and the signification that is accorded to the so-called fractionation: based on an exhaustive review of the literature, we show how, sometimes large deviations may appear. It is shown that when comparing the non-exchangeable fraction of organically bound tritium (neOBT) to another fraction of tritium (e.g. tritiated water) the preparation of samples and the measurement of neOBT reported frequently led to underestimation of the ratio of tritium to hydrogen (T/H) in the non-exchangeable compartment by a factor of 5% to 50%. In the present study, corrections are proposed for most of the biological matrices studied so far. Nevertheless, the values of isotopic fractionation reported in the literature remain difficult to compare with each other, especially since the physical quantities and units often vary between authors. Some improvements are proposed to better define what should encompass the concepts of exchangeable and non-exchangeable fractions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Toward mechanical systems biology in bone.

    Science.gov (United States)

    Trüssel, Andreas; Müller, Ralph; Webster, Duncan

    2012-11-01

    Cyclic mechanical loading is perhaps the most important physiological factor regulating bone mass and shape in a way which balances optimal strength with minimal weight. This bone adaptation process spans multiple length and time scales. Forces resulting from physiological exercise at the organ scale are sensed at the cellular scale by osteocytes, which reside inside the bone matrix. Via biochemical pathways, osteocytes orchestrate the local remodeling action of osteoblasts (bone formation) and osteoclasts (bone resorption). Together these local adaptive remodeling activities sum up to strengthen bone globally at the organ scale. To resolve the underlying mechanisms it is required to identify and quantify both cause and effect across the different scales. Progress has been made at the different scales experimentally. Computational models of bone adaptation have been developed to piece together various experimental observations at the different scales into coherent and plausible mechanisms. However additional quantitative experimental validation is still required to build upon the insights which have already been achieved. In this review we discuss emerging as well as state of the art experimental and computational techniques and how they might be used in a mechanical systems biology approach to further our understanding of the mechanisms governing load induced bone adaptation, i.e., ways are outlined in which experimental and computational approaches could be coupled, in a quantitative manner to create more reliable multiscale models of bone.

  5. Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

    Science.gov (United States)

    2011-01-01

    Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

  6. Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

    Science.gov (United States)

    Degrazio, Dominick

    Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

  7. Radionuclide Imaging Technologies for Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Howell, Calvin R. [Duke Univ., Durham, NC (United States); Reid, Chantal D. [Duke Univ., Durham, NC (United States); Weisenberger, Andrew G. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2014-05-14

    The main objective of this project is to develop technologies and experimental techniques for studying the dynamics of physiological responses of plants to changes in their interface with the local environment and to educate a new generation of scientists in an interdisciplinary environment of biology, physics and engineering. Also an important goal is to perform measurements to demonstrate the new data that can be produced and made available to the plant-biology community using the imaging technologies and experimental techniques developed in this project. The study of the plant-environment interface includes a wide range of topics in plant physiology, e.g., the root-soil interface, resource availability, impact of herbivores, influence of microbes on root surface, and responses to toxins in the air and soil. The initial scientific motivation for our work is to improve understanding of the mechanisms for physiological responses to abrupt changes in the local environment, in particular, the responses that result in short-term adjustments in resource (e.g., sugars, nutrients and water) allocations. Data of time-dependent responses of plants to environmental changes are essential in developing mechanistic models for substance intake and resource allocation. Our approach is to use radioisotope tracing techniques to study whole-plant and plant organ (e.g., leaves, stems, roots) dynamical responses to abrupt changes in environmental conditions such as concentration of CO2 in the atmosphere, nutrient availability and lighting. To this aim we are collaborating with the Radiation Detector and Imaging Group at the Thomas Jefferson National Laboratory Facility (JLab) to develop gamma-ray and beta particle imaging systems optimized for plant studies. The radioisotope tracing measurements are conducted at the Phytotron facility at Duke University. The Phytotron is a controlled environment plant research facility with a variety of plant growth chambers. One chamber

  8. Hazardous materials in aquatic environments of the Mississippi River Basin. Quarterly project status report, July 1, 1994--September 30, 1994

    International Nuclear Information System (INIS)

    1994-01-01

    This document references information pertaining to the presence of hazardous materials in the Mississippi River Basin. Topics discussed include: The biological fate, transport, and ecotoxicity of toxic and hazardous wastes; biological uptake and metabolism; sentinels of aquatic contamination; bioremediation; microorganisms; biomarkers of exposure and ecotoxicity; expert geographical information systems for assessing hazardous wastes in aquatic environments; and enhancement of environmental education at Tulane and Xavier

  9. Study on the mercury evolution in a laboratory multi specific aquatic system by using instrumental neutron activation analysis

    International Nuclear Information System (INIS)

    Bubach, Debora; Guevara, Sergio Ribeiro; Arribere, Maria A.; Pechen de d'Angelo, Ana; Ferrari, Ana; Venturino, Andres

    1999-01-01

    A preliminary study on the evolution of mercury in the organisms of a laboratory multi specific aquatic system was performed using Instrumental Neutron Activation Analysis (INAA). Some of the possible effects of mercury toxicity were monitored by analyzing early biochemical indicators. The system consisted of an aquarium with bed sediments, aquatic macrophytes (Myriophyllum sp.), bivalves (Diplodom sp.) and exotic fish, simulating a long term contamination situation of unknown causes, where the sediments are the contaminant reservoir. Samples of the abiotic components of the system were analyzed at the beginning of the experiment, and again when the organisms were sampled. Fish carcass, kidney and liver samples, bivalve hepatopancreas, and whole macrophytes were extracted ana analyzed for mercury and other elements by INAA at the beginning of the experiment, and after 48 and 96 hours. Since some crustal elements such as Sc and La were detected in the hepatopancreas and macrophyte samples, enrichment factors for mercury, with respect to the <63 μm sediment fraction, were computed to discriminate the metabolized Hg content from that associated to the particulate. The hepatopancreas index, some indicators of oxidative stress (γ-Glutamyl-cysteinyl-glycine content and lipid peroxidation) and brain acetilcolinesterasa were measured as early indicators of toxicity. (author)

  10. Design and setup of intermittent-flow respirometry system for aquatic organisms

    DEFF Research Database (Denmark)

    Svendsen, Morten Bo Søndergaard; Bushnell, P.G.; Steffensen, John Fleng

    2016-01-01

    Intermittent-flow respirometry is an experimental protocol for measuring oxygen consumption in aquatic organisms that utilizes the best features of closed (stop-flow) and flow-through respirometry while eliminating (or at least reducing) some of their inherent problems. By interspersing short...... and software further reduces error by allowing many measurements to be made over long periods thereby minimizing animal stress due to acclimation issues. This paper describes some of the fundamental principles that need to be considered when designing and carrying out automated intermittent-flow respirometry...

  11. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Nielsen, Jens; Jewett, Michael Christopher

    2008-01-01

    in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

  12. Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

    DEFF Research Database (Denmark)

    Green, Sara; Serban, Maria; Scholl, Raphael

    2018-01-01

    of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

  13. Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

    NARCIS (Netherlands)

    Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

    2015-01-01

    There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

  14. Breeding system and pollination biology of the semidomesticated ...

    African Journals Online (AJOL)

    Breeding system and pollination biology of the semidomesticated fruit tree, Tamarindus indica L. (Leguminosae: Caesalpinioideae ): Implications for fruit production, selective breeding, and conservation of genetic resources.

  15. How do biological systems escape 'chaotic' state?

    Indian Academy of Sciences (India)

    B J Rao

    2018-02-13

    Feb 13, 2018 ... Lorencova 2016), sociology, physics, computer science, economics and even biology ... dynamic complexity associated with them at multiple levels? .... Social anthropology and the science of chaos (Oxford: Berghahn Books).

  16. Model description of trophodynamic behavior of methylmercury in a marine aquatic system

    International Nuclear Information System (INIS)

    Tong Yindong; Zhang Wei; Hu Xindi; Ou Langbo; Hu Dan; Yang Tianjun; Wei Wen; Wang Xuejun

    2012-01-01

    A marine food web in Bohai Bay, China, was selected to study methylmercury (MeHg) bioaccumulation, and an aquivalence-based mass balance model was established to explore the possibility of predicting the MeHg concentrations and quantifying MeHg bioaccumulation in the food web. Results showed that both total mercury (THg) and MeHg were biomagnified in the food web. The calculated MeHg concentrations in the selected species agreed well with the measured values, which shows the model could be a useful tool in MeHg concentration prediction in food web. Model outputs also showed that metabolism and growth dilution could be the dominant mechanisms for the reduction of MeHg levels in aquatic organisms. With the increase of trophic level, the contribution of food as a MeHg source for organism is increasing, and MeHg from prey was the dominant source. - Highlights: ► We model the bioaccumulation of methylmercury in a marine aquatic food web. ► Aquivalence-based mass balance model could quantify MeHg trophic transfer. ► Metabolism and growth dilution are dominant mechanisms of MeHg reduction in organisms. ► With increase of trophic levels, contribution of food as MeHg source is increasing. - Aquivalence-based mass balance model was established to study methylmercury bioaccumulation in a marine food web.

  17. Analysis of nitrogen saturation potential in Rocky Mountain tundra and forest: implications for aquatic systems

    Science.gov (United States)

    Baron, Jill S.; Ojima, Dennis S.; Holland, Elisabeth A.; Parton, William J.

    1994-01-01

    We employed grass and forest versions of the CENTURY model under a range of N deposition values (0.02–1.60 g N m−2 y−1) to explore the possibility that high observed lake and stream N was due to terrestrial N saturation of alpine tundra and subalpine forest in Loch Vale Watershed, Rocky Mountain National Park, Colorado. Model results suggest that N is limiting to subalpine forest productivity, but that excess leachate from alpine tundra is sufficient to account for the current observed stream N. Tundra leachate, combined with N leached from exposed rock surfaces, produce high N loads in aquatic ecosystems above treeline in the Colorado Front Range. A combination of terrestrial leaching, large N inputs from snowmelt, high watershed gradients, rapid hydrologic flushing and lake turnover times, and possibly other nutrient limitations of aquatic organisms constrain high elevation lakes and streams from assimilating even small increases in atmospheric N. CENTURY model simulations further suggest that, while increased N deposition will worsen the situation, nitrogen saturation is an ongoing phenomenon.

  18. Aquatic systems in semi-arid Brazil: limnology and management Ecossistemas aquáticos do semi-árido brasileiro: aspectos limnológicos e manejo

    Directory of Open Access Journals (Sweden)

    José Etham de Lucena Barbosa

    2012-03-01

    Full Text Available Aquatic systems in semi-arid Brazil include natural shallow lakes, artificial reservoirs and intermittent streams and rivers. These systems are distinctive features in the semi-arid landscape and comprise a range of associated systems functioning as an ever-changing mosaic of dry/wet patches. Lakes and reservoirs in semi-arid Brazil are subject to important periods of water shortages, whereas rivers and streams are characterized as highly variable and driven by the extremes of water flow and its absence. Within this view a catchment-scale approach must be used to create a holistic model to conceptualize and comprehend these aquatic systems, since the aquatic environment types in the semi-arid region of Brazil incorporate broader aspects within the catchment scale such as geomorphology, vegetation, climate and land use. This paper summarizes some of the information on the aquatic systems of the Brazilian semi-arid region and shows the importance of limnological studies in this region. It also attempts to establish perspectives for future research considering the catchment as a scale for surveying biological processes and limnological characteristics of the various aquatic systems. It is presented information on their overall structure and functioning, as well as characteristics of some biological communities, such as phytoplankton, periphyton, aquatic macrophytes, benthic invertebrates and fish. The importance of the understanding of eutrophication in reservoirs and the role of the dry phase in streams is emphasized, and information on possible actions of planning and management to improve water quality of reservoirs are presented.Os ecossistemas no semiárido brasileiro englobam lagos rasos naturais, reservatórios artificiais e rios e riachos intermitentes. Estes sistemas são particularidades na paisagem do semiárida e compreendem uma grande variedade de sistemas associados, funcionando como um mosaico em constante mudança entre épocas de

  19. Passive aquatic listener (PAL): An adoptive underwater acoustic recording system for the marine environment

    International Nuclear Information System (INIS)

    Anagnostou, Marios N.; Nystuen, Jeffrey A.; Anagnostou, Emmanouil N.; Papadopoulos, Anastasios; Lykousis, Vassilios

    2011-01-01

    The ambient sound field in the ocean is a combination of natural and manmade sounds. Consequently, the interpretation of the ambient sound field can be used to quantify these processes. In the frequency range from 1 to 50 kHz, the general character of ocean ambient sound is a slowly changing background that is closely associated with local wind speed, interspersed with shorter time scale events such as rain storms, ships and animal calls. At lower frequencies the underwater ambient sound budget includes geologically generated sound activities including underwater volcanic eruptions, seismic and seepage faults that generate bubbles, etc. that can also potentially be classified and quantified. Acoustic data are collected on hydrophones. Hydrophones are simple, robust sensors that can be deployed on most ocean instrumentation systems including surface or sub-surface moorings, bottom mounted systems, drifters, ARGO floats or autonomous underwater platforms. A dedicated oceanic underwater recorder called a passive acoustic listener (PAL) has been developed. A principal issue is to accurately distinguish different sound sources so that they can be quantified as part of a sound budget, and then quantified if appropriate. Based on ongoing data collected from the Poseidon II network the retrieval potential of multi-parameters from underwater sound, including meteorological (i.e., precipitation and winds) and in general geophysical, anthropogenetic (i.e., ships, submarines, etc.) and biological (whales, etc.) sources is presented.

  20. Passive aquatic listener (PAL): An adoptive underwater acoustic recording system for the marine environment

    Energy Technology Data Exchange (ETDEWEB)

    Anagnostou, Marios N., E-mail: managnostou@ath.hcmr.g [Hellenic Center for Marine Research, Department of Inland Waters, Anavissos (Greece); Nystuen, Jeffrey A. [Hellenic Center for Marine Research, Department of Inland Waters, Anavissos (Greece); Applied Physics Laboratory, University of Washington, Seattle, WA (United States); Anagnostou, Emmanouil N. [Hellenic Center for Marine Research, Department of Inland Waters, Anavissos (Greece); Department of Civil and Environmental Engineering, University of Connecticut, CT (United States); Papadopoulos, Anastasios [Hellenic Center for Marine Research, Department of Inland Waters, Anavissos (Greece); Lykousis, Vassilios [Hellenic Center for Marine Research, Department of Oceanography, Anavissos (Greece)

    2011-01-21

    The ambient sound field in the ocean is a combination of natural and manmade sounds. Consequently, the interpretation of the ambient sound field can be used to quantify these processes. In the frequency range from 1 to 50 kHz, the general character of ocean ambient sound is a slowly changing background that is closely associated with local wind speed, interspersed with shorter time scale events such as rain storms, ships and animal calls. At lower frequencies the underwater ambient sound budget includes geologically generated sound activities including underwater volcanic eruptions, seismic and seepage faults that generate bubbles, etc. that can also potentially be classified and quantified. Acoustic data are collected on hydrophones. Hydrophones are simple, robust sensors that can be deployed on most ocean instrumentation systems including surface or sub-surface moorings, bottom mounted systems, drifters, ARGO floats or autonomous underwater platforms. A dedicated oceanic underwater recorder called a passive acoustic listener (PAL) has been developed. A principal issue is to accurately distinguish different sound sources so that they can be quantified as part of a sound budget, and then quantified if appropriate. Based on ongoing data collected from the Poseidon II network the retrieval potential of multi-parameters from underwater sound, including meteorological (i.e., precipitation and winds) and in general geophysical, anthropogenetic (i.e., ships, submarines, etc.) and biological (whales, etc.) sources is presented.

  1. Bioassessment of bioremediation products in aquatic systems using cytotoxic and in vitro immune function assays

    International Nuclear Information System (INIS)

    Rice, C.D.; Roszell, L.E.

    1995-01-01

    Estuarine sediments and overlying water were collected from Back Bay Mississippi and placed in five 7.5 x 61 cm. glass-column mesocosms with a peristaltic recirculating system. Four columns received a sample of artificially weathered Louisiana Crude Oil spiked with either N + P, a PAH-metabolizing bacterial consortium collected in situ, or both. A fifth column excluded oil, bacteria, and nutrients. Aliphatic and aromatic fractions were extracted from each system and diluted in iso-octane. Poecoliopsis Hepatoma Cells (PLHC-1) and Rat Hepatoma Cells (H4IIE) were treated with 1/100--1/800 dilutions of each extract and protein synthesis, RNA synthesis, DNA synthesis, Cytochrome P4501A induction, and viability were determined. ∝-CD3 and ∝-IgM-stimulated proliferation of mouse lymphocytes, PWM-stimulated proliferation and PMA-stimulated oxidative burst activity of catfish lymphocytes and phagocytes, respective, were also determined. All extracts were overtly toxic to cell cultures compared to controls at a 1/100 dilution but only aliphatic fractions affected viability at higher dilutions. Aromatic fractions increased protein and RNA synthesis as well as induced P4501A at 1/400 and 1/800 dilutions. Fertilization with P + N increased toxic responses. Lymphocyte proliferation and fish phagocyte responses were more sensitive to aliphatic extracts. This approach may be useful for investigating the toxicity and biological impact of effluents

  2. Aquatic Chemistry

    International Nuclear Information System (INIS)

    Kim, Dong Yeun; Kim, Oh Sik; Kim, Chang Guk; Park, Cheong Gil; Lee, Gwi Hyeon; Lee, Cheol Hui

    1987-07-01

    This book deals aquatic chemistry, which treats water and environment, chemical kinetics, chemical balance like dynamical characteristic, and thermodynamics, acid-base chemistry such as summary, definition, kinetics, and PH design for mixture of acid-base chemistry, complex chemistry with definition, and kinetics, precipitation and dissolution on summary, kinetics of precipitation and dissolution, and balance design oxidation and resolution with summary, balance of oxidation and resolution.

  3. Industrial systems biology and its impact on synthetic biology of yeast cell factories.

    Science.gov (United States)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-06-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  4. Industrial systems biology and its impact on synthetic biology of yeast cell factories

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

  5. Nutrient uptake from liquid digestate using ornamental aquatic macrophytes (Canna indica, Iris pseudacorus, Typha latifolia) in a constructed wetland system

    Science.gov (United States)

    Ediviani, W.; Priadi, C. R.; Moersidik, S. S.

    2018-05-01

    Indonesia has implemented energy recovery from organic (food) waste by anaerobic digestion method, but the digestate was commonly treated only by composting, and still as a separated treatment (not integrated into a resource recovery system). Whilst not getting any pretreatment, the digestate was disposed to the environment and then act as a pollutant. Yet it contains nutrients which could be recovered as a nutrient source for plants. The study was about how ornamental aquatic macrophytes could uptake nitrogen from liquid digestate in a constructed wetland method. Canna indica, Iris pseudacorus, and Typha latifolia were the experimented ornamental aquatic macrophytes used to uptake the nutrient (nitrogen—N) from liquid digestate. The study showed that the highest N uptake was done by C. indica (25.1%) which has the highest biomass increment as well (80.5%). Effluent quality improvement also shown by N removal by C. indica (68.5—76.4% TN), I. pseudacorus (61.8—71.3% TN), and T. latifolia (61.6—74.5%). This research proved that C. indica has the performance for the N uptake, best N removal efficiency, with a great growth rate as well. This system using C. indica could also improve the water quality of the effluent and add the aesthetic of environment.

  6. Riparian swallows as integrators of landscape change in a multiuse river system: implications for aquatic-to-terrestrial transfers of contaminants.

    Science.gov (United States)

    Alberts, Jeremy M; Sullivan, S Mažeika P; Kautza, A

    2013-10-01

    Recent research has highlighted the transfer of contaminants from aquatic to terrestrial ecosystems via predation of aquatic emergent insects by riparian consumers. The influence of adjacent land use and land cover (LULC) on aquatic-to-terrestrial contaminant transfer, however, has received limited attention. From 2010 to 2012, at 11 river reaches in the Scioto River basin (OH, USA), we investigated the relationships between LULC and selenium (Se) and mercury (Hg) concentrations in four species of riparian swallows. Hg concentrations in swallows were significantly higher at rural reaches than at urban reaches (t=-3.58, Pemergent insects. For example, tree swallows (Tachycineta bicolor) at urban reaches exhibited a higher proportion of aquatic prey in their diet, fed at a higher trophic level, and exhibited elevated Se levels. We also found that both Se and Hg concentrations in adult swallows were significantly higher than those observed in nestlings at both urban and rural reaches (Se: t=-2.83, P=0.033, df=3; Hg: t=-3.22, P=0.024, df=3). Collectively, our results indicate that riparian swallows integrate contaminant exposure in linked aquatic-terrestrial systems and that LULC may strongly regulate aquatic contaminant flux to terrestrial consumers. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-05-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched between a bio-functionalized sensor surface and bio-functionalized magnetic beads. This method has been used very successfully in different application, but its execution requires a rather elaborate procedure including several washing and incubation steps. This dissertation investigates a new magnetic biosensor concept, which enables a simple and effective detection of biological targets. The biosensor takes advantage of the size difference between bare magnetic beads and compounds of magnetic beads and biological targets. First, the detection of super-paramagnetic beads via magnetic tunnel junction (MTJ) sensors is implemented. Frequency modulation is used to enhance the signal-to-noise ratio, enabling the detection of a single magnetic bead. Second, the concept of the magnetic biosensor is investigated theoretically. The biosensor consists of an MTJ sensor, which detects the stray field of magnetic beads inside of a trap on top of the MTJ. A microwire between the trap and the MTJ is used to attract magnetic beads to the trapping well by applying a current to it. The MTJ sensor’s output depends on the number of beads inside the trap. If biological targets are in the sample solution, the beads will form bead compounds consisting of beads linked to the biological targets. Since bead compounds are larger than bare beads, the number of beads inside the trapping well will depend on the presence of biological targets. Hence, the output of the MTJ sensor will depend on the biological targets. The dependences of sensor signals on the sizes of the MTJ sensor, magnetic beads and biological targets are studied to find the optimum constellations for the detection of specific biological targets. The optimization is demonstrated

  8. The aims of systems biology: between molecules and organisms.

    Science.gov (United States)

    Noble, D

    2011-05-01

    The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

  9. Arsenic speciation in biological environmental samples of aquatic ecosystems by using HPLC-ICP-MS; Speciation von Arsen in biologischen Umweltproben aus aquatischen Oekosystemen mittels HPLC-ICP-MS

    Energy Technology Data Exchange (ETDEWEB)

    Falk, K.

    1999-09-01

    The physicochemical forms of arsenic (arsenic species) which are present in the environment vary significantly with respect to toxicity, bioavailability, stability and transport behaviour. Therefore, it is necessary for an assessment of the toxic potential to humans and the environment to investigate not only the total arsenic concentrations but also to differentiate the single species. By that the knowledge about ecological correlations and pathways will be increased. The present thesis reports the results of a Ph.D. study on the development and optimisation of analytical methods for arsenic speciation and their application to biological samples from different aquatic ecosystems in Germany. The method development included separation of 12 naturally occurring arsenic species by high-performance liquid chromatography (HPLC) followed by an arsenic selective detection by inductively coupled plasma-mass spectrometry (ICP-MS). The arsenic species As (III), As (V), monomethylarsonic acid (MMA), dimethylarsinic acid (DMA), arsenobetaine (AB), arsenocholine (AC), trimethylarsine oxid (TMAO) and tetramethylarsonium (Tetra) were separated with ion-exchange chromatography, whereas reversed-phase chromatography was used for the separation of four arsenosugars. Because of the partly low arsenic concentration in biological samples a very good detection power was required. Therefore, an HPLC-ICP-MS system was tested with different nebulizers. Using the high efficiency nebulizer HHPN (Hydraulic High Pressure Nebulizer), detection limits in the low pg-range could be achieved. The developed analytical methods were applied to arsenic speciation in four marine matrices, which are representative of different trophic levels in the food chain. All samples originated from an ecosystem in the North Sea.

  10. Morphogenesis and pattern formation in biological systems experiments and models

    CERN Document Server

    Noji, Sumihare; Ueno, Naoto; Maini, Philip

    2003-01-01

    A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

  11. A review of imaging techniques for systems biology

    Directory of Open Access Journals (Sweden)

    Po Ming J

    2008-08-01

    Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

  12. Hierarchical structure of biological systems: a bioengineering approach.

    Science.gov (United States)

    Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

    2014-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

  13. On the interplay between mathematics and biology: hallmarks toward a new systems biology.

    Science.gov (United States)

    Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

    2015-03-01

    This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Programming Morphogenesis through Systems and Synthetic Biology.

    Science.gov (United States)

    Velazquez, Jeremy J; Su, Emily; Cahan, Patrick; Ebrahimkhani, Mo R

    2018-04-01

    Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Monitoring aquatic environment pollution : a major component of environment management system part-II

    International Nuclear Information System (INIS)

    Khan, I.H.; Khan, M.H.; Sheikh, I.M.

    1999-01-01

    The quality of water suitable for simple disinfection and filtration is presented in this article. Aquatic monitoring requires sampling frequencies along the alignment of surface water bodies. It is necessary to control the industrial effluents discharge in to river and sewers. Unlike wastes from entirely domestic sources, however industrial effluents may contain a very large variety of unnatural components which necessitates greater considerations in setting suitable discharge limits and, perhaps closer surveillance to ensure that standards are met. Several suggestion and example of different types of effluent have been described. All the examples given are sufficiently convincing that Pakistan can learn a great deal from international experiences in environmental pollution to avoid catastrophes. (A.B.)

  16. Do environmental dynamics matter in fate models? Exploring scenario dynamics for a terrestrial and an aquatic system.

    Science.gov (United States)

    Morselli, Melissa; Terzaghi, Elisa; Di Guardo, Antonio

    2018-01-24

    Nowadays, there is growing interest in inserting more ecological realism into risk assessment of chemicals. On the exposure evaluation side, this can be done by studying the complexity of exposure in the ecosystem, niche partitioning, e.g. variation of the exposure scenario. Current regulatory predictive approaches, to ensure simplicity and predictive ability, generally keep the scenario as static as possible. This could lead to under or overprediction of chemical exposure depending on the chemical and scenario simulated. To account for more realistic exposure conditions, varying temporally and spatially, additional scenario complexity should be included in currently used models to improve their predictive ability. This study presents two case studies (a terrestrial and an aquatic one) in which some polychlorinated biphenyls (PCBs) were simulated with the SoilPlusVeg and ChimERA models to show the importance of scenario variation in time (biotic and abiotic compartments). The results outlined the importance of accounting for planetary boundary layer variation and vegetation dynamics to accurately predict air concentration changes and the timing of chemical dispersion from the source in terrestrial systems. For the aquatic exercise, the results indicated the need to account for organic carbon forms (particulate and dissolved organic carbon) and vegetation biomass dynamics. In both cases the range of variation was up to two orders of magnitude depending on the congener and scenario, reinforcing the need for incorporating such knowledge into exposure assessment.

  17. Network science of biological systems at different scales: A review

    Science.gov (United States)

    Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

    2018-03-01

    Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

  18. SEEK: a systems biology data and model management platform.

    NARCIS (Netherlands)

    Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

    2015-01-01

    Background: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems

  19. Monitoring aquatic environment pollution: a major component of environment management systems

    International Nuclear Information System (INIS)

    Khan, I.H.; Khan, M.H.; Sheikh, I.M.

    1999-01-01

    The paper is based on the international experiences mostly of the UK (United Kingdom) and Europe on monitoring aquatic pollution and controlling water pollution which have a long history of the legislation involved. The U.K. control of water pollution and regulatory laws are very effective as in shown by the fact that 96 percent of rivers in England and Wales are suitable for potable supplies with conventional water treatment. Current British legislation is basically contained n the 1951, 1960 and 1974 acts of parliament in the U.K. A common feature of all this environment legislation is the high level of consultation which has taken place between government and all concerned and al those concerned in the development of legislation and drawing up regulations etc. and involved in implementation of them. Similarly considerable discussion takes place with the controlling authorities by dischargers over the detailed implementation of legislation in the U.K. Consequently these harmonious attitudes have been responsible for the effectiveness of the U.K. legislation. In the U.K. control of discharges of industrial effluents to sewers and to all natural waters including underground water is vested in the regional water authorities, which on application, issue consent permitting discharges of industrial effluents to sewers and to all natural waters including underground waters in vested in the regional water authorities, which on application, issue consent permitting discharges to be made subject to conditions and limitations in the consent/authorisation/approval. The paper critically reviews major aspects of the philosophy of aquatic pollution control and monitoring, as statistics reveal deadly state of liquid effluent contamination water bodies in Pakistan. Without prompt installation of treatment plants we may face a tragedy of catastrophic magnitude. (author)

  20. Plant Systems Biology at the Single-Cell Level.

    Science.gov (United States)

    Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

    2017-11-01

    Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Tracing organizing principles: Learning from the history of systems biology

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

    on this historical background in order to increase the understanding of the motivation behind the search for general principles and to clarify different epistemic aims within systems biology. We pinpoint key aspects of earlier approaches that also underlie the current practice. These are i) the focus on relational......With the emergence of systems biology, the identification of organizing principles is being highlighted as a key research aim. Researchers attempt to “reverse engineer” the functional organization of biological systems using methodologies from mathematics, engineering and computer science while...... taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-twentieth century. The aim of this paper is to draw...

  2. Yeast systems biology to unravel the network of life

    DEFF Research Database (Denmark)

    Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

    2006-01-01

    Systems biology focuses on obtaining a quantitative description of complete biological systems, even complete cellular function. In this way, it will be possible to perform computer-guided design of novel drugs, advanced therapies for treatment of complex diseases, and to perform in silico design....... Furthermore, it serves as an industrial workhorse for production of a wide range of chemicals and pharmaceuticals. Systems biology involves the combination of novel experimental techniques from different disciplines as well as functional genomics, bioinformatics and mathematical modelling, and hence no single...... laboratory has access to all the necessary competences. For this reason the Yeast Systems Biology Network (YSBN) has been established. YSBN will coordinate research efforts, in yeast systems biology and, through the recently obtained EU funding for a Coordination Action, it will be possible to set...

  3. Deliverable 4.2-2: Stressor propagation through surface-groundwater linkages and its effect on aquatic systems

    DEFF Research Database (Denmark)

    Kaandorp, Vince; de Louw, Perry; Bloomfield, John

    2017-01-01

    The good ecological status of Europe’s freshwaters is still lacking. This paper reviews the role of groundwater in these systems and demonstrates that it is an important factor to include in surface water management. Groundwater influences streamflow, water chemistry and water temperature...... and connects rivers and streams with their catchment and thus functions as a pathway for stressors to reach the surface water. A new ‘Groundwater DPS’ framework is proposed which shows how groundwater fits in the system of a stressed aquatic ecosystem. The functioning of this framework is demonstrated using...... examples from four different European lowland catchments: the Thames, Odense, Regge and Dinkel catchments. The importance of groundwater varies between scales, between catchments and within catchments. The Groundwater DPS will aid water managers in understanding the importance of groundwater...

  4. Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

    Science.gov (United States)

    Jalili, Mahdi

    2018-03-01

    I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

  5. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    NARCIS (Netherlands)

    He, F.; Murabito, E.; Westerhoff, H.V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

  6. Biological Detection System Technologies Technology and Industrial Base Study. A Primer on Biological Detection Technologies

    National Research Council Canada - National Science Library

    2001-01-01

    .... and Canadian military personnel. In light of these concerns both defense departments have increased efforts to develop and field biological agent detection systems to help protect their military forces and fixed assets...

  7. Surface-water quantity and quality, aquatic biology, stream geomorphology, and groundwater-flow simulation for National Guard Training Center at Fort Indiantown Gap, Pennsylvania, 2002-05

    Science.gov (United States)

    Langland, Michael J.; Cinotto, Peter J.; Chichester, Douglas C.; Bilger, Michael D.; Brightbill, Robin A.

    2010-01-01

    Base-line and long-term monitoring of water resources of the National Guard Training Center at Fort Indiantown Gap in south-central Pennsylvania began in 2002. Results of continuous monitoring of streamflow and turbidity and monthly and stormflow water-quality samples from two continuous-record long-term stream sites, periodic collection of water-quality samples from five miscellaneous stream sites, and annual collection of biological data from 2002 to 2005 at 27 sites are discussed. In addition, results from a stream-geomorphic analysis and classification and a regional groundwater-flow model are included. Streamflow at the facility was above normal for the 2003 through 2005 water years and extremely high-flow events occurred in 2003 and in 2004. Water-quality samples were analyzed for nutrients, sediments, metals, major ions, pesticides, volatile and semi-volatile organic compounds, and explosives. Results indicated no exceedances for any constituent (except iron) above the primary and secondary drinking-water standards or health-advisory levels set by the U.S. Environmental Protection Agency. Iron concentrations were naturally elevated in the groundwater within the watershed because of bedrock lithology. The majority of the constituents were at or below the method detection limit. Sediment loads were dominated by precipitation due to the remnants of Hurricane Ivan in September 2004. More than 60 percent of the sediment load measured during the entire study was transported past the streamgage in just 2 days during that event. Habitat and aquatic-invertebrate data were collected in the summers of 2002-05, and fish data were collected in 2004. Although 2002 was a drought year, 2003-05 were above-normal flow years. Results indicated a wide diversity in invertebrates, good numbers of taxa (distinct organisms), and on the basis of a combination of metrics, the majority of the 27 sites indicated no or slight impairment. Fish-metric data from 25 sites indicated results

  8. Insect-gene-activity detection system for chemical and biological warfare agents and toxic industrial chemicals

    Science.gov (United States)

    Mackie, Ryan S.; Schilling, Amanda S.; Lopez, Arturo M.; Rayms-Keller, Alfredo

    2002-02-01

    Detection of multiple chemical and biological weapons (CBW) agents and/or complex mixtures of toxic industrial chemicals (TIC) is imperative for both the commercial and military sectors. In a military scenario, a multi-CBW attack would create confusion, thereby delaying decontamination and therapeutic efforts. In the commercial sector, polluted sites invariably contain a mixture of TIC. Novel detection systems capable of detecting CBW and TIC are sorely needed. While it may be impossible to build a detector capable of discriminating all the possible combinations of CBW, a detection system capable of statistically predicting the most likely composition of a given mixture is within the reach of current emerging technologies. Aquatic insect-gene activity may prove to be a sensitive, discriminating, and elegant paradigm for the detection of CBW and TIC. We propose to systematically establish the expression patterns of selected protein markers in insects exposed to specific mixtures of chemical and biological warfare agents to generate a library of biosignatures of exposure. The predicting capabilities of an operational library of biosignatures of exposures will allow the detection of emerging novel or genetically engineered agents, as well as complex mixtures of chemical and biological weapons agents. CBW and TIC are discussed in the context of war, terrorism, and pollution.

  9. Multi-metal contamination with uranium trend impact on aquatic environment and consequences for fish immune system and adaptive responses

    Energy Technology Data Exchange (ETDEWEB)

    Le Guernic, A.; Gagnaire, B. [IRSN/PRP-ENV/SERIS/LECO (France); Sanchez, W. [Institut national de l' environnement industriel et des risques - INERIS (France); Betoulle, S. [Champagne Ardenne University (France)

    2014-07-01

    Human activities have conducted to an increase of concentrations of various metals in aquatic ecosystems, including uranium. Its extraction and use have been rapidly magnified because of its role in the nuclear fuel cycle. These activities have led to high concentrations of uranium in the aquatic environment and thus a potential risk to exposed organisms, including fish. Consequences can be observed through metabolic and physiological responses, called biomarkers. Some biomarkers are interesting in order to evaluate the effects of metal contamination, among other immunotoxicity markers, antioxidant defenses and genotoxicity. The aims of this study are: i) to investigate the effects of a multi-metal contamination on a fish, the three-spined stickleback, Gasterosteus aculeatus, and ii) to observe the adaptive capacity of fish due to a combination of stress (chemical stress and biological stress). To meet the first objective, six water bodies (ponds and lakes) located in two departments (Cantal and Haute-Vienne, France) were chosen according to their proximity to old uranium mines and to their levels of metal contamination related to chemical processes appeared during extraction. 240 three-spined sticklebacks were caged for 28 days in the six selected sites. A battery of biomarkers was measured in fish sampled after 14 and 28 of caging. The results for the Haute-Vienne department showed that caged fish in the pond with the highest uranium concentration (20 μg.L{sup -1}) presented the most DNA damage after 14 days of caging. Leukocyte phagocytosis (marker of immunotoxicity) of caged fish in this pond was lower at 14 days and greater at 28 days compared to other ponds without uranium. The multi-metal contamination negatively affected other parameters such as the condition index, oxidative activity, viability of lysosomal membrane and leukocytes distribution. In order to study the response of fish to a combined stress (chemical + biological) (objective ii), a second

  10. The Systems Biology Research Tool: evolvable open-source software

    Directory of Open Access Journals (Sweden)

    Wright Jeremiah

    2008-06-01

    Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

  11. Scaling for Dynamical Systems in Biology.

    Science.gov (United States)

    Ledder, Glenn

    2017-11-01

    Asymptotic methods can greatly simplify the analysis of all but the simplest mathematical models and should therefore be commonplace in such biological areas as ecology and epidemiology. One essential difficulty that limits their use is that they can only be applied to a suitably scaled dimensionless version of the original dimensional model. Many books discuss nondimensionalization, but with little attention given to the problem of choosing the right scales and dimensionless parameters. In this paper, we illustrate the value of using asymptotics on a properly scaled dimensionless model, develop a set of guidelines that can be used to make good scaling choices, and offer advice for teaching these topics in differential equations or mathematical biology courses.

  12. Magnetic biosensor system to detect biological targets

    KAUST Repository

    Li, Fuquan

    2012-09-01

    Magneto-resistive sensors in combination with magnetic beads provide sensing platforms, which are small in size and highly sensitive. These platforms can be fully integrated with microchannels and electronics to enable devices capable of performing complex tasks. Commonly, a sandwich method is used that requires a specific coating of the sensor\\'s surface to immobilize magnetic beads and biological targets on top of the sensor. This paper concerns a micro device to detect biological targets using magnetic concentration, magnetic as well as mechanical trapping and magnetic sensing. Target detection is based on the size difference between bare magnetic beads and magnetic beads with targets attached. This method remedies the need for a coating layer and reduces the number of steps required to run an experiment. © 2012 IEEE.

  13. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    Science.gov (United States)

    Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

    2017-03-28

    Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. EPA Region 7 Aquatic Focus Areas (ECO_RES.R7_AQUATIC_FOCUS_AREAS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — This shapefile consists of 347 individual Aquatic Ecological System (AES) polygons that are the Aquatic Conservation Focus Areas for EPA Region 7. The focus areas...

  15. Expert geographical information system for assessing hazardous materials in aquatic environments

    International Nuclear Information System (INIS)

    Regens, J.L.; White, L.; Wright, J.D.; Rene, A.; Mielke, H.; Bakeer, R.; Belkhouche, B.; Barber, M.

    1993-01-01

    Hazardous substances, including radionuclides, heavy metals, chlorinated hydrocarbons, and industrial solvents, pose unique challenges in terms of environmental restoration and waste management, especially in aquatic environments. When stored, used or disposed of improperly, hazardous materials including transuranic wastes, high level wastes, low level wastes, greater than class C wastes, mixed wastes or chemical wastes can contaminate an array of environmental receptors ranging from soils, sediments, groundwater to surface water. Depending on the specific hazardous substance and site attributes, environmental restoration and waste management can be a complex, problematic activity. This is particularly true for the major Defense Programs facilities managed by the Department of Energy (DOE). This research cluster consists of two discrete elements. Project Element No. 1 develops and applies GIS-based approaches to decision support for environmental restoration by delineating potential exposures and health risks at the Rocky Flats Plant and profiling contemporary and historical demographic/land use patterns at Sandia National Laboratories. Project Element No. 2 develops ESS software for surface water and ground water contaminants in the Mississippi River Basin

  16. Infrared tomographic PIV and 3D motion tracking system applied to aquatic predator–prey interaction

    International Nuclear Information System (INIS)

    Adhikari, Deepak; Longmire, Ellen K

    2013-01-01

    Infrared tomographic PIV and 3D motion tracking are combined to measure evolving volumetric velocity fields and organism trajectories during aquatic predator–prey interactions. The technique was used to study zebrafish foraging on both non-evasive and evasive prey species. Measurement volumes of 22.5 mm × 10.5 mm × 12 mm were reconstructed from images captured on a set of four high-speed cameras. To obtain accurate fluid velocity vectors within each volume, fish were first masked out using an automated visual hull method. Fish and prey locations were identified independently from the same image sets and tracked separately within the measurement volume. Experiments demonstrated that fish were not influenced by the infrared laser illumination or the tracer particles. Results showed that the zebrafish used different strategies, suction and ram feeding, for successful capture of non-evasive and evasive prey, respectively. The two strategies yielded different variations in fluid velocity between the fish mouth and the prey. In general, the results suggest that the local flow field, the direction of prey locomotion with respect to the predator and the relative accelerations and speeds of the predator and prey may all be significant in determining predation success. (paper)

  17. Phytoremediation of organochlorine and pyrethroid pesticides by aquatic macrophytes and algae in freshwater systems.

    Science.gov (United States)

    Riaz, Ghazala; Tabinda, Amtul Bari; Iqbal, Shakir; Yasar, Abdullah; Abbas, Mateen; Khan, Abdul Muqeet; Mahfooz, Yusra; Baqar, Mujtaba

    2017-10-03

    Extensive use of Pesticides in agriculture and its surface runoff in river water is a major environmental concern. The present study evaluated the phytoremediation potential of Eichornia crassipes, Pistia strateotes and algae (Chaetomorpha sutoria, Sirogonium sticticum and Zygnema sp.) for organochlorine and pyrethroid pesticides. Water and plant samples were extracted by liquid phase and solid phase extraction respectively and analyzed by high-performance liquid chromatography. Eleven treatments (T1-T11) with and without plants were used for phytoremediation of organochlorine and pyrethroid pesticides. During the experiment, P. strateotes, E. crassipes and algae (C. sutoria, S. sticticum and Zygnema sp.) showed the highest removal efficiency with 62 (71% root, 29% shoot), 60 (67% root, 33% shoot), and 58% respectively for organochlorine and 76 (76% root, 24% shoot), 68 (69% root, 31% shoot), and 70% respectively for pyrethroids for the respective aquatic plants. Dissipation rate constant of treatments with plants (T2, T3, T5, T6, T8, and T9) was significantly higher (p < 0.05) as compared to that of treatments without plants (T10 and T11, control) for both organochlorine and pyrethroid. The bioconcentration factor of pyrethroid treatments (T3, T6, and T9) was significantly higher (p < 0.05) as compared to that of organochlorine treatments (T2, T5 and T8). The removal efficiency of E. crassipes, P. strateotes and algae (C. sutoria, S. sticticum and Zygnema sp.) for pyrethroids was significantly higher (p < 0.01) as compared to that of organochlorine.

  18. Pollution-Induced Community Tolerance To Diagnose Hazardous Chemicals in Multiple Contaminated Aquatic Systems.

    Science.gov (United States)

    Rotter, Stefanie; Gunold, Roman; Mothes, Sibylle; Paschke, Albrecht; Brack, Werner; Altenburger, Rolf; Schmitt-Jansen, Mechthild

    2015-08-18

    Aquatic ecosystems are often contaminated with large numbers of chemicals, which cannot be sufficiently addressed by chemical target analyses. Effect-directed analysis (EDA) enables the identification of toxicants in complex contaminated environmental samples. This study suggests pollution-induced community tolerance (PICT) as a confirmation tool for EDA to identify contaminants which actually impact on local communities. The effects of three phytotoxic compounds local periphyton communities, cultivated at a reference (R-site) and a polluted site (P-site), were assessed to confirm the findings of a former EDA study on sediments. The sensitivities of R- and P-communities to prometryn, tributyltin (TBT) and N-phenyl-2-naphthylamine (PNA) were quantified in short-term toxicity tests and exposure concentrations were determined. Prometryn and PNA concentrations were significantly higher at the P-site, whereas TBT concentrations were in the same range at both sites. Periphyton communities differed in biomass, but algal class composition and diatom diversity were similar. Community tolerance of P-communities was significantly enhanced for prometryn, but not for PNA and TBT, confirming site-specific effects on local periphyton for prometryn only. Thus, PICT enables in situ effect confirmation of phytotoxic compounds at the community level and seems to be suitable to support confirmation and enhance ecological realism of EDA.

  19. Assessment of relative accuracy in the determination of organic matter concentrations in aquatic systems

    Science.gov (United States)

    Aiken, G.; Kaplan, L.A.; Weishaar, J.

    2002-01-01

    Accurate determinations of total (TOC), dissolved (DOC) and particulate (POC) organic carbon concentrations are critical for understanding the geochemical, environmental, and ecological roles of aquatic organic matter. Of particular significance for the drinking water industry, TOC measurements are the basis for compliance with US EPA regulations. The results of an interlaboratory comparison designed to identify problems associated with the determination of organic matter concentrations in drinking water supplies are presented. The study involved 31 laboratories and a variety of commercially available analytical instruments. All participating laboratories performed well on samples of potassium hydrogen phthalate (KHP), a compound commonly used as a standard in carbon analysis. However, problems associated with the oxidation of difficult to oxidize compounds, such as dodecylbenzene sulfonic acid and caffeine, were noted. Humic substances posed fewer problems for analysts. Particulate organic matter (POM) in the form of polystyrene beads, freeze-dried bacteria and pulverized leaf material were the most difficult for all analysts, with a wide range of performances reported. The POM results indicate that the methods surveyed in this study are inappropriate for the accurate determination of POC and TOC concentration. Finally, several analysts had difficulty in efficiently separating inorganic carbon from KHP solutions, thereby biasing DOC results.

  20. Behaviors of tritium in terrestrial biological system

    International Nuclear Information System (INIS)

    Inomata, Tsuyako

    1983-01-01

    The in vivo behaviors of HTO- 3 H in food chain models in experimental animals were described. Of pregnant mice that had ingested HTO and drinking water alone for 19 days, the total 3 H content in the tissue/wet weight was greater by 20% in fetuses and newborns than in mothers, and the proportion of tissue-bound 3 H was 8-24% in mothers and 3% in fetuses. The mean 3 H concentration in the free water in tissues was about 36% of ingested HTO. When only 3 H foods were ingested for 18 days, the total 3 H content in the tissue/wet weight showed no marked difference among the mother, fetuses and newborns, nor did the bound 3 H level show great differences. With respect to the tissue distribution of 3 H, only the incorporation rate by the mother's brain from HTO was satisfactory, whereas in other organs, the mother, fetuses and newborns showed higher incorporation rates from 3 H foods. The ratio of specific radioactivity of soft tissue 3 H in mothers to HTO in drinking water exceeded 1 only for the spleen, but other tissues showed no biological concentration. Again, no biological concentration was observed with 3 H foods. Environmental HTO did not result in biological concentration of 3 H in mother mice that had ingested 3 H foods, but 3 H was rather diluted. Tissues other than the spleen showed similar values of 3 H ingestion from environmental HTO through all routes. However, the proportion of bound 3 H in the total 3 H in the soft tissue was about 1.4-1.6 times that on ingestion of HTO alone. (Chiba, N.)

  1. Optical Biosensors to Explore Biological Systems

    DEFF Research Database (Denmark)

    Palanco, Marta Espina; Mogensen, Klaus Bo; Andersen, Nils H. Skovgaard

    2016-01-01

    their capability to work in biosensor devices. For example, Raman spectroscopy can be non-invasive and can provide 1 μm of spatial resolution in 1 second of collection time, well suited for sensing. Moreover, it may give information at the single cell and even approaching the single molecule scale. Here we present...... protein may be used as an efficient sensor in an organic environment via a biomimetic membrane model. The combination of both biomimetic membranes and protein membranes as a signal transduction medium has interesting applications in biology and medicine. It is crucial that the matrix where a protein...

  2. ZOONOSIS OF AQUATICAL ORGANISMS

    Directory of Open Access Journals (Sweden)

    Božidar Kurtović

    2001-12-01

    Full Text Available Aquatic organisms play a very important role in human nutrition. They also pose a real threat for human health by causing various diseases. Parasites, bacteria and viruses may either directly or indirectly be carried from aquatic organisms to humans. Disease outbreaks are influenced by many factors among which decreased immune response and feeding habits and higyene are most important. More frequent occuence of foodborne diseases has a number of reasons, including international travel and trade, microbial adaptation and changes in the food production system. Parasitic diseases occur most frequently as a result of human role in parasites life cycles. The prevalence is further increased by consuming raw fish and shellfish. The main feature of bacterial infections is facultative pathogenicity of most ethiological agents. In most cases disease occures as a result of decreased immunoreactivity. Several bacteria are, however, hightly pathogenic and capable of causing high morbidity and mortality in human. To date it has not been reported the case of human infection with viruses specific for aquatic organisms. Human infections are caused with human viruses and aquatic organisms play role only as vechicles. The greatest risk in that respect present shellfish. Fish and particularly shellfish are likely to cause food poisoning in humans. In most cases the cause are toxins of phithoplancton origins accumulating in shellfish and fish.

  3. Evaluation of the radiological impact in the aquatic system in the surrounding of IPEN-CNEN/SP

    International Nuclear Information System (INIS)

    Jacomino, V.M.F.; Gordon, A.M.P.L.; Venturini, L.

    1989-12-01

    In order to control the discharges of radioactive material in the aquatic system (Jaguare stream and Pinheiros river) in the vicinity of IPEN-CNEN/SP an effluent monitoring program was established on a routine basis. This control is carried out by measuring the activity of the radionuclides present in the liquid effluents (source term) using gamma spectrometry and/or spectrophotometry. The results obtained are then compared with the discharge limits adopted by CNEN when a decision is made upon the discharge of the effluent under consideration. In 1988 the total activity discharged by the nuclear installations available was 1997, 9x10 6 Bq in a total volume of 2421,4 m 3 . The next step was to evaluate the effective equivalent dose in the general public by using the results of the source term and the information available concerning the environment. It was assumed that the only critical pathway is the external gamma irradiation of the people that work in the nearby of the discharge points in Pinheiros river. The effective equivalent dose obtained was 39,4η Sv and the most relevant radionuclides that should be considered 60 Co, 137 Cs, 131 I and 226 Ra. This result is less than 1/10 of the maximum admissible dose limit adopted by the Radiological Protection Standards which is 10 -3 Sv/year. In order to measure the level of radioactivity in the environment, samples of ground water, water and sediments of Pinheiros river were collected and analyzed by using gamma spectrometry and fluorimetry. The radionuclides found were 226 Ra, 22228 Ra, U Nat, 40 K and 7 Be with activities corresponding to the background levels. The analysis of these results and the evaluation of the equivalent dose show that the radiological impact in the aquatic systems considered is insignificant. (author) [pt

  4. ANN Model for Predicting the Impact of Submerged Aquatic Weeds Existence on the Hydraulic Performance of Branched Open Channel System Accompanied by Water Structures

    International Nuclear Information System (INIS)

    Abdeen, Mostafa A. M.; Abdin, Alla E.

    2007-01-01

    The existence of hydraulic structures in a branched open channel system urges the need for considering the gradually varied flow criterion in evaluating the different hydraulic characteristics in this type of open channel system. Computations of hydraulic characteristics such as flow rates and water surface profiles in branched open channel system with hydraulic structures require tremendous numerical effort especially when the flow cannot be assumed uniform. In addition, the existence of submerged aquatic weeds in this branched open channel system adds to the complexity of the evaluation of the different hydraulic characteristics for this system. However, this existence of aquatic weeds can not be neglected since it is very common in Egyptian open channel systems. Artificial Neural Network (ANN) has been widely utilized in the past decade in civil engineering applications for the simulation and prediction of the different physical phenomena and has proven its capabilities in the different fields. The present study aims towards introducing the use of ANN technique to model and predict the impact of submerged aquatic weeds existence on the hydraulic performance of branched open channel system. Specifically the current paper investigates a branched open channel system that consists of main channel supplies water to two branch channels that are infested by submerged aquatic weeds and have water structures such as clear over fall weirs and sluice gates. The results of this study showed that ANN technique was capable, with small computational effort and high accuracy, of predicting the impact of different infestation percentage for submerged aquatic weeds on the hydraulic performance of branched open channel system with two different hydraulic structures

  5. Search for the evidence of endocrine disruption in the aquatic environment: Lessons to be learned from joint biological and chemical monitoring in the European Project COMPREHEND

    NARCIS (Netherlands)

    Eggen, R.I.L.; Bengtsson, B.E.; Bowmer, C.T.; Gerritsen, A.A.M.; Gibert, M.; Hylland, K.; Johnson, A.C.; Leonards, P.E.G.; Nakari, T.; Norrgren, L.; Sumpter, J.P.; Suter, M.J.F.; Svenson, A.; Pickering, A.D.

    2003-01-01

    Between January 1999 and December 2001, the European Community project COMPREHEND was performed. The overall aim of COMPREHEND was to assess endocrine disruption in the aquatic environment in Europe, consequent to effluent discharge, with emphasis on estrogenic activity. COMPREHEND demonstrated the

  6. Noninvasive biological sensor system for detection of drunk driving.

    Science.gov (United States)

    Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

    2011-01-01

    Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

  7. Biochemical Space: A Framework for Systemic Annotation of Biological Models

    Czech Academy of Sciences Publication Activity Database

    Klement, M.; Děd, T.; Šafránek, D.; Červený, Jan; Müller, Stefan; Steuer, Ralf

    2014-01-01

    Roč. 306, JUL (2014), s. 31-44 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * cyanobacteria Subject RIV: EH - Ecology, Behaviour

  8. Review of "Stochastic Modelling for Systems Biology" by Darren Wilkinson

    Directory of Open Access Journals (Sweden)

    Bullinger Eric

    2006-12-01

    Full Text Available Abstract "Stochastic Modelling for Systems Biology" by Darren Wilkinson introduces the peculiarities of stochastic modelling in biology. This book is particularly suited to as a textbook or for self-study, and for readers with a theoretical background.

  9. A systems biology approach to study systemic inflammation.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2014-01-01

    Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

  10. Multi-level and hybrid modelling approaches for systems biology.

    Science.gov (United States)

    Bardini, R; Politano, G; Benso, A; Di Carlo, S

    2017-01-01

    During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

  11. Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

    Science.gov (United States)

    Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

    2015-08-21

    In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

  12. Genome Scale Modeling in Systems Biology: Algorithms and Resources

    Science.gov (United States)

    Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

    2014-01-01

    In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

  13. Sensitivity analysis approaches applied to systems biology models.

    Science.gov (United States)

    Zi, Z

    2011-11-01

    With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

  14. Evaluation of Colloidal Stability and Ecotoxicity of Metal-based Nanoparticles in the Aquatic and Terrestrial Systems

    Science.gov (United States)

    Pokhrel, Lok Raj

    NPs, ZnONPs, or their ions. Overall, various metal-based nanoparticles revealed lower toxicity than their ions against multiple organisms. This study showed that particle size, surface properties, and ion release kinetics of AgNPs modify following release into aquatic environment, suggesting potential implications to ecosystem health and functions, and that caution be applied when extending one species toxicity results to another because obvious differences in organism biology---supporting species sensitivity paradigm---can significantly alter nanoparticle or ionic toxicity.

  15. A system for success: BMC Systems Biology, a new open access journal

    OpenAIRE

    Webb Penelope A; Hodgkinson Matt J

    2007-01-01

    Abstract BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  16. A system for success: BMC Systems Biology, a new open access journal.

    Science.gov (United States)

    Hodgkinson, Matt J; Webb, Penelope A

    2007-09-04

    BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  17. Systems biology of neutrophil differentiation and immune response

    DEFF Research Database (Denmark)

    Theilgaard-Mönch, Kim; Porse, Bo T; Borregaard, Niels

    2005-01-01

    Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies. These stu......Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies....... These studies have identified a plethora of novel effector proteins stored in the granules of neutrophils. In addition, these studies provide evidence that neutrophil differentiation and immune response are governed by a highly coordinated transcriptional programme that regulates cellular fate and function...

  18. Advancing metabolic engineering through systems biology of industrial microorganisms.

    Science.gov (United States)

    Dai, Zongjie; Nielsen, Jens

    2015-12-01

    Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Advancing metabolic engineering through systems biology of industrial microorganisms

    DEFF Research Database (Denmark)

    Dai, Zongjie; Nielsen, Jens

    2015-01-01

    resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review......Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

  20. Systems biology approaches to the study of cardiovascular drugs

    NARCIS (Netherlands)

    Nikolsky, Y.; Kleemann, R.

    2010-01-01

    Atherogenic lipids and chronic inflammation drive the development of cardiovascular disorders such as atherosclerosis. Many cardiovascular drugs target the liver which is involved in the formation of lipid and inflammatory risk factors. With robust systems biology tools and comprehensive

  1. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

    2016-01-01

    function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material...... and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active...... performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii...

  2. Category of Metabolic-Replication Systems in Biology and Medicine

    OpenAIRE

    I. C. Baianu

    2012-01-01

    Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life's origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important questio...

  3. Stochastic chemical kinetics theory and (mostly) systems biological applications

    CERN Document Server

    Érdi, Péter; Lente, Gabor

    2014-01-01

    This volume reviews the theory and simulation methods of stochastic kinetics by integrating historical and recent perspectives, presents applications, mostly in the context of systems biology and also in combustion theory. In recent years, due to the development in experimental techniques, such as optical imaging, single cell analysis, and fluorescence spectroscopy, biochemical kinetic data inside single living cells have increasingly been available. The emergence of systems biology brought renaissance in the application of stochastic kinetic methods.

  4. Exploring Synthetic and Systems Biology at the University of Edinburgh.

    Science.gov (United States)

    Fletcher, Liz; Rosser, Susan; Elfick, Alistair

    2016-06-15

    The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  5. Fast removal of oxygen from biological systems

    International Nuclear Information System (INIS)

    Dewey, D.L.; Michael, B.D.

    1975-01-01

    Reference is made to the fact that if radiation is given at a high enough dose rate, the biological effect of oxygen is less than at low dose rates. Examples are given of 'break-point' experiments showing the effect. It is stated that the rapid removal of a substance by radiation is not confined to oxygen: the only criterion required to demonstrate the effect is that the chemical causes a measurable sensitization or protection at a concentration small enough so that it can be depleted at a relatively low dose of radiation. Sufficient confidence is now placed in the effect that it can be used the other way round; that is, to measure the position of the break-point and from this measurement determine the oxygen concentration at the target site at the instant before irradiation. Examples are given of the use of the high dose rate technique for measuring the oxygen concentration inside mammalian cells (Chinese hamster cells). The effects of partial pressures of inert gases, and the effect of elevated gas pressures, are discussed. (U.K.)

  6. Primary energy-transformations in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Lehninger, A.L.

    1980-10-01

    In this paper I shall review the main outlines of current research on the molecular aspects of the primary energy-coupling mechanisms in cells, those carried out by energy-transducing membranes. They include the capture of solar energy by the chloroplast membranes of green plants, used to generate carbohydrates and molecular oxygen from carbon dioxide and water, and the counterpart of photosynthesis, the process of respiration in heterotrophic organisms, in which reduced organic products generated by photosynthesis are oxidized at the expense of dioxygen to form carbon dioxide and water. Although the cycling of dioxygen, carbon dioxide, and organic matter between the plant and animal worlds is well known, it is not generally appreciated that the magnitude of biological energy flux in these cycles is huge compared to the total energy flux in man-made devices. A major consequence is that the concentration of carbon dioxide in the atmosphere has been increasing at a significant rate, at a time when there is also a decrease, at least in some parts of the world, in the counterbalancing utilization of CO/sub 2/ by green plants, due to deforestation. The greenhouse effect of increased atmospheric CO/sub 2/ may not only change the earth's climate, but also may influence the rate of photosynthesis. It is also not generally appreciated that energy flow in the biosphere leads to production of enormous amounts of organic matter potentially useful in furnishing man's energy requirements.

  7. An outline of a model-based expert system to identify optimal remedial strategies for restoring contaminated aquatic ecosystems: the project MOIRA

    International Nuclear Information System (INIS)

    Appelgren, A.; Bergstrom, U.; Brittain, J.; Monte, L.

    1996-10-01

    The present report describes the fundamental principles of the research programme MOIRA (a model based computerized system for management support to Identify optimal remedial strategies for Restoring radionuclide contaminated Aquatic ecosystems and drainage areas) financed by the EC (European Community) (Contract N F14P-CT96-0036). The interventions to restore radionuclides contaminated aquatic systems may result in detrimental ecological, social and economical effects. Decision makers must carefully evaluate these impacts. The main aim of the MOIRA project is the development of an expert system based on validated models predicting the evolution of the radioactive contamination of fresh water systems following countermeasure applications and their relevant ecological, social and economical impacts. The expert system will help decision makers, that are not necessarily gifted with experience in environmental modeling, to identify optimal remedial strategies for restoring contaminated fresh water systems

  8. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...

  9. A Generic Language for Biological Systems based on Bigraphs

    DEFF Research Database (Denmark)

    Damgaard, Troels Christoffer; Krivine, Jean

    Several efforts have shown that process calculi developed for reasoning about concurrent and mobile systems may be employed for modelling biological systems at the molecular level. In this paper, we initiate investigation of the meta-language framework bigraphical reactive systems, due to Milner et...

  10. Biocellion: accelerating computer simulation of multicellular biological system models.

    Science.gov (United States)

    Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

    2014-11-01

    Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Biological oceanography of the red oceanic system

    Science.gov (United States)

    Theil, Hjalmar; Weikert, Horst

    1. In 1977, 1979 and 1980-81, investigations were carried out which aimed at evaluating the potential risks from mining metalliferous muds precipating in the Atlantis II Deep of the central Red Sea. This environmental research was initiated by the Saudi Sudanese Red Sea Joint Commission in order to avoid any danger for the Red Sea ecosystem. The broad environmental research programme coherent studies in physical, chemical, biological, and geological oceanography as well as toxicological investigations in the oceanic and in reef zones. We summarise the results from our biological fiels studies in the open sea. 2. The biological investigations were concentrated on the area of the Atlantis II Deep. Benthos was sampled between 700-2000m. For comparison a few samples were also taken further north in the central Red Sea, and to east and west along the flanking deep terraces (500-1000m). Plankton studies covered the total water column above the Deep, and were extended along the axial through to north and south. 3. Benthos sampling was carried out using a heavy closing trawl, a large box grab (box size 50 × 50 cm), Van Veen grabs and traps; photographic surveys were made a phototrap and a photosled. Community respiration was measured with a ship-board method using grab subsamples. Nutrient concentrations, seston and phytoplankton standing stocks as well as in situ primary production were determined from hydrocast samples. Data on zooplankton and micronekton composition and standing stock were obtained from samples collected using different multiple opening-and-closing nets equipped with 100 μm, 300 μm, and 1000 μm mesh sizes. Daily and ontogenetical vertical migration patterns were studied by comparisons of data from midday and midnight tows. 4. Throughout the whole area the sediment is a pteropod ooze containing low contentrations of organic matter; measured organic carbon and nitrogen contents were 0.5 and 0.05% respectively, and chloroplastic pigment equivalents

  12. Modeling life the mathematics of biological systems

    CERN Document Server

    Garfinkel, Alan; Guo, Yina

    2017-01-01

    From predator-prey populations in an ecosystem, to hormone regulation within the body, the natural world abounds in dynamical systems that affect us profoundly. This book develops the mathematical tools essential for students in the life sciences to describe these interacting systems and to understand and predict their behavior. Complex feedback relations and counter-intuitive responses are common in dynamical systems in nature; this book develops the quantitative skills needed to explore these interactions. Differential equations are the natural mathematical tool for quantifying change, and are the driving force throughout this book. The use of Euler’s method makes nonlinear examples tractable and accessible to a broad spectrum of early-stage undergraduates, thus providing a practical alternative to the procedural approach of a traditional Calculus curriculum. Tools are developed within numerous, relevant examples, with an emphasis on the construction, evaluation, and interpretation of mathematical models ...

  13. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  14. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  15. Circadian systems biology: When time matters

    Directory of Open Access Journals (Sweden)

    Luise Fuhr

    2015-01-01

    In this manuscript we review the combination of experimental methodologies, bioinformatics and theoretical models that have been essential to explore this remarkable timing-system. Such an integrative and interdisciplinary approach may provide new strategies with regard to chronotherapeutic treatment and new insights concerning the restoration of the circadian timing in clock-associated diseases.

  16. Statistical Model Checking for Biological Systems

    DEFF Research Database (Denmark)

    David, Alexandre; Larsen, Kim Guldstrand; Legay, Axel

    2014-01-01

    Statistical Model Checking (SMC) is a highly scalable simulation-based verification approach for testing and estimating the probability that a stochastic system satisfies a given linear temporal property. The technique has been applied to (discrete and continuous time) Markov chains, stochastic...

  17. Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system.

    Science.gov (United States)

    Jiang, Jing-Zhe; Zhao, Wang; Liu, Guang-Feng; Wang, Jiang-Yong

    2017-01-01

    An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling.

  18. Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system.

    Directory of Open Access Journals (Sweden)

    Jing-Zhe Jiang

    Full Text Available An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone, producers (algae or a substrate, and the environment (water. DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems

  19. Stream classification of the Apalachicola-Chattahoochee-Flint River System to support modeling of aquatic habitat response to climate change

    Science.gov (United States)

    Elliott, Caroline M.; Jacobson, Robert B.; Freeman, Mary C.

    2014-01-01

    A stream classification and associated datasets were developed for the Apalachicola-Chattahoochee-Flint River Basin to support biological modeling of species response to climate change in the southeastern United States. The U.S. Geological Survey and the Department of the Interior’s National Climate Change and Wildlife Science Center established the Southeast Regional Assessment Project (SERAP) which used downscaled general circulation models to develop landscape-scale assessments of climate change and subsequent effects on land cover, ecosystems, and priority species in the southeastern United States. The SERAP aquatic and hydrologic dynamics modeling efforts involve multiscale watershed hydrology, stream-temperature, and fish-occupancy models, which all are based on the same stream network. Models were developed for the Apalachicola-Chattahoochee-Flint River Basin and subbasins in Alabama, Florida, and Georgia, and for the Upper Roanoke River Basin in Virginia. The stream network was used as the spatial scheme through which information was shared across the various models within SERAP. Because these models operate at different scales, coordinated pair versions of the network were delineated, characterized, and parameterized for coarse- and fine-scale hydrologic and biologic modeling. The stream network used for the SERAP aquatic models was extracted from a 30-meter (m) scale digital elevation model (DEM) using standard topographic analysis of flow accumulation. At the finer scale, reaches were delineated to represent lengths of stream channel with fairly homogenous physical characteristics (mean reach length = 350 m). Every reach in the network is designated with geomorphic attributes including upstream drainage basin area, channel gradient, channel width, valley width, Strahler and Shreve stream order, stream power, and measures of stream confinement. The reach network was aggregated from tributary junction to tributary junction to define segments for the

  20. A framework for ecological risk assessment of metal mixtures in aquatic systems.

    Science.gov (United States)

    Nys, Charlotte; Van Regenmortel, Tina; Janssen, Colin R; Oorts, Koen; Smolders, Erik; De Schamphelaere, Karel A C

    2018-03-01

    Although metal mixture toxicity has been studied relatively intensely, there is no general consensus yet on how to incorporate metal mixture toxicity into aquatic risk assessment. We combined existing data on chronic metal mixture toxicity at the species level with species sensitivity distribution (SSD)-based in silico metal mixture risk predictions at the community level for mixtures of Ni, Zn, Cu, Cd, and Pb, to develop a tiered risk assessment scheme for metal mixtures in freshwater. Generally, independent action (IA) predicts chronic metal mixture toxicity at the species level most accurately, whereas concentration addition (CA) is the most conservative model. Mixture effects are noninteractive in 69% (IA) and 44% (CA) and antagonistic in 15% (IA) and 51% (CA) of the experiments, whereas synergisms are only observed in 15% (IA) and 5% (CA) of the experiments. At low effect sizes (∼ 10% mixture effect), CA overestimates metal mixture toxicity at the species level by 1.2-fold (i.e., the mixture interaction factor [MIF]; median). Species, metal presence, or number of metals does not significantly affect the MIF. To predict metal mixture risk at the community level, bioavailability-normalization procedures were combined with CA or IA using SSD techniques in 4 different methods, which were compared using environmental monitoring data of a European river basin (the Dommel, The Netherlands). We found that the simplest method, in which CA is directly applied to the SSD (CA SSD ), is also the most conservative method. The CA SSD has median margins of safety (MoS) of 1.1 and 1.2 respectively for binary mixtures compared with the theoretically more consistent methods of applying CA or IA to the dose-response curve of each species individually prior to estimating the fraction of affected species (CA DRC or IA DRC ). The MoS increases linearly with an increasing number of metals, up to 1.4 and 1.7 for quinary mixtures (median) compared with CA DRC and IA DRC

  1. Systems identification: a theoretical method applied to tracer kinetics in aquatic microcosms

    International Nuclear Information System (INIS)

    Halfon, E.; Georgia Univ., Athens

    1974-01-01

    A mathematical model of radionuclide kinetics in a laboratory microcosm was built and the transfer parameters estimated by multiple regression and system identification techniques. Insight into the functioning of the system was obtained from analysis of the model. Methods employed have allowed movements of radioisotopes not directly observable in the experimental systems to be distinguished. Results are generalized to whole ecosystems

  2. Aquatic Ecology Section

    International Nuclear Information System (INIS)

    Brocksen, R.W.

    1978-01-01

    Population studies were concerned with predicting long-term consequences of mortality imposed on animal populations by man's activities. These studies consisted of development of a generalized life cycle model and an empirical impingement model for use in impact analysis. Chemical effects studies were conducted on chlorine minimization; fouling by the Asiatic clam; identification of halogenated organics in cooling water; and effects of halogenated organics in cooling systems on aquatic organisms. Ecological transport studies were conducted on availability of sediment-bound 137 Cs and 60 Co to fish; 137 Cs and 60 Co in White Oak Lake fish; and chromium levels in fish from a lake chronically contaminated with chromates from cooling towers. Progress is also reported on the following: effects of irradiation on thermal tolerance of mosquito fish; toxicity of nickel to the developing eggs and larvae of carp; accumulation of selected heavy metals associated with fly ash; and environmental monitoring of aquatic ecosystems

  3. An online model composition tool for system biology models.

    Science.gov (United States)

    Coskun, Sarp A; Cicek, A Ercument; Lai, Nicola; Dash, Ranjan K; Ozsoyoglu, Z Meral; Ozsoyoglu, Gultekin

    2013-09-05

    There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user's input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.

  4. Impact of long-term radiation exposure on aquatic biota within the Chernobyl exclusion zone: 30 years after accident

    International Nuclear Information System (INIS)

    Gudkov, D.I.; Pomortseva, N.A.; Shevtsova, N.L.; Dzyubenko, E.V.; Nazarov, A.B.

    2016-01-01

    Self-purification of closed water bodies within the Chernobyl exclusion zone (EZ) is an extremely slow process. Therefore, ecosystems of the majority of lakes, dead channels and crawls possess high levels of radionuclide contamination of all components. Along with natural decontamination processes in aquatic ecosystems such as physical decay of radionuclides and their water transport outside the EZ, there is a change of physical and chemical forms of radioactive substances in soils of catchment areas, their transformation and transition in the mobile and bioavailable state, washout to the closed aquatic ecosystems and accumulation by hydrobionts. This essentially deteriorates the radiation situation in closed aquatic ecosystems, which are some kind of 'storage system' of radioactive substances in the EZ and results in increase of radiation dose to aquatic species and manifests in a variety of radiation effects at different levels of biological systems. We established dose-related effects in hydrobionts of lakes within the EZ which indicates a damage of biological systems at subcellular, cellular, tissue, organ, organism and population levels as a result of chronic exposure to low doses of ionizing radiation. The rate of chromosomal aberrations in cells of aquatic species, many-a-times exceeds the level of spontaneous mutagenesis level to aquatic biota. Increased levels of chromosome damages may be a manifestation of radiation-induced genetic instability, which is one of the main mechanisms for the protection of living organisms from exposure to stressors with subsequent implementation at higher levels of organization of biological systems. (author)

  5. Systematic integration of experimental data and models in systems biology.

    Science.gov (United States)

    Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

    2010-11-29

    The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

  6. Thermostability of biological systems: fundamentals, challenges, and quantification.

    Science.gov (United States)

    He, Xiaoming

    2011-01-01

    This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.

  7. Standards, Data Exchange and Intellectual Property Rights in Systems Biology

    DEFF Research Database (Denmark)

    van Zimmeren, Esther; Rutz, Berthold; Minssen, Timo

    2016-01-01

    ” of scientists. In 2015, Biotechnology Journal published a report from an expert meeting on “Synthetic Biology & Intellectual Property Rights” organized by the Danish Agency for Science, Technology and Innovation sponsored by the European Research Area Network (ERA-Net) in Synthetic Biology (ERASynBio), in which...... we provided a number of recommendations for a variety of stakeholders. The current article offers some deeper reflections about the interface between IPRs, standards and data exchange in Systems Biology resulting from an Expert Meeting funded by another ERA-Net, ERASysAPP. The meeting brought...... together experts and stakeholders (e.g. scientists, company representatives, officials from public funding organizations) in systems biology (SysBio) from different countries.  Despite the different profiles of the stakeholders at the meeting and the variety of interests, many concerns and opinions were...

  8. Applications of dynamical systems in biology and medicine

    CERN Document Server

    Radunskaya, Ami

    2015-01-01

    This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

  9. Biological indicators for monitoring water quality of MTF canals system

    Science.gov (United States)

    Sethi, S. L.

    1975-01-01

    Biological models, diversity indexes, were developed to predict environmental effects of NASA's Mississippi test facility (MTF) chemical operations on canal systems in the area. To predict the effects on local streams, a physical model of unpolluted streams was established. The model is fed by artesian well water free of background levels of pollutants. The species diversity and biota composition of unpolluted MTF stream was determined; resulting information will be used to form baseline data for future comparisons. Biological modeling was accomplished by adding controlled quantities or kinds of chemical pollutants and evaluating the effects of these chemicals on the biological life of the stream.

  10. Systems-biology dissection of eukaryotic cell growth

    Directory of Open Access Journals (Sweden)

    Andrews Justen

    2010-05-01

    Full Text Available Abstract A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth. See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

  11. Biota connect aquatic habitats throughout freshwater ecosystem mosaics

    Science.gov (United States)

    Schofield, Kate A.; Alexander, Laurie C.; Ridley, Caroline E.; Vanderhoof, Melanie; Fritz, Ken M.; Autrey, Bradley; DeMeester, Julie; Kepner, William G.; Lane, Charles R.; Leibowitz, Scott; Pollard, Amina I.

    2018-01-01

    Freshwater ecosystems are linked at various spatial and temporal scales by movements of biota adapted to life in water. We review the literature on movements of aquatic organisms that connect different types of freshwater habitats, focusing on linkages from streams and wetlands to downstream waters. Here, streams, wetlands, rivers, lakes, ponds, and other freshwater habitats are viewed as dynamic freshwater ecosystem mosaics (FEMs) that collectively provide the resources needed to sustain aquatic life. Based on existing evidence, it is clear that biotic linkages throughout FEMs have important consequences for biological integrity and biodiversity. All aquatic organisms move within and among FEM components, but differ in the mode, frequency, distance, and timing of their movements. These movements allow biota to recolonize habitats, avoid inbreeding, escape stressors, locate mates, and acquire resources. Cumulatively, these individual movements connect populations within and among FEMs and contribute to local and regional diversity, resilience to disturbance, and persistence of aquatic species in the face of environmental change. Thus, the biological connections established by movement of biota among streams, wetlands, and downstream waters are critical to the ecological integrity of these systems. Future research will help advance our understanding of the movements that link FEMs and their cumulative effects on downstream waters.

  12. Nuclear magnetic resonance studies of biological systems

    International Nuclear Information System (INIS)

    Antypas, W.G. Jr.

    1988-01-01

    The difference between intracellular and extracellular proton relaxation rates provides the basis for the determination of the mean hemoglobin concentration (MHC) in red blood cells. The observed water T 1 relaxation data from red blood cell samples under various conditions were fit to the complete equation for the time-dependent decay of magnetization for a two-compartment system including chemical exchange. The MHC for each sample was calculated from the hematocrit and the intracellular water fraction as determined by NMR. The binding of the phosphorylcholine (PC) analogue, 2-(trimethylphosphonio)-ethylphosphate (phosphoryl-phosphocholine, PPC) to the PC binding myeloma proteins TEPC-15, McPC 603, and MOPC 167 was studied by 31 P NMR

  13. Modeling of biological intelligence for SCM system optimization.

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  14. Dietary antioxidant synergy in chemical and biological systems.

    Science.gov (United States)

    Wang, Sunan; Zhu, Fan

    2017-07-24

    Antioxidant (AOX) synergies have been much reported in chemical ("test-tube" based assays focusing on pure chemicals), biological (tissue culture, animal and clinical models), and food systems during the past decade. Tentative synergies differ from each other due to the composition of AOX and the quantification methods. Regeneration mechanism responsible for synergy in chemical systems has been discussed. Solvent effects could contribute to the artifacts of synergy observed in the chemical models. Synergy in chemical models may hardly be relevant to biological systems that have been much less studied. Apparent discrepancies exist in understanding the molecular mechanisms in both chemical and biological systems. This review discusses diverse variables associated with AOX synergy and molecular scenarios for explanation. Future research to better utilize the synergy is suggested.

  15. Modeling of Biological Intelligence for SCM System Optimization

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  16. Modeling of Biological Intelligence for SCM System Optimization

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

  17. Tritium isotope fractionation in biological systems and in analytical procedures

    International Nuclear Information System (INIS)

    Kim, M.A.; Baumgaertner, Franz

    1989-01-01

    The organically bound tritium (OBT) is evaluated in biological systems by determining the tritium distribution ratio (R-value), i.e. tritium concentrations in organic substance to cell water. The determination of the R-value always involves isotope fractionation is applied analytical procedures and hence the evaluation of the true OBT -value in a given biological system appears more complicated than hitherto known in the literature. The present work concentrates on the tritium isotope fractionation in the cell water separation and on the resulting effects on the R-value. The analytical procedures examined are vacuum freeze drying under equilibrium and non-equilibrium conditions and azeotropic distillation. The vaporization isotope effects are determined separately in the phase transition of solid or liquid to gas in pure tritium water systems as well as in real biological systems, e.g. corn plant. The results are systematically analyzed and the influence of isotope effects on the R-value is rigorously quantified

  18. Vibrational resonances in biological systems at microwave frequencies.

    Science.gov (United States)

    Adair, Robert K

    2002-03-01

    Many biological systems can be expected to exhibit resonance behavior involving the mechanical vibration of system elements. The natural frequencies of such resonances will, generally, be in the microwave frequency range. Some of these systems will be coupled to the electromagnetic field by the charge distributions they carry, thus admitting the possibility that microwave exposures may generate physiological effects in man and other species. However, such microwave excitable resonances are expected to be strongly damped by interaction with their aqueous biological environment. Although those dissipation mechanisms have been studied, the limitations on energy transfers that follow from the limited coupling of these resonances to the electromagnetic field have not generally been considered. We show that this coupling must generally be very small and thus the absorbed energy is so strongly limited that such resonances cannot affect biology significantly even if the systems are much less strongly damped than expected from basic dissipation models.

  19. Dissolved Organic In Natural and Polluted Waters: Methodology and Results of Running Control of Chemical Oxygen Demand (cod) For The Inland and Marine Aquatic System

    Science.gov (United States)

    Melentyev, K. V.; Worontsov, A. M.

    Current control of dissolved organic matter in natural and waste waters is the definition traditionally of chemical oxygen demand (COD) -- one of the basic parameters of quality of water. According to the International Standard (ISO 6060), it requires not less than one hour, while in many cases the operative information about amount of dissolved organic matter in aquatic environments have importance for prevention of an emergency. The standard method is applicable to waters with meaning of COD above 30 mg O2/l and, as the chloride ion prevents, it could be difficult for assessment of organic matter in sea water. Besides it is based on dichromate oxidation of the sum of organic substances in strong acid conditions at the presence of silver and mercury, that resulted in formation toxic pollutants. Till now attempts of automation of the COD definition in aquatic system were limited, basically, to duplication of the technology submitted the above standard (automatic COD analyzers "SERES Co."-- France, or "Tsvet Co." - Russia). The system of ozone-chemiluminescence automatic control of organic matter in water (CS COD) is offered and designed. Its based on the ozone oxidation of these substances in flowing water system and measurement arising from luminescent effects. CS COD works in real time. An instrument uses for reaction the atmospheric air, doesn't require fill of reagents and doesn't make new toxic pollutants. The system was tested in laboratory, and biochemical control of organic matter in water samples gathered from the river Neva and other polluted inland water areas and basins in St. Petersburg region was fulfilled (distilled water was used as "zero" media). The results of systematization of these measurements are presented. The new special ozone generator and flowing reactor for real-time running control of different waters in natural conditions were developed, and several series of large - scale field experiments onboard research ship were provided

  20. Investigating cholesterol metabolism and ageing using a systems biology approach.

    Science.gov (United States)

    Morgan, A E; Mooney, K M; Wilkinson, S J; Pickles, N A; Mc Auley, M T

    2017-08-01

    CVD accounted for 27 % of all deaths in the UK in 2014, and was responsible for 1·7 million hospital admissions in 2013/2014. This condition becomes increasingly prevalent with age, affecting 34·1 and 29·8 % of males and females over 75 years of age respectively in 2011. The dysregulation of cholesterol metabolism with age, often observed as a rise in LDL-cholesterol, has been associated with the pathogenesis of CVD. To compound this problem, it is estimated by 2050, 22 % of the world's population will be over 60 years of age, in culmination with a growing resistance and intolerance to pre-existing cholesterol regulating drugs such as statins. Therefore, it is apparent research into additional therapies for hypercholesterolaemia and CVD prevention is a growing necessity. However, it is also imperative to recognise this complex biological system cannot be studied using a reductionist approach; rather its biological uniqueness necessitates a more integrated methodology, such as that offered by systems biology. In this review, we firstly discuss cholesterol metabolism and how it is affected by diet and the ageing process. Next, we describe therapeutic strategies for hypercholesterolaemia, and finally how the systems biology paradigm can be utilised to investigate how ageing interacts with complex systems such as cholesterol metabolism. We conclude by emphasising the need for nutritionists to work in parallel with the systems biology community, to develop novel approaches to studying cholesterol metabolism and its interaction with ageing.

  1. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  2. Fish associated with aquatic macrophytes in the Chacororé-Sinhá Mariana Lake system and Mutum River, Pantanal of Mato Grosso, Brazil.

    Science.gov (United States)

    Pacheco, E B; Da-Silva, C J

    2009-02-01

    On the left bank of the Cuibá River, one of the main tributaries of the Pantanal in Mato Grosso, are located the Chacororé and Sinhá Mariana Lakes and the Mutum River, the littoral regions of which are covered with aquatic macrophytes, dominated by the species Eichhornia crassipes and Eichhornia azurea. To examine the ichthyofauna associated with this vegetation, in the year 2003, 3510 fish were collected, distributed among 83 species, and the limnological variables verified near the macrophyte stands where they were sampled. The most abundant and richest order was the Characiformes, followed by the Gymnotiformes and Siluriformes. Analysis of similarity showed a very low, or null, index that the limnological conditions and morphology of the aquatic macrophyte species provide habitat sufficiently homogeneous to give. The limnological conditions and morphology of the aquatic macrophyte species provide a sufficient habitat heterogeneity to give very low, or null, index values. Thus, environmental conservation measures should be more effective in promoting the conservation of the species, given the high levels of biological diversity found in the habitats studied.

  3. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Ihekwaba, Adoha

    2007-01-01

    A. Ihekwaba, R. Mardare. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems. Case study: NFkB system. In Proc. of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2...

  4. Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

    DEFF Research Database (Denmark)

    Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk

    2013-01-01

    Improve the System A "systems biology" approach may clarify, for example, how particular proteins determine sensitivity of bacteria to extremes of temperature. Chang et al. (p. 1220) integrated information on protein structure with a model of metabolism, thus associating the protein structure of ...

  5. Hepatocellular carcinoma: a systems biology perspective

    Directory of Open Access Journals (Sweden)

    Lorenza Alice D'alessandro

    2013-02-01

    Full Text Available Hepatocellular carcinomas (HCC have different etiology and heterogenic genomic alterations lead to high complexity. The molecular features of HCC have largely been studied by gene expression and proteome profiling focusing on the correlations between the expression of specific markers and clinical data. Integration of the increasing amounts of data in databases has facilitated the link of genomic and proteomic profiles of HCC to disease state and clinical outcome. Despite the current knowledge, specific molecular markers remain to be identified and new strategies are required to establish novel targeted therapies. In the last years, mathematical models reconstructing gene and protein networks based on experimental data of HCC have been developed providing powerful tools to predict candidate interactions and potential targets for therapy. Furthermore, the combination of dynamic and logical mathematical models with quantitative data allows detailed mechanistic insights into system properties. To address effects at the organ level, mathematical models reconstructing the three-dimensional organization of liver lobules were developed. In the future, integration of different modeling approaches capturing the effects at the cellular up to the organ level is required to address the complex properties of HCC and to enable the discovery of new targets for HCC prevention or treatment.

  6. Viscosity and not biological mechanisms often controls the effects of temperature on ciliary activity and swimming velocity of small aquatic organisms

    DEFF Research Database (Denmark)

    Larsen, Poul Scheel; Riisgård, H. U.

    2009-01-01

    organisms using cilia or small appendages for propulsion. Here we summarize results from the literature and from own studies on bio-mechanical activities in response to changing temperature or manipulated viscosity at constant temperature, both having the same change in kinematic viscosity. The survey......A number of studies have shown that temperature-dependent viscosity of the ambient water controls or strongly affects bio-mechanical activity such as beat frequency of water-pumping cilia in mussels and ascidians, swimming velocity of sperm cells, ciliates and small (micro- and meso-scale) aquatic...

  7. SEEK: a systems biology data and model management platform.

    Science.gov (United States)

    Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L; Mueller, Wolfgang; Goble, Carole

    2015-07-11

    Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and

  8. Biología reproductiva de la serpiente semiacuática Liophis semiaureus (Serpentes, Colubridae en el nordeste de Argentina Reproductive biology of the semi-aquatic snake Liophis semiaureus (Serpentes, Colubridae in the north-east of Argentina

    Directory of Open Access Journals (Sweden)

    SOLEDAD M LÓPEZ

    2009-06-01

    Full Text Available Las serpientes tienen una notable flexibilidad y diversidad en sus tácticas reproductivas, a pesar de ello, los estudios acerca de la biología reproductiva de especies sudamericanas en zonas subtropicales-templadas son escasos. Se analizó la biología reproductiva de Liophis semiaureus en el nordeste de Argentina, incluyendo la madurez y dimorfismo sexual, fecundidad y ciclo reproductivo. Las hembras maduras fueron significativamente más largas, presentaron mayor peso corporal y alcanzaron la madurez sexual a una longitud mayor que los machos. Los machos tuvieron colas más largas que las hembras. El ciclo reproductivo fue estacional con mayor actividad en los períodos templados del año aunque previos a la época de inundaciones. Liophis semiaureus invirtió más energía en la reproducción que en el crecimiento, lo que posibilita que comiencen a reproducirse con tamaños más pequeños con respecto a otras poblaciones, sin retrasar su reproducción hasta alcanzar mayores tamaños. Esta puede ser una estrategia ventajosa en climas estacionales. Las características reproductivas y de dimorfismo sexual en L. semiaureus se encontrarían influenciadas por aspectos filogenéticos, geográficos y ecológicos, lo que determina que la especie responda de manera general al patrón reproductivo del grupo taxonómico pero con particularidades propias determinadas por los factores geográficos y los requerimientos ecológicos.Snakes in subtropical warm zones have a wide flexibility and diversity in your reproductive tactics. In spite of it, the studies in South America about that are scanty yet. We analyzed sexual dimorphism, sexual maturity, fecundity and reproductive cycle of a semi-aquatic snake, Liophis semiaureus, in north-east of Argentina. Females were significantly longer and heavier than the males. Females reach sexual maturity with longer snout-vent length than the males. Males had longer tails than the females. The reproductive cycle was

  9. Endocrine active contaminants in aquatic systems and intersex in common sport fishes

    Science.gov (United States)

    Lee Pow, Crystal S. D.; Law, J. Mac; Kwak, Thomas J.; Cope, W. Gregory; Rice, James A.; Kullman, Seth W.; Aday, D. Derek

    2017-01-01

    Male fish are susceptible to developing intersex, a condition characterized by the presence of testicular oocytes. In the present study, the relationship between intersex and exposure to estrogenic endocrine active contaminants (EACs) was assessed for 2 genera of sport fish, Micropterus and Lepomis, at 20 riverine sites. Seasonal trends and relationships between EACs and intersex (prevalence and severity) were examined at varying putative sources of EACs throughout North Carolina, identified as point sources, nonpoint sources, and reference sites. Intersex was identified in both genera, which was documented for the first time in wild-caught Lepomis. Intersex was more prevalent (59.8%) and more severe (1.6 mean rank) in Micropterus, which was highly correlation to EACs in sediment. In contrast, intersex was less common (9.9%) and less severe (0.2 mean rank) in Lepomis and was highly correlated to EACs in the water column. The authors found that concentrations of polycyclic aromatic hydrocarbons, polychlorinated biphenyls, industrial EACs, and estrogens were highest at point source sites; however, no source type variation was identified in the prevalence or severity of intersex, nor were there seasonal trends in intersex or EAC concentrations. The authors’ results associate genus-specific prevalence of intersex with specific EAC classes in common sport fishes having biological, ecological, and conservation implications.

  10. Application of modeling tools for risk assessment of engineered nanomaterials in aquatic systems

    CSIR Research Space (South Africa)

    Ondiaka, M

    2012-04-01

    Full Text Available Globally, engineered nanomaterials (ENMs) are increasingly being used in nanoproducts to improve their performance. The multi-stage lifecycle of ENMs increases their potential risk profiles to different environmental systems, for example, due...

  11. Cell-Based Sensor System Using L6 Cells for Broad Band Continuous Pollutant Monitoring in Aquatic Environments

    Directory of Open Access Journals (Sweden)

    Evamaria Stütz

    2012-03-01

    Full Text Available Pollution of drinking water sources represents a continuously emerging problem in global environmental protection. Novel techniques for real-time monitoring of water quality, capable of the detection of unanticipated toxic and bioactive substances, are urgently needed. In this study, the applicability of a cell-based sensor system using selected eukaryotic cell lines for the detection of aquatic pollutants is shown. Readout parameters of the cells were the acidification (metabolism, oxygen consumption (respiration and impedance (morphology of the cells. A variety of potential cytotoxic classes of substances (heavy metals, pharmaceuticals, neurotoxins, waste water was tested with monolayers of L6 cells (rat myoblasts. The cytotoxicity or cellular effects induced by inorganic ions (Ni2+ and Cu2+ can be detected with the metabolic parameters acidification and respiration down to 0.5 mg/L, whereas the detection limit for other substances like nicotine and acetaminophen are rather high, in the range of 0.1 mg/L and 100 mg/L. In a close to application model a real waste water sample shows detectable signals, indicating the existence of cytotoxic substances. The results support the paradigm change from single substance detection to the monitoring of overall toxicity.

  12. Synthetic and systems biology for microbial production of commodity chemicals.

    Science.gov (United States)

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

    2016-01-01

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

  13. Continuum analysis of biological systems conserved quantities, fluxes and forces

    CERN Document Server

    Suraishkumar, G K

    2014-01-01

    This book addresses the analysis, in the continuum regime, of biological systems at various scales, from the cellular level to the industrial one. It presents both fundamental conservation principles (mass, charge, momentum and energy) and relevant fluxes resulting from appropriate driving forces, which are important for the analysis, design and operation of biological systems. It includes the concept of charge conservation, an important principle for biological systems that is not explicitly covered in any other book of this kind. The book is organized in five parts: mass conservation; charge conservation; momentum conservation; energy conservation; and multiple conservations simultaneously applied. All mathematical aspects are presented step by step, allowing any reader with a basic mathematical background (calculus, differential equations, linear algebra, etc.) to follow the text with ease. The book promotes an intuitive understanding of all the relevant principles and in so doing facilitates their applica...

  14. Learning (from) the errors of a systems biology model.

    Science.gov (United States)

    Engelhardt, Benjamin; Frőhlich, Holger; Kschischo, Maik

    2016-02-11

    Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many cases itself incomplete and uncertain. A major problem in this context is that biological systems are open. Missed or unknown external influences as well as erroneous interactions in the model could thus lead to severely misleading results. Here we introduce the dynamic elastic-net, a data driven mathematical method which automatically detects such model errors in ordinary differential equation (ODE) models. We demonstrate for real and simulated data, how the dynamic elastic-net approach can be used to automatically (i) reconstruct the error signal, (ii) identify the target variables of model error, and (iii) reconstruct the true system state even for incomplete or preliminary models. Our work provides a systematic computational method facilitating modelling of open biological systems under uncertain knowledge.

  15. Overview of case studies on recovery of aquatic systems from disturbance

    Science.gov (United States)

    Niemi, Gerald J.; Devore, Philip; Detenbeck, Naomi; Taylor, Debra; Lima, Ann; Pastor, John; Yount, J. David; Naiman, Robert J.

    1990-09-01

    An extensive review of the published literature identified more than 150 case studies in which some aspect of resilience in freshwater systems was reported. Approximately 79% of systems studied were lotic and the remainder lentic. Most of the stressor types were chemical with DDT (N=29) and rotenone (N=15) the most common. The most common nonchemical stressors were logging activity (N=16), flooding (N=8), dredging (N=3), and drought (N=7). The variety of endpoints to which recovery could be measured ranged from sparse data for phytoplankton (N=13), periphyton (N=6), and macrophytes (N=8) to relatively more data for fish (N=412) and macroinvertebrates (N=698). Unfortunately the same characteristics were rarely measured consistently among sites. For example, with respect to fish, more than 30 different species were studied and recovery was measured in many ways, most commonly on the basis of: (1) first reappearance of the species, (2) return time of predisturbance densities, and (3) return time of predisturbance average individual size. Based on these criteria, all systems in these studies seem to be resilient to most disturbances with most recovery times being less than three years. Exceptions included when (1) the disturbance resulted in physical alteration of the existing habitat, (2) residual pollutants remained in the system, or (3) the system was isolated and recolonization was suppressed.

  16. Advances in Structural Biology and the Application to Biological Filament Systems.

    Science.gov (United States)

    Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

    2018-04-01

    Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  17. Conception of a sub aquatic lighting system for nuclear fuels storage pools

    International Nuclear Information System (INIS)

    Bracco, P.; Rosenthal, E.

    1990-01-01

    Restrictions like contaminated water, irradiated fuel elements in racks located on the bottom of the pool and the impossibility of removing the water, require a non conventional design of pool lamps. The model developed is independent of the pool, permitting easily fabrication and maintenance. They are made of stainless steel tubes with borosilicate windows, where floodlight or light are located. The lamp assembly is fixed at the border of the pool. The system offers advantages over the conventional pool lighting systems in fabrication, operation and maintenance. (author)

  18. Glycoengineering in CHO cells: Advances in systems biology

    DEFF Research Database (Denmark)

    Tejwani, Vijay; Andersen, Mikael Rørdam; Nam, Jong Hyun

    2018-01-01

    are not well understood. A systems biology approach combining different technologies is needed for complete understanding of the molecular processes accounting for this variability and to open up new venues in cell line development. In this review, we describe several advances in genetic manipulation, modeling......For several decades, glycoprotein biologics have been successfully produced from Chinese hamster ovary (CHO) cells. The therapeutic efficacy and potency of glycoprotein biologics are often dictated by their post translational modifications, particularly glycosylation, which unlike protein synthesis....... Recently, CHO cells have also been explored for production of therapeutic glycosaminoglycans (e.g. heparin), which presents similar challenges as producing glycoproteins biologics. Approaches to controlling heterogeneity in CHO cells and directing the biosynthetic process toward desired glycoforms...

  19. Optical sensors and their applications for probing biological systems

    DEFF Research Database (Denmark)

    Palanco, Marta Espina

    There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant and mammal......There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant...... of a trapped cell. The project could provide new insights into the desired biosensor for future membrane-protein cell studies....

  20. The Systems Biology Research Tool: evolvable open-source software

    OpenAIRE

    Wright, J; Wagner, A

    2008-01-01

    Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform calle...

  1. Cadmium (II) distribution in complex aquatic systems containing ferrihydrite, bacteria and an organic ligand: The effect of bioactivity

    International Nuclear Information System (INIS)

    Song Yantao; Swift, Simon; Swedlund, Peter J.; Singhal, Naresh

    2011-01-01

    Highlights: → Cd 2+ and ferrihydrite did not inhibit H 2 L p degradation by Comamonas spp. → In systems lacking ferrihydrite, Cd 2+ sorption onto live bacteria exceeded dead bacteria for pH > 6. → With ferrihydrite present, no difference in Cd 2+ sorption to live and dead bacteria was observed. → Cd 2+ sorption to ferrihydrite and bacterial was successfully modeled by neglecting H 2 L p degradation. - Abstract: The distribution of Cd 2+ in the presence of phthalic acid (H 2 L p ), ferrihydrite and bacteria (Comamonas spp.) was investigated in biologically active systems involving H 2 L p biodegradation. Tests showed that Cd 2+ sorption onto bacteria, ferrihydrite and bacteria-ferrihydrite mixture increased with pH in all systems, irrespective of H 2 L p degradation or not. The use of bacterial growth medium, Bushnell Hass Broth modified for low phosphate, had negligible effect on Cd sorption. In the presence of ferrihydrite, no difference was observed between Cd 2+ sorption in the ferrihydrite-live bacteria and in the ferrihydrite-dead bacteria systems as ferrihydrite proved to be the dominant sorption phase. Cadmium sorption to ferrihydrite and to bacterial cells was described using the diffuse layer model and a nonelectrostatic 4-site model, respectively, which were developed for systems lacking H 2 L p degradation. For systems experiencing H 2 L p degradation this modeling approach predicted the general trend of Cd 2+ sorption-edge shift and gave good fits to the observed sorption data. The results obtained demonstrate that Cd 2+ sorption in the biologically active system was reasonably estimated by a model developed for biologically inactive systems, although uncertainty exists due to processes involving H 2 L p biodegradation products and changes in the bacterial population.

  2. Closed-loop system for growth of aquatic biomass and gasification thereof

    Science.gov (United States)

    Oyler, James R.

    2017-09-19

    Processes, systems, and methods for producing combustible gas from wet biomass are provided. In one aspect, for example, a process for generating a combustible gas from a wet biomass in a closed system is provided. Such a process may include growing a wet biomass in a growth chamber, moving at least a portion of the wet biomass to a reactor, heating the portion of the wet biomass under high pressure in the reactor to gasify the wet biomass into a total gas component, separating the gasified component into a liquid component, a non-combustible gas component, and a combustible gas component, and introducing the liquid component and non-combustible gas component containing carbon dioxide into the growth chamber to stimulate new wet biomass growth.

  3. Systems Biology of Meridians, Acupoints, and Chinese Herbs in Disease

    Directory of Open Access Journals (Sweden)

    Li-Ling Lin

    2012-01-01

    Full Text Available Meridians, acupoints, and Chinese herbs are important components of traditional Chinese medicine (TCM. They have been used for disease treatment and prevention and as alternative and complementary therapies. Systems biology integrates omics data, such as transcriptional, proteomic, and metabolomics data, in order to obtain a more global and complete picture of biological activity. To further understand the existence and functions of the three components above, we reviewed relevant research in the systems biology literature and found many recent studies that indicate the value of acupuncture and Chinese herbs. Acupuncture is useful in pain moderation and relieves various symptoms arising from acute spinal cord injury and acute ischemic stroke. Moreover, Chinese herbal extracts have been linked to wound repair, the alleviation of postmenopausal osteoporosis severity, and anti-tumor effects, among others. Different acupoints, variations in treatment duration, and herbal extracts can be used to alleviate various symptoms and conditions and to regulate biological pathways by altering gene and protein expression. Our paper demonstrates how systems biology has helped to establish a platform for investigating the efficacy of TCM in treating different diseases and improving treatment strategies.

  4. Collaborative Systems Biology Projects for the Military Medical Community.

    Science.gov (United States)

    Zalatoris, Jeffrey J; Scheerer, Julia B; Lebeda, Frank J

    2017-09-01

    This pilot study was conducted to examine, for the first time, the ongoing systems biology research and development projects within the laboratories and centers of the U.S. Army Medical Research and Materiel Command (USAMRMC). The analysis has provided an understanding of the breadth of systems biology activities, resources, and collaborations across all USAMRMC subordinate laboratories. The Systems Biology Collaboration Center at USAMRMC issued a survey regarding systems biology research projects to the eight U.S.-based USAMRMC laboratories and centers in August 2016. This survey included a data call worksheet to gather self-identified project and programmatic information. The general topics focused on the investigators and their projects, on the project's research areas, on omics and other large data types being collected and stored, on the analytical or computational tools being used, and on identifying intramural (i.e., USAMRMC) and extramural collaborations. Among seven of the eight laboratories, 62 unique systems biology studies were funded and active during the final quarter of fiscal year 2016. Of 29 preselected medical Research Task Areas, 20 were associated with these studies, some of which were applicable to two or more Research Task Areas. Overall, studies were categorized among six general types of objectives: biological mechanisms of disease, risk of/susceptibility to injury or disease, innate mechanisms of healing, diagnostic and prognostic biomarkers, and host/patient responses to vaccines, and therapeutic strategies including host responses to therapies. We identified eight types of omics studies and four types of study subjects. Studies were categorized on a scale of increasing complexity from single study subject/single omics technology studies (23/62) to studies integrating results across two study subject types and two or more omics technologies (13/62). Investigators at seven USAMRMC laboratories had collaborations with systems biology experts

  5. Portable Instrument to Measure CDOM Light Absorption in Aquatic Systems: WPI Success Story

    Science.gov (United States)

    2001-01-01

    World Precision Instruments, Inc. (WPI), of Sarasota, FL, in collaboration with NASA's John C. Stennis Space Center, has developed an innovative instrument to accurately measure Colored Dissolved Organic Matter (CDOM) absorption in the field. This successful collaboration has culminated in an exciting new device, called the UltraPath, now commercially available through WPI. Traditional methods of measuring absorption of dissolved materials require special handling and storage prior to measurement. Use of laboratory spectrophotometers as the measuring devices have proven time consuming, cumbersome, and delicate to handle. The UltraPath provides a low-cost, highly sensitive, rugged, portable system that is capable of high sensitivity measurements in widely divergent waters.

  6. Implementation of the aquatic radionuclide transport models RIVTOX and COASTOX into the RODOS System

    International Nuclear Information System (INIS)

    Gofman, D.; Lyashenko, G.; Marinets, A.; Mezhueva, I.; Shepeleva, T.; Tkalich, P.; Zheleznyak, M.

    1996-01-01

    The one -dimensional model of radionuclide transport in a network of river channel RIVTOX and two-dimensional lateral-longitudinal model of radionuclide transport in rivers, reservoirs and shallow lakes COASTOX have been implemented into the hydrological model chain of the decision support system RODOS. The software framework is developed to operate the models and to support their coupling with the other parts of RODOS hydrological model chain. The validation studies were performed for RIVTOX and COASTOX on the base of the data sets from Ukrainian, German and United States rivers

  7. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  8. Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.

    Science.gov (United States)

    Stéphanou, Angélique; Fanchon, Eric; Innominato, Pasquale F; Ballesta, Annabelle

    2018-05-09

    Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.

  9. A distributed approach for parameters estimation in System Biology models

    International Nuclear Information System (INIS)

    Mosca, E.; Merelli, I.; Alfieri, R.; Milanesi, L.

    2009-01-01

    Due to the lack of experimental measurements, biological variability and experimental errors, the value of many parameters of the systems biology mathematical models is yet unknown or uncertain. A possible computational solution is the parameter estimation, that is the identification of the parameter values that determine the best model fitting respect to experimental data. We have developed an environment to distribute each run of the parameter estimation algorithm on a different computational resource. The key feature of the implementation is a relational database that allows the user to swap the candidate solutions among the working nodes during the computations. The comparison of the distributed implementation with the parallel one showed that the presented approach enables a faster and better parameter estimation of systems biology models.

  10. Can aquatic macrophytes mobilize technetium by oxidizing their rhizosphere?

    International Nuclear Information System (INIS)

    Sheppard, S.C.; Evenden, W.G.

    1991-01-01

    Technetium (Tc) is very mobile in aerated surface environments, but is essentially immobile and biologically unavailable in anaerobic sediments. Aquatic macrophyte roots penetrate anaerobic sediments, carrying O 2 downward and frequently creating oxidizing conditions in their rhizosphere. The authors hypothesized that this process could mobilize otherwise unavailable Tc, possibly leading to incorporation of Tc into human or animal foods. Through experiments with rice (Oryza sativa L.), and with a novel artificial macrophyte root, they concluded that this pathway is unlikely to be important for annual plants, especially in soils with a high biological oxygen demand. The relatively slow oxidation of Tc limited its mobilization by short-lived root systems

  11. Tetrodotoxin-Producing Bacteria: Detection, Distribution and Migration of the Toxin in Aquatic Systems

    Directory of Open Access Journals (Sweden)

    Timur Yu. Magarlamov

    2017-05-01

    Full Text Available This review is devoted to the marine bacterial producers of tetrodotoxin (TTX, a potent non-protein neuroparalytic toxin. In addition to the issues of the ecology and distribution of TTX-producing bacteria, this review examines issues relating to toxin migration from bacteria to TTX-bearing animals. It is shown that the mechanism of TTX extraction from toxin-producing bacteria to the environment occur through cell death, passive/active toxin excretion, or spore germination of spore-forming bacteria. Data on TTX microdistribution in toxic organs of TTX-bearing animals indicate toxin migration from the digestive system to target organs through the transport system of the organism. The role of symbiotic microflora in animal toxicity is also discussed: despite low toxin production by bacterial strains in laboratory conditions, even minimal amounts of TTX produced by intestinal microflora of an animal can contribute to its toxicity. Special attention is paid to methods of TTX detection applicable to bacteria. Due to the complexity of toxin detection in TTX-producing bacteria, it is necessary to use several methods based on different methodological approaches. Issues crucial for further progress in detecting natural sources of TTX investigation are also considered.

  12. Properties and reactivity of aquatic organic matter from an Amazonian floodplain system

    Science.gov (United States)

    Perez, M. A. P.; Benedetti, M. F.; Moreira-Turcq, P.

    2009-04-01

    The aim of this study was to characterize the nature of the bulk dissolved organic matter (DOM) in different types of environments in the Amazon River-floodplain system and determine the importance of two different fractions of dissolved organic matter onto adsorption processes that occurs through the transport of organic matter in the Amazon Basin. Seven samples were collected in the Amazon River - "Lago Grande de Curuai" floodplain system, in rising water levels cruise (March 2006). The samples were taken in the Amazon main stem, in white and black floodplain waters, and in the middle of a phytoplaktonic bloom. The bulk, dissolved (i.e. acid-base titration) were characterized for these fractions. Adsorption experiments onto mineral phase from de surface sediment of the Curuai floodplain lake (rich in smectite and kaolinite) were realized with HPO and TPH fractions. The OC concentrations in the natural organic matter (Bulk and < 0.22 micrometer fractions) varied between 3.7-5.7 mg/L. The OC and TN concentrations varied between 510 - 528 mg C/g in the HPO fraction, and 408 - 462 mg C/g in the TPH compounds and between 14.3 - 17.6 mg N/g (HPO), and 22.1 - 30.0 mg N/g (TPH). The molecular weight of both fractions (HPO and TPH) didn't present significant variation. Both fractions presented high aromaticity and they were rich in carboxylic groups, although smaller values are systematically reported for the HPO fractions. The OM of the main stem was the most adsorbed, followed by the white water lake, the phytoplanktonic bloom, and black water lake sample. These results helped us to strengthen the hypothesis that the organic matter carried from the river and sediment in the floodplain is closely associated with mineral phase.

  13. Ecological effects assessment of anionic surfactant on aquatic ecosystem using microcosm system; Microcosm wo mochiita in ion kaimen kasseizai no suiken seitaikei ni oyobosu eikyo hyoka

    Energy Technology Data Exchange (ETDEWEB)

    Takamatsu, Y. [University of Tsukuba, Tsukuba (Japan); Inamori, Y. [National Institute for Environmental Studies, Tsukuba (Japan); Sudo, R. [Tohoku University, Sendai (Japan). Faculty of Engineering; Kurihara, Y. [Ou Univ., Fukushima (Japan). Faculty of Engineering; Matsumura, M. [University of Tsukuba, Tsukuba (Japan). Institute of Applied Biochemical

    1997-11-10

    Microcosm system was applied to assess effect of anionic surfactant (LAS) on aquatic ecosystem. Anionic surfactant such as LAS was added to an flask microcosm consisting of four species of bacteria as decomposer, one species of ciliate protozoa (Cyclidium glaucoma), two rotifers (Philodina sp. and Lepadella sp.) and one aquatic oligochaete (Aeolosoma hemprichi) as predator, and a green alga (Chlorella sp.) and a filamentous blue-green alga (Tolypothrix sp.) as producer, comparing with that of an natural lake model ecosystem derived from natural lake water. In the flask microcosm system and the natural lake model ecosystem, biodegradation rates of LAS were almost same and NOECs (no observed effect concentration) of LAS were also below 1.5 mg{center_dot} l{sup -1}. It was found that flask microcosm test could provide precise ecological effect assessment of LAS on number of microorganisms because the system showed higher reproducibility and stability than natural take model ecosystem. It was suggested that flask microcosm test was useful ecological effect assessment method which can reflect natural aquatic ecosystem. 10 refs., 4 figs., 2 tabs.

  14. The importance of recording physical and chemical variables simultaneously with remote radiological surveillance of aquatic systems: a perspective for environmental modelling

    International Nuclear Information System (INIS)

    Abril, J.M.; El-Mrabet, R.; Barros, H.

    2004-01-01

    Modern nuclear metrological tools allow the remote surveillance of the radiological status of the aquatic systems, providing an important advance in the protection of the environment. Nevertheless, the significance of the radiological data could be highly improved through simultaneous recording of physical and chemical variables that govern the behaviour and bioavailability of radionuclides in these aquatic systems. This work reviews some of these variables from the point of view of the environmental modelling. The amount, nature and dynamics of the suspended loads and bottom sediments strongly influence the behaviour of particle-reactive radionuclides. The kinetics of this process has a very fast component, as it is shown from our recent studies with 241 Am, 239 Pu and 133 Ba in several aquatic systems from southern Spain. Changes in pH, temperature and in the electrical conductivity are influencing the uptake kinetics and the final partitioning of the radioactivity. Water currents govern the radionuclide transport and dispersion. These points are illustrated with modelling exercises in the scenarios of the Suez Canal (Egypt) and the Haersvatten Lake (Sweden)

  15. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  16. Request for Travel Funds for Systems Radiation Biology Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Barcellos-Hoff, Mary Helen [NYU School of Medicine

    2014-03-22

    The 3rd International Systems Radiation Biology Workshop brought together the major European, US and Japanese research programs on radiation risk as well as selected experts representing systems biological approaches to discuss how the new methodologies could be best exploited for low dose research. A significant part of the workshop was devoted to discussions organised as breakout group sessions. To facilitate discussions number of participants was limited to 60 persons. To achieve the goals of this symposium in this international conference, support from DOE is vital. Hence, this proposal requested support in the amount of $15,000 to cover the travel expenses of international experts and radiation biology scientists from the United States. This supporting mechanism was clearly identified to the selected US participants as a conference support award from the DOE (See attached PDF). The workshop was an outstanding opportunity to strengthen interactions between leading experts in the emerging areas of radiation sciences, and will also provide opportunities for younger scientists to meet with experts and discuss their results. This workshop was designed to endorse active engagement in international collaboration. A major objective of this conference was to effectively communicate research results, in order to ensure that current thinking reflects sound science of radiation biology. Further, this international event addressed the use and success of scientific initiatives in radiation biology for policymakers, standard-setters, and the general public.

  17. Biological removal of algae in an integrated pond system

    CSIR Research Space (South Africa)

    Meiring, PGJ

    1995-01-01

    Full Text Available A system of oxidation ponds in series with a biological trickling filter is described. It was known that this arrangement was incapable of reducing effectively the levels of algae present in the pond liquid even though nitrification was effected...

  18. The role of analytical sciences in medical systems biology

    NARCIS (Netherlands)

    Greef, J. van der; Stroobant, P.; Heijden, R. van der

    2004-01-01

    Medical systems biology has generated widespread interest because of its bold conception and exciting potential, but the field is still in its infancy. Although there has been tremendous progress achieved recently in generating, integrating and analysing data in the medical and pharmaceutical field,

  19. Systems Biology for Mapping Genotype-Phenotype Relations in Yeast

    KAUST Repository

    Nielsen, Jens

    2016-01-01

    . Besides its wide industrial use, S. cerevisiae serves as an eukaryal model organism, and many systems biology tools have therefore been developed for this organism. Among these genome-scale metabolic models have shown to be most successful as they easy

  20. Separating intrinsic from extrinsic fluctuations in dynamic biological systems.

    Science.gov (United States)

    Hilfinger, Andreas; Paulsson, Johan

    2011-07-19

    From molecules in cells to organisms in ecosystems, biological populations fluctuate due to the intrinsic randomness of individual events and the extrinsic influence of changing environments. The combined effect is often too complex for effective analysis, and many studies therefore make simplifying assumptions, for example ignoring either intrinsic or extrinsic effects to reduce the number of model assumptions. Here we mathematically demonstrate how two identical and independent reporters embedded in a shared fluctuating environment can be used to identify intrinsic and extrinsic noise terms, but also how these contributions are qualitatively and quantitatively different from what has been previously reported. Furthermore, we show for which classes of biological systems the noise contributions identified by dual-reporter methods correspond to the noise contributions predicted by correct stochastic models of either intrinsic or extrinsic mechanisms. We find that for broad classes of systems, the extrinsic noise from the dual-reporter method can be rigorously analyzed using models that ignore intrinsic stochasticity. In contrast, the intrinsic noise can be rigorously analyzed using models that ignore extrinsic stochasticity only under very special conditions that rarely hold in biology. Testing whether the conditions are met is rarely possible and the dual-reporter method may thus produce flawed conclusions about the properties of the system, particularly about the intrinsic noise. Our results contribute toward establishing a rigorous framework to analyze dynamically fluctuating biological systems.

  1. CINRG: Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2013-10-01

    Contract W81XWH-09-1-0726 SYSTEMS BIOLOGY OF GLUCOCORTICOIDS IN MUSCLE DISEASE Introduction Duchenne muscular dystrophy (DMD) is the most... muscle and enable the development of better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant...common and incurable muscular dystrophy of childhood. Muscle regeneration fails with advancing age, leading to considerable fibrosis. Corticosteroid

  2. System as metaphor in the psychology and biology of shame.

    Science.gov (United States)

    Maunder, R

    1996-01-01

    Biological theories of brain and psychological theories of mind are two systems of explanation that seem related to one another. The nature of the relationship is problematic and constitutes the age-old mind-body problem. The most prominent solutions currently are variations of materialism. While psychological theories can be consistent with materialism, there remains a difficulty in comprehending nonphysical (social, psychological) causes of physical effects. This difficulty is an obstacle to integration in psychiatry, where we routinely assume that illnesses that include or depend on biological dysfunction are caused multifactorially by causal agents such as perceived parental warmth, parental loss, stressful life events, genetics, and personality (Hammen et al. 1992; Kendler et al. 1993). Unity theory adopts the stance that neurobiological theories and psychological theories are essentially disparate explanations of the same psychobiological events; thus the relationship of mind to brain is one of shared reference (Goodman 1991; Maunder 1995). In Goodman's model the gap between biological and psychological systems is not bridgeable. Different conceptual categories refer to the same referents but cannot interact with each other. Stepping into the breach, systems theory has been presented as offering a language that can bridge the gap between psychological and biological theories of causation (Schwartz 1981; Weiner 1989). Thus, there is a controversy about the applicability of systems theory for integration in psychiatry.

  3. FIELD INVESTIGATION OF BIOLOGICAL TOILET SYSTEMS AND GREY WATER TREATMENT

    Science.gov (United States)

    The objective of the field program was to determine the operational characteristics and overall acceptability of popular models of biological toilets and a few select grey water systems. A field observation scheme was devised to take advantage of in-use sites throughout the State...

  4. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. Small programs as building unit. Why PERL? Why not BioPerl? Why not PERL modules? Advantage of independent programs. Language independent; Can be run independently.

  5. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. A journey from simple computer programs to drug/vaccine informatics. Limitations of existing web services. History repeats (Web to Standalone); Graphics vs command mode. General purpose ...

  6. Advances in reproductive biology and seed production systems of ...

    African Journals Online (AJOL)

    Eucalyptus globulus is the main eucalypt species grown in Australian plantations. The focus on seedling deployment systems, coupled with exploitation of large, open-pollinated base populations for breeding purposes over the last two decades, has required a detailed understanding of the reproductive biology of this ...

  7. Pristine aquatic systems in a Long Term Ecological Research (LTER) site of the Brazilian Cerrado.

    Science.gov (United States)

    Fonseca, Bárbara Medeiros; de Mendonça-Galvão, Luciana

    2014-12-01

    The maintenance of limnological monitoring programs in the Cerrado Domain is crucial as a provision of useful information about temporal variations in land use and their respective water quality responses, considering its importance as water source for different Brazilian hydrographic basins. The purpose of this research was to describe limnological variables of low-order lotic systems located in the Cerrado Long Term Ecological Research (LTER) site (Environmental Protection Area (APA) Gama and Cabeça de Veado, Federal District of Brazil). Altogether, nine different streams were considered in this study. Samplings were conducted between 2010 and 2012, concentrated in the dry and rainy seasons. The sampling sites were generally characterized by low nutrient concentrations (e.g., medians, TP = 14.8 μg L(-1), TN = 20.0 μg L(-1), NO3 = 13.8 μg L(-1)) and slightly acidic waters (median, pH = 5.3), with quite low electrical conductivity values (median = 6.4 μS cm(-1)). However, water quality degradation as a response to diffuse pollution was reported in some sampling points (e.g., Onça and Gama streams), expressed by relatively higher N and P concentrations, which were probably highlighted by the good water quality of the data set as whole. Although there was a trend to higher values of nitrogen forms during the dry season, significant statistical differences between the seasonal periods were reported only for the variables temperature and dissolved silica, which were higher in the dry and rainy season, respectively. The streams located in the preserved areas inside the ecological stations of APA Gama and Cabeça de Veado can still be considered good examples of reference lotic systems in the Cerrado Domain; notwithstanding, this study reported incipient signs of water quality degradation which cannot be overlooked in future limnological monitoring.

  8. Chemical behaviour of plutonium in natural, aquatic systems: Hydrolysis, carbonate complexation and redox reactions

    International Nuclear Information System (INIS)

    Lierse, C.

    1985-01-01

    In order to clear up the geochemical behaviour of plutonium and its migration mechanisms in groundwater, hydrolysis, redox behaviour, compound formation in carbonate solutions and colloid formation were examined in groundwater conditions, i.e. at pH values between 5 and 8 and at redox potentials of between -300 and +700 mV. Solubility measurements, spectroscopic processes (UV, VIS, IR spectroscopy and laser induced photoacoustic spectroscopy) and electrochemical processes (cyclic voltammetry, differential pulse polarography) are used as methods of investigation. The hydrolysis constants of Pu IV and Pu VI and the solubility product of Pu (OH) 4 were determined and hydrolysis products of divalent and trivalent type are described. From solubility experiments, the stability constants for Pu (IV) carbonate compounds and the solubility product for the carbonate system of stable bodies of Pu (OH) 2 CO 3 were calculated. Using absorption spectroscopy, the disproportionate kinetics of Pu (V) in carbonate was determined at various pH values. A slow, but continuous, reduction in Pu (VI) was found in carbonate solution, which was derived from radiolytic effects. The speed of this auto-reduction was determined, depending on various experimental parameters. (orig./RB) [de

  9. Aquatic systems in and adjacent to Agulhas National Park with particular reference to the fish fauna

    Directory of Open Access Journals (Sweden)

    I.A. Russell

    2006-12-01

    Full Text Available The study aimed to determine the distribution and relative abundance of freshwater fishes in and adjacent to Agulhas National Park. Fourteen fish species were collected during surveys carried out in the Heuningnes and Ratel river systems and a variety of endorheic pans from 2003 to 2005. Seven of the species are marine fishes tolerant of low salinity (Mugil cephalus, Liza richardsonii, Monodactylus falciformis, Caffrogobius gilchristi, Rhabdosargus holubi, Solea bleekeri, Gilchristella aestuaria with the remaining seven species being primary freshwater fishes. Three are indigenous, including Pseudobarbus burchelli, Sandelia capensis, and Galaxias zebratus of which two morphological forms were recorded within Agulhas National Park. The remaining four species are invasive aliens (Cyprinus carpio, Lepomis macrochirus, Micropterus salmoides, Micropterus punctulatus. Classification using physico-chemical variables indicated four major wetland groups, with fishes occurring predominantly in the group comprising palustrine, lacustrine and riverine wetlands, and in one instance in a brackish endorheic pan. Management actions which should facilitate conservation of indigenous fishes in the Agulhas region are suggested.

  10. Thermoactivated persulfate oxidation of pesticide chlorpyrifos in aquatic system: kinetic and mechanistic investigations.

    Science.gov (United States)

    Zhou, Lei; Zhang, Ya; Ying, Rongrong; Wang, Guoqing; Long, Tao; Li, Jianhua; Lin, Yusuo

    2017-04-01

    The widespread occurrence of organophosphorus pesticides (OPPs) in the environment poses risks to both ecologic system as well as human health. This study investigated the oxidation kinetics of chlorpyrifos (CP), one of the typical OPPs, by thermoactivated persulfate (PS) oxidation process, and evaluated the influence of key kinetic factors, such as PS concentrations, pH, temperature, bicarbonate, and chloride ions. The reaction pathways and mechanisms were also proposed based on products identification by LC-MS techniques. Our results revealed that increasing initial PS concentration and temperature favored the decomposition of CP, whereas the oxidation efficiency was not affected by pH change ranging from 3 to 11. Bicarbonate was found to play a detrimental role on CP removal rates, while chloride showed no effect. The oxidation pathways including initial oxidation of P=S bond to P=O, dechlorination, dealkylation, and the dechlorination-hydroxylation were proposed, and the detailed underlying mechanisms were also discussed. Molecular orbital (MO) calculations indicated that P=S bond was the most favored oxidation site of the molecule. The toxicity of reaction solution was believed to increase due to the formation of products with P=O structures. This work demonstrates that OPPs can readily react with SO 4 ·- and provides important information for further research on the oxidation of these contaminants.

  11. Determining CDOM Absorption Spectra in Diverse Aquatic Environments Using a Multiple Pathlength, Liquid Core Waveguide System

    Science.gov (United States)

    Miller, Richard L.; Belz, Mathias; DelCastillo, Carlos; Trzaska, Rick

    2001-01-01

    We evaluated the accuracy, sensitivity and precision of a multiple pathlength, liquid core waveguide (MPLCW) system for measuring colored dissolved organic matter (CDOM) absorption in the UV-visible spectral range (370-700 nm). The MPLCW has four optical paths (2.0, 9.8, 49.3, and 204 cm) coupled to a single Teflon AF sample cell. Water samples were obtained from inland, coastal and ocean waters ranging in salinity from 0 to 36 PSU. Reference solutions for the MPLCW were made having a refractive index of the sample. CDOM absorption coefficients, aCDOM, and the slope of the log-linearized absorption spectra, S, were compared with values obtained using a dual-beam spectrophotometer. Absorption of phenol red secondary standards measured by the MPLCW at 558 nm were highly correlated with spectrophotometer values and showed a linear response across all four pathlengths. Values of aCDOM measured using the MPLCW were virtually identical to spectrophotometer values over a wide range of concentrations. The dynamic range of aCDOM for MPLCW measurements was 0.002 - 231.5 m-1. At low CDOM concentrations spectrophotometric aCDOM were slightly greater than MPLCW values and showed larger fluctuations at longer wavelengths due to limitations in instrument precision. In contrast, MPLCW spectra followed an exponential to 600 nm for all samples.

  12. EPR spectroscopy of complex biological iron-sulfur systems.

    Science.gov (United States)

    Hagen, Wilfred R

    2018-02-21

    From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

  13. Applications of membrane computing in systems and synthetic biology

    CERN Document Server

    Gheorghe, Marian; Pérez-Jiménez, Mario

    2014-01-01

    Membrane Computing was introduced as a computational paradigm in Natural Computing. The models introduced, called Membrane (or P) Systems, provide a coherent platform to describe and study living cells as computational systems. Membrane Systems have been investigated for their computational aspects and employed to model problems in other fields, like: Computer Science, Linguistics, Biology, Economy, Computer Graphics, Robotics, etc. Their inherent parallelism, heterogeneity and intrinsic versatility allow them to model a broad range of processes and phenomena, being also an efficient means to solve and analyze problems in a novel way. Membrane Computing has been used to model biological systems, becoming with time a thorough modeling paradigm comparable, in its modeling and predicting capabilities, to more established models in this area. This book is the result of the need to collect, in an organic way, different facets of this paradigm. The chapters of this book, together with the web pages accompanying th...

  14. Journal of Aquatic Sciences

    African Journals Online (AJOL)

    The Journal of Aquatic Sciences publishes articles on problems and issues in Aquatic Sciences from all ... The journal accepts for publication manuscripts of very high international standard containing reports of original scientific research.

  15. Predicting biological system objectives de novo from internal state measurements

    Directory of Open Access Journals (Sweden)

    Maranas Costas D

    2008-01-01

    Full Text Available Abstract Background Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells to optimally produce byproducts of commercial value, such as bioethanol, as well as molecular compounds for disease therapy. Flux balance analysis (FBA is an optimization framework that aids in this interrogation by generating predictions of optimal flux distributions in cellular networks. Critical features of FBA are the definition of a biologically relevant objective function (e.g., maximizing the rate of synthesis of biomass, a unit of measurement of cellular growth and the subsequent application of linear programming (LP to identify fluxes through a reaction network. Despite the success of FBA, a central remaining challenge is the definition of a network objective with biological meaning. Results We present a novel method called Biological Objective Solution Search (BOSS for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables. Specifically, BOSS identifies a system objective by defining a putative stoichiometric "objective reaction," adding this reaction to the existing set of stoichiometric constraints arising from known interactions within a network, and maximizing the putative objective reaction via LP, all the while minimizing the difference between the resultant in silico flux distribution and available experimental (e.g., isotopomer flux data. This new approach allows for discovery of objectives with previously unknown stoichiometry, thus extending the biological relevance from earlier methods. We verify our approach on the well-characterized central metabolic network of Saccharomyces cerevisiae. Conclusion We illustrate how BOSS offers insight into the functional organization of biochemical networks

  16. Inverse Problems in Systems Biology: A Critical Review.

    Science.gov (United States)

    Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

    2018-01-01

    Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

  17. Patterns of transuranic uptake by aquatic organisms: consequences and implications

    International Nuclear Information System (INIS)

    Eyman, L.D.; Trabalka, J.R.

    1980-01-01

    Literature on the behavior of plutonium and transuranic elements in aquatic organisms is reviewed. The commonality of observed distribution coefficients over a wide array of aquatic environments (both freshwater and marine) and the lack of biomagnification in aquatic food chains from these environments are demonstrated. These findings lead to the conclusion that physical processes dominate in the transfer of transuranic elements from aquatic environments to man. The question of the nature of the association of plutonium with aquatic biota (surface sorption vs biological incorporation) is discussed as well as the importance of short food chains in the transfer of plutonium to man

  18. Time changes in radiocesium concentration in aquatic systems affected by the Fukushima Daiichi NPP accident

    Science.gov (United States)

    Onda, Yuichi; Taniguchi, Keisuke; Kato, Hiroaki; Yoshimura, Kazuya; Wakiyama, Yoshifumi; Iwagami, Sho; Tsujimura, Maki; Sakaguchi, Aya; Yamamoto, Masatoshi

    2015-04-01

    important insights into the future prediction of the radiocesium wash-off from catchments from different land uses. The decerasing trend of river system vaired with catchments. Our analysis suggest that these differences can be explained by upstream landuse with different decreasing trend.

  19. Nutrients and bioactive substances in aquatic organisms

    International Nuclear Information System (INIS)

    Devadasan, K.; Mukundan, M.K.; Antony, P.D.; Viswanathan Nair, P.G.; Perigreen, P.A.; Joseph, Jose

    1994-01-01

    The International Symposium on Nutrients and Bioactive Substances in Aquatic Organisms, was held during 16-17 September 1993 by the Society of Fisheries Technologists (India) to review the progress of research in this area in India and elsewhere. The papers presented indicate that scientific productivity in this field is substantial and that some of the bioactive materials isolated from aquatic organisms have potential application in human health, nutrition and therapy. The symposium focussed attention on toxicants, nutrients and bioactive substances in aquatic organisms in general, and also on pollution of aquatic systems due to thermal effluents. Paper relevant to INIS database is indexed separately. (M.K.V.)

  20. A survey of chemicals inducing lipid peroxidation in biological systems.

    Science.gov (United States)

    Kappus, H

    1987-01-01

    A great number of drugs and chemicals are reviewed which have been shown to stimulate lipid peroxidation in any biological system. The underlying mechanisms, as far as known, are also dealt with. Lipid peroxidation induced by iron ions, organic hydroperoxides, halogenated hydrocarbons, redox cycling drugs, glutathione depleting chemicals, ethanol, heavy metals, ozone, nitrogen dioxide and a number of miscellaneous compounds, e.g. hydrazines, pesticides, antibiotics, are mentioned. It is shown that lipid peroxidation is stimulated by many of these compounds. However, quantitative estimates cannot be given yet and it is still impossible to judge the biological relevance of chemical-induced lipid peroxidation.