WorldWideScience

Sample records for chemical systems biology

  1. 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).

  2. Computational systems chemical biology.

    Science.gov (United States)

    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) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  3. Discovery of Chemical Toxicity via Biological Networks and Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, Edward; Habib, Tanwir; Guan, Xin; Escalon, Barbara; Falciani, Francesco; Chipman, J.K.; Antczak, Philipp; Edwards, Stephen; Taylor, Ronald C.; Vulpe, Chris; Loguinov, Alexandre; Van Aggelen, Graham; Villeneuve, Daniel L.; Garcia-Reyero, Natalia

    2010-09-30

    Both soldiers and animals are exposed to many chemicals as the result of military activities. Tools are needed to understand the hazards and risks that chemicals and new materials pose to soldiers and the environment. We have investigated the potential of global gene regulatory networks in understanding the impact of chemicals on reproduction. We characterized effects of chemicals on ovaries of the model animal system, the Fathead minnow (Pimopheles promelas) connecting chemical impacts on gene expression to circulating blood levels of the hormones testosterone and estradiol in addition to the egg yolk protein vitellogenin. We describe the application of reverse engineering complex interaction networks from high dimensional gene expression data to characterize chemicals that disrupt the hypothalamus-pituitary-gonadal endocrine axis that governs reproduction in fathead minnows. The construction of global gene regulatory networks provides deep insights into how drugs and chemicals effect key organs and biological pathways.

  4. 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...

  5. 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.

  6. Modeling drug- and chemical- induced hepatotoxicity with systems biology approaches

    Directory of Open Access Journals (Sweden)

    Sudin eBhattacharya

    2012-12-01

    Full Text Available We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of ‘toxicity pathways’ is described in the context of the 2007 US National Academies of Science report, Toxicity testing in the 21st Century: A Vision and A Strategy. Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically-based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular virtual tissue model of the liver lobule that combines molecular circuits in individual hepatocytes with cell-cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the AhR toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsymTM to understand drug-induced liver injury (DILI, the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.

  7. Stochastic chemical kinetics theory and (mostly) systems biological applications

    CERN Document Server

    Érdi, Péter

    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.

  8. Chemical imaging of biological systems with the scanning electrochemical microscope.

    Science.gov (United States)

    Gyurcsányi, Róbert E; Jágerszki, Gyula; Kiss, Gergely; Tóth, Klára

    2004-06-01

    A brief overview on recent advances in the application of scanning electrochemical microscopy (SECM) to the investigation of biological systems is presented. Special emphasis is given to the mapping of local enzyme activity by SECM, which is exemplified by relevant original systems. PMID:15110274

  9. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.;

    2016-01-01

    The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies....... for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems....

  10. Biological and Chemical Security

    Energy Technology Data Exchange (ETDEWEB)

    Fitch, P J

    2002-12-19

    The LLNL Chemical & Biological National Security Program (CBNP) provides science, technology and integrated systems for chemical and biological security. Our approach is to develop and field advanced strategies that dramatically improve the nation's capabilities to prevent, prepare for, detect, and respond to terrorist use of chemical or biological weapons. Recent events show the importance of civilian defense against terrorism. The 1995 nerve gas attack in Tokyo's subway served to catalyze and focus the early LLNL program on civilian counter terrorism. In the same year, LLNL began CBNP using Laboratory-Directed R&D investments and a focus on biodetection. The Nunn-Lugar-Domenici Defense Against Weapons of Mass Destruction Act, passed in 1996, initiated a number of U.S. nonproliferation and counter-terrorism programs including the DOE (now NNSA) Chemical and Biological Nonproliferation Program (also known as CBNP). In 2002, the Department of Homeland Security was formed. The NNSA CBNP and many of the LLNL CBNP activities are being transferred as the new Department becomes operational. LLNL has a long history in national security including nonproliferation of weapons of mass destruction. In biology, LLNL had a key role in starting and implementing the Human Genome Project and, more recently, the Microbial Genome Program. LLNL has over 1,000 scientists and engineers with relevant expertise in biology, chemistry, decontamination, instrumentation, microtechnologies, atmospheric modeling, and field experimentation. Over 150 LLNL scientists and engineers work full time on chemical and biological national security projects.

  11. Group behaviour in physical, chemical and biological systems

    Indian Academy of Sciences (India)

    Cihan Saçlioğlu; Önder Pekcan; Vidyanand Nanjundiah

    2014-04-01

    Groups exhibit properties that either are not perceived to exist, or perhaps cannot exist, at the individual level. Such `emergent’ properties depend on how individuals interact, both among themselves and with their surroundings. The world of everyday objects consists of material entities. These are, ultimately, groups of elementary particles that organize themselves into atoms and molecules, occupy space, and so on. It turns out that an explanation of even the most commonplace features of this world requires relativistic quantum field theory and the fact that Planck’s constant is discrete, not zero. Groups of molecules in solution, in particular polymers (`sols’), can form viscous clusters that behave like elastic solids (`gels’). Sol-gel transitions are examples of cooperative phenomena. Their occurrence is explained by modelling the statistics of inter-unit interactions: the likelihood of either state varies sharply as a critical parameter crosses a threshold value. Group behaviour among cells or organisms is often heritable and therefore can evolve. This permits an additional, typically biological, explanation for it in terms of reproductive advantage, whether of the individual or of the group. There is no general agreement on the appropriate explanatory framework for understanding group-level phenomena in biology.

  12. Group behaviour in physical, chemical and biological systems.

    Science.gov (United States)

    Saçlioğlu, Cihan; Pekcan, Önder; Nanjundiah, Vidyanand

    2014-04-01

    Groups exhibit properties that either are not perceived to exist, or perhaps cannot exist, at the individual level. Such 'emergent' properties depend on how individuals interact, both among themselves and with their surroundings. The world of everyday objects consists of material entities. These are, ultimately, groups of elementary particles that organize themselves into atoms and molecules, occupy space, and so on. It turns out that an explanation of even the most commonplace features of this world requires relativistic quantum field theory and the fact that Planck's constant is discrete, not zero. Groups of molecules in solution, in particular polymers ('sols'), can form viscous clusters that behave like elastic solids ('gels'). Sol-gel transitions are examples of cooperative phenomena. Their occurrence is explained by modelling the statistics of inter-unit interactions: the likelihood of either state varies sharply as a critical parameter crosses a threshold value. Group behaviour among cells or organisms is often heritable and therefore can evolve. This permits an additional, typically biological, explanation for it in terms of reproductive advantage, whether of the individual or of the group. There is no general agreement on the appropriate explanatory framework for understanding group-level phenomena in biology. PMID:24736152

  13. Nonequilibrium thermodynamics transport and rate processes in physical, chemical and biological systems

    CERN Document Server

    Demirel, Yasar

    2014-01-01

    Natural phenomena consist of simultaneously occurring transport processes and chemical reactions. These processes may interact with each other and may lead to self-organized structures, fluctuations, instabilities, and evolutionary systems. Nonequilibrium Thermodynamics, 3rd edition emphasizes the unifying role of thermodynamics in analyzing the natural phenomena. This third edition updates and expands on the first and second editions by focusing on the general balance equations for coupled processes of physical, chemical, and biological systems. The new edition contains a new chapte

  14. Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

    Science.gov (United States)

    Dreuw, Andreas

    2006-11-13

    With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented. PMID:17009357

  15. Improving integrative searching of systems chemical biology data using semantic annotation

    Directory of Open Access Journals (Sweden)

    Chen Bin

    2012-03-01

    Full Text Available Abstract Background Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. Results We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i simplifies the process of building SPARQL queries, (ii enables useful new kinds of queries on the data and (iii makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Availability Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

  16. In situ combined chemical and biological assessment of estrogenic pollution in a water recycling system.

    Science.gov (United States)

    Chi, Yulang; Huang, Qiansheng; Zhang, Huanteng; Chen, Yajie; Dong, Sijun

    2016-05-01

    Estrogenic pollution and its control in aquatic systems have drawn substantial attention around the world. The chemical and biological assessment approaches currently utilized in the laboratory or field cannot give an integrated assessment of the pollution when used separately. In this study, in situ chemical and biological methods were combined to detect pollution in a water recycling system. Data for the water quality index (WQI) demonstrated that the water treatment resulted in the decline of pollution from upstream to downstream. Wild male Nile tilapia, Oreochromis niloticus, was sampled in June and September. The concentrations of four common endocrine disrupting chemicals (EDCs) were determined in the tilapia liver by chromatographic analysis methods. The level of 17β-estradiol (E2) declined from upstream to downstream in both months. In contrast, the levels of bisphenol A (BPA), di-(2-ethylhcxyl) phthalate (DEHP), and perfluorooctane sulfonate (PFOS) did not display this declining tendency. The highest relative expression of vitellogenin 1 (VTG1) was observed in tilapia from upstream, then the level significantly decreased along the water system. The relative expression levels of CYP1A1 in the water system were also significantly higher than that of the control. However, no declining trend could be observed along the water system. The change of VTG1 expression corresponded well with that of E2 levels in the tilapia liver. Overall, our study assessed the pollution by endocrine disruptors using chemical and biological data with good correspondence. This study also demonstrated the effectiveness of the water recycling system in eliminating estrogen pollution in municipal sewage. PMID:27155427

  17. Chemical and Biological Kinetics

    Science.gov (United States)

    Emanuel', N. M.

    1981-10-01

    Examples of the application of the methods and ideas of chemical kinetics in various branches of chemistry and biology are considered and the results of studies on the kinetics and mechanisms of autoxidation and inhibited and catalysed oxidation of organic substances in the liquid phase are surveyed. Problems of the kinetics of the ageing of polymers and the principles of their stabilisation are discussed and certain trends in biological kinetics (kinetics of tumour growth, kinetic criteria of the effectiveness of chemotherapy, problems of gerontology, etc.) are considered. The bibliography includes 281 references.

  18. Indoor Air Nuclear, Biological, and Chemical Health Modeling and Assessment System

    Energy Technology Data Exchange (ETDEWEB)

    Stenner, Robert D.; Hadley, Donald L.; Armstrong, Peter R.; Buck, John W.; Hoopes, Bonnie L.; Janus, Michael C.

    2001-03-01

    Indoor air quality effects on human health are of increasing concern to public health agencies and building owners. The prevention and treatment of 'sick building' syndrome and the spread of air-borne diseases in hospitals, for example, are well known priorities. However, increasing attention is being directed to the vulnerability of our public buildings/places, public security and national defense facilities to terrorist attack or the accidental release of air-borne biological pathogens, harmful chemicals, or radioactive contaminants. The Indoor Air Nuclear, Biological, and Chemical Health Modeling and Assessment System (IA-NBC-HMAS) was developed to serve as a health impact analysis tool for use in addressing these concerns. The overall goal was to develop a user-friendly fully functional prototype Health Modeling and Assessment system, which will operate under the PNNL FRAMES system for ease of use and to maximize its integration with other modeling and assessment capabilities accessible within the FRAMES system (e.g., ambient air fate and transport models, water borne fate and transport models, Physiologically Based Pharmacokinetic models, etc.). The prototype IA-NBC-HMAS is designed to serve as a functional Health Modeling and Assessment system that can be easily tailored to meet specific building analysis needs of a customer. The prototype system was developed and tested using an actual building (i.e., the Churchville Building located at the Aberdeen Proving Ground) and release scenario (i.e., the release and measurement of tracer materials within the building) to ensure realism and practicality in the design and development of the prototype system. A user-friendly "demo" accompanies this report to allow the reader the opportunity for a "hands on" review of the prototype system's capability.

  19. Compatible biological and chemical control systems for Rhizoctonia solani in potato

    NARCIS (Netherlands)

    Boogert, van den P.H.J.F.; Luttikholt, A.J.G.

    2004-01-01

    A series of chemical and biological control agents were tested for compatibility with the Rhizoctonia-specific biocontrol fungus Verticillium biguttatum aimed at designing novel control strategies for black scurf (Rhizoctonia solani) and other tuber diseases in potato. The efficacy of chemicals, alo

  20. Chemical and biological warfare: Detection and warning systems. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning the detection, identification, verification, and warning systems of chemical and biological warfare agents. Citations discuss agents sampling, monitoring, and assessment. Techniques include chromotography, biosensing, chemical analysis, and DNA probes. Land pollution, soil tests, and skin protection are examined. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  1. Electrostatic thin film chemical and biological sensor

    Science.gov (United States)

    Prelas, Mark A.; Ghosh, Tushar K.; Tompson, Jr., Robert V.; Viswanath, Dabir; Loyalka, Sudarshan K.

    2010-01-19

    A chemical and biological agent sensor includes an electrostatic thin film supported by a substrate. The film includes an electrostatic charged surface to attract predetermined biological and chemical agents of interest. A charge collector associated with said electrostatic thin film collects charge associated with surface defects in the electrostatic film induced by the predetermined biological and chemical agents of interest. A preferred sensing system includes a charge based deep level transient spectroscopy system to read out charges from the film and match responses to data sets regarding the agents of interest. A method for sensing biological and chemical agents includes providing a thin sensing film having a predetermined electrostatic charge. The film is exposed to an environment suspected of containing the biological and chemical agents. Quantum surface effects on the film are measured. Biological and/or chemical agents can be detected, identified and quantified based on the measured quantum surface effects.

  2. Methods and systems for carrying out a pH-influenced chemical and/or biological reaction

    Energy Technology Data Exchange (ETDEWEB)

    Stern, Michael C.; Simeon, Fritz; Hatton, Trevor Alan

    2016-04-05

    The present invention generally relates to methods and systems for carrying out a pH-influenced chemical and/or biological reaction. In some embodiments, the pH-influenced reaction involves the conversion of CO.sub.2 to a dissolved species.

  3. Nanomaterial based detection and degradation of biological and chemical contaminants in a microfluidic system

    Science.gov (United States)

    Jayamohan, Harikrishnan

    Monitoring and remediation of environmental contaminants (biological and chemical) form the crux of global water resource management. There is an extant need to develop point-of-use, low-power, low-cost tools that can address this problem effectively with minimal environmental impact. Nanotechnology and microfluidics have made enormous advances during the past decade in the area of biosensing and environmental remediation. The "marriage" of these two technologies can effectively address some of the above-mentioned needs. In this dissertation, nanomaterials were used in conjunction with microfluidic techniques to detect and degrade biological and chemical pollutants. In the first project, a point-of-use sensor was developed for detection of trichloroethylene (TCE) from water. A self-organizing nanotubular titanium dioxide (TNA) synthesized by electrochemical anodization and functionalized with photocatalytically deposited platinum (Pt/TNA) was applied to the detection. The morphology and crystallinity of the Pt/TNA sensor was characterized using field emission scanning electron microscope, energy dis- persive x-ray spectroscopy, and X-ray diffraction. The sensor could detect TCE in the concentrations ranging from 10 to 1000 ppm. The room-temperature operation capability of the sensor makes it less power intensive and can potentially be incorporated into a field-based sensor. In the second part, TNA synthesized on a foil was incorporated into a flow-based microfluidic format and applied to degradation of a model pollutant, methylene blue. The system was demonstrated to have enhanced photocatalytic performance at higher flow rates (50-200 muL/min) over the same microfluidic format with TiO2 nanoparticulate (commercial P25) catalyst. The microfluidic format with TNA catalyst was able to achieve 82% fractional conversion of 18 mM methylene blue in comparison to 55% in the case of the TiO2 nanoparticulate layer at a flow rate of 200 L/min. The microfluidic device was

  4. The aesthetics of chemical biology.

    Science.gov (United States)

    Parsons, Glenn

    2012-12-01

    Scientists and philosophers have long reflected on the place of aesthetics in science. In this essay, I review these discussions, identifying work of relevance to chemistry and, in particular, to the field of chemical biology. Topics discussed include the role of aesthetics in scientific theory choice, the aesthetics of molecular images, the beauty-making features of molecules, and the relation between the aesthetics of chemical biology and the aesthetics of industrial design.

  5. Human Pluripotent Stem Cell Based Developmental Toxicity Assays for Chemical Safety Screening and Systems Biology Data Generation.

    Science.gov (United States)

    Shinde, Vaibhav; Klima, Stefanie; Sureshkumar, Perumal Srinivasan; Meganathan, Kesavan; Jagtap, Smita; Rempel, Eugen; Rahnenführer, Jörg; Hengstler, Jan Georg; Waldmann, Tanja; Hescheler, Jürgen; Leist, Marcel; Sachinidis, Agapios

    2015-01-01

    Efficient protocols to differentiate human pluripotent stem cells to various tissues in combination with -omics technologies opened up new horizons for in vitro toxicity testing of potential drugs. To provide a solid scientific basis for such assays, it will be important to gain quantitative information on the time course of development and on the underlying regulatory mechanisms by systems biology approaches. Two assays have therefore been tuned here for these requirements. In the UKK test system, human embryonic stem cells (hESC) (or other pluripotent cells) are left to spontaneously differentiate for 14 days in embryoid bodies, to allow generation of cells of all three germ layers. This system recapitulates key steps of early human embryonic development, and it can predict human-specific early embryonic toxicity/teratogenicity, if cells are exposed to chemicals during differentiation. The UKN1 test system is based on hESC differentiating to a population of neuroectodermal progenitor (NEP) cells for 6 days. This system recapitulates early neural development and predicts early developmental neurotoxicity and epigenetic changes triggered by chemicals. Both systems, in combination with transcriptome microarray studies, are suitable for identifying toxicity biomarkers. Moreover, they may be used in combination to generate input data for systems biology analysis. These test systems have advantages over the traditional toxicological studies requiring large amounts of animals. The test systems may contribute to a reduction of the costs for drug development and chemical safety evaluation. Their combination sheds light especially on compounds that may influence neurodevelopment specifically. PMID:26132533

  6. Target identification strategies in plant chemical biology

    OpenAIRE

    Dejonghe, Wim; Russinova, Eugenia

    2014-01-01

    The current needs to understand gene function in plant biology increasingly require more dynamic and conditional approaches opposed to classic genetic strategies. Gene redundancy and lethality can substantially complicate research, which might be solved by applying a chemical genetics approach. Now understood as the study of small molecules and their effect on biological systems with subsequent target identification, chemical genetics is a fast developing field with a strong history in pharma...

  7. Reducing Mortality from Terrorist Releases of Chemical and Biological Agents: I. Filtration for Ventilation Systems in Commercial Building

    Energy Technology Data Exchange (ETDEWEB)

    Thatcher, Tracy L.; Daisey, Joan M.

    1999-09-01

    There is growing concern about potential terrorist attacks involving releases of chemical and/or biological (CB) agents, such as sarin or anthrax, in and around buildings. For an external release, the CB agent can enter the building through the air intakes of a building's mechanical ventilation system and by infiltration through the building envelope. For an interior release in a single room, the mechanical ventilation system, which often recirculates some fraction of the air within a building, may distribute the released CB agent throughout the building. For both cases, installing building systems that remove chemical and biological agents may be the most effective way to protect building occupants. Filtration systems installed in the heating, ventilating and air-conditioning (HVAC) systems of buildings can significantly reduce exposures of building occupants in the event of a release, whether the release is outdoors or indoors. Reduced exposures can reduce the number of deaths from a terrorist attack. The purpose of this report is to provide information and examples of the design of filtration systems to help building engineers retrofit HVAC systems. The report also provides background information on the physical nature of CB agents and brief overviews of the basic principles of particle and vapor filtration.

  8. Biological and Chemical Information Technologies

    DEFF Research Database (Denmark)

    Amos, Martyn; Dittrich, Peter; McCaskill, John;

    2011-01-01

    Biological and chemical information technologies (bio/chem IT) have the potential to reshape the scientific and technological landscape. In this paper we briefly review the main challenges and opportunities in the field, before presenting several case studies based on ongoing FP7 research projects....

  9. History of chemical and biological warfare agents.

    Science.gov (United States)

    Szinicz, L

    2005-10-30

    Chemical and biological warfare agents constitute a low-probability, but high-impact risk both to the military and to the civilian population. The use of hazardous materials of chemical or biological origin as weapons and for homicide has been documented since ancient times. The first use of chemicals in terms of weapons of mass destruction goes back to World War I, when on April 22, 1915 large amounts of chlorine were released by German military forces at Ypres, Belgium. Until around the 1970s of the 20th century, the awareness of the threat by chemical and biological agents had been mainly confined to the military sector. In the following time, the development of increasing range delivery systems by chemical and biological agents possessors sensitised public attention to the threat emanating from these agents. Their proliferation to the terrorists field during the 1990s with the expanding scale and globalisation of terrorist attacks suggested that these agents are becoming an increasing threat to the whole world community. The following article gives a condensed overview on the history of use and development of the more prominent chemical and biological warfare agents. PMID:16111798

  10. The chemical biology of sirtuins.

    Science.gov (United States)

    Chen, Bing; Zang, Wenwen; Wang, Juan; Huang, Yajun; He, Yanhua; Yan, Lingling; Liu, Jiajia; Zheng, Weiping

    2015-08-01

    The sirtuin family of enzymes are able to catalyze the N(ε)-acyl-lysine deacylation reaction on histone and non-histone protein substrates. Over the past years since the discovery of its founding member (i.e. the yeast silent information regulator 2 (sir2) protein) in 2000, the sirtuin-catalyzed deacylation reaction has been demonstrated to play an important regulatory role in multiple crucial cellular processes such as transcription, DNA damage repair, and metabolism. This reaction has also been regarded as a current therapeutic target for human diseases such as cancer, and metabolic and neurodegenerative diseases. The unique β-nicotinamide adenine dinucleotide (β-NAD(+) or NAD(+))-dependent nature of the sirtuin-catalyzed deacylation reaction has also engendered extensive mechanistic studies, resulting in a mechanistic view of the enzyme chemistry supported by several lines of experimental evidence. On the journey toward these knowledge advances, chemical biological means have constituted an important functional arsenal; technically, a variety of chemical probes and modulators (inhibitors and activators) have been developed and some of them have been employed toward an enhanced mechanistic and functional (pharmacological) understanding of the sirtuin-catalyzed deacylation reaction. On the other hand, an enhanced mechanistic understanding has also facilitated the development of a variety of chemical probes and modulators. This article will review the tremendous accomplishments achieved during the past few years in the field of sirtuin chemical biology. It is hoped that this would also help to set a stage for how outstanding mechanistic and functional questions for the sirtuin-catalyzed deacylation reaction could be addressed in the future from the chemical biology perspective. PMID:25955411

  11. IMOS National Reference Stations: A Continental-Wide Physical, Chemical and Biological Coastal Observing System

    Science.gov (United States)

    Lynch, Tim P.; Morello, Elisabetta B.; Evans, Karen; Richardson, Anthony J.; Rochester, Wayne; Steinberg, Craig R.; Roughan, Moninya; Thompson, Peter; Middleton, John F.; Feng, Ming; Sherrington, Robert; Brando, Vittorio; Tilbrook, Bronte; Ridgway, Ken; Allen, Simon; Doherty, Peter; Hill, Katherine; Moltmann, Tim C.

    2014-01-01

    Sustained observations allow for the tracking of change in oceanography and ecosystems, however, these are rare, particularly for the Southern Hemisphere. To address this in part, the Australian Integrated Marine Observing System (IMOS) implemented a network of nine National Reference Stations (NRS). The network builds on one long-term location, where monthly water sampling has been sustained since the 1940s and two others that commenced in the 1950s. In-situ continuously moored sensors and an enhanced monthly water sampling regime now collect more than 50 data streams. Building on sampling for temperature, salinity and nutrients, the network now observes dissolved oxygen, carbon, turbidity, currents, chlorophyll a and both phytoplankton and zooplankton. Additional parameters for studies of ocean acidification and bio-optics are collected at a sub-set of sites and all data is made freely and publically available. Our preliminary results demonstrate increased utility to observe extreme events, such as marine heat waves and coastal flooding; rare events, such as plankton blooms; and have, for the first time, allowed for consistent continental scale sampling and analysis of coastal zooplankton and phytoplankton communities. Independent water sampling allows for cross validation of the deployed sensors for quality control of data that now continuously tracks daily, seasonal and annual variation. The NRS will provide multi-decadal time series, against which more spatially replicated short-term studies can be referenced, models and remote sensing products validated, and improvements made to our understanding of how large-scale, long-term change and variability in the global ocean are affecting Australia's coastal seas and ecosystems. The NRS network provides an example of how a continental scaled observing systems can be developed to collect observations that integrate across physics, chemistry and biology. PMID:25517905

  12. IMOS National Reference Stations: a continental-wide physical, chemical and biological coastal observing system.

    Directory of Open Access Journals (Sweden)

    Tim P Lynch

    Full Text Available Sustained observations allow for the tracking of change in oceanography and ecosystems, however, these are rare, particularly for the Southern Hemisphere. To address this in part, the Australian Integrated Marine Observing System (IMOS implemented a network of nine National Reference Stations (NRS. The network builds on one long-term location, where monthly water sampling has been sustained since the 1940s and two others that commenced in the 1950s. In-situ continuously moored sensors and an enhanced monthly water sampling regime now collect more than 50 data streams. Building on sampling for temperature, salinity and nutrients, the network now observes dissolved oxygen, carbon, turbidity, currents, chlorophyll a and both phytoplankton and zooplankton. Additional parameters for studies of ocean acidification and bio-optics are collected at a sub-set of sites and all data is made freely and publically available. Our preliminary results demonstrate increased utility to observe extreme events, such as marine heat waves and coastal flooding; rare events, such as plankton blooms; and have, for the first time, allowed for consistent continental scale sampling and analysis of coastal zooplankton and phytoplankton communities. Independent water sampling allows for cross validation of the deployed sensors for quality control of data that now continuously tracks daily, seasonal and annual variation. The NRS will provide multi-decadal time series, against which more spatially replicated short-term studies can be referenced, models and remote sensing products validated, and improvements made to our understanding of how large-scale, long-term change and variability in the global ocean are affecting Australia's coastal seas and ecosystems. The NRS network provides an example of how a continental scaled observing systems can be developed to collect observations that integrate across physics, chemistry and biology.

  13. HExpoChem: a systems biology resource to explore human exposure to chemicals

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Jacobsen, Ulrik Plesner; Kalhauge, Christian Gram;

    2013-01-01

    Summary: Humans are exposed to diverse hazardous chemicals daily. Although an exposure to these chemicals is suspected to have adverse effects on human health, mechanistic insights into how they interact with the human body are still limited. Therefore, acquisition of curated data and development....... Availability: HExpoChem is available at http://www.cbs.dtu.dk/services/HExpoChem-1.0/. Contact: karine@cbs.dtu.dk Supplementary information: Supplementary data are available at Bioinformatics online....

  14. Olefin Metathesis for Chemical Biology

    Science.gov (United States)

    Binder, Joseph B; Raines, Ronald T

    2009-01-01

    Summary Chemical biology relies on effective synthetic chemistry for building molecules to probe and modulate biological function. Olefin metathesis in organic solvents is a valuable addition to this armamentarium, and developments during the previous decade are enabling metathesis in aqueous solvents for the manipulation of biomolecules. Functional group-tolerant ruthenium metathesis catalysts modified with charged moieties or hydrophilic polymers are soluble and active in water, enabling ring-opening metathesis polymerization, cross metathesis, and ring-closing metathesis. Alternatively, conventional hydrophobic ruthenium complexes catalyze a similar array of metathesis reactions in mixtures of water and organic solvents. This strategy has enabled cross metathesis on the surface of a protein. Continuing developments in catalyst design and methodology will popularize the bioorthogonal reactivity of metathesis. PMID:18935975

  15. Olefin metathesis for chemical biology.

    Science.gov (United States)

    Binder, Joseph B; Raines, Ronald T

    2008-12-01

    Chemical biology relies on effective synthetic chemistry for building molecules to probe and modulate biological function. Olefin metathesis in organic solvents is a valuable addition to this armamentarium, and developments during the previous decade are enabling metathesis in aqueous solvents for the manipulation of biomolecules. Functional group-tolerant ruthenium metathesis catalysts modified with charged moieties or hydrophilic polymers are soluble and active in water, enabling ring-opening metathesis polymerization, cross metathesis, and ring-closing metathesis. Alternatively, conventional hydrophobic ruthenium complexes catalyze a similar array of metathesis reactions in mixtures of water and organic solvents. This strategy has enabled cross metathesis on the surface of a protein. Continuing developments in catalyst design and methodology will popularize the bioorthogonal reactivity of metathesis. PMID:18935975

  16. ChemProt: A disease chemical biology database

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    2013-01-01

    The integration of chemistry, biology, and informatics to study drug actions across multiple biological targets, pathways, and biological systems is an emerging paradigm in drug discovery. Rather than reducing a complex system to simplistic models, fields such as chemogenomics and translational...... chemical biology, drug repurposing, and off-target effects prediction....

  17. Chemical and biological properties of supramolecular polymer systems based on oligocaprolactones

    NARCIS (Netherlands)

    Dankers, Patricia Y. W.; van Leeuwen, Ellen N. M.; van Gemert, Gaby M. L.; Spiering, A. J. H.; Harmsen, Martin C.; Brouwer, Linda A.; Janssen, Henk M.; Bosman, Anton W.; van Luyn, Maria J. A.; Meijer, E. W.

    2006-01-01

    We show that materials with a diverse range of mechanical and biological properties can be obtained using a modular approach by simply mixing different ratios of oligocaprolactones that are either end-functionalized or chain-extended with quadruple hydrogen bonding ureido-pyrimidinone (UPy) moieties

  18. Systems Biology Approach for Understanding MOA, Dose-Response and Susceptibility to Environmental Chemicals

    Science.gov (United States)

    There is an increasing need for assays for the rapid and efficient assessment of toxicities of large numbers of environmental chemicals. To meet this need, we have developed a battery of cell-based reporter assays that measure the activation of key cellular stress pathways. These...

  19. Design and development of a miniaturised total chemical analysis system for on-line lactate and glucose monitoring in biological samples

    NARCIS (Netherlands)

    Dempsey, Eithne; Diamond, Dermot; Smyth, Malcolm R.; Urban, Gerald; Jobst, Gerhard; Moser, Isabella; Verpoorte, Elisabeth M.J.; Manz, Andreas; Widmer, H. Michael; Rabenstein, Kai; Freaney, Rosemarie

    1997-01-01

    A miniaturised Total chemical Analysis System (μTAS) for glucose and lactate measurement in biological samples constructed based on an integrated microdialysis sampling and detection system. The complete system incorporates a microdialysis probe for intravascular monitoring in an ex vivo mini-shunt

  20. Biology Today. Thinking Chemically about Biology.

    Science.gov (United States)

    Flannery, Maura C.

    1990-01-01

    Discussed are applications of biochemistry. Included are designed drugs, clever drugs, carcinogenic structures, sugary wine, caged chemicals, biomaterials, marine chemistry, biopolymers, prospecting bacteria, and plant chemistry. (CW)

  1. Effects of head pruning and different nutritional systems (chemical, biological and integrated on seed yield and oil content in medicinal pumpkin (Cucurbita pepo L.

    Directory of Open Access Journals (Sweden)

    Zarei Dariush

    2016-01-01

    Full Text Available To evaluate the effect of head pruning and different nutritional systems (chemical, biological and integrated on yield and seed oil content in medicinal pumpkin (Cucurbita pepo L., an experiment was conducted in Kermanshah/Iran during the 2013 growing season. The experimental treatments consisted of two levels - no head pruning, control (Co and head pruning (C1 allocated to the main plots. Four levels of different fertilizing systems - control (without fertilizer (T0, chemical (T1, biological (a combination of nitrogen fixing bacteria, Azospirillum brasilense and Glomus mosseae (T2, and integrated fertilizing system (biological fertilizer + 50% chemical fertilizer (T3 were assigned to the sub-plots. The experimental treatments were arranged as a split plot based on a randomized complete block design with three replications. The results showed that the highest percentage of seed oil was obtained (37% in the integrated nutritional system along with the head pruning treatment. The highest grain yields of 53 and 50 g per square meter were obtained in integrated and chemical fertilizing systems, respectively while no pruning was applied. The highest fruit yields of 3,710 and 3,668 kg per hectare were produced by chemical and integrated fertilizing systems, respectively. The biological nutrition system required more time to demonstrate its positive effect on the growth and yield of medicinal pumpkin.

  2. Biological and Chemical Renovation of Wastewater with a Soil Infiltrator Low-Pressure Distribution System

    OpenAIRE

    DiPaola, Tracey Stickley

    1998-01-01

    An alternative on-site wastewater treatment and disposal system (OSWTDS) consisting of a soil infiltrator with low pressure distribution was evaluated in a soil that was unsuitable for a conventional OSWTDS under current Commonwealth of Virginia Sewage Handling and Disposal Regulations, due to a shallow seasonally perched water table and low hydraulic conductivity. The absorption field consisted of two subsystems numbered as 1 and 2 with effluent design loading rates of 5.1 and 10.2 Lpd/m2, ...

  3. Challenges and opportunities in synthetic biology for chemical engineers

    OpenAIRE

    Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

    2012-01-01

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunitie...

  4. ChemProt: a disease chemical biology database

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Nielsen, Sonny Kim; Audouze, Karine Marie Laure;

    2011-01-01

    Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network...... biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700 000 unique chemicals with biological annotation for 30...... evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram...

  5. Challenges and opportunities in synthetic biology for chemical engineers

    Energy Technology Data Exchange (ETDEWEB)

    Luo, YZ; Lee, JK; Zhao, HM

    2013-11-15

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. (C) 2012 Elsevier Ltd. All rights reserved.

  6. Opportunities for Merging Chemical and Biological Synthesis

    OpenAIRE

    Wallace, Stephen; Balskus, Emily P.

    2014-01-01

    Organic chemists and metabolic engineers use largely orthogonal technologies to access small molecules like pharmaceuticals and commodity chemicals. As the use of biological catalysts and engineered organisms for chemical production grows, it is becoming increasingly evident that future efforts for chemical manufacture will benefit from the integration and unified expansion of these two fields. This review will discuss approaches that combine chemical and biological synthesis for small molecu...

  7. Systems interface biology

    OpenAIRE

    Francis J Doyle; Stelling, Jörg

    2006-01-01

    The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological networks. In particular, systems engineering methods are finding unique opportunities in characterizing the rich behaviour exhibited by biological systems. In the same manner, these new classes of biological problems are motivating novel developments in theoretical systems approaches. Henc...

  8. A new methodology for studying nanoparticle interactions in biological systems: Dispersing titania in biocompatible media using chemical stabilisers

    Science.gov (United States)

    Ramirez-Garcia, Sonia; Chen, Lan; Morris, Michael A.; Dawson, Kenneth A.

    2011-11-01

    We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates using citrate stabilisations between 45 and 55 nm at concentrations of up to 10 mg mL-1. The optimum pH for this type of suspension was 7, resulting in ζ-potentials of approximately -50 mV. The stabilised aggregates were the subject of dialysis to produce stable dispersions without the chemical stabiliser, thus allowing studies in the absence of potentially toxic chemicals. Different sizing techniques such as Dynamic Light Scattering (DLS), Nanoparticle Tracking Analysis (NTA) and Differential Centrifuge Sedimentation (DCS) were used to characterise the different suspensions. The results obtained with each of these techniques are compared and a critical analysis of the suitability of each technique is given.We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates

  9. Testing and Risk Assessment of Chemicals that Impact Highly Adaptive Biological Systems: The Case of Endocrine Systems

    Science.gov (United States)

    Animals have evolved a variety of mechanisms for responding to toxic chemicals of both natural and anthropogenic origin. Well-known examples include activation of cellular repair pathways and induction of metabolizing enzymes. From a governmental regulatory perspective, these a...

  10. Effects of head pruning and different nutritional systems (chemical, biological and integrated) on seed yield and oil content in medicinal pumpkin (Cucurbita pepo L.)

    OpenAIRE

    Zarei Dariush; Shabani Ghobad; Chaichi Reza Mohammad; Akbarabadi Ali

    2016-01-01

    To evaluate the effect of head pruning and different nutritional systems (chemical, biological and integrated) on yield and seed oil content in medicinal pumpkin (Cucurbita pepo L.), an experiment was conducted in Kermanshah/Iran during the 2013 growing season. The experimental treatments consisted of two levels - no head pruning, control (Co) and head pruning (C1) allocated to the main plots. Four levels of different fertilizing systems - control (without ...

  11. CHEMICAL EFFECTS IN BIOLOGICAL SYSTEMS – DATA DICTIONARY (CEBS-DD): A COMPENDIUM OF TERMS FOR THE CAPTURE AND INTEGRATION OF BIOLOGICAL STUDY DESIGN DESCRIPTION, CONVENTIONAL PHENOTYPES AND ‘OMICS’ DATA

    Science.gov (United States)

    A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical pathology and histopathology). A Study is generally an experiment carried out du...

  12. Chemical Biology Strategies for Biofilm Control.

    Science.gov (United States)

    Yang, Liang; Givskov, Michael

    2015-08-01

    Microbes live as densely populated multicellular surface-attached biofilm communities embedded in self-generated, extracellular polymeric substances (EPSs). EPSs serve as a scaffold for cross-linking biofilm cells and support development of biofilm architecture and functions. Biofilms can have a clear negative impact on humans, where biofilms are a common denominator in many chronic diseases in which they prime development of destructive inflammatory conditions and the failure of our immune system to efficiently cope with them. Our current assortment of antimicrobial agents cannot efficiently eradicate biofilms. For industrial applications, the removal of biofilms within production machinery in the paper and hygienic food packaging industry, cooling water circuits, and drinking water manufacturing systems can be critical for the safety and efficacy of those processes. Biofilm formation is a dynamic process that involves microbial cell migration, cell-to-cell signaling and interactions, EPS synthesis, and cell-EPS interactions. Recent progress of fundamental biofilm research has shed light on novel chemical biology strategies for biofilm control. In this article, chemical biology strategies targeting the bacterial intercellular and intracellular signaling pathways will be discussed.

  13. Engineering scalable biological systems

    OpenAIRE

    Lu, Timothy K.

    2010-01-01

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

  14. 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.

  15. Nanotechnologies and chemical tools for cell biology

    Science.gov (United States)

    Chen, Xing

    This dissertation describes several nanotechnologies and chemical tools that I have developed to probe living cells. Chapter one gives a brief overview on the current status of biomedical and biotechnological applications of carbon nanotubes (CNTs). In this chapter, strategies for functionalization of CNTs with emphasis on biological applications are reviewed. Representative developments in biosensing, bioimaging, intracellular delivery, and tissue engineering are presented. Recent studies on toxicity of CNTs are also discussed. Chapter two describes the development of a nanoscale cell injector for delivery of cargo to the interior of living cells without physiological harm. A CNT attached to an atomic force microscope tip was functionalized with cargo via a disulfide linker. Penetration of cell membranes with this "nanoneedle", followed by reductive cleavage of the disulfide bonds within the cell's interior, resulted in the release of cargo inside the cells. Chapter three presents a biomimetic functionalization strategy for interfacing CNTs with biological systems. The potential biological applications of CNTs have been limited by their insolubility in aqueous environment and their intrinsic toxicity. We developed a biomimetic surface modification of CNTs using glycosylated polymers designed to mimic natural cell surface mucin glycoproteins interactions. Chapter four further extends the biomimetic strategy for functionalization of CNTs to glycosylated dendrimers. We developed a new class of amphiphilic bifunctional glycodendrimers that comprised carbohydrate units displayed in the periphery and a pyrene tail that bound to SWNT surface via pi-pi interactions. The glycodendrimer-coated CNTs were soluble in water, and noncytotoxic. We also demonstrated that the coated CNTs could interface with biological systems including proteins and cells. Chapter five presents a biosensing application of glycodenderimer-coated CNTs. SWNTN-FETs coated with glycodendrimers were

  16. A numerical model (MISER) for the simulation of coupled physical, chemical and biological processes in soil vapor extraction and bioventing systems

    Science.gov (United States)

    Rathfelder, Klaus M.; Lang, John R.; Abriola, Linda M.

    2000-05-01

    The efficiency and effectiveness of soil vapor extraction (SVE) and bioventing (BV) systems for remediation of unsaturated zone soils is controlled by a complex combination of physical, chemical and biological factors. The Michigan soil vapor extraction remediation (MISER) model, a two-dimensional numerical simulator, is developed to advance our ability to investigate the performance of field scale SVE and BV systems by integrating processes of multiphase flow, multicomponent compositional transport with nonequilibrium interphase mass transfer, and aerobic biodegradation. Subsequent to the model presentation, example simulations of single well SVE and BV systems are used to illustrate the interplay between physical, chemical and biological processes and their potential influence on remediation efficiency and the pathways of contaminant removal. Simulations of SVE reveal that removal efficiency is controlled primarily by the ability to engineer gas flow through regions of organic liquid contaminated soil and by interphase mass transfer limitations. Biodegradation is found to play a minor role in mass removal for the examined SVE scenarios. Simulations of BV systems suggest that the effective supply of oxygen may not be the sole criterion for efficient BV performance. The efficiency and contaminant removal pathways in these systems can be significantly influenced by interdependent dynamics involving biological growth factors, interphase mass transfer rates, and air injection rates. Simulation results emphasize the need for the continued refinement and validation of predictive interphase mass transfer models applicable under a variety of conditions and for the continued elucidation and quantification of microbial processes under unsaturated field conditions.

  17. Recovery from chemical, biological, and radiological incidents :

    Energy Technology Data Exchange (ETDEWEB)

    Franco, David Oliver; Yang, Lynn I.; Hammer, Ann E.

    2012-06-01

    To restore regional lifeline services and economic activity as quickly as possible after a chemical, biological or radiological incident, emergency planners and managers will need to prioritize critical infrastructure across many sectors for restoration. In parallel, state and local governments will need to identify and implement measures to promote reoccupation and economy recovery in the region. This document provides guidance on predisaster planning for two of the National Disaster Recovery Framework Recovery Support Functions: Infrastructure Systems and Economic Recovery. It identifies key considerations for infrastructure restoration, outlines a process for prioritizing critical infrastructure for restoration, and identifies critical considerations for promoting regional economic recovery following a widearea disaster. Its goal is to equip members of the emergency preparedness community to systematically prioritize critical infrastructure for restoration, and to develop effective economic recovery plans in preparation for a widearea CBR disaster.

  18. ChemProt: a disease chemical biology database.

    Science.gov (United States)

    Taboureau, Olivier; Nielsen, Sonny Kim; Audouze, Karine; Weinhold, Nils; Edsgärd, Daniel; Roque, Francisco S; Kouskoumvekaki, Irene; Bora, Alina; Curpan, Ramona; Jensen, Thomas Skøt; Brunak, Søren; Oprea, Tudor I

    2011-01-01

    Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700,000 unique chemicals with biological annotation for 30,578 proteins. We gathered over 2-million chemical-protein interactions, which were integrated in a quality scored human PPI network of 428,429 interactions. The PPI network layer allows for studying disease and tissue specificity through each protein complex. ChemProt can assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram, an antidepressant, with osteogenesis imperfect and leukemia and bisphenol A, an endocrine disruptor, with certain types of cancer, respectively. The server can be accessed at http://www.cbs.dtu.dk/services/ChemProt/. PMID:20935044

  19. Progress in Nano-Electro-Optics VII Chemical, Biological, and Nanophotonic Technologies for Nano-Optical Devices and Systems

    CERN Document Server

    Ohtsu, Motoichi

    2010-01-01

    This book focuses on chemical and nanophotonic technology to be used to develop novel nano-optical devices and systems. It begins with temperature- and photo-induced phase transition of ferromagnetic materials. Further topics include: energy transfer in artificial photosynthesis, homoepitaxial multiple quantum wells in ZnO, near-field photochemical etching and nanophotonic devices based on a nonadiabatic process and optical near-field energy transfer, respectively and polarization control in the optical near-field for optical information security. Taken as a whole, this overview will be a valuable resource for engineers and scientists working in the field of nano-electro-optics.

  20. [Systems biology of cancer].

    Science.gov (United States)

    Barillot, Emmanuel; Calzone, Laurence; Zinovyev, Andrei

    2009-01-01

    Cancer Systems Biology is now accepted and recognized as a promising field both in biological and clinical research. It relies on a rigorous formalization of regulation networks into precise and unambiguous languages. It provides both detailed and modular views of the complex biological system of interest (which in cancer research is typically an interaction network governing essential cellular events such as proliferation, differentiation, cell death...) in order to facilitate the interpretation of molecular profiles of tumors. The translation of these networks into mathematical models allows prediction of the evolution of the system in time and under certain perturbations. As a result, it can not only propose specific target points for pharmaceutical purposes, but also anticipate the evolution of tumors as well as their classifications. These characteristics emphasize the important role of Systems Biology of Cancer in the future of biomedical research.

  1. Chemical Force Microscopy of Chemical and Biological Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Noy, A

    2006-01-02

    Interactions between chemical functionalities define outcomes of the vast majority of important events in chemistry, biology and materials science. Chemical Force Microscopy (CFM)--a technique that uses direct chemical functionalization of AFM probes with specific functionalities--allows researchers to investigate these important interactions directly. We review the basic principles of CFM, some examples of its application, and theoretical models that provide the basis for understanding the experimental results. We also emphasize application of modern kinetic theory of non-covalent interactions strength to the analysis of CFM data.

  2. Cellular Biology in Terms of Stochastic Nonlinear Biochemical Dynamics: Emergent Properties, Isogenetic Variations and Chemical System Inheritability

    Science.gov (United States)

    Qian, Hong

    2010-12-01

    Based on a stochastic, nonlinear, open biochemical reaction system perspective, we present an analytical theory for cellular biochemical processes. The chemical master equation (CME) approach provides a unifying mathematical framework for cellular modeling. We apply this theory to both self-regulating gene networks and phosphorylation-dephosphorylation signaling modules with feedbacks. Two types of bistability are illustrated in mesoscopic biochemical systems: one that has a macroscopic, deterministic counterpart and another that does not. In certain cases, the latter stochastic bistability is shown to be a "ghost" of the extinction phenomenon. We argue the thermal fluctuations inherent in molecular processes do not disappear in mesoscopic cell-sized nonlinear systems; rather they manifest themselves as isogenetic variations on a different time scale. Isogenetic biochemical variations in terms of the stochastic attractors can have extremely long lifetime. Transitions among discrete stochastic attractors spend most of the time in "waiting", exhibit punctuated equilibria. It can be naturally passed to "daughter cells" via a simple growth and division process. The CME system follows a set of nonequilibrium thermodynamic laws that include non-increasing free energy F( t) with external energy drive Q hk ≥0, and total entropy production rate e p =- dF/ dt+ Q hk ≥0. In the thermodynamic limit, with a system's size being infinitely large, the nonlinear bistability in the CME exhibits many of the characteristics of macroscopic equilibrium phase transition.

  3. Kinetic Modeling of Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Petzold, Linda; Pettigrew, Michel F.

    2009-04-21

    The dynamics of how its constituent components interact define the spatio-temporal response of a natural system to stimuli. Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multiscale problems, and possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods, and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided.

  4. Systems cell biology.

    Science.gov (United States)

    Mast, Fred D; Ratushny, Alexander V; Aitchison, John D

    2014-09-15

    Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology.

  5. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    OpenAIRE

    Hill, D. P.; Adams, N.; Bada, M.; Batchelor, C.; Berardini, T. Z.; H. Dietze; Drabkin, H.J.; Ennis, M.; Foulger, R. E.; Harris, M. A.; Hastings, J.; Kale, N. S.; Matos, P.; Mungall, C. J.; Owen, G.

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Inte...

  6. Estimation of Biological Oxygen Demand and Chemical Oxygen Demand for Combined Sewer Systems Using Synchronous Fluorescence Spectra

    Directory of Open Access Journals (Sweden)

    Dae-Hee Park

    2010-03-01

    Full Text Available Real-time monitoring of water quality for sewer system is required for efficient sewer network design because it provides information on the precise loading of pollutant to wastewater treatment facilities and the impact of loading on receiving water. In this study, synchronous fluorescence spectra and its first derivatives were investigated using a number of wastewater samples collected in sewer systems in urban and non-urban areas, and the optimum fluorescence feature was explored for the estimation of biochemical oxygen demand (BOD and chemical oxygen demand (COD concentrations of sewer samples. The temporal variations in BOD and COD showed a regular pattern for urban areas whereas they were relatively irregular for non-urban areas. Irrespective of the sewer pipes and the types of the areas, two distinct peaks were identified from the synchronous fluorescence spectra, which correspond to protein-like fluorescence (PLF and humic-like fluorescence (HLF, respectively. HLF in sewer samples appears to be associated with fluorescent whitening agents. Five fluorescence characteristics were selected from the synchronous spectra and the first-derivatives. Among the selected fluorescence indices, a peak in the PLF region (i.e., Index I showed the highest correlation coefficient with both BOD and COD. A multiple regression approach based on suspended solid (SS and Index I used to compensate for the contribution of SS to BOD and COD revealed an improvement in the estimation capability, showing good correlation coefficients of 0.92 and 0.94 for BOD and COD, respectively.

  7. 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...

  8. Chemical approaches to studying stem cell biology

    Institute of Scientific and Technical Information of China (English)

    Wenlin Li; Kai Jiang; Wanguo Wei; Yan Shi; Sheng Ding

    2013-01-01

    Stem cells,including both pluripotent stem cells and multipotent somatic stem cells,hold great potential for interrogating the mechanisms of tissue development,homeostasis and pathology,and for treating numerous devastating diseases.Establishment of in vitro platforms to faithfully maintain and precisely manipulate stem cell fates is essential to understand the basic mechanisms of stem cell biology,and to translate stem cells into regenerative medicine.Chemical approaches have recently provided a number of small molecules that can be used to control cell selfrenewal,lineage differentiation,reprogramming and regeneration.These chemical modulators have been proven to be versatile tools for probing stem cell biology and manipulating cell fates toward desired outcomes.Ultimately,this strategy is promising to be a new frontier for drug development aimed at endogenous stem cell modulation.

  9. Nanotechnology Applications for Chemical and Biological Sensors

    Directory of Open Access Journals (Sweden)

    M. K. Patra

    2008-09-01

    Full Text Available Recent discoveries indicate that when the materials are brought down to sizes in the range 1–100 nm, theseexhibit unique electrical, optical, magnetic, chemical, and mechanical properties. Methods have now beenestablished to obtain the monodisperse nanocrystals of various metallic and semiconducting materials, single-walled and multi-walled nanotubes of carbon and other metallic and non-metallic materials together withorganic nanomaterials such as supra-molecular nanostructures, dendrimers, hybrid composites with tailoredfunctionalities. The high surface-to-volume ratio with an added element of porosity makes these highly potentialcandidates for chemical and biological sensor applications with higher degree of sensitivity and selectivity ascompared to their bulk counterparts. The paper reviews the recent developments and applications of chemicaland biological sensors based on nanomaterials of various structural forms.Defence Science Journal, 2008, 58(5, pp.636-649, DOI:http://dx.doi.org/10.14429/dsj.58.1686

  10. 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 ‘‘...

  11. 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."

  12. Applicability of computational systems biology in toxicology.

    Science.gov (United States)

    Kongsbak, Kristine; Hadrup, Niels; Audouze, Karine; Vinggaard, Anne Marie

    2014-07-01

    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. However, computational systems biology offers more advantages than providing a high-throughput literature search; it may form the basis for establishment of hypotheses on potential links between environmental chemicals and human diseases, which would be very difficult to establish experimentally. This is possible due to the existence of comprehensive databases containing information on networks of human protein-protein interactions and protein-disease associations. Experimentally determined targets of the specific chemical of interest can be fed into these networks to obtain additional information that can 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 in the hypothesis-generating phase of toxicological research.

  13. Integrative radiation systems biology.

    Science.gov (United States)

    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. PMID:24411063

  14. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    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

  15. Systems biology, emergence and antireductionism.

    Science.gov (United States)

    Kesić, Srdjan

    2016-09-01

    This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed. Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist-antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.

  16. Systems biology in animal sciences

    NARCIS (Netherlands)

    Woelders, H.; Pas, te M.F.W.; Bannink, A.; Veerkamp, R.F.; Smits, M.A.

    2011-01-01

    Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes an

  17. Innovation in academic chemical screening: Filling the gaps in chemical biology

    OpenAIRE

    Hasson, Samuel A.; Inglese, James

    2013-01-01

    Academic screening centers across the world have endeavored to discover small molecules that can modulate biological systems. To increase the reach of functional-genomic and chemical screening programs, universities, research institutes, and governments have followed their industrial counterparts in adopting high-throughput paradigms. As academic screening efforts have steadily grown in scope and complexity, so have the ideas of what is possible with the union of technology and biology. This ...

  18. Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems)

    International Nuclear Information System (INIS)

    Integration, re-use and meta-analysis of high content study data, typical of DNA microarray studies, can increase its scientific utility. Access to study data and design parameters would enhance the mining of data integrated across studies. However, without standards for which data to include in exchange, and common exchange formats, publication of high content data is time-consuming and often prohibitive. The MGED Society ( (www.mged.org)) was formed in response to the widespread publication of microarray data, and the recognition of the utility of data re-use for meta-analysis. The NIEHS has developed the Chemical Effects in Biological Systems (CEBS) database, which can manage and integrate study data and design from biological and biomedical studies. As community standards are developed for study data and metadata it will become increasingly straightforward to publish high content data in CEBS, where they will be available for meta-analysis. Different exchange formats for study data are being developed: Standard for Exchange of Nonclinical Data (SEND; (www.cdisc.org)); Tox-ML ( (www.Leadscope.com)) and Simple Investigation Formatted Text (SIFT) from the NIEHS. Data integration can be done at the level of conclusions about responsive genes and phenotypes, and this workflow is supported by CEBS. CEBS also integrates raw and preprocessed data within a given platform. The utility and a method for integrating data within and across DNA microarray studies is shown in an example analysis using DrugMatrix data deposited in CEBS by Iconix Pharmaceuticals

  19. Assessment of full-scale biological nutrient removal systems upgraded with physico-chemical processes for the removal of emerging pollutants present in wastewaters from Mexico.

    Science.gov (United States)

    Estrada-Arriaga, Edson Baltazar; Cortés-Muñoz, Juana Enriqueta; González-Herrera, Arturo; Calderón-Mólgora, César Guillermo; de Lourdes Rivera-Huerta, Ma; Ramírez-Camperos, Esperanza; Montellano-Palacios, Leticia; Gelover-Santiago, Silvia Lucila; Pérez-Castrejón, Sara; Cardoso-Vigueros, Lina; Martín-Domínguez, Alejandra; García-Sánchez, Liliana

    2016-11-15

    Two full-scale biological nutrient removal systems upgraded with three physico-chemical processes (coagulation, chemical precipitation, and neutral Fenton) were evaluated in order to determine the removal of emerging pollutants (EPs) present in municipal wastewater from Mexico. Between 41 and 55 EPs were detected in the influents of two wastewater treatment plants (WWTPs), including personal care products (PPCPs), antibiotics, analgesics, antiepileptics, antilipidemics, antihypertensives, antiseptics, stimulants, and hormones. Emerging pollutants were detected at concentrations ranging from 0.69ng/L to 94,600ng/L. High concentrations of emerging pollutants were found during dry season. WWTP 1, integrated by oxidation ditches and UV light lamps, showed removal efficiencies of EPs between 20% and 22%. On the other hand, WWTP 2 consisted of anaerobic/anoxic/aerobic tanks coupled with two disinfection processes; chlorine dioxide and UV light lamps, for which the removal of EPs was significant (up to 80%). The concentrations of emerging pollutants in WWTP 1 effluent was found within a rangetreatment for the two effluents from the WWTPs is promising for the removal of emerging pollutants (up to 100%) and for assuring high quality of treated water. PMID:27457673

  20. Estimation of Biological Oxygen Demand and Chemical Oxygen Demand for Combined Sewer Systems Using Synchronous Fluorescence Spectra

    OpenAIRE

    Dae-Hee Park; Tae-Hwan Lee; Bo-Mi Lee; Jin Hur

    2010-01-01

    Real-time monitoring of water quality for sewer system is required for efficient sewer network design because it provides information on the precise loading of pollutant to wastewater treatment facilities and the impact of loading on receiving water. In this study, synchronous fluorescence spectra and its first derivatives were investigated using a number of wastewater samples collected in sewer systems in urban and non-urban areas, and the optimum fluorescence feature was explored for the es...

  1. 面向专利的化合物和生物实体识别系统%Chemical and Biological Entity Recognition System from Patent Documents

    Institute of Scientific and Technical Information of China (English)

    赖鸿昌; 朱礼军; 徐硕

    2015-01-01

    It is crucial to explore the chemical and biological space covered by patent documents. In order to recognize chemical and biological entities, a recognition system is developed on the basis of open-source machine learning and natural language processing (NLP) toolkits. The system processing pipeline consists of three major components:pre-processing (sentence detection, tokenization), recognition (conditional random field (CRF) based approach), and post-processing (rule-based approach). The paper introduces each part in detail. Finally, extensive experiments on annotated chemical patent corpus are conducted, and the balanced-F measure is 69.20% with 10-fold cross validation. The results indicates that the performance on patent documents is slightly lower than that of counterpart on paper and news corpus.%探索专利文献中的化合物和生物知识变得至关重要。为了识别化合物实体和生物实体,开发了面向专利的化合物和生物实体识别系统。系统基于开源的机器学习和自然语言工具进行开发。系统按照流水线模式进行,本文将详细阐述其三个主要过程:预处理(句子分割、词条化),识别(基于条件随机场的方法),后处理(基于规则的方法)。最后,利用系统在已标注的化合物专利语料库进行大量实验,进行十折交叉验证,得到了69.20%的F值。但是,从结果可以看到,在专利文献上的实验表现,要低于论文和新闻语料库中的表现。

  2. A roadmap for hazard monitoring and risk assessment of marine biotoxins on the basis of chemical and biological test systems.

    Science.gov (United States)

    Daneshian, Mardas; Botana, Luis M; Dechraoui Bottein, Marie-Yasmine; Buckland, Gemma; Campàs, Mònica; Dennison, Ngaire; Dickey, Robert W; Diogène, Jorge; Fessard, Valérie; Hartung, Thomas; Humpage, Andrew; Leist, Marcel; Molgó, Jordi; Quilliam, Michael A; Rovida, Costanza; Suarez-Isla, Benjamin A; Tubaro, Aurelia; Wagner, Kristina; Zoller, Otmar; Dietrich, Daniel

    2013-01-01

    Aquatic food accounts for over 40% of global animal food products, and the potential contamination with toxins of algal origin--marine biotoxins--poses a health threat for consumers. The gold standards to assess toxins in aquatic food have traditionally been in vivo methods, i.e., the mouse as well as the rat bioassay. Besides ethical concerns, there is also a need for more reliable test methods because of low inter-species comparability, high intra-species variability, the high number of false positive and negative results as well as questionable extrapolation of quantitative risk to humans. For this reason, a transatlantic group of experts in the field of marine biotoxins was convened from academia and regulatory safety authorities to discuss future approaches to marine biotoxin testing. In this report they provide a background on the toxin classes, on their chemical characterization, the epidemiology, on risk assessment and management, as well as on their assumed mode of action. Most importantly, physiological functional assays such as in vitro bioassays and also analytical techniques, e.g., liquid chromatography coupled mass spectrometry (LC-MS), as substitutes for the rodent bioassay are reviewed. This forms the basis for recommendations on methodologies for hazard monitoring and risk assessment, establishment of causality of intoxications in human cases, a roadmap for research and development of human-relevant functional assays, as well as new approaches for a consumer directed safety concept.

  3. 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.

  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. 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....

  6. The biological and chemical variability of yacon.

    Science.gov (United States)

    Valentová, Katerina; Lebeda, Ales; Dolezalová, Ivana; Jirovský, David; Simonovska, Breda; Vovk, Irena; Kosina, Pavel; Gasmanová, Nikol; Dziechciarková, Marta; Ulrichová, Jitka

    2006-02-22

    This paper focuses on the biological and chemical variability of four yacon (Smallanthus sonchifolius) accessions cultivated under field conditions. Significant variations in tuber shape, weight, content of oligofructans, as well as in leaf isozymes, phenolics, and relative DNA contents were found. Accessions 6 and 88 were the most productive (up to 3.01 and 3.74 kg/plant); accession 48 was the most balanced from the yield aspect in three vegetative periods. A significantly higher content of beta-(2-->1) oligofructans was noted in accessions 48 and 88 as compared to 6 and 60. No difference in sucrose, glucose, and fructose level was observed. Only accession 6 exhibited separate acid phosphatase and esterase isoforms. Accessions 6 and 60 had the highest content of phenolics, and accession 88 had the lowest relative DNA content. Large yacon intraspecific variation may be useful in future detailed research as a good background for breeding, growing, and utilization in industrial processing. PMID:16478259

  7. ECO-BIOLOGICAL SYSTEM MODELING

    Directory of Open Access Journals (Sweden)

    T. I. Burak

    2015-01-01

    Full Text Available The methodology for computer modeling of complex eco-biological models is presented in this paper. It is based on system approach of J. Forrester. Developed methodology is universal for complex ecological and biological systems. Modeling algorithm considers specialties of eco-biological systems and shows adequate and accurate results in practice. 

  8. Chemical and biological warfare: Biology, chemistry, and toxicology. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning the physiological effects, physicochemical effects, and toxicology of chemical and biological warfare agents. Citations discuss toxic chemicals, chemical agent simulants, detoxification and decontamination, environmental toxicity, and land pollution. Detection techniques and warning systems are examined in a separate bibliography. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  9. Chemical and biological warfare: Biology, chemistry, and toxicology. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The bibliography contains citations concerning the physiological effects, physicochemical effects, and toxicology of chemical and biological warfare agents. Citations discuss toxic chemicals, chemical agent simulants, detoxification and decontamination, environmental toxicity, and land pollution. Detection techniques and warning systems are examined in a separate bibliography. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  10. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

    Lina Yang; Shujuan Guo; Yang Li; Shumin Zhou; Shengce Tao

    2011-01-01

    Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer,diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics,proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as highthroughput, miniaturized, and capable of parallel analysis,protein microarrays have already become an important technology platform for systems biology, In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays,and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

  11. CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

    Science.gov (United States)

    Waters, Michael; Stasiewicz, Stanley; Merrick, B Alex; Tomer, Kenneth; Bushel, Pierre; Paules, Richard; Stegman, Nancy; Nehls, Gerald; Yost, Kenneth J; Johnson, C Harris; Gustafson, Scott F; Xirasagar, Sandhya; Xiao, Nianqing; Huang, Cheng-Cheng; Boyer, Paul; Chan, Denny D; Pan, Qinyan; Gong, Hui; Taylor, John; Choi, Danielle; Rashid, Asif; Ahmed, Ayazaddin; Howle, Reese; Selkirk, James; Tennant, Raymond; Fostel, Jennifer

    2008-01-01

    CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. CEBS is designed to permit the user to query the data using the study conditions, the subject responses and then, having identified an appropriate set of subjects, to move to the microarray module of CEBS to carry out gene signature and pathway analysis. Scope of CEBS: CEBS currently holds 22 studies of rats, four studies of mice and one study of Caenorhabditis elegans. CEBS can also accommodate data from studies of human subjects. Toxicogenomics studies currently in CEBS comprise over 4000 microarray hybridizations, and 75 2D gel images annotated with protein identification performed by MALDI and MS/MS. CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Additionally, clinical chemistry and histopathology findings from over 1500 animals are included in CEBS. CEBS/BID: The BID (Biomedical Investigation Database) is another component of the CEBS system. BID is a relational database used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee (in preparation). BID has been shared with Health Canada and the US Environmental Protection Agency. CEBS is available at http://cebs.niehs.nih.gov. BID can be accessed via the user interface from https://dir-apps.niehs.nih.gov/arc/. Requests for a copy of BID and for depositing data into CEBS or BID are available at http://www.niehs.nih.gov/cebs-df/.

  12. Autonomous chemical and biological miniature wireless-sensor

    Science.gov (United States)

    Goldberg, Bar-Giora

    2005-05-01

    The presentation discusses a new concept and a paradigm shift in biological, chemical and explosive sensor system design and deployment. From large, heavy, centralized and expensive systems to distributed wireless sensor networks utilizing miniature platforms (nodes) that are lightweight, low cost and wirelessly connected. These new systems are possible due to the emergence and convergence of new innovative radio, imaging, networking and sensor technologies. Miniature integrated radio-sensor networks, is a technology whose time has come. These network systems are based on large numbers of distributed low cost and short-range wireless platforms that sense and process their environment and communicate data thru a network to a command center. The recent emergence of chemical and explosive sensor technology based on silicon nanostructures, coupled with the fast evolution of low-cost CMOS imagers, low power DSP engines and integrated radio chips, has created an opportunity to realize the vision of autonomous wireless networks. These threat detection networks will perform sophisticated analysis at the sensor node and convey alarm information up the command chain. Sensor networks of this type are expected to revolutionize the ability to detect and locate biological, chemical, or explosive threats. The ability to distribute large numbers of low-cost sensors over large areas enables these devices to be close to the targeted threats and therefore improve detection efficiencies and enable rapid counter responses. These sensor networks will be used for homeland security, shipping container monitoring, and other applications such as laboratory medical analysis, drug discovery, automotive, environmental and/or in-vivo monitoring. Avaak"s system concept is to image a chromatic biological, chemical and/or explosive sensor utilizing a digital imager, analyze the images and distribute alarm or image data wirelessly through the network. All the imaging, processing and communications

  13. LIDAR for Detection of Chemical and Biological Warfare Agents

    Directory of Open Access Journals (Sweden)

    S Veerabuthiran

    2011-04-01

    Full Text Available Remote detection of chemical and biological warfare agents and toxic gases in the atmosphere is of current interest to both the military and civilian agencies. Out of all currently available techniques, no single technique provides efficient detection against such threats at significant standoff distances. Light detection and ranging (LIDAR technologies, based on the transmission of laser pulses and analysis of the return signals, have demonstrated impressive capabilities in remote detection of such toxic chemicals. LIDAR is a highly sensitive tool to detect the extremely low concentrations of various toxic agents present in the form of thin clouds at distances of few kilometer. The detection of these toxic clouds is based on the approach of first detecting and measuring the range of the clouds using the scattering phenomena and subsequently identifying the composition of toxic clouds using absorption and fluorescence phenomena. Laser Science and Technology Centre (LASTEC, Delhi has been working on the design and development of LIDAR systems for detection of chemical and biological warfare (CBW agents. In this paper, theoretical analysis of differential absorption LIDAR (DIAL for detection of chemical agents and fluorescence LIDAR for detection of biological agents has been discussed. For some typical parametric conditions, the received power levels from different ranges to detect specific concentrations of chemical or biological clouds have been computed and discussed. The technical details of the indigenously developed backscattering LIDAR, which detects and measures the distance of cloud layers up to 5 km is also presented.Defence Science Journal, 2011, 61(3, pp.241-250, DOI:http://dx.doi.org/10.14429/dsj.61.556

  14. Molecular codes in biological and chemical reaction networks.

    Directory of Open Access Journals (Sweden)

    Dennis Görlich

    Full Text Available Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio- chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries, biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades, an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

  15. Aromatic rings in chemical and biological recognition: energetics and structures.

    Science.gov (United States)

    Salonen, Laura M; Ellermann, Manuel; Diederich, François

    2011-05-16

    This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations. PMID:21538733

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  17. Application of the Raven UAV for chemical and biological detection

    Science.gov (United States)

    Altenbaugh, Ryan; Barton, Jeff; Chiu, Christopher; Fidler, Ken; Hiatt, Dan; Hawthorne, Chad; Marshall, Steven; Mohos, Joe; McHugh, Vince; Nicoloff, Bill

    2010-04-01

    This paper presents the plume tracking algorithms developed for a series of outdoor chemical-stimulant testing conducted at Dugway Proving Ground in 2008 and 2009 employing a Raven UAV equipped with a real-time chemical sensor. The flights were conducted as part of the a program under the sponsorship of the Army JPM NBC Contamination Avoidance and in conjunction with the Army PM-Unmanned Aircraft Systems, the Defense Threat Reduction Agency, and Edgewood Chemical Biological Center. This test demonstrated the Raven's ability to autonomously detect and track a chemical plume during a variety of atmospheric conditions. During the testing, the Raven conducted over a dozen flights, tracking outdoor releases of simulated chemical weapons over significant distances. The Raven was cued to the releases with standoff detection systems through Cursor on Target messages. Upon reaching the plume, the Raven used on-board sensors and on-board meteorological data to track the plume autonomously and determine the extent of the plume. Results were provided in real-time to the UAV operator.

  18. 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 ...

  19. Comparison of Chemical Sensitivity of Fresh and Long-Stored Heat Resistant Neosartorya fischeri Environmental Isolates Using BIOLOG Phenotype MicroArray System.

    Directory of Open Access Journals (Sweden)

    Jacek Panek

    Full Text Available Spoilage of heat processed food and beverage by heat resistant fungi (HRF is a major problem for food industry in many countries. Neosartorya fischeri is the leading source of spoilage in thermally processed products. Its resistance to heat processing and toxigenicity makes studies about Neosartorya fischeri metabolism and chemical sensitivity essential. In this study chemical sensitivity of two environmental Neosartorya fischeri isolates were compared. One was isolated from canned apples in 1923 (DSM3700, the other from thermal processed strawberry product in 2012 (KC179765, used as long-stored and fresh isolate, respectively. The study was conducted using Biolog Phenotype MicroArray platforms of chemical sensitivity panel and traditional hole-plate method. The study allowed for obtaining data about Neosartorya fischeri growth inhibitors. The fresh isolate appeared to be much more resistant to chemical agents than the long-stored isolate. Based on phenotype microarray assay nitrogen compounds, toxic cations and membrane function compounds were the most effective in growth inhibition of N. fischeri isolates. According to the study zaragozic acid A, thallium(I acetate and sodium selenate were potent and promising N. fischeri oriented fungicides which was confirmed by both chemical sensitivity microplates panel and traditional hole-plate methods.

  20. 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.

  1. Telemetry System of Biological Parameters

    OpenAIRE

    2005-01-01

    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 consum...

  2. A Systems Biology-Based Approach to Uncovering the Molecular Mechanisms Underlying the Effects of Dragon's Blood Tablet in Colitis, Involving the Integration of Chemical Analysis, ADME Prediction, and Network Pharmacology

    OpenAIRE

    Haiyu Xu; Yanqiong Zhang; Yun Lei; Xiumei Gao; Huaqiang Zhai; Na Lin; Shihuan Tang; Rixin Liang; Yan Ma; Defeng Li; Yi Zhang; Guangrong Zhu; Hongjun Yang; Luqi Huang

    2014-01-01

    Traditional Chinese medicine (TCM) is one of the oldest East Asian medical systems. The present study adopted a systems biology-based approach to provide new insights relating to the active constituents and molecular mechanisms underlying the effects of dragon's blood (DB) tablets for the treatment of colitis. This study integrated chemical analysis, prediction of absorption, distribution, metabolism, and excretion (ADME), and network pharmacology. Firstly, a rapid, reliable, and accurate ult...

  3. 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....

  4. 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...... that were in concordance with their effects in experimental animals. In project II, I profiled the effects on rat liver gene expression levels following exposure to a 14-chemical mixture ± the presence of an endocrine disrupting chemical. This project helped us shed light on the mechanism of action...... of the 14-chemical mixture and the endocrine disrupting chemical. In project III, I modeled a predictive signature for an in vivo endpoint that is sensitive to endocrine disruption. I used publicly available data generated for the purpose of modeling predictive signatures for various in vivo endpoints. From...

  5. 化学铁盐辅助除磷对生物除磷的影响研究%Effect of Chemical Addition on Biological Phosphorus Removal System

    Institute of Scientific and Technical Information of China (English)

    樊杰; 胡晗

    2013-01-01

    Biological phosphorus removal which is assisted by chemical dose has potential impact on phosphorus accumulating organism.The simultaneous phosphorus removal was done to treat domestic wastewater in the college by adding ferrous sulphate.Considering confused constituent of phosphorus precipitation which interferes with biological phosphorus analysis, chemically pure ferric phosphate and ferric hydroxide were chosen to represent phosphorus precipitation.Phosphorus removal by PAO was calculated according to potassium and mol ratio of K/P in order to evaluate the effect of chemical dose on biological phosphorus removal.Results showed that continuous addition of FeSO4 resulted in decrease of phosphorus release and adsorption by PAO.Ferric phosphate of 0.075 mmol/L stimulated the phosphorus release and adsorption of PAO by 25%, while ferric phosphate of 0.15 mmol/L had inhibition on phosphorus release.Phosphorus release and initial adsorption by PAO were inhibited by ferric hydroxide.There was interaction between biological sludge and chemical sludge.%化学辅助除磷有助于污水厂实现磷达标,但其对生物系统存在潜在的影响.针对除磷药剂对生物除磷过程的影响展开研究,选用硫酸亚铁进行化学辅助除磷.药剂形成的化学污泥干扰生物除磷过程且成分复杂,故以磷酸铁、氢氧化铁模拟化学污泥,由钾离子、K/P摩尔比计算出同步除磷中的生物除磷,来探讨化学污泥对聚磷菌释磷暇磷过程的影响.结果表明,连续投加硫酸亚铁使聚磷菌的释磷量、吸磷量降低;系统中磷酸铁含量0.075 mmol/L时聚磷菌的释磷和吸磷能力提高了约25%,磷酸铁含量0.15 mmol/L时对聚磷菌吸磷有抑制作用;氢氧化铁对聚磷菌释磷、好氧初期吸磷均有抑制作用.生物污泥与化学污泥存在交互作用.

  6. Innovation in academic chemical screening: filling the gaps in chemical biology.

    Science.gov (United States)

    Hasson, Samuel A; Inglese, James

    2013-06-01

    Academic screening centers across the world have endeavored to discover small molecules that can modulate biological systems. To increase the reach of functional-genomic and chemical screening programs, universities, research institutes, and governments have followed their industrial counterparts in adopting high-throughput paradigms. As academic screening efforts have steadily grown in scope and complexity, so have the ideas of what is possible with the union of technology and biology. This review addresses the recent conceptual and technological innovation that has been propelling academic screening into its own unique niche. In particular, high-content and whole-organism screening are changing how academics search for novel bioactive compounds. Importantly, we recognize examples of successful chemical probe development that have punctuated the changing technology landscape. PMID:23683346

  7. 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),...

  8. Chemical biology: How to minimalize antibodies

    Science.gov (United States)

    Rader, Christoph

    2015-02-01

    The success of antibodies as pharmaceuticals has triggered interest in crafting much smaller mimics. A crucial step forward has been taken with the chemical synthesis of small molecules that recruit immune cells to attack cancer cells.

  9. 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...... of nutritional research is, therefore, to borrow methods that are well established in medical and pharmacological research. In this thesis, we use advanced data-mining tools for the construction of a database with available, state-of-the-art information concerning the interaction of food and its molecular...

  10. Chemical, Biological, and Explosive Sensors for Field Measurements

    Energy Technology Data Exchange (ETDEWEB)

    Kevin Kyle, Manuel Manard, Stephan Weeks

    2009-01-31

    Special Technologies Laboratory (STL) is developing handheld chemical, biological, and explosive (CBE) detection systems and sensor motes for wireless networked field operations. The CBE sensors are capable of detecting and identifying multiple targeted toxic industrial chemicals (TICs) and high-explosive vapor components. The CBE devices are based on differential mobility spectrometry (DMS) coupled with fast gas chromatography (GC) or mass spectrometry. The systems all include the concepts of: 1. Direct air/particulate “smart” sampling 2. Selective, continuous real-time (~1 sec) alert monitoring using DMS 3. Highly selective, rapid dual technology separation/verification analysis The biosensor technology is based on Raman aerosol particle flow cytometry for target detection and identification. Monitoring and identifying trace level chemical vapors directly from ambient air will allow First Responders to quickly adapt situational response strategies and personal protective equipment needs to the specific response scenario being encountered. First Responders require great confidence in the measurements and ability of a given system to detect CBE below threshold levels without interferences. The concept of determining the background matrix in near real-time to allow subsequent automated field-programmable method selection and cueing of high-value assets in a wide range of environs will be presented. This provides CBE information for decisions prior to First Responders entering the response site or sending a portable mobile unit for a remote site survey of the hazards. The focus is on real-time information needed by those responsible for emergency response and national security.

  11. Chemical, Biological, and Explosive Sensors for Field Measurements

    International Nuclear Information System (INIS)

    Special Technologies Laboratory (STL) is developing handheld chemical, biological, and explosive (CBE) detection systems and sensor motes for wireless networked field operations. The CBE sensors are capable of detecting and identifying multiple targeted toxic industrial chemicals (TICs) and high-explosive vapor components. The CBE devices are based on differential mobility spectrometry (DMS) coupled with fast gas chromatography (GC) or mass spectrometry. The systems all include the concepts of: (1) Direct air/particulate 'smart' sampling; (2) Selective, continuous real-time (∼1 sec) alert monitoring using DMS; and (3) Highly selective, rapid dual technology separation/verification analysis The biosensor technology is based on Raman aerosol particle flow cytometry for target detection and identification. Monitoring and identifying trace level chemical vapors directly from ambient air will allow First Responders to quickly adapt situational response strategies and personal protective equipment needs to the specific response scenario being encountered. First Responders require great confidence in the measurements and ability of a given system to detect CBE below threshold levels without interferences. The concept of determining the background matrix in near real-time to allow subsequent automated field-programmable method selection and cueing of high-value assets in a wide range of environs will be presented. This provides CBE information for decisions prior to First Responders entering the response site or sending a portable mobile unit for a remote site survey of the hazards. The focus is on real-time information needed by those responsible for emergency response and national security

  12. Cutaneous reactions in nuclear, biological and chemical warfare

    Directory of Open Access Journals (Sweden)

    Arora Sandeep

    2005-03-01

    Full Text Available Nuclear, biological and chemical warfare have in recent times been responsible for an increasing number of otherwise rare dermatoses. Many nations are now maintaining overt and clandestine stockpiles of such arsenal. With increasing terrorist threats, these agents of mass destruction pose a risk to the civilian population. Nuclear and chemical attacks manifest immediately while biological attacks manifest later. Chemical and biological attacks pose a significant risk to the attending medical personnel. The large scale of anticipated casualties in the event of such an occurrence would need the expertise of all physicians, including dermatologists, both military and civilian. Dermatologists are uniquely qualified in this respect. This article aims at presenting a review of the cutaneous manifestations in nuclear, chemical and biological warfare and their management.

  13. Aging and computational systems biology.

    Science.gov (United States)

    Mooney, Kathleen M; Morgan, Amy E; Mc Auley, Mark T

    2016-01-01

    Aging research is undergoing a paradigm shift, which has led to new and innovative methods of exploring this complex phenomenon. The systems biology approach endeavors to understand biological systems in a holistic manner, by taking account of intrinsic interactions, while also attempting to account for the impact of external inputs, such as diet. A key technique employed in systems biology is computational modeling, which involves mathematically describing and simulating the dynamics of biological systems. Although a large number of computational models have been developed in recent years, these models have focused on various discrete components of the aging process, and to date no model has succeeded in completely representing the full scope of aging. Combining existing models or developing new models may help to address this need and in so doing could help achieve an improved understanding of the intrinsic mechanisms which underpin aging.

  14. Chemical and biological sensing using tuning forks

    Science.gov (United States)

    Tao, Nongjian; Boussaad, Salah

    2012-07-10

    A device for sensing a chemical analyte is disclosed. The device is comprised of a vibrating structure having first and second surfaces and having an associated resonant frequency and a wire coupled between the first and second surfaces of the vibrating structure, wherein the analyte interacts with the wire and causes a change in the resonant frequency of the vibrating structure. The vibrating structure can include a tuning fork. The vibrating structure can be comprised of quartz. The wire can be comprised of polymer. A plurality of vibrating structures are arranged in an array to increase confidence by promoting a redundancy of measurement or to detect a plurality of chemical analytes. A method of making a device for sensing a chemical analyte is also disclosed.

  15. Modelling coordination in biological systems

    OpenAIRE

    Clarke, David; Oliveira Costa, de, David; Arbab, Farhad

    2004-01-01

    We present an application of the Reo coordination paradigm to provide a compositional formal model for describing and reasoning about the behaviour of biological systems, such as regulatory gene networks. Reo governs the interaction and flow of data between components by allowing the construction of connector circuits which have a precise formal semantics. When applied to systems biology, the result is a graphical model, which is comprehensible, mathematically precise, and flexible

  16. Optimization in computational systems biology

    OpenAIRE

    Banga Julio R

    2008-01-01

    Abstract Optimization aims to make a system or design as effective or functional as possible. Mathematical optimization methods are widely used in engineering, economics and science. This commentary is focused on applications of mathematical optimization in computational systems biology. Examples are given where optimization methods are used for topics ranging from model building and optimal experimental design to metabolic engineering and synthetic biology. Finally, several perspectives for ...

  17. Guidelines to improve airport preparedness against chemical and biological terrorism.

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, Donna M.; Price, Phillip N. (Lawrence Berkeley National Laboratory, Berkeley, CA); Gordon, Susanna P.; Gadgil, Ashok (Lawrence Berkeley National Laboratory, Berkeley, CA)

    2005-05-01

    Guidelines to Improve Airport Preparedness Against Chemical and Biological Terrorism is a 100-page document that makes concrete recommendations on improving security and assessing vulnerable areas and helps its readers understand the nature of chemical and biological attacks. The report has been turned over to Airports Council International (ACI) and the American Association of Airport Executives (AAAE), two organizations that together represent the interests of thousands of airport personnel and facilities in the U.S. and around the world.

  18. 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...

  19. Electrochemical approaches for chemical and biological analysis on Mars

    Science.gov (United States)

    Kounaves, Samuel P.

    2003-01-01

    Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and

  20. Informing Biological Design by Integration of Systems and Synthetic Biology

    OpenAIRE

    Smolke, Christina D.; Silver, Pamela A.

    2011-01-01

    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.

  1. Chemical and Biological Evaluation of Whey

    International Nuclear Information System (INIS)

    This Study has been carried out to extract whey protein concentrate (WPC) from sweet whey and to study the chemical composition, amino acids composition, amino acid scores and to investigate the possible role of WPC in ameliorating some biochemical disorders induced in γ-irradiated rats. Animals were divided into 4 groups. Group 1, fed on normal diet during experimental period. Group 2, fed on diet containing 15% WPC instead of soybean protein. Group 3, rats exposed to whole body γ-radiation with single dose of 5 Gy and fed on the normal diet. Group 4, rats exposed to 5 Gy then fed on diet containing 15% WPC. The rats were decapitated 14 and 28 days post irradiation. Chemical analysis of WPC revealed that it contains high amounts of protein (44%), total amino acids (71%) and all essential amino acids (EAA), phenylalanine (37%), isoleucine cystine and threonine were the major EAA and high amounts of sulphur amino acids. Methionine gave rich chemical score (102.67%) also, isoleucine (119.95%) and phenylalanine+ tyrosine gave maximum chemical score (198.8%), respectively. Exposure to γ-irradiation caused significant elevation of serum cholesterol, triglycerides, low density lipoprotein (LDL), lipid per oxidation end product (TBARS) and iron (Fe) with significant decrease in high density lipoprotein (HDL), glutathione (GSH) and catalase (CAT) in serum. Also, irradiated rats had significant decrease in copper (Cu), magnesium (Mg) and zinc (Zn) in serum. The histological examination of cardiac tissue showed severe structural damage. Irradiated rats fed on WPC revealed significant improvement of some biochemical parameters. It could be concluded that WPC must be added to diet for reducing radiation injury via metabolic pathway

  2. The chemical and biological versatility of riboflavin.

    Science.gov (United States)

    Massey, V

    2000-01-01

    Since their discovery and chemical characterization in the 1930s, flavins have been recognized as being capable of both one- and two-electron transfer processes, and as playing a pivotal role in coupling the two-electron oxidation of most organic substrates to the one-electron transfers of the respiratory chain. In addition, they are now known as versatile compounds that can function as electrophiles and nucleophiles, with covalent intermediates of flavin and substrate frequently being involved in catalysis. Flavins are thought to contribute to oxidative stress through their ability to produce superoxide, but at the same time flavins are frequently involved in the reduction of hydroperoxides, products of oxygen-derived radical reactions. Flavoproteins play an important role in soil detoxification processes via the hydroxylation of many aromatic compounds, and a simple flavoprotein in liver microsomes catalyses many reactions similar to those carried out by cytochrome P450 enzymes. Flavins are involved in the production of light in bioluminescent bacteria, and are intimately connected with light-initiated reactions such as plant phototropism and nucleic acid repair processes. Recent reports also link them to programmed cell death. The chemical versatility of flavoproteins is clearly controlled by specific interactions with the proteins with which they are bound. One of the main thrusts of current research is to try to define the nature of these interactions, and to understand in chemical terms the various steps involved in catalysis by flavoprotein enzymes. PMID:10961912

  3. Circadian systems biology in Metazoa.

    Science.gov (United States)

    Lin, Li-Ling; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2015-11-01

    Systems biology, which can be defined as integrative biology, comprises multistage processes that can be used to understand components of complex biological systems of living organisms and provides hierarchical information to decoding life. Using systems biology approaches such as genomics, transcriptomics and proteomics, it is now possible to delineate more complicated interactions between circadian control systems and diseases. The circadian rhythm is a multiscale phenomenon existing within the body that influences numerous physiological activities such as changes in gene expression, protein turnover, metabolism and human behavior. In this review, we describe the relationships between the circadian control system and its related genes or proteins, and circadian rhythm disorders in systems biology studies. To maintain and modulate circadian oscillation, cells possess elaborative feedback loops composed of circadian core proteins that regulate the expression of other genes through their transcriptional activities. The disruption of these rhythms has been reported to be associated with diseases such as arrhythmia, obesity, insulin resistance, carcinogenesis and disruptions in natural oscillations in the control of cell growth. This review demonstrates that lifestyle is considered as a fundamental factor that modifies circadian rhythm, and the development of dysfunctions and diseases could be regulated by an underlying expression network with multiple circadian-associated signals.

  4. 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

  5. Systems biology and cancer, [Editorial

    OpenAIRE

    Soto, A M; Sonnenschein, C; Maini, P.K.

    2011-01-01

    The systems approach to complex biological problems has rapidly gained ground during the first decade of this century. There are several reasons for this development. An important one is that while the achievement of sequencing the complete human genome, and those of other species, has been of great benefit to fundamental science, for example in comparative genomics and evolutionary biology, it has not led to the expected quick and simple solutions to multifactorial diseases (2010). On the co...

  6. Enhanced formulations for neutralization of chemical, biological and industrial toxants

    Science.gov (United States)

    Tucker, Mark D [Albuqueque, NM

    2008-06-24

    An enhanced formulation and method of making that neutralizes the adverse health effects of both chemical and biological compounds, especially chemical warfare (CW) and biological warfare (BW) agents, and toxic industrial chemicals. The enhanced formulation according to the present invention is non-toxic and non-corrosive and can be delivered by a variety of means and in different phases. The formulation provides solubilizing compounds that serve to effectively render the chemical and biological compounds, particularly CW and BW compounds, susceptible to attack, and at least one reactive compound that serves to attack (and detoxify or kill) the compound. The formulation includes at least one solubilizing agent, a reactive compound, a bleaching activator and water.

  7. 78 FR 55326 - Determinations Regarding Use of Chemical Weapons in Syria Under the Chemical and Biological...

    Science.gov (United States)

    2013-09-10

    ... Determinations Regarding Use of Chemical Weapons in Syria Under the Chemical and Biological Weapons Control and..., 22 U.S.C. 5604(a), that the Government of Syria has used chemical weapons in violation of... Under Secretary of State for Political Affairs: (1) Determined that the Government of Syria has...

  8. Estimating Escherichia coli loads in streams based on various physical, chemical, and biological factors

    OpenAIRE

    Dwivedi, Dipankar; Mohanty, Binayak P.; Lesikar, Bruce J.

    2013-01-01

    Microbes have been identified as a major contaminant of water resources. Escherichia coli (E. coli) is a commonly used indicator organism. It is well recognized that the fate of E. coli in surface water systems is governed by multiple physical, chemical, and biological factors. The aim of this work is to provide insight into the physical, chemical, and biological factors along with their interactions that are critical in the estimation of E. coli loads in surface streams. There are various mo...

  9. 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...... perspective about the contribution of genes and genetic variants to disease is a key reason 'omics' has failed to deliver the anticipated breakthroughs. We then point out the critical utility of key concepts from physiology like homeostasis, regulated systems and redundancy as major intellectual tools...... 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...

  10. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    Directory of Open Access Journals (Sweden)

    Janna Hastings

    Full Text Available Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA.

  11. Chemical industrial wastewater treated by combined biological and chemical oxidation process.

    Science.gov (United States)

    Guomin, Cao; Guoping, Yang; Mei, Sheng; Yongjian, Wang

    2009-01-01

    Wastewaters from phenol and rubber synthesis were treated by the activated sludge process in a large-scale chemical factory in Shanghai, but the final effluent quality cannot conform with the local discharge limit without using river water for dilution. Therefore, this chemical factory had to upgrade its wastewater treatment plant. To fully use the present buildings and equipment during upgrading of the chemical factory's wastewater treatment plant and to save operation costs, a sequential biological pre-treatement, chemical oxidation, and biological post-treatment (or BCB for short) process had been proposed and investigated in a pilot trial. The pilot trial results showed that about 80% COD in the chemical wastewater could be removed through anoxic and aerobic degradation in the biological pre-treatement section, and the residual COD in the effluent of the biological pre-treatment section belongs to refractory chemicals which cannot be removed by the normal biological process. The refractory chemicals were partial oxidized using Fenton's reagent in the chemical oxidation section to improve their biodegradability; subsequently the wastewater was treated by the SBR process in the biological post-treatment section. The final effluent COD reached the first grade discharge limit (process, the operation cost of the BCB process increased by about 0.5 yuan (RMB) per cubic metre wastewater, but about 1,240,000 m(3) a(-1) dilution water could be saved and the COD emission could be cut down by 112 tonne each year.

  12. Bridging the gap between systems biology and synthetic biology

    OpenAIRE

    Liu, Di; Hoynes-O’Connor, Allison; Zhang, Fuzhong

    2013-01-01

    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, syst...

  13. Language Based Techniques for Systems Biology

    DEFF Research Database (Denmark)

    Pilegaard, Henrik

    calculi have similarly been used for the study of bio-chemical reactive systems. In this dissertation it is argued that techniques rooted in the theory and practice of programming languages, language based techniques if you will, constitute a strong basis for the investigation of models of biological......Process calculus is the common denominator for a class of compact, idealised, domain-specific formalisms normally associated with the study of reactive concurrent systems within Computer Science. With the rise of the interactioncentred science of Systems Biology a number of bio-inspired process...... systems as formalised in a process calculus. In particular it is argued that Static Program Analysis provides a useful approach to the study of qualitative properties of such models. In support of this claim a number of static program analyses are developed for Regev’s BioAmbients – a bio-inspired variant...

  14. 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’.

  15. Chemical and biological characterization of urban particulate matter

    International Nuclear Information System (INIS)

    Airborne particulate matter has been collected on glass fiber filter by high volume sampling in the Goeteborg urban area. The samples were, after extraction with respect to organic components, tested for biological effect in the Salmonella mutagenicity assay, affinity to the cytosol TCDD receptor and toxicity towards a mammalian cell system and analysed chemically for selected polycyclic aromatic compounds. A series of samples collected simultaneously at a street level location and a rooftop site showed that most parameters associated with the organic compounds adsorbed to airborne particulate matter has similar concentrations at the two levels. The differences observed for the mutagenic effect in different strains and conditions showed that the rooftop samples had a different composition compared to the street samples indicating that atmospheric transformations have occurred. Chemical fractionation of representative samples showed that the distribution of mutagenic activity among different fractions is dissimilar to the distribution obtained in the fractionation of both gasoline and diesel engine exhaust particles. Partial least squares regression analysis showed qualitatively that diesel exhaust is a major source of airborne particulate mutagenic activity and source apportionment with chemical mass balance and multilinear regression corroborated this quantitatively. The multilinear regression analysis gave the result that the airborne activity in Salmonella TA90-S9 originated to 54±4% from diesel exhaust and to 26±3% from gasoline exhaust. The contribution is more equal for the activity measured with TA98+S9. The usefulness of short-term bioassays as an addition to chemical analysis of airborne particulate matter depends on whether only polycylic aromatic hydrocarbons (PAH) are major carcinogens, as has been suggested in the literature, or whether also other polycyclic aromatic compound (PAC) are of importance. (au)

  16. 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

  17. Chemical and biological nonproliferation program. FY99 annual report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    This document is the first of what will become an annual report documenting the progress made by the Chemical and Biological Nonproliferation Program (CBNP). It is intended to be a summary of the program's activities that will be of interest to both policy and technical audiences. This report and the annual CBNP Summer Review Meeting are important vehicles for communication with the broader chemical and biological defense and nonproliferation communities. The Chemical and Biological Nonproliferation Program Strategic Plan is also available and provides additional detail on the program's context and goals. The body of the report consists of an overview of the program's philosophy, goals and recent progress in the major program areas. In addition, an appendix is provided with more detailed project summaries that will be of interest to the technical community.

  18. Assessing estrogenic activity in surface water and sediment of the Liao River system in northeast China using combined chemical and biological tools

    Energy Technology Data Exchange (ETDEWEB)

    Wang Li [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Ying Guangguo, E-mail: guangguo.ying@gmail.co [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Zhao Jianliang; Liu Shan; Yang Bin; Zhou Lijun; Tao Ran; Su Haochang [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China)

    2011-01-15

    This paper investigated some selected estrogenic compounds (4-t-octylphenol: 4-t-OP; 4-nonylphenols: 4-NP; bisphenol-A: BPA; diethylstilbestrol: DES; estrone: E1; 17{beta}-estradiol: E2; 17{alpha}-Ethinylestradiol: EE2; triclosan: TCS) and estrogenicity in the Liao River system using the combined chemical and in vitro yeast screen bioassay and assessed their ecological risks to aquatic organisms. The estrogenic compounds 4-t-OP, 4-NP, BPA, E1, E2 and TCS were detected in most of the samples, with their concentrations up to 52.1 2065.7, 755.6, 55.8, 7.4 and 81.3 ng/L in water, and up to 8.6, 558.4, 33.8, 7.9, system. - Estrogenic risks to aquatic organisms were assessed by using combined chemical analysis and in vitro bioassay.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  20. Modelling coordination in biological systems

    NARCIS (Netherlands)

    Clarke, D.G.; Oliveira Costa, D.F. de; Arbab, F.

    2004-01-01

    We present an application of the Reo coordination paradigm to provide a compositional formal model for describing and reasoning about the behaviour of biological systems, such as regulatory gene networks. Reo governs the interaction and flow of data between components by allowing the construction of

  1. 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...

  2. Seeking the chemical roots of darwinism: bridging between chemistry and biology.

    Science.gov (United States)

    Pross, Addy

    2009-08-24

    Chemistry and biology are intimately connected sciences yet the chemistry-biology interface remains problematic and central issues regarding the very essence of living systems remain unresolved. In this essay we build on a kinetic theory of replicating systems that encompasses the idea that there are two distinct kinds of stability in nature-thermodynamic stability, associated with "regular" chemical systems, and dynamic kinetic stability, associated with replicating systems. That fundamental distinction is utilized to bridge between chemistry and biology by demonstrating that within the parallel world of replicating systems there is a second law analogue to the second law of thermodynamics, and that Darwinian theory may, through scientific reductionism, be related to that second law analogue. Possible implications of these ideas to the origin of life problem and the relationship between chemical emergence and biological evolution are discussed.

  3. Chemical reaction systems with toric steady states

    CERN Document Server

    Millan, Mercedes Perez; Shiu, Anne; Conradi, Carsten

    2011-01-01

    Mass-action chemical reaction systems are frequently used in Computational Biology. The corresponding polynomial dynamical systems are often large, consisting of tens or even hundreds of ordinary differential equations, and poorly parameterized (due to noisy measurement data and a small number of data points and repetitions). Therefore, it is often difficult to establish the existence of (positive) steady states or to determine whether more complicated phenomena such as multistationarity exist. If, however, the steady state ideal of the system is a binomial ideal, then we show that these questions can be answered easily. The focus of this work is on systems with this property, and we say that such systems have toric steady states. Our main result gives sufficient conditions for a chemical reaction system to have toric steady states. Furthermore, we analyze the capacity of such a system to exhibit positive steady states and multistationarity. Examples of systems with toric steady states include weakly-reversib...

  4. Chemical sensor system

    Science.gov (United States)

    Darrach, Murray R. (Inventor); Chutjian, Ara (Inventor)

    2008-01-01

    A chemical sensing apparatus and method for the detection of sub parts-per-trillion concentrations of molecules in a sample by optimizing electron utilization in the formation of negative ions is provided. A variety of media may be sampled including air, seawater, dry sediment, or undersea sediment. An electrostatic mirror is used to reduce the kinetic energy of an electron beam to zero or near-zero kinetic energy.

  5. MECs: "Building Blocks" for Creating Biological and Chemical Instruments.

    Science.gov (United States)

    Hill, Douglas A; Anderson, Lindsey E; Hill, Casey J; Mostaghim, Afshin; Rodgers, Victor G J; Grover, William H

    2016-01-01

    The development of new biological and chemical instruments for research and diagnostic applications is often slowed by the cost, specialization, and custom nature of these instruments. New instruments are built from components that are drawn from a host of different disciplines and not designed to integrate together, and once built, an instrument typically performs a limited number of tasks and cannot be easily adapted for new applications. Consequently, the process of inventing new instruments is very inefficient, especially for researchers or clinicians in resource-limited settings. To improve this situation, we propose that a family of standardized multidisciplinary components is needed, a set of "building blocks" that perform a wide array of different tasks and are designed to integrate together. Using these components, scientists, engineers, and clinicians would be able to build custom instruments for their own unique needs quickly and easily. In this work we present the foundation of this set of components, a system we call Multifluidic Evolutionary Components (MECs). "Multifluidic" conveys the wide range of fluid volumes MECs operate upon (from nanoliters to milliliters and beyond); "multi" also reflects the multiple disciplines supported by the system (not only fluidics but also electronics, optics, and mechanics). "Evolutionary" refers to the design principles that enable the library of MEC parts to easily grow and adapt to new applications. Each MEC "building block" performs a fundamental function that is commonly found in biological or chemical instruments, functions like valving, pumping, mixing, controlling, and sensing. Each MEC also has a unique symbol linked to a physical definition, which enables instruments to be designed rapidly and efficiently using schematics. As a proof-of-concept, we use MECs to build a variety of instruments, including a fluidic routing and mixing system capable of manipulating fluid volumes over five orders of magnitude, an

  6. Biological control in greenhouse systems.

    Science.gov (United States)

    Paulitz, T C; Bélanger, R R

    2001-01-01

    The controlled environment of greenhouses, the high value of the crops, and the limited number of registered fungicides offer a unique niche for the biological control of plant diseases. During the past ten years, over 80 biocontrol products have been marketed worldwide. A large percentage of these have been developed for greenhouse crops. Products to control soilborne pathogens such as Sclerotinia, Pythium, Rhizoctonia and Fusarium include Coniothyrium minitans, species of Gliocladium, Trichoderma, Streptomyces, and Bacillus, and nonpathogenic Fusarium. Products containing Trichoderma, Ampelomyces quisqualis, Bacillus, and Ulocladium are being developed to control the primary foliar diseases, Botrytis and powdery mildew. The development of Pseudomonas for the control of Pythium diseases in hydroponics and Pseudozyma flocculosa for the control of powdery mildew by two Canadian research programs is presented. In the future, biological control of diseases in greenhouses could predominate over chemical pesticides, in the same way that biological control of greenhouse insects predominates in the United Kingdom. The limitations in formulation, registration, and commercialization are discussed, along with suggested future research priorities. PMID:11701861

  7. Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Borodina, Irina; Li, Mingji

    2015-01-01

    biology has the potential to bring down this cost by improving our ability to predictably engineer biological systems. This review highlights synthetic biology applications for design, assembly, and optimization of non-native biochemical pathways in baker's yeast Saccharomyces cerevisiae. We describe......-of-concept chemicals have been made in yeast, only a very small fraction of those has reached commercial-scale production so far. The limiting factor is the high research cost associated with the development of a robust cell factory that can produce the desired chemical at high titer, rate, and yield. Synthetic...

  8. Very Large Chemical Sensor Array for Mimicking Biological Olfaction

    Science.gov (United States)

    Beccherelli, R.; Zampetti, E.; Pantalei, S.; Bernabei, M.; Persaud, K. C.

    2009-05-01

    Olfactory receptor neurons (ORN) in the mammalian olfactory system, transduce molecular properties of the odorants into electrical signals and project these into the olfactory bulb (OB). In the biological system several millions of receptor neurons of a few hundred types create redundancy and the massive convergence of the ORNs to the OB, is thought to enhance the sensitivity and selectivity of the system. To explore this concept, the NEUROCHEM project will build a polymeric chemical sensor array consisting of 216 (65536) sensors with tens of different types. To interface such a large sensor array, a topological array configuration with n rows and m columns, has been adopted, to reduce the total wiring connections to n+m. A method of addressing a single element in the array in isolation of the rest of the network has been developed. Over the array ten different conductive polymers with different sensing characteristics will be deposited by means of electrodeposition and inkjet printing. A smaller prototype of 64 elements has been investigated and the results are here reported and discussed.

  9. Biological Effects and Chemical Measurements in Irish Marine Waters

    OpenAIRE

    Giltrap, Michelle, (Thesis); McHugh, Brendan; Ronan, Jenny; Wilson, James; MCGOVERN Evin

    2014-01-01

    The overall aim of this project was to increase Ireland’s capacity for the generation of integrated monitoring of biological effects and chemical measurement data and for the completion of a pilot scale assessment of the quality of the Irish marine environment at a number of selected locations.

  10. Chemical and biological weapons in the 'new wars'.

    Science.gov (United States)

    Ilchmann, Kai; Revill, James

    2014-09-01

    The strategic use of disease and poison in warfare has been subject to a longstanding and cross-cultural taboo that condemns the hostile exploitation of poisons and disease as the act of a pariah. In short, biological and chemical weapons are simply not fair game. The normative opprobrium is, however, not fixed, but context dependent and, as a social phenomenon, remains subject to erosion by social (or more specifically, antisocial) actors. The cross cultural understanding that fighting with poisons and disease is reprehensible, that they are taboo, is codified through a web of interconnected measures, principal amongst these are the 1925 Geneva Protocol; the Biological Weapons Convention; and the Chemical Weapons Convention. Whilst these treaties have weathered the storm of international events reasonably well, their continued health is premised on their being 'tended to' in the face of contextual changes, particularly facing changes in science and technology, as well as the changed nature and character of conflict. This article looks at the potential for normative erosion of the norm against chemical and biological weapons in the face of these contextual changes and the creeping legitimization of chemical and biological weapons. PMID:24132385

  11. Chemical and biological rhizosphere interactions in low zinc soils

    NARCIS (Netherlands)

    Duffner, A.

    2014-01-01

    Abstract of the PhD thesis entitled “Chemical and biological rhizosphere interactions in low zinc soils” by Andreas Duffner Soil provides ecosystem services critical for life. The availability of micronutrients, such as zinc (Zn), in soils is an essenti

  12. On the transition period from chemical to biological evolution

    International Nuclear Information System (INIS)

    We discuss the consequences of the hypothesis that biological evolution was contemporary with an important event in chemical evolution, namely, the induction of a small chiral bias by the electroweak neutral interaction, amplified by the Salam enhancement factor, which we discuss in terms of familiar crystallographic terms. (author). 18 refs, 3 tabs

  13. System biology of gene regulation.

    Science.gov (United States)

    Baitaluk, Michael

    2009-01-01

    ) questions of biological relevance. Thus systems biology could be treated as such a socioscientific phenomenon and a new approach to both experiments and theory that is defined by the strategy of pursuing integration of complex data about the interactions in biological systems from diverse experimental sources using interdisciplinary tools and personnel. PMID:19623486

  14. 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.

  15. Robust Design of Biological Circuits: Evolutionary Systems Biology Approach

    OpenAIRE

    Bor-Sen Chen; Chih-Yuan Hsu; Jing-Jia Liou

    2011-01-01

    Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter ...

  16. 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.

  17. Looming Threat of Chemical and Biological Warfare Agents

    Directory of Open Access Journals (Sweden)

    A.K. Goel

    2016-09-01

    Full Text Available In the recent past, a dramatic shift has been observed in the strategies of warfare from conventional to non-conventional. Now-a-days, traditional power is of less importance than it used to be earlier. Weapons of mass destruction, which comprise of nuclear weapons, and chemical and biological warfare agents, are posing a great peril to the world due to their devastating potential. Though, there are several bilateral as well as multilateral treaties to control the use and proliferation of these weapons, yet the risk of use of such agents by non-state actors cannot be overlooked. Chances of use of chemical and biological agents are more likely than the nuclear weapons. A comparison of nuclear, chemical and biological weapons in terms of technology, cost, signature, effectiveness on protected and un-protected troops shows that chemical and biological weapon programmes require much lower level of technology and cost than the nuclear weapon programme. Further, there is no or least distinctive and readily observable signature in biological weapon programme in comparison to nuclear and chemical weapon facilities. There can be two possibilities of use of these agents in terrorist attacks. First, there is a risk of transfer of material or know-how of these weapons to terrorists for using against the adversaries and second, the risk of these agents being pilfered due to poor security, thereby sabotaging the national security. The International Committee of Red Cross in February 1918 reckoned these agents as ‘barbarous inventions’ that can ‘only be called criminal’.

  18. Bridging the gaps in systems biology

    OpenAIRE

    Marija Cvijovic; Joachim Almquist; Jonas Hagmar; Stefan Hohmann; Hans\\u2011Michael Kaltenbach; Edda Klipp; Marcus Krantz; Pedro Mendes; Sven Nelander; Jens Nielsen; Andrea Pagnani; Natasa Przulj; Andreas Raue; J\\xf6rg Stelling; Szymon Stoma

    2014-01-01

    International audience Systems biology aims at creating mathematical models, i.e., computational reconstructions of biological systems and processes that will result in a new level of understanding-the elucidation of the basic and presumably conserved "design" and "engineering" principles of biomolecular systems. Thus, systems biology will move biology from a phenomenological to a predictive science. Mathematical modeling of biological networks and processes has already greatly improved ou...

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

    OpenAIRE

    Bor-Sen Chen; Chia-Chou Wu

    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...

  20. Recent Developments in the Application of Biologically Inspired Computation to Chemical Sensing

    Science.gov (United States)

    Marco, S.; Gutierrez-Gálvez, A.

    2009-05-01

    Biological olfaction outperforms chemical instrumentation in specificity, response time, detection limit, coding capacity, time stability, robustness, size, power consumption, and portability. This biological function provides outstanding performance due, to a large extent, to the unique architecture of the olfactory pathway, which combines a high degree of redundancy, an efficient combinatorial coding along with unmatched chemical information processing mechanisms. The last decade has witnessed important advances in the understanding of the computational primitives underlying the functioning of the olfactory system. In this work, the state of the art concerning biologically inspired computation for chemical sensing will be reviewed. Instead of reviewing the whole body of computational neuroscience of olfaction, we restrict this review to the application of models to the processing of real chemical sensor data.

  1. Novel integrated mechanical biological chemical treatment (MBCT) systems for the production of levulinic acid from fraction of municipal solid waste: A comprehensive techno-economic analysis.

    Science.gov (United States)

    Sadhukhan, Jhuma; Ng, Kok Siew; Martinez-Hernandez, Elias

    2016-09-01

    This paper, for the first time, reports integrated conceptual MBCT/biorefinery systems for unlocking the value of organics in municipal solid waste (MSW) through the production of levulinic acid (LA by 5wt%) that increases the economic margin by 110-150%. After mechanical separation recovering recyclables, metals (iron, aluminium, copper) and refuse derived fuel (RDF), lignocelluloses from remaining MSW are extracted by supercritical-water for chemical valorisation, comprising hydrolysis in 2wt% dilute H2SO4 catalyst producing LA, furfural, formic acid (FA), via C5/C6 sugar extraction, in plug flow (210-230°C, 25bar, 12s) and continuous stirred tank (195-215°C, 14bar, 20min) reactors; char separation and LA extraction/purification by methyl isobutyl ketone solvent; acid/solvent and by-product recovery. The by-product and pulping effluents are anaerobically digested into biogas and fertiliser. Produced biogas (6.4MWh/t), RDF (5.4MWh/t), char (4.5MWh/t) are combusted, heat recovered into steam generation in boiler (efficiency: 80%); on-site heat/steam demand is met; balance of steam is expanded into electricity in steam turbines (efficiency: 35%).

  2. Novel integrated mechanical biological chemical treatment (MBCT) systems for the production of levulinic acid from fraction of municipal solid waste: A comprehensive techno-economic analysis.

    Science.gov (United States)

    Sadhukhan, Jhuma; Ng, Kok Siew; Martinez-Hernandez, Elias

    2016-09-01

    This paper, for the first time, reports integrated conceptual MBCT/biorefinery systems for unlocking the value of organics in municipal solid waste (MSW) through the production of levulinic acid (LA by 5wt%) that increases the economic margin by 110-150%. After mechanical separation recovering recyclables, metals (iron, aluminium, copper) and refuse derived fuel (RDF), lignocelluloses from remaining MSW are extracted by supercritical-water for chemical valorisation, comprising hydrolysis in 2wt% dilute H2SO4 catalyst producing LA, furfural, formic acid (FA), via C5/C6 sugar extraction, in plug flow (210-230°C, 25bar, 12s) and continuous stirred tank (195-215°C, 14bar, 20min) reactors; char separation and LA extraction/purification by methyl isobutyl ketone solvent; acid/solvent and by-product recovery. The by-product and pulping effluents are anaerobically digested into biogas and fertiliser. Produced biogas (6.4MWh/t), RDF (5.4MWh/t), char (4.5MWh/t) are combusted, heat recovered into steam generation in boiler (efficiency: 80%); on-site heat/steam demand is met; balance of steam is expanded into electricity in steam turbines (efficiency: 35%). PMID:27085988

  3. Organic Chemistry and Biology: Chemical Biology Through the Eyes of Collaboration

    Science.gov (United States)

    Hruby, Victor J.

    2011-01-01

    From a scientific perspective, efforts to understand biology including what constitutes health and disease has become a chemical problem. However, chemists and biologists “see” the problems of understanding biology from different perspectives, and this has retarded progress in solving the problems especially as they relate to health and disease. This suggests that close collaboration between chemists and biologists is not only necessary but essential for progress in both the biology and chemistry that will provide solutions to the global questions of biology. This perspective has directed my scientific efforts for the past 45 years, and in this overview I provide my perspective of how the applications of synthetic chemistry, structural design, and numerous other chemical principles have intersected in my collaborations with biologists to provide new tools, new science, and new insights that were only made possible and fruitful by these collaborations. PMID:20000552

  4. Biological effects of low level exposures to chemicals and radiation

    International Nuclear Information System (INIS)

    In May 1990 a group of scientists representing several federal agencies, the International Society of Regulatory Toxicology and Pharmacology, the private sector, and academia met to develop a strategy to encourage the study of the biological effects of low level exposures (BELLE) to chemical agents and radioactivity. A workshop was held in 1991 with seven invited speakers focusing on the toxicological implications of biological adaptations. The selection of topics and speakers was designed to consider critically the concept of hormesis, not only in a broad, conceptual manner, but also at the molecular and biochemical levels. These presentations offered a complementary perspective on the diverse range of molecular mechanisms that can become activated at low levels of toxicant exposure. In addition to chemical toxicology research, an overview of current research on 'Effects of low-dose radiation on the immune response' was presented as well as 'Cellular adaptation as an important response during chemical carcinogenesis'. The final presentation was devoted to biostatistical considerations when designing studies that address issues associated with the biological responses to low doses of chemicals and radiation, as well as issues in interpretation of the findings from such studies

  5. Preparedness for terrorism: managing nuclear, biological and chemical threats.

    Science.gov (United States)

    Koenig, Kristi L

    2009-12-01

    The management of nuclear, biological and chemical (NBC) terrorism events is critical to reducing morbidity and mortality in the next decade; however, initial patient care considerations and protective actions for staff are unfamiliar to most front-line clinicians. High explosive events (bomb and blast) remain the most common type of terrorism and are easy to detect. Conversely, some types of terrorist attacks are more likely to be unsuspected or covert. This paper explains the current threat of terrorism and describes clues for detection that an event has occurred. Specific criteria that should lead to a high suspicion for terrorism are illustrated. The manuscript outlines initial actions and clinical priorities for management and treatment of patients exposed to nuclear/radiological, biological, chemical and combined agents (for example an explosion involving a chemical agent). Examples of terrorist events include: a nuclear explosion, an aerosolised release of anthrax (biological), dissemination of sarin in a subway (chemical), and the detonation of a radiologic dispersion device or "dirty bomb" (combined explosive and radiological). Basic principles of decontamination include potential risks to healthcare providers from secondary exposure and contamination. Unique issues may hinder clinical actions. These include coordination with law enforcement for a crime scene, public health entities for surveillance and monitoring, hazardous materials teams for decontamination, and the media for risk communications. Finally, the importance of personal preparedness is discussed.

  6. 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...

  7. A Chemical/biological Information System Based on SEURAT%构建基于SEURAT的化学/生物信息系统

    Institute of Scientific and Technical Information of China (English)

    李丰; Andreas Witte; Matt Wessel; 王正

    2012-01-01

    In modern drug design scientists need to handle massive data every day and it is a key to success to manage all these data systematically. Most technologies needed to handle chemicaL/biologi- cal information are built up in recent decades but there are no low-priced solutions to fulfill these needs in contemporary pharmaceutical companies. We created a system based on SEURAT according to our demands. It supplied an easy-to-use platform to our scientists to fulfill their routine.%在现代药物研发中,科学家们每天都会面对海量的数据。因此,能系统化的组织并迅速处理这些数据成为研发新药的关键。对于药物研发所需的生物化学数据的存储、检索等技术已经在过去几十年中逐步发展起来,但对中小型的药物研发企业来说,要将这些技术组合起来,建立真正系统化的解决方隶,仍旧耗资巨大。依据日常所需,基于Schrodinger公司的SEURAT软件,建立了一个公司内部的化学/生物信息系统,管理了公司内部药物研发所产生的海量数据,满足了广大科研人员的日常需求。

  8. [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.

  9. 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.

  10. Chemical and structural features influencing the biological activity of curcumin.

    Science.gov (United States)

    Priyadarsini, K Indira

    2013-01-01

    Curcumin, a polyphenolic natural product, exhibits therapeutic activity against a number of diseases, attributed mainly to its chemical structure and unique physical, chemical, and biological properties. It is a diferuloyl methane molecule [1,7-bis (4-hydroxy-3- methoxyphenyl)-1,6-heptadiene-3,5-dione)] containing two ferulic acid residues joined by a methylene bridge. It has three important functionalities: an aromatic o-methoxy phenolic group, α, β-unsaturated β-diketo moiety and a seven carbon linker. Extensive research in the last two decades has provided evidence for the role of these different functional groups in its crucial biological activities. A few highlights of chemical structural features associated with the biological activity of curcumin are: The o-methoxyphenol group and methylenic hydrogen are responsible for the antioxidant activity of curcumin, and curcumin donates an electron/ hydrogen atom to reactive oxygen species. Curcumin interacts with a number of biomolecules through non-covalent and covalent binding. The hydrogen bonding and hydrophobicity of curcumin, arising from the aromatic and tautomeric structures along with the flexibility of the linker group are responsible for the non-covalent interactions. The α, β-unsaturated β-diketone moiety covalently interacts with protein thiols, through Michael reaction. The β-diketo group forms chelates with transition metals, there by reducing the metal induced toxicity and some of the metal complexes exhibit improved antioxidant activity as enzyme mimics. New analogues with improved activity are being developed with modifications on specific functional groups of curcumin. The physico-chemical and structural features associated with some of the biological activities of curcumin and important analogues are summarized in this article. PMID:23116315

  11. Chemical and biological rhizosphere interactions in low zinc soils

    OpenAIRE

    Duffner, A.

    2014-01-01

    Abstract of the PhD thesis entitled “Chemical and biological rhizosphere interactions in low zinc soils” by Andreas Duffner Soil provides ecosystem services critical for life. The availability of micronutrients, such as zinc (Zn), in soils is an essential factor for normal healthy growth and reproduction of plants. Zinc deficiency is, however, a global problem in crop production due to low Zn bioavailability in soils to plants. The bioavailable Zn fraction in soils is controlled ...

  12. Biologically inspired large scale chemical sensor arrays and embedded data processing

    Science.gov (United States)

    Marco, S.; Gutiérrez-Gálvez, A.; Lansner, A.; Martinez, D.; Rospars, J. P.; Beccherelli, R.; Perera, A.; Pearce, T.; Vershure, P.; Persaud, K.

    2013-05-01

    Biological olfaction outperforms chemical instrumentation in specificity, response time, detection limit, coding capacity, time stability, robustness, size, power consumption, and portability. This biological function provides outstanding performance due, to a large extent, to the unique architecture of the olfactory pathway, which combines a high degree of redundancy, an efficient combinatorial coding along with unmatched chemical information processing mechanisms. The last decade has witnessed important advances in the understanding of the computational primitives underlying the functioning of the olfactory system. EU Funded Project NEUROCHEM (Bio-ICT-FET- 216916) has developed novel computing paradigms and biologically motivated artefacts for chemical sensing taking inspiration from the biological olfactory pathway. To demonstrate this approach, a biomimetic demonstrator has been built featuring a large scale sensor array (65K elements) in conducting polymer technology mimicking the olfactory receptor neuron layer, and abstracted biomimetic algorithms have been implemented in an embedded system that interfaces the chemical sensors. The embedded system integrates computational models of the main anatomic building blocks in the olfactory pathway: the olfactory bulb, and olfactory cortex in vertebrates (alternatively, antennal lobe and mushroom bodies in the insect). For implementation in the embedded processor an abstraction phase has been carried out in which their processing capabilities are captured by algorithmic solutions. Finally, the algorithmic models are tested with an odour robot with navigation capabilities in mixed chemical plumes

  13. Biological, chemical, electrochemical, and photochemical fractionation of Fe isotopes

    Science.gov (United States)

    John, S.; King, A.; Hutchins, D.; Adkins, J. F.; Fu, F.; Wasson, A.; Hodierne, C.

    2012-12-01

    Iron is an important nutrient for life in the ocean, where low Fe concentrations often limit the growth of marine phytoplankton. Fe stable isotope ratios (δ56Fe) are a potentially valuable new tool for studying the marine biological cycling of Fe. In order to effectively use Fe isotopes as a biological tracer, however, it is important to parameterize the isotope effect for biological uptake. We have therefore measured the biological fractionation of Fe isotopes by the marine diatoms Thalassiosira pseudonana, T. oceanica, and Phaeodactylum tricornutum in culture. During biological Fe acquisition, Fe(III) is often first reduced from Fe(III) to Fe(II), either in seawater or at the cell surface. Therefore, we have also measured the isotope effect for Fe(III) reduction by chemical, electrochemical, and photochemical processes. Diatoms were cultured in EDTA or NTA buffered media under varying Fe concentrations from Fe-sufficiency to Fe-limitation. Biological fractionation of Fe isotopes was determined by comparing δ56Fe of phytoplankton to the media. The use of a cell wash allows us to distinguish between isotopic fractionation during extracellular adsorption and intracellular uptake. The biological fractionation of Fe isotopes is highly dependent on culture conditions with Δδ56Fe ranging from +0.6 ‰ to -0.5 ‰ depending on ligand composition, species, and Fe-limitation status. Isotope effects for chemical, electrochemical, and photochemical reduction of Fe(III) to Fe(II) span an even larger range. For example, chemical reduction of Fe(III)-EDTA with hydroxylamine hydrochloride has an isotope effect of Δδ56Fe = -2.8 ‰. By contrast, photochemical reduction of Fe(III)-EDTA has an isotope effect of Δδ56Fe = +0.9 ‰. Isotope effects for electrochemical reduction of Fe(III) using a rotating disc electrode allow for greater control of experimental conditions, such as differentiating between the effects of electric potential (voltage) and mass transport (diffusion

  14. Recent advances in the chemical biology of nitroxyl (HNO) detection and generation.

    Science.gov (United States)

    Miao, Zhengrui; King, S Bruce

    2016-07-01

    Nitroxyl or azanone (HNO) represents the redox-related (one electron reduced and protonated) relative of the well-known biological signaling molecule nitric oxide (NO). Despite the close structural similarity to NO, defined biological roles and endogenous formation of HNO remain unclear due to the high reactivity of HNO with itself, soft nucleophiles and transition metals. While significant work has been accomplished in terms of the physiology, biology and chemistry of HNO, important and clarifying work regarding HNO detection and formation has occurred within the last 10 years. This review summarizes advances in the areas of HNO detection and donation and their application to normal and pathological biology. Such chemical biological tools allow a deeper understanding of biological HNO formation and the role that HNO plays in a variety of physiological systems. PMID:27108951

  15. 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.

  16. 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.

  17. 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.

  18. Suitability of Gray Water for Hydroponic Crop Production Following Biological and Physical Chemical and Biological Subsystems

    Science.gov (United States)

    Bubenheim, David L.; Harper, Lynn D.; Wignarajah, Kanapathipillai; Greene, Catherine

    1994-01-01

    The water present in waste streams from a human habitat must be recycled in Controlled Ecological Life Support Systems (CELSS) to limit resupply needs and attain self-sufficiency. Plants play an important role in providing food, regenerating air, and producing purified water via transpiration. However, we have shown that the surfactants present in hygiene waste water have acute toxic effects on plant growth (Bubenheim et al. 1994; Greene et al., 1994). These phytotoxic affects can be mitigated by allowing the microbial population on the root surface to degrade the surfactant, however, a significant suppression (several days) in crop performance is experienced prior to reaching sub-toxic surfactant levels and plant recovery. An effective alternative is to stabilize the microbial population responsible for degradation of the surfactant on an aerobic bioreactor and process the waste water prior to utilization in the hydroponic solution (Wisniewski and Bubenheim, 1993). A sensitive bioassay indicates that the surfactant phytotoxicity is suppressed by more than 90% within 5 hours of introduction of the gray water to the bioreactor; processing for more than 12 hours degrades more than 99% of the phytotoxin. Vapor Compression Distillation (VCD) is a physical / chemical method for water purification which employees sequential distillation steps to separate water from solids and to volatilize contaminants. The solids from the waste water are concentrated in a brine and the pure product water (70 - 90% of the total waste water volume depending on operating conditions) retains non of the phytotoxic effects. Results of the bioassay were used to guide evaluations of the suitability of recovered gray water following biological and VCD processing for hydroponic lettuce production in controlled environments. Lettuce crops were grown for 28 days with 100% of the input water supplied with recovered water from the biological processor or VCD. When compared with the growth of plants

  19. Chemical Specification of Autonomic Systems

    OpenAIRE

    Banâtre, Jean-Pierre; Fradet, Pascal; Radenac, Yann

    2004-01-01

    Autonomic computing provides a vision of information systems allowing self-management of many predefined properties. Such systems take care of their own behavior and of their interactions with other components without any external intervention. One of the major challenges concerns the expression of properties and constraints of autonomic systems. We believe that the {\\em chemical programming paradigm} (represented here by the Gamma formalism) is well-suited to the specification of autonomic s...

  20. Emergency response to nuclear, biological and chemical incidents:challenges and countermeasures

    Institute of Scientific and Technical Information of China (English)

    Hai-Long Li; Wen-Jun Tang; Ya-Kun Ma; Ji-Min Jia; Rong-Li Dang; Er-Chen Qiu

    2015-01-01

    Given the multiple terrorist attacks that have occurred in recent years in China, medical rescue teams and specialized incident assessment teams have been established by the government; however, medical rescue after nuclear, biological, and chemical incidents remains challenging and is often inefficient. In the present article, problems were analyzed regarding the assessment of responder countermeasures, training of professionals and the management of emergency medical incidents related to nuclear, biological and chemical attacks. Countermeasures, the establishment of response coordination, public education, practical training and exercise, and a professional consultant team or system should be the focus of emergency medical response facilities. Moreover, the government was offered professionals who are involved in managing nuclear, biological and chemical incidents.

  1. Yeast systems biology to unravel the network of life

    DEFF Research Database (Denmark)

    Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

    2006-01-01

    of advanced cell factories for production of fuels, chemicals, food ingredients and pharmaceuticals. The yeast Saccharomyces cerevisiae represents an excellent model system; the density of biological information available on this organism allows it to serve as a eukaryotic model for studying human diseases....... 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...... appropriate guidelines, establish an appropriate infrastructure for the network and organize courses, meetings and conferences that will consolidate the network and promote systems biology. This paper discusses the impacts of systems biology and how YSBN may play a role in the future development of the field...

  2. Analyzing the Biology on the System Level

    Institute of Scientific and Technical Information of China (English)

    Wei Tong

    2004-01-01

    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, and summarizes the analysis methods, experimental technologies, research developments, and so on in the four key fields of systems biology-systemic structures, dynamics, control methods, and design principles.

  3. 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.

  4. Microbiology and atmospheric processes: chemical interactions of primary biological aerosols

    Directory of Open Access Journals (Sweden)

    L. Deguillaume

    2008-07-01

    Full Text Available This paper discusses the influence of primary biological aerosols (PBA on atmospheric chemistry and vice versa through microbiological and chemical properties and processes. Several studies have shown that PBA represent a significant fraction of air particulate matter and hence affect the microstructure and water uptake of aerosol particles. Moreover, airborne micro-organisms, namely fungal spores and bacteria, can transform chemical constituents of the atmosphere by metabolic activity. Recent studies have emphasized the viability of bacteria and metabolic degradation of organic substances in cloud water. On the other hand, the viability and metabolic activity of airborne micro-organisms depend strongly on physical and chemical atmospheric parameters such as temperature, pressure, radiation, pH value and nutrient concentrations. In spite of recent advances, however, our knowledge of the microbiological and chemical interactions of PBA in the atmosphere is rather limited. Further targeted investigations combining laboratory experiments, field measurements, and modelling studies will be required to characterize the chemical feedbacks, microbiological activities at the air/snow/water interface supplied to the atmosphere.

  5. The chemical and biological weapon terrorism by the Aum Shnirikyo

    International Nuclear Information System (INIS)

    The Aum Shinrikyo, an obscure cult religious group, attacked the Tokyo subways employing sarin gas in March 1995, which was viewed as a mark of a new era in terrorism. The Aum Shinrikyo remains the one empirical example of a religiously motivated cult with an affluent amount of financial and human resources and motivations to use unconventional weapons. The Aum Shinrikyo's leaders included the scientific elite of a young generation as well as former Yakuza members who had close ties with organized crime networks. Aum succeeded in establishing an extensive network to procure weapons, material, and drug, primarily in Russia but also other countries including the United States and even North Korea. Despite the fact that the law enforcement authority had already obtained various pieces of information that reasonably indicated that Aum was producing sarin by late 1994, the law enforcement authority became too cautious to advance its investigation to arrest Aum members until it was too late. Japan's experience with the Aum Shinrikyo's threats provides valuable insights for democratic governments seeking to thwart the deadly plans of religiously motivated non-state actors. It reveals the tremendous difficulties for a democratic society to confront the terrorists who were willing to pursue their deadly 'divine' objectives, especially when the society had no experience to encounter such a threat. This presentation will explain the chemical and biological weapon programs of the Aum Shinrikyo, especially focusing on the following elements: Intention and capability of the Aum Shinrikyo; Weapon systems and mode of attacks, including their target selections; The lessons learned from this case for the prevention and crisis/consequence management n the event of CBW terrorism. The views expressed here are those of the author and do not represent those of the Research Institute for Science and Technology for Society or its research sponsors.(author)

  6. Modeling biological systems with Answer Set Programming

    OpenAIRE

    Thiele, Sven

    2012-01-01

    Biology has made great progress in identifying and measuring the building blocks of life. The availability of high-throughput methods in molecular biology has dramatically accelerated the growth of biological knowledge for various organisms. The advancements in genomic, proteomic and metabolomic technologies allow for constructing complex models of biological systems. An increasing number of biological repositories is available on the web, incorporating thousands of biochemical reactions and ...

  7. Integrating systems biology models and biomedical ontologies

    Directory of Open Access Journals (Sweden)

    de Bono Bernard

    2011-08-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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.

  8. Principles of Systems Biology, No. 8.

    Science.gov (United States)

    2016-08-01

    Advances in biological engineering headline this month's Cell Systems call (Cell Systems 1, 307), alongside intriguing applications of modeling from the Elf, Goentoro, and Wolf groups. Check out our recent blogpost: http://crosstalk.cell.com/blog/a-call-for-papers-on-biological-engineering-and-synthetic-biology. PMID:27559920

  9. Chemical Abstracts Service Chemical Registry System: History, Scope, and Impacts.

    Science.gov (United States)

    Weisgerber, David W.

    1997-01-01

    Describes the history, scope, and applications of the Chemical Abstracts Service Chemical Registry System, a computerized database that uniquely identifies chemical substances on the basis of their molecular structures. Explains searching the system is and discusses its use as an international resource. (66 references) (Author/LRW)

  10. A Review on Pyrazole chemical entity and Biological Activity

    Directory of Open Access Journals (Sweden)

    Md. Jahangir Alam

    2015-12-01

    Full Text Available Aromatic organic heterocycle containing pyrimidine scaffolds possesses two nitrogen atoms of Five-membered ring. These Pyrazole skeletons comprise various ranges of pharmacological activities such as analgesic, antipyretic, anticancer, antiviral, anti-inflammatory, antioxidants, antimicrobial, anti-diabetic, anticonvulsant, ant arrhythmic activities. Pyrazole is a multipurpose lead compound developed by chemical architecture for effective molecules which are biologically active. Several synthetic routes are accorded to the development of pyrazole containing reactions to afford a novel molecule which is an enormous opportunity in the field of medicinal chemistry. The existing collection of exertions on research to provide information about the synthesis and innumerable biological activities of pyrazole and their outcomes during the past year.

  11. Chemical and Biological Warfare: Should Rapid Detection Techniques Be Researched To Dissuade Usage? A Review

    Directory of Open Access Journals (Sweden)

    Mark R. Hurst

    2005-01-01

    Full Text Available Chemistry, microbiology and genetic engineering have opened new doorways for the human race to propel itself to a better future. However, there is a darker side to Bioengineering. One element of this is the manufacture and proliferation of biological and chemical weapons. It is clearly in the interest of humankind to prevent the future use of such weapons of mass destruction. Though many agents have been proposed as potential biological and chemical weapons, the feasibility of these weapons is a matter of conjecture. The unpredictable and indiscriminate devastation caused by natural epidemics and hazardous chemicals during wartime without medical treatment should warn humans of the dangers of employing them as weapons. This study argues rapid detection techniques may dissuade future use. Many agents are far less toxic to treatment. A quick response time to most attacks will decrease the chances of serious health issues. The agent will be less effective and discourage the attacker from using the weapon. Fortunately, the Chemical and Biological Weapons Convention (CWCIBWC allows defensive work in the area of biological and chemical weapons. Consequently, the review will discuss history, delivery/dispersal systems and specific agents of the warfare. The study presents current developments in biosensors for toxic materials of defense interest. It concludes with future directions for biosensor development.

  12. Chemical and biological factors affecting bioavailability of contaminants in seawater

    International Nuclear Information System (INIS)

    This paper discusses the influence that salinity has on the bioavailability of the two largest classes of contaminants, trace metals and organic compounds will be discussed. Although data on contaminant toxicity will be used to draw inferences about chemical availability, this discussion will focus on the properties that contaminants are likely to exhibit in waters of varying salinities. In addition, information on physiological changes that are affected by salinity will be used to illustrate how biological effects can alter the apparent availability of contaminants

  13. Terrorist threat, chemical, biological, radiological, nuclear medical approach

    International Nuclear Information System (INIS)

    The different aspects linked to the use of nuclear, radiological, biological and or chemical weapons are gathered in this work. They concern history, fundamental aspect, diagnosis, therapy and prevention. The part devoted to the nuclear aspect concern the accidents in relation with ionizing radiations, the radiation syndrome, the contribution and limits of dosimetry, the treatment of medullary aplasia, the evaluation and treatment of an internal contamination, new perspectives on the use of cytokine for the treatment of accidental irradiated persons, alternative to the blood transfusion. (N.C.)

  14. Biological and chemical technologies research. FY 1995 annual summary report

    Energy Technology Data Exchange (ETDEWEB)

    None

    1996-03-01

    The annual summary report presents the fiscal year (FY) 1995 research activities and accomplishments for the United States Department of Energy (DOE) Biological and Chemical Technologies Research (BCTR) Program. This BCTR program resides within the Office of Industrial Technologies (OIT) of the Office of Energy Efficiency and Renewable Energy (EE). The annual summary report for 1995 (ASR 95) contains the following: program description (including BCTR program mission statement, historical background, relevance, goals and objectives); program structure and organization, selected technical and programmatic highlights for 1995; detailed descriptions of individual projects; a listing of program output, including a bibliography of published work; patents; and awards arising from work supported by the BCTR.

  15. Smart phones: platform enabling modular, chemical, biological, and explosives sensing

    Science.gov (United States)

    Finch, Amethist S.; Coppock, Matthew; Bickford, Justin R.; Conn, Marvin A.; Proctor, Thomas J.; Stratis-Cullum, Dimitra N.

    2013-05-01

    Reliable, robust, and portable technologies are needed for the rapid identification and detection of chemical, biological, and explosive (CBE) materials. A key to addressing the persistent threat to U.S. troops in the current war on terror is the rapid detection and identification of the precursor materials used in development of improvised explosive devices, homemade explosives, and bio-warfare agents. However, a universal methodology for detection and prevention of CBE materials in the use of these devices has proven difficult. Herein, we discuss our efforts towards the development of a modular, robust, inexpensive, pervasive, archival, and compact platform (android based smart phone) enabling the rapid detection of these materials.

  16. Simaroubaceae family: botany, chemical composition and biological activities

    Directory of Open Access Journals (Sweden)

    Iasmine A.B.S. Alves

    2014-08-01

    Full Text Available The Simaroubaceae family includes 32 genera and more than 170 species of trees and brushes of pantropical distribution. The main distribution hot spots are located at tropical areas of America, extending to Africa, Madagascar and regions of Australia bathed by the Pacific. This family is characterized by the presence of quassinoids, secondary metabolites responsible of a wide spectrum of biological activities such as antitumor, antimalarial, antiviral, insecticide, feeding deterrent, amebicide, antiparasitic and herbicidal. Although the chemical and pharmacological potential of Simaroubaceae family as well as its participation in official compendia; such as British, German, French and Brazilian pharmacopoeias, and patent registration, many of its species have not been studied yet. In order to direct further investigation to approach detailed botanical, chemical and pharmacological aspects of the Simaroubaceae, the present work reviews the information regarding the main genera of the family up to 2013.

  17. Plant chemical biology: Are we meeting the promise?

    Directory of Open Access Journals (Sweden)

    Glenn R. Hicks

    2014-09-01

    Full Text Available As an early adopter of plant chemical genetics to the study of endomembrane trafficking, we have observed the growth of small molecule approaches. Within the field, we often describe the strengths of the approach in a broad, generic manner, such as the ability to address redundancy and lethality. But, we are now in a much better position to evaluate the demonstrated value of the approach based on examples. In this perspective, we offer an assessment of chemical genetics in plants and where its applications may be of particular utility from the perspective of the cell biologist. Beyond this, we suggest areas to be addressed to provide broader access and enhance the effectiveness of small molecule approaches in plant biology.

  18. Chemical and biological treatment technologies for leather tannery chemicals and wastewaters: a review.

    Science.gov (United States)

    Lofrano, Giusy; Meriç, Sureyya; Zengin, Gülsüm Emel; Orhon, Derin

    2013-09-01

    Although the leather tanning industry is known to be one of the leading economic sectors in many countries, there has been an increasing environmental concern regarding the release of various recalcitrant pollutants in tannery wastewater. It has been shown that biological processes are presently known as the most environmental friendly but inefficient for removal of recalcitrant organics and micro-pollutants in tannery wastewater. Hence emerging technologies such as advanced oxidation processes and membrane processes have been attempted as integrative to biological treatment for this sense. This paper, as the-state-of-the-art, attempts to revise the over world trends of treatment technologies and advances for pollution prevention from tannery chemicals and wastewater. It can be elucidated that according to less extent advances in wastewater minimization as well as in leather production technology and chemicals substitution, biological and chemical treatment processes have been progressively studied. However, there has not been a full scale application yet of those emerging technologies using advanced oxidation although some of them proved good achievements to remove xenobiotics present in tannery wastewater. It can be noted that advanced oxidation technologies integrated with biological processes will remain in the agenda of the decision makers and water sector to apply the best prevention solution for the future tanneries.

  19. Chemical and biological treatment technologies for leather tannery chemicals and wastewaters: a review.

    Science.gov (United States)

    Lofrano, Giusy; Meriç, Sureyya; Zengin, Gülsüm Emel; Orhon, Derin

    2013-09-01

    Although the leather tanning industry is known to be one of the leading economic sectors in many countries, there has been an increasing environmental concern regarding the release of various recalcitrant pollutants in tannery wastewater. It has been shown that biological processes are presently known as the most environmental friendly but inefficient for removal of recalcitrant organics and micro-pollutants in tannery wastewater. Hence emerging technologies such as advanced oxidation processes and membrane processes have been attempted as integrative to biological treatment for this sense. This paper, as the-state-of-the-art, attempts to revise the over world trends of treatment technologies and advances for pollution prevention from tannery chemicals and wastewater. It can be elucidated that according to less extent advances in wastewater minimization as well as in leather production technology and chemicals substitution, biological and chemical treatment processes have been progressively studied. However, there has not been a full scale application yet of those emerging technologies using advanced oxidation although some of them proved good achievements to remove xenobiotics present in tannery wastewater. It can be noted that advanced oxidation technologies integrated with biological processes will remain in the agenda of the decision makers and water sector to apply the best prevention solution for the future tanneries. PMID:23735721

  20. The smallest chemical reaction system with bistability

    Directory of Open Access Journals (Sweden)

    Wilhelm Thomas

    2009-09-01

    Full Text Available Abstract Background Bistability underlies basic biological phenomena, such as cell division, differentiation, cancer onset, and apoptosis. So far biologists identified two necessary conditions for bistability: positive feedback and ultrasensitivity. Results Biological systems are based upon elementary mono- and bimolecular chemical reactions. In order to definitely clarify all necessary conditions for bistability we here present the corresponding minimal system. According to our definition, it contains the minimal number of (i reactants, (ii reactions, and (iii terms in the corresponding ordinary differential equations (decreasing importance from i-iii. The minimal bistable system contains two reactants and four irreversible reactions (three bimolecular, one monomolecular. We discuss the roles of the reactions with respect to the necessary conditions for bistability: two reactions comprise the positive feedback loop, a third reaction filters out small stimuli thus enabling a stable 'off' state, and the fourth reaction prevents explosions. We argue that prevention of explosion is a third general necessary condition for bistability, which is so far lacking discussion in the literature. Moreover, in addition to proving that in two-component systems three steady states are necessary for bistability (five for tristability, etc., we also present a simple general method to design such systems: one just needs one production and three different degradation mechanisms (one production, five degradations for tristability, etc.. This helps modelling multistable systems and it is important for corresponding synthetic biology projects. Conclusion The presented minimal bistable system finally clarifies the often discussed question for the necessary conditions for bistability. The three necessary conditions are: positive feedback, a mechanism to filter out small stimuli and a mechanism to prevent explosions. This is important for modelling bistability with

  1. Total, chemical, and biological oxygen consumption of the sediments in the Ziya River watershed, China.

    Science.gov (United States)

    Rong, Nan; Shan, Baoqing

    2016-07-01

    Sediment oxygen demand (SOD) is a critical dissolved oxygen (DO) sink in many rivers. Understanding the relative contributions of the biological and chemical components of SOD would improve our knowledge of the potential environmental harm SOD could cause and allow appropriate management systems to be developed. A various inhibitors addition technique was conducted to measure the total, chemical, and biological SOD of sediment samples from 13 sites in the Ziya River watershed, a severely polluted and anoxic river system in the north of China. The results showed that the major component of SOD was chemical SOD due to iron predominate. The ferrous SOD accounted for 21.6-78.9 % of the total SOD and 33.26-96.79 % of the chemical SOD. Biological SOD represented 41.13 % of the overall SOD averagely. Sulfide SOD accounted for 1.78-45.71 % of the total SOD and it was the secondary predominate of the chemical SOD. Manganous SOD accounted for 1.2-16.6 % of the total SOD and it was insignificant at many sites. Only four kinds of benthos were collected in the Ziya River watershed, resulting from the low DO concentration in the sediment surface due to SOD. This study would be helpful for understanding and preventing the potential sediment oxygen depletion during river restoration.

  2. Spatial Aspects in Biological System Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Costa, Michelle N.; Shankaran, Harish

    2011-01-30

    Mathematical models of the dynamical properties of biological systems aim to improve our understanding of the studied system with the ultimate goal of being able to predict system responses in the absence of experimentation. Despite the enormous advances that have been made in biological modeling and simulation, the inherently multiscale character of biological systems and the stochasticity of biological processes continue to present significant computational and conceptual challenges. Biological systems often consist of well-organized structural hierarchies, which inevitably lead to multiscale problems. This chapter introduces and discusses the advantages and shortcomings of several simulation methods that are being used by the scientific community to investigate the spatio-temporal properties of model biological systems. We first describe the foundations of the methods and then describe their relevance and possible application areas with illustrative examples from our own research. Possible ways to address the encountered computational difficulties are also discussed.

  3. The diverse biological properties of the chemically inert noble gases.

    Science.gov (United States)

    Winkler, David A; Thornton, Aaron; Farjot, Géraldine; Katz, Ira

    2016-04-01

    The noble gases represent an intriguing scientific paradox. They are extremely inert chemically but display a remarkable spectrum of clinically useful biological properties. Despite a relative paucity of knowledge of their mechanisms of action, some of the noble gases have been used successfully in the clinic. Studies with xenon have suggested that the noble gases as a class may exhibit valuable biological properties such as anaesthesia; amelioration of ischemic damage; tissue protection prior to transplantation; analgesic properties; and a potentially wide range of other clinically useful effects. Xenon has been shown to be safe in humans, and has useful pharmacokinetic properties such as rapid onset, fast wash out etc. The main limitations in wider use are that: many of the fundamental biochemical studies are still lacking; the lighter noble gases are likely to manifest their properties only under hyperbaric conditions, impractical in surgery; and administration of xenon using convectional gaseous anaesthesia equipment is inefficient, making its use very expensive. There is nonetheless a significant body of published literature on the biochemical, pharmacological, and clinical properties of noble gases but no comprehensive reviews exist that summarize their properties and the existing knowledge of their models of action at the molecular (atomic) level. This review provides such an up-to-date summary of the extensive, useful biological properties of noble gases as drugs and prospects for wider application of these atoms. PMID:26896563

  4. How chemistry supports cell biology: the chemical toolbox at your service.

    Science.gov (United States)

    Wijdeven, Ruud H; Neefjes, Jacques; Ovaa, Huib

    2014-12-01

    Chemical biology is a young and rapidly developing scientific field. In this field, chemistry is inspired by biology to create various tools to monitor and modulate biochemical and cell biological processes. Chemical contributions such as small-molecule inhibitors and activity-based probes (ABPs) can provide new and unique insights into previously unexplored cellular processes. This review provides an overview of recent breakthroughs in chemical biology that are likely to have a significant impact on cell biology. We also discuss the application of several chemical tools in cell biology research.

  5. The giant cold-water coral mound as a nested microbial/metazoan system: physical, chemical, biological and geological picture (ESF EuroDiversity MiCROSYSTEMS)

    OpenAIRE

    Henriet, J.-P.; The MICROSYSTEMS Team

    2009-01-01

    The MiCROSYSTEMS project under the ESF EUROCORES EuroDiversity scheme is a holistic and multi-scale approach in studying microbial diversity and functionality in a nested microbial/metazoan system, which thrives in deep waters: the giant cold-water coral mound. Studies on prolific cold-water coral sites have been carried out from the canyons of the Bay of Biscay to the fjords of the Norwegian margin, while the Pen Duick carbonate mound province off Morocco developed into a joint natural lab f...

  6. Tritium Exchange in Biological Systems

    International Nuclear Information System (INIS)

    Whenever tritium-labelled water is employed as a test solute or tracer in biological systems, an appreciable exchange between tritium and labile hydrogen atoms occurs that frequently affects the nature and interpretation of experimental results. The studies reported here are concerned with the magnitude of the effect that tritium exchange introduces into measurements of total body water and water metabolism in animals and humans. Direct measurements of exchange were made in rats, guinea pigs, pigeons, and rabbits. Tritium-labelled water was administered intravenously or by mouth, and tritium space and turnover determined from the concentration of tritium in blood. The animals were then desiccated to constant weight in vacuo. The specific activity of water collected periodically during desiccation increased by 50% as a result of isotope effects. Water from combustion of dried rabbit tissues contained about 2% of the tritium originally given to the animal. Adipose tissue alone contained little or no exchange tritium. The dried tissues of the other animals were rehydrated with inactive water and the appearance of tritium in the water observed. The specific activity of the water increased in exponential fashion, i.e., 1-exp. (kt), with about 90% of exchange occurring with a half-time of 1 h, and the remaining 10% with a half-time of 10 h. The total tritium extracted accounted for 1.5 to 3.5% of the dose given to the animal, which agrees with the difference between the tritium space and total body water determined by desiccation. An indirect estimate of exchange in humans was derived from concurrent measurements of tritium and antipyrene spaces. The average difference of about 2% in water volume agrees with the direct estimates of exchanges in animals. It is evident that tritium space should be reduced by about 2% to identify it with total body water. The magnitude and relatively slow rate of exchange may also influence the interpretation of metabolic studies with

  7. The giant cold-water coral mound as a nested microbial/metazoan system: physical, chemical, biological and geological picture (ESF EuroDiversity MiCROSYSTEMS)

    Science.gov (United States)

    Henriet, J. P.; Microsystems Team

    2009-04-01

    The MiCROSYSTEMS project under the ESF EUROCORES EuroDiversity scheme is a holistic and multi-scale approach in studying microbial diversity and functionality in a nested microbial/metazoan system, which thrives in deep waters: the giant cold-water coral mound. Studies on prolific cold-water coral sites have been carried out from the canyons of the Bay of Biscay to the fjords of the Norwegian margin, while the Pen Duick carbonate mound province off Morocco developed into a joint natural lab for studying in particular the impact of biogeochemical and microbial processes on modern sedimentary diagenesis within the reef sediments, in complement to the studies on I0DP Exp. 307 cores (Challenger Mound, off Ireland). Major outcomes of this research can be summarized as follows. • IODP Exp. 307 on Challenger Mound had revealed a significant prokaryotic community both within and beneath the carbonate mound. MiCROSYSTEMS unveils a remarkable degree of compartmentalization in such community from the seawater, the coral skeleton surface and mucus to the reef sediments. The occurrence of such multiple and distinct microbial compartments associated with cold-water coral ecosystems promotes opportunities for microbial diversity in the deep ocean. • New cases of co-habitation of cold-water corals and giant deep-water oysters were discovered in the Bay of Biscay, which add a new facet of macrofaunal diversity to cold-water coral reef systems. • The discovery of giant, ancient coral graveyards on the Moroccan mounds not only fuels the debate about natural versus anthropogenic mass extinction, but these open frameworks simultaneously invite for the study of bio-erosion and early diagenesis, in particular organo-mineralization, and of the possible role and significance of these thick, solid rubble patches in 3D mound-building and consolidation. • The assessment of the carbonate budget of a modern cold-water coral mound (Challenger Mound) reveals that only 33 to 40 wt % of

  8. Efeito do Fogo nas Características Químicas e Biológicas do Solo no Sistema Agroflorestal da Bracatinga Effects of Burning Harvesting Residues on Soil Chemical and Biological Characteristics Under Agroforestry System With Bracatinga

    Directory of Open Access Journals (Sweden)

    Danielle Janaina Westphalen Pomianoski

    2011-03-01

    Full Text Available

    Avaliou-se o efeito do fogo nas características químicas e biológicas do solo no sistema agroflorestal tradicional da bracatinga (Mimosa scabrella Bentham. A queima dos resíduos da exploração é utilizada para regenerar o bracatingal, como forma de controlar as plantas invasoras e facilitar a implantação de lavouras. Os tratamentos consistiram no uso e não uso do fogo e mata nativa como testemunha. O período amostrado foi entre maio de 2002 e agosto de 2003, onde foram analisadas variáveis químicas e biológicas do solo, em diferentes períodos. A queima dos resíduos da colheita da bracatinga aumenta inicialmente a  concentração dos nutrientes, principalmente do fósforo, nas camadas de 1 a 2 cm e influenciam a quantidade de carbono da biomassa microbiana, no primeiro ano. A manutenção da cobertura vegetal de bracatinga em sistema agroflorestal tradicional, sem o uso do fogo, controla a erosão e mantém os nutrientes no solo, melhorando a sustentabilidade desta atividade florestal. 
    The effect of burning residues was evaluated on soil chemical and biological characteristics under bracatinga (Mimosa scabrella Bentham agroforestry system. This system uses to burn residues to assure revegetation of new harvest and to control weeds. Treatments tested were revegetation using fire and without fire and a test plot consisting of native forest. The period of sampling started on May 2002 until August 2003, and soil samplings for chemical and biological analyses were on different dates. Burning harvesting residues of bracatinga increases initially soil nutrient concentration, mainly P in 1 and 2 cm surface soil layers, and influenced the amount of C in the microbe biomass in the first year. Maintaining soil cover with bracatinga harvesting residues, without using fire, may control soil erosion and the nutrients will be slowly released, promoting site sustainability on this

  9. Network systems biology for targeted cancer therapies

    Institute of Scientific and Technical Information of China (English)

    Ting-Ting Zhou

    2012-01-01

    The era of targeted cancer therapies has arrived.However,due to the complexity of biological systems,the current progress is far from enough.From biological network modeling to structural/dynamic network analysis,network systems biology provides unique insight into the potential mechanisms underlying the growth and progression of cancer cells.It has also introduced great changes into the research paradigm of cancer-associated drug discovery and drug resistance.

  10. Biological efficiency of interaction between various radiation and chemicals

    International Nuclear Information System (INIS)

    This research project has been carried out jointly with INP (Poland) to develop technologies to assess the biological efficiency of interaction between radiation and chemicals. Through the cooperative project, KAERI and INP have established wide variety of bioassay techniques applicable to radiation bioscience, human monitoring, molecular epidemiology and environmental science. The joint experiment, in special, made it possible to utilize the merits of both institutes and to upgrade and verify KAERI's current technology level. All results of the cooperative research will be jointly published in high standard scientific journals listed in the Science Citation Index (SCI), which can make the role of fundamental basis for improving relationship between Korea and Poland. Research skills such as Trad-MCN assay, SCGE assay, immunohistochemical assay and molecular assay developed through joint research will be further elaborated and will be continuously used for the collaboration between two institutes

  11. Using ChemBank to probe chemical biology.

    Science.gov (United States)

    Petri Seiler, Kathleen; Kuehn, Heidi; Pat Happ, Mary; Decaprio, Dave; Clemons, Paul A

    2008-06-01

    ChemBank (http://chembank.broad.harvard.edu/) is a public, Web-based informatics environment. ChemBank stores and makes freely available data derived from small molecules and small-molecule screens and has resources for relating and studying these data. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays performed at the Broad Institute screening center. Web-based analysis tools are available within ChemBank to study the relationships between small molecules, cell measurements, and cell states. This unit demonstrates the use of ChemBank data to ask and answer questions relating to chemical biology and screening experiments contained within ChemBank. PMID:18551413

  12. BCTR: Biological and Chemical Technologies Research 1994 annual summary report

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, G.

    1995-02-01

    The annual summary report presents the fiscal year (FY) 1994 research activities and accomplishments for the United States Department of Energy (DOE) Biological and Chemical Technologies Research (BCTR) Program of the Advanced Industrial Concepts Division (AICD). This AICD program resides within the Office of Industrial Technologies (OIT) of the Office of Energy Efficiency and Renewable Energy (EE). Although the OIT was reorganized in 1991 and AICD no longer exists, this document reports on efforts conducted under the former structure. The annual summary report for 1994 (ASR 94) contains the following: program description (including BCTR program mission statement, historical background, relevance, goals and objectives); program structure and organization, selected technical and programmatic highlights for 1994; detailed descriptions of individual projects; a listing of program output, including a bibliography of published work; patents, and awards arising from work supported by BCTR.

  13. Respiratory Protection Against Chemical and Biological Warfare Agents

    Directory of Open Access Journals (Sweden)

    G.K. Prasad

    2008-09-01

    Full Text Available Chemical and biological warfare (CBW agents pose unavoidable threat, both to soldiers and civilians.Exposure to such deadly agents amidst the CBW agents contaminated environment can be avoided bytaking proper protective measures. Respiratory protection is indispensable when the soldiers or civiliansare surrounded by such deadly environment as contamination-free air is needed for respiration purposes.In this context, an attempt has been made to review the literature for the past five decades on developmentof various protective devices for respiratory protection against aerosols, gases, and vapours of CBWagents. This review covers structural, textural, and adsorption properties of materials used in gas filtersand mechanical filters for the removal of CBW agents.Defence Science Journal, 2008, 58(5, pp.686-697, DOI:http://dx.doi.org/10.14429/dsj.58.1692

  14. Chemical Constituents of Descurainia sophia L. and its Biological Activity

    Directory of Open Access Journals (Sweden)

    Nawal H. Mohamed

    2009-01-01

    Full Text Available Seven coumarin compounds were isolated for the first time from the aerial parts of DescurainiaSophia L. identified as scopoletine, scopoline, isoscopoline, xanthtoxol, xanthtoxin, psoralene and bergaptane.Three flavonoids namely kaempferol, quercetine and isorhamnetine and three terpenoid compounds -sitosterol-amyrine and cholesterol were also isolated and identified by physical and chemical methods; melting point, Rfvalues, UV and 1H NMR spectroscopy. Qualitative and quantitative analyses of free and protein amino acidsusing amino acid analyzer were performed. The plant contains 15 amino acids as free and protein amino acidswith different range of concentrations. Fatty acid analysis using GLC, revealed the presence of 10 fatty acids,the highest percentage was palmitic acid (27.45 % and the lowest was lauric acid (0.13%. Biological screeningof alcoholic extract showed that the plant is highly safe and has analgesic, antipyretic and anti-inflammatoryeffects.

  15. Microcantilever technology for law enforcement and anti-terrorism applications: chemical, biological, and explosive material detection

    Science.gov (United States)

    Adams, J. D.; Rogers, B.; Whitten, R.

    2005-05-01

    The remarkable sensitivity, compactness, low cost, low power-consumption, scalability, and versatility of microcantilever sensors make this technology among the most promising solutions for detection of chemical and biological agents, as well as explosives. The University of Nevada, Reno, and Nevada Nanotech Systems, Inc (NNTS) are currently developing a microcantilever-based detection system that will measure trace concentrations of explosives, toxic chemicals, and biological agents in air. A baseline sensor unit design that includes the sensor array, electronics, power supply and air handling has been created and preliminary demonstrations of the microcantilever platform have been conducted. The envisioned device would measure about two cubic inches, run on a small watch battery and cost a few hundred dollars. The device could be operated by untrained law enforcement personnel. Microcantilever-based devices could be used to "sniff out" illegal and/or hazardous chemical and biological agents in high traffic public areas, or be packaged as a compact, low-power system used to monitor cargo in shipping containers. Among the best detectors for such applications at present is the dog, an animal which is expensive, requires significant training and can only be made to work for limited time periods. The public is already accustomed to explosives and metal detection systems in airports and other public venues, making the integration of the proposed device into such security protocols straightforward.

  16. Weber's law for biological responses in autocatalytic networks of chemical reactions.

    Science.gov (United States)

    Inoue, Masayo; Kaneko, Kunihiko

    2011-07-22

    Biological responses often obey Weber's law, according to which the magnitude of the response depends only on the fold change in the external input. In this study, we demonstrate that a system involving a simple autocatalytic reaction shows such a response when a chemical is slowly synthesized by the reaction from a faster influx process. We also show that an autocatalytic reaction process occurring in series or in parallel can obey Weber's law with an oscillatory adaptive response. Considering the simplicity and ubiquity of the autocatalytic process, our proposed mechanism is thought to be commonly observed in biological reactions. PMID:21867048

  17. Nucleic Acid Nanostructures for Chemical and Biological Sensing.

    Science.gov (United States)

    Chandrasekaran, Arun Richard; Wady, Heitham; Subramanian, Hari K K

    2016-05-01

    The nanoscale features of DNA have made it a useful molecule for bottom-up construction of nanomaterials, for example, two- and three-dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA-based nanostructures is in chemical and biological sensing, where they have proven to be cost-effective, sensitive and have shown promise as point-of-care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure-based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA-based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed. PMID:27040036

  18. 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...

  19. 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.

  20. Preparing Federal Coordinating Officers (FCOs) to operate in Chemical, Biological, Radiological, and Nuclear (CBRN) environments

    OpenAIRE

    Russell, Tony.

    2008-01-01

    CHDS State/Local In this thesis the Federal Emergency Management Agency's (FEMA) Federal Coordinating Officer (FCO) function is examined as it relates to Chemical, Biological, Radiological and Nuclear (CBRN) operations. It is suggested that targeted changes can be made to ensure the FCOs are better prepared to manage the additional complexities of a CBRN environment. The changes include addressing the FCOs from the systems approach- internally to improve the FCO personal and professio...

  1. Lignin valorization through integrated biological funneling and chemical catalysis.

    Science.gov (United States)

    Linger, Jeffrey G; Vardon, Derek R; Guarnieri, Michael T; Karp, Eric M; Hunsinger, Glendon B; Franden, Mary Ann; Johnson, Christopher W; Chupka, Gina; Strathmann, Timothy J; Pienkos, Philip T; Beckham, Gregg T

    2014-08-19

    Lignin is an energy-dense, heterogeneous polymer comprised of phenylpropanoid monomers used by plants for structure, water transport, and defense, and it is the second most abundant biopolymer on Earth after cellulose. In production of fuels and chemicals from biomass, lignin is typically underused as a feedstock and burned for process heat because its inherent heterogeneity and recalcitrance make it difficult to selectively valorize. In nature, however, some organisms have evolved metabolic pathways that enable the utilization of lignin-derived aromatic molecules as carbon sources. Aromatic catabolism typically occurs via upper pathways that act as a "biological funnel" to convert heterogeneous substrates to central intermediates, such as protocatechuate or catechol. These intermediates undergo ring cleavage and are further converted via the β-ketoadipate pathway to central carbon metabolism. Here, we use a natural aromatic-catabolizing organism, Pseudomonas putida KT2440, to demonstrate that these aromatic metabolic pathways can be used to convert both aromatic model compounds and heterogeneous, lignin-enriched streams derived from pilot-scale biomass pretreatment into medium chain-length polyhydroxyalkanoates (mcl-PHAs). mcl-PHAs were then isolated from the cells and demonstrated to be similar in physicochemical properties to conventional carbohydrate-derived mcl-PHAs, which have applications as bioplastics. In a further demonstration of their utility, mcl-PHAs were catalytically converted to both chemical precursors and fuel-range hydrocarbons. Overall, this work demonstrates that the use of aromatic catabolic pathways enables an approach to valorize lignin by overcoming its inherent heterogeneity to produce fuels, chemicals, and materials. PMID:25092344

  2. 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.

  3. 15 CFR Supplement No. 1 to Part 742 - Nonproliferation of Chemical and Biological Weapons

    Science.gov (United States)

    2010-01-01

    ... Biological Weapons No. Supplement No. 1 to Part 742 Commerce and Foreign Trade Regulations Relating to...—Nonproliferation of Chemical and Biological Weapons Note: Exports and reexports of items in performance of...: (i) Equipment (for producing chemical weapon precursors and chemical warfare agents) described...

  4. Systems Medicine: Evolution of Systems Biology From Bench To Bedside

    OpenAIRE

    Wang, Rui-Sheng; Maron, Bradley A.; Loscalzo, Joseph

    2015-01-01

    High-throughput experimental techniques for generating genomes, transcriptomes, proteomes, metabolomes, and interactomes have provided unprecedented opportunities to interrogate biological systems and human diseases on a global level. Systems biology integrates the mass of heterogeneous high-throughput data and predictive computational modeling to understand biological functions as system-level properties. Most human diseases are biological states caused by multiple components of perturbed pa...

  5. Genomes, phylogeny, and evolutionary systems biology

    OpenAIRE

    Medina, Monica

    2005-01-01

    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 c...

  6. Developmental systems biology flourishing on new technologies

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies,and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems Biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches.

  7. Developmental systems biology flourishing on new technologies.

    Science.gov (United States)

    Han, Jing-Dong J; Liu, Yi; Xue, Huiling; Xia, Kai; Yu, Hong; Zhu, Shanshan; Chen, Zhang; Zhang, Wei; Huang, Zheng; Jin, Chunyu; Xian, Bo; Li, Jing; Hou, Lei; Han, Yixing; Niu, Chaoqun; Alcon, Timothy C

    2008-10-01

    Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies, and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems Biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches. PMID:18937914

  8. The bioartificial pancreas (BAP): Biological, chemical and engineering challenges.

    Science.gov (United States)

    Iacovacci, Veronica; Ricotti, Leonardo; Menciassi, Arianna; Dario, Paolo

    2016-01-15

    The bioartificial pancreas (BAP) represents a viable solution for the treatment of type 1 diabetes (T1D). By encapsulating pancreatic cells in a semipermeable membrane to allow nutrient, insulin and glucose exchange, the side effects produced by islets and whole organ transplantation-related immunosuppressive therapy can be circumvented. Several factors, mainly related to materials properties, capsule morphology and biological environment, play a key role in optimizing BAP systems. The BAP is an extremely complex delivery system for insulin. Despite considerable efforts, in some instances meeting with limited degree of success, a BAP capable of restoring physiological pancreas functions without the need for immunosuppressive drugs and of controlling blood glucose levels especially in large animal models and a few clinical trials, does not exist. The state of the art in terms of materials, fabrication techniques and cell sources, as well as the current status of commercial devices and clinical trials, are described in this overview from an interdisciplinary viewpoint. In addition, challenges to the creation of effective BAP systems are highlighted including future perspectives in terms of component integration from both a biological and an engineering viewpoint.

  9. Systems Biology Analysis of Heterocellular Signaling.

    Science.gov (United States)

    Tape, Christopher J

    2016-08-01

    Tissues comprise multiple heterotypic cell types (e.g., epithelial, mesenchymal, and immune cells). Communication between heterotypic cell types is essential for biological cohesion and is frequently dysregulated in disease. Despite the importance of heterocellular communication, most systems biology techniques do not report cell-specific signaling data from mixtures of cells. As a result, our existing perspective of cellular behavior under-represents the influence of heterocellular signaling. Recent technical advances now permit the resolution of systems-level cell-specific signaling data. This review discusses how new physical, spatial, and isotopic resolving methods are facilitating unique systems biology studies of heterocellular communication. PMID:27087613

  10. Facile: a command-line network compiler for systems biology

    OpenAIRE

    Ollivier Julien F; Siso-Nadal Fernando; Swain Peter S

    2007-01-01

    Abstract Background A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unknown. It is therefore important to be able to easily investigate the effects of adding or removing reactions and to easily perform a bifurcation analysis, which shows the qualitative dynamics of a model for a range of parameter values. Results We present Facile, a Perl...

  11. 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

  12. Chemical Tracking Systems: Not Your Usual Global Positioning System!

    Science.gov (United States)

    Roy, Ken

    2007-01-01

    The haphazard storing and tracking of chemicals in the laboratory is a serious safety issue facing science teachers. To get control of your chemicals, try implementing a "chemical tracking system". A chemical tracking system (CTS) is a database of chemicals used in the laboratory. If implemented correctly, a CTS will reduce purchasing costs,…

  13. Recycling of dyehouse effluents by biological and chemical treatment

    Energy Technology Data Exchange (ETDEWEB)

    Krull, R.; Doepkens, E. [Inst. of Biochemical Engineering, Technical Univ. of Braunschweig, Braunschweig (Germany)

    2003-07-01

    The introduction of the production integrated environmental protection by closing raw material cycles is shown exemplary for the textile finishing industry. Colored process water with a high content of dissolved organic dyes has always been a non-trivial problem for the sewage engineering sector. The recycling of process water of textile mills is often hindered by remaining color of water-soluable azo dyes after conventional wastewater treatment. Rising costs of emitted wastewater, lawful limits and restricted availability of water makes it of great interest to introduce sophisticated techniques helping to purify dye effluents and to recycle process water. A combined biological and chemical process of purification and recycling of residual dyehouse split flows into the production was developed, investigated and installed by a textile finishing company which produces 330,000 m{sup 3} colored wastewater effluents per year. The process contains anaerobic dye-cleavage, aerobic mineralization of cleavage-products and the decolorization and partial oxidation of traces of dyeresiduals by advanced oxidation. (orig.)

  14. Terahertz technology in biological and chemical sensing for defence

    Science.gov (United States)

    Woodward, Ruth M.

    2004-12-01

    The terahertz (1 THz = 1012 Hz, 3 mm or 33 cm-1) region of the electromagnetic spectrum is typically defined in the frequency range 100 GHz to 10 THz, corresponding to a wavelength range of 3 mm to 30 microns. Owing to a lack of suitable coherent sources and detectors, this region has only been investigated in earnest in the last ten years for terrestrial imaging and spectroscopy applications. Its role in the medical, pharmaceutical, non-destructive testing and more recently security industries is now being examined. The terahertz frequency range is of particular interest since it is able to probe several molecular interactions including the intermolecular vibrations, large amplitude vibrations and twisting and torsional modes. Molecules have also shown polarization sensitivity to the incident terahertz radiation. The ability of terahertz radiation to investigate conformational change makes it an important part of the electromagnetic spectrum. Terahertz radiation has the potential to provide additional information, which may complement other optically based sensing technologies. The use of terahertz technology in the security and defence industry is discussed, with a specific focus on biological and chemical sensing. The challenges faced in bringing terahertz technology into the market place will be discussed.

  15. Pereskia aculeata Muller (Cactaceae) Leaves: Chemical Composition and Biological Activities.

    Science.gov (United States)

    Souza, Lucèia Fàtima; Caputo, Lucia; Inchausti De Barros, Ingrid Bergman; Fratianni, Florinda; Nazzaro, Filomena; De Feo, Vincenzo

    2016-01-01

    The aims of this work were to study the chemical composition of the essential oil from the leaves of Pereskia aculeata and to evaluate some biological activities of three leaf extracts. The phenolic content, antioxidant activity, and in vitro antimicrobial and antifungal activities were determined. The methanol extract showed antioxidant activity (EC50 7.09 mg/mL) and high polyphenols content (15.04 ± 0.31 mg gallic acid equivalents (GAE)/g). The petroleum ether extract exhibited potent antibacterial activity against Escherichia coli, whereas the chloroform extract showed inhibitory activity against Bacillus cereus and Staphylococcus aureus. The petroleum ether and methanol extracts were more effective in inhibiting the growth of Aspergillus versicolor. The possible cytotoxicity of extracts on neuroblastoma SH-SY5Y cancer cell line and the influence on adenylate cyclase (ADCY) expression was also studied. P. aculeata chloroform extract showed antiproliferative activity with an IC50 value of 262.83 µg/mL. Treatments of SH-SY5Y neuroblastoma cells with 100 µg/mL of methanol extract significantly reduced ADCY1 expression. PMID:27598154

  16. Chemical, Biological, Radiological and Nuclear Regional Centres of Excellence Initiative

    International Nuclear Information System (INIS)

    This series of slides presents the initiative launched in May 2010 by the European Union to develop at national and regional levels the necessary institutional capacity to fight against the CBRN (Chemical, Biological, Radiological and Nuclear) risk. The origin of the risk can be: -) criminal (proliferation, theft, sabotage and illicit traffics), -) accidental (industrial catastrophes, transport accidents...) and -) natural (mainly pandemics). The initiative consists in the creation of Centres of Excellence for providing assistance and cooperation in the field of CBRN risk and the creation of experts networks for sharing best practices, reviewing laws and regulation, developing technical capacities in order to mitigate the CBRN risk. The initiative is complementary to the instrument for nuclear safety cooperation. Regional Centres of Excellence are being set up in 6 regions: South East Europe, South East Asia, North Africa, West Africa, Middle East, and Central Asia covering nearly 40 countries. A global budget of 100 million Euros will be dedicated to this initiative for the 2009-2013 period. (A.C.)

  17. [Nuclear, radiological, biological, and chemical dangers and risks].

    Science.gov (United States)

    Maillard, Stéphane

    2008-01-01

    In contrast to military conflicts natural events, industrial disasters as well as terror attacks can surprise our society without warning. In all these events nuclear, radiological, biological or chemical dangers can be involved as well. The acute or retarded health effects on the public, first responders and society are well known. The psychological strain and disconcertion have also to be considered as well. Conditions to respond to these events with success are the early recognition and introduction of appropriate immediate measures. The early recognition is as such important because these events don't only have to start with an explosion. The early recognition should maybe base on the delayed appearance of atypical symptoms or with the increase of rare illnesses. The response to some incidence will inevitable includes drastical safety precautions such as evacuations, limitations of passenger traffic or food consumption. Precautions will only be carried out if they are understood by the public. Objective information and sensiblisation of the public and all concerned by this matter is crucial; without minimization or paranoia.

  18. Chemical and Biological Characterization of Oleanane Triterpenoids from Soy

    Directory of Open Access Journals (Sweden)

    David G. Popovich

    2009-08-01

    Full Text Available Soyasaponins are a group of complex and structural diverse oleanane triterpenoids found in soy (Glycine max and other legumes. They are primarily classified into two main groups − group A and B − based on the attachment of sugar moieties at positions C-3 and C-22 of the ring structures. Group A soyasaponins are bidesmosidic, while group B soyasaponins are monodesmosidic. Group B soyasaponins are further classified into two subcategories known as 2,3-dihydro-2,5-dihydroxy-6 -methyl-4H-pyran-4-one (DDMP and non-DDMP conjugated molecules. The preparation and purification of soyasaponin molecules is complicated by the presence of bioactive soy isoflavones, which often overlap with soyasaponin in polarity and must removed from extracts before biological assessment. Soyasaponin extracts, aglycones of group A and B and individual group B soyasaponins such as soyasaponin I have been reported to posses specific bioactive properties, such as in vitro anti-cancer properties by modulating the cell cycle and inducing apoptosis. The isolation, chemical characterization and detection strategies by HPLC and HPLC-MS are reviewed, along with the reported bioactive effects of soyasaponin extracts and individual molecules in cultured cancer cell experiments.

  19. Stability and its manifestation in the chemical and biological worlds.

    Science.gov (United States)

    Pascal, Robert; Pross, Addy

    2015-11-21

    Bridging between the phenomenologically distinct biological and physical worlds has been a major scientific challenge since Boltzmann's probabilistic formulation of the second law of thermodynamics. In this review we summarize our recent theoretical attempts to bridge that divide through analysis of the thermodynamic-kinetic interplay in chemical processes and the manner in which that interplay impacts on material stability. Key findings are that the term 'stability' manifests two facets - time and energy - and that stability's time facet, expressed as persistence, is more general than its energy facet. That idea, together with the proposed existence of a logical law of nature, the persistence principle, leads to the mathematically-based insight that stability can come about through either Boltzmann's probabilistic considerations or Malthusian kinetics. Two mathematically-based forms of material persistence then lead directly to the physical likelihood of two material forms, animate and inanimate. Significantly, the incorporation of kinetic considerations into the stability concept appears to bring us closer to enabling two of the central theories in science - the second law of thermodynamics and Darwin's theory of evolution - to be reconciled within a single conceptual framework. PMID:26465292

  20. Stability and its manifestation in the chemical and biological worlds.

    Science.gov (United States)

    Pascal, Robert; Pross, Addy

    2015-11-21

    Bridging between the phenomenologically distinct biological and physical worlds has been a major scientific challenge since Boltzmann's probabilistic formulation of the second law of thermodynamics. In this review we summarize our recent theoretical attempts to bridge that divide through analysis of the thermodynamic-kinetic interplay in chemical processes and the manner in which that interplay impacts on material stability. Key findings are that the term 'stability' manifests two facets - time and energy - and that stability's time facet, expressed as persistence, is more general than its energy facet. That idea, together with the proposed existence of a logical law of nature, the persistence principle, leads to the mathematically-based insight that stability can come about through either Boltzmann's probabilistic considerations or Malthusian kinetics. Two mathematically-based forms of material persistence then lead directly to the physical likelihood of two material forms, animate and inanimate. Significantly, the incorporation of kinetic considerations into the stability concept appears to bring us closer to enabling two of the central theories in science - the second law of thermodynamics and Darwin's theory of evolution - to be reconciled within a single conceptual framework.

  1. Pereskia aculeata Muller (Cactaceae) Leaves: Chemical Composition and Biological Activities

    Science.gov (United States)

    Souza, Lucèia Fàtima; Caputo, Lucia; Inchausti De Barros, Ingrid Bergman; Fratianni, Florinda; Nazzaro, Filomena; De Feo, Vincenzo

    2016-01-01

    The aims of this work were to study the chemical composition of the essential oil from the leaves of Pereskia aculeata and to evaluate some biological activities of three leaf extracts. The phenolic content, antioxidant activity, and in vitro antimicrobial and antifungal activities were determined. The methanol extract showed antioxidant activity (EC50 7.09 mg/mL) and high polyphenols content (15.04 ± 0.31 mg gallic acid equivalents (GAE)/g). The petroleum ether extract exhibited potent antibacterial activity against Escherichia coli, whereas the chloroform extract showed inhibitory activity against Bacillus cereus and Staphylococcus aureus. The petroleum ether and methanol extracts were more effective in inhibiting the growth of Aspergillus versicolor. The possible cytotoxicity of extracts on neuroblastoma SH-SY5Y cancer cell line and the influence on adenylate cyclase (ADCY) expression was also studied. P. aculeata chloroform extract showed antiproliferative activity with an IC50 value of 262.83 µg/mL. Treatments of SH-SY5Y neuroblastoma cells with 100 µg/mL of methanol extract significantly reduced ADCY1 expression. PMID:27598154

  2. Bioferroelectricity and optical properties of biological systems

    Science.gov (United States)

    Bystrov, Vladimir; Bystrova, Natalia

    2003-08-01

    A bioferroelectric approach to analysis of ferroelectric behavior of biological systems is presented. The optical properties of nerve fibers, biomembrane ion channels, and purple membrane films containing bacteriorhodopsin are analyzed. The features, influence of the proton subsystem and proton transfer on the hydrogen-bonded biomolecular structures are analyzed within the ferroelectric liquid-crystal model and possible biomedical applications discussed. The ferroelectric behavior of biological systems and the set of various bioferroelectric effects are considered within the limits of phenomenological theory of ferroelectrics. The nonlinear response to weak actions under conditions critical to human organism is one of specific features characterizing biological objects on molecular, cell and organism levels.

  3. Assessment of the use potential of edible sea urchins (Paracentrotus lividus) processing waste within the agricultural system: influence on soil chemical and biological properties and bean (Phaseolus vulgaris) and wheat (Triticum vulgare) growth in an amended acidic soil.

    Science.gov (United States)

    Garau, Giovanni; Castaldi, Paola; Deiana, Salvatore; Campus, Paolo; Mazza, Antonio; Deiana, Pietrino; Pais, Antonio

    2012-10-30

    assessed in a pot experiment. Plant growth was unaffected (wheat) or stimulated (bean) by the amendment addition in the 0.5-3.0% range while the higher amendment rate (i.e. 5.0%) was detrimental for both plant species indicating a phytotoxic effect which could be due to different factors such as an excess of calcium in soil, a suppression of Mg uptake or the higher EC values detected at the highest amendment rate. It is concluded that ground P. lividus endoskeletons have potential as a soil amendment to ameliorate chemical and biological properties of acidic Mediterranean soils. This seems particularly relevant, especially at the lower amendment rates, since for the first time, a sustainable management system is proposed for P. lividus processing waste, which foresees economic value in the sea urchin by-product through its re-use within the agricultural production system. PMID:22659645

  4. Effects of timber harvest on river food webs: physical, chemical and biological responses.

    Directory of Open Access Journals (Sweden)

    J Timothy Wootton

    Full Text Available I compared physical, chemical and biological characteristics of nine rivers running through three timber harvest regimes to investigate the effects of land use on river ecosystems, to determine whether these corresponded to changes linked with downstream location, and to compare the response of different types of indicator variables. Physical variables changed with downstream location, but varied little with timber harvest. Most chemical variables increased strongly with timber harvest, but not with downstream location. Most biological variables did not vary systematically with either timber harvest or downstream location. Dissolved organic carbon did not vary with timber harvest or downstream location, but correlated positively with salmonid abundance. Nutrient manipulations revealed no general pattern of nutrient limitation with timber harvest or downstream location. The results suggest that chemical variables most reliably indicate timber harvest impact in these systems. The biological variables most relevant to human stakeholders were surprisingly insensitive to timber harvest, however, apparently because of decoupling from nutrient responses and unexpectedly weak responses by physical variables.

  5. Chemical and biological sensors based on optically confined birefringent chalcopyrite heterostructures

    International Nuclear Information System (INIS)

    This paper introduces and discusses the design and application(s) of a new and unique integrated solid-state molecular sensor (SSMS) system. The SSMS is based on optically confined birefringent heterostructure technology, which has the capability of recognizing target chemicals and biological molecules in an ambient environment. The SSMS technology is applicable for miniaturized sensor devices that can be used for quick, remote screening and recognition of chemical hazards in the environment. For example, trace impurities related to air/water pollution can be continuously monitored. Just as important, however, the SSMS technology will have a worldwide impact--economically as well as technologically--when used in the detection of chemical and biological agents, as well as for a variety of medical sensing applications, such as to identify and monitor complex biological structures, test for allergic reactions and screen for common diseases. Moreover, it could hasten the time of development and introduction into the marketplace of critically needed new drugs by the monitoring of biochemical and molecular cellular responses to the candidate drugs. Materials selection criteria, growth parameters and device architecture requirements are given and discussed. In addition, the results of a recent phase matching calculation, substantiating the feasibility of the SSMS, are given and discussed

  6. TOPICAL REVIEW: Biological and chemical sensors for cancer diagnosis

    Science.gov (United States)

    Simon, Elfriede

    2010-11-01

    The great challenge for sensor systems to be accepted as a relevant diagnostic and therapeutic tool for cancer detection is the ability to determine the presence of relevant biomarkers or biomarker patterns comparably to or even better than the traditional analytical systems. Biosensor and chemical sensor technologies are already used for several clinical applications such as blood glucose or blood gas measurements. However, up to now not many sensors have been developed for cancer-related tests because only a few of the biomarkers have shown clinical relevance and the performance of the sensor systems is not always satisfactory. New genomic and proteomic tools are used to detect new molecular signatures and identify which combinations of biomarkers may detect best the presence or risk of cancer or monitor cancer therapies. These molecular signatures include genetic and epigenetic signatures, changes in gene expressions, protein biomarker profiles and other metabolite profile changes. They provide new changes in using different sensor technologies for cancer detection especially when complex biomarker patterns have to be analyzed. To address requirements for this complex analysis, there have been recent efforts to develop sensor arrays and new solutions (e.g. lab on a chip) in which sampling, preparation, high-throughput analysis and reporting are integrated. The ability of parallelization, miniaturization and the degree of automation are the focus of new developments and will be supported by nanotechnology approaches. This review recaps some scientific considerations about cancer diagnosis and cancer-related biomarkers, relevant biosensor and chemical sensor technologies, their application as cancer sensors and consideration about future challenges.

  7. 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...

  8. Systems biology: leading the revolution in ecotoxicology.

    Science.gov (United States)

    Garcia-Reyero, Natàlia; Perkins, Edward J

    2011-02-01

    The rapid development of new technologies such as transcriptomics, proteomics, and metabolomics (Omics) are changing the way ecotoxicology is practiced. The data deluge has begun with genomes of over 65 different aquatic species that are currently being sequenced, and many times that number with at least some level of transcriptome sequencing. Integrating these top-down methodologies is an essential task in the field of systems biology. Systems biology is a biology-based interdisciplinary field that focuses on complex interactions in biological systems, with the intent to model and discover emergent properties of the system. Recent studies demonstrate that Omics technologies provide valuable insight into ecotoxicity, both in laboratory exposures with model organisms and with animals exposed in the field. However, these approaches require a context of the whole animal and population to be relevant. Powerful approaches using reverse engineering to determine interacting networks of genes, proteins, or biochemical reactions are uncovering unique responses to toxicants. Modeling efforts in aquatic animals are evolving to interrelate the interacting networks of a system and the flow of information linking these elements. Just as is happening in medicine, systems biology approaches that allow the integration of many different scales of interaction and information are already driving a revolution in understanding the impacts of pollutants on aquatic systems.

  9. Chemical probes of quorum sensing: from compound development to biological discovery.

    Science.gov (United States)

    Welsh, Michael A; Blackwell, Helen E

    2016-09-01

    Bacteria can utilize chemical signals to coordinate the expression of group-beneficial behaviors in a method of cell-cell communication called quorum sensing (QS). The discovery that QS controls the production of virulence factors and biofilm formation in many common pathogens has driven an explosion of research aimed at both deepening our fundamental understanding of these regulatory networks and developing chemical agents that can attenuate QS signaling. The inherently chemical nature of QS makes studying these pathways with small molecule tools a complementary approach to traditional microbiology techniques. Indeed, chemical tools are beginning to yield new insights into QS regulation and provide novel strategies to inhibit QS. Here, we review the most recent advances in the development of chemical probes of QS systems in Gram-negative bacteria, with an emphasis on the opportunistic pathogen Pseudomonas aeruginosa We first describe reports of novel small molecule modulators of QS receptors and QS signal synthases. Next, in several case studies, we showcase how chemical tools have been deployed to reveal new knowledge of QS biology and outline lessons for how researchers might best target QS to combat bacterial virulence. To close, we detail the outstanding challenges in the field and suggest strategies to overcome these issues.

  10. A review of chemical gradient systems for cell analysis.

    Science.gov (United States)

    Somaweera, Himali; Ibraguimov, Akif; Pappas, Dimitri

    2016-02-11

    Microfluidic spatial and temporal gradient generators have played an important role in many biological assays such as in the analysis of wound healing, inflammation, and cancer metastasis. Chemical gradient systems can also be applied to other fields such as drug design, chemical synthesis, chemotaxis, etc. Microfluidic systems are particularly amenable to gradient formation, as the length scales used in chips enable fluid processes that cannot be conducted in bulk scale. In this review we discuss new microfluidic devices for gradient generation and applications of those systems in cell analysis.

  11. 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...

  12. Computational systems biology in cancer brain metastasis.

    Science.gov (United States)

    Peng, Huiming; Tan, Hua; Zhao, Weiling; Jin, Guangxu; Sharma, Sambad; Xing, Fei; Watabe, Kounosuke; Zhou, Xiaobo

    2016-01-01

    Brain metastases occur in 20-40% of patients with advanced malignancies. A better understanding of the mechanism of this disease will help us to identify novel therapeutic strategies. In this review, we will discuss the systems biology approaches used in this area, including bioinformatics and mathematical modeling. Bioinformatics has been used for identifying the molecular mechanisms driving brain metastasis and mathematical modeling methods for analyzing dynamics of a system and predicting optimal therapeutic strategies. We will illustrate the strategies, procedures, and computational techniques used for studying systems biology in cancer brain metastases. We will give examples on how to use a systems biology approach to analyze a complex disease. Some of the approaches used to identify relevant networks, pathways, and possibly biomarkers in metastasis will be reviewed into details. Finally, certain challenges and possible future directions in this area will also be discussed.

  13. Thermodynamically predicted oscillations in closed chemical systems

    CERN Document Server

    Zilbergleyt, B

    2010-01-01

    All known up to now models of chemical oscillations are based exclusively on kinetic considerations. The chemical gross-process equation is split usually by elementary steps, each step is supplied by an arrow and a differential equation, joint solution to such a construction under certain, often ad hoc chosen conditions and with ad hoc numerical coefficients leads to chemical oscillations. Kinetic perception of chemical oscillations reigns without exclusions. However, as it was recently shown by the author for the laser and for the electrochemical systems, chemical oscillations follow also from solutions to the basic expressions of discrete thermodynamics of chemical equilibria. Graphically those solutions are various fork bifurcation diagrams, and, in certain types of chemical systems, oscillations are well pronounced in the bistable bifurcation areas. In this work we describe a general thermodynamic approach to chemical oscillations as opposite to kinetic models, and depict some of their new features like s...

  14. 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...... timed automata and most recently hybrid systems using the tool Uppaal SMC. In this paper we enable the application of SMC to complex biological systems, by combining Uppaal SMC with ANIMO, a plugin of the tool Cytoscape used by biologists, as well as with SimBiology®, a plugin of Matlab to simulate...

  15. Implementation of algorithms to discriminate chemical/biological airbursts from high explosive airbursts utilizing acoustic signatures

    Science.gov (United States)

    Hohil, Myron E.; Desai, Sachi; Morcos, Amir

    2006-05-01

    The Army is currently developing acoustic sensor systems that will provide extended range surveillance, detection, and identification for force protection and tactical security. A network of such sensors remotely deployed in conjunction with a central processing node (or gateway) will provide early warning and assessment of enemy threats, near real-time situational awareness to commanders, and may reduce potential hazards to the soldier. In contrast, the current detection of chemical/biological (CB) agents expelled into a battlefield environment is limited to the response of chemical sensors that must be located within close proximity to the CB agent. Since chemical sensors detect hazardous agents through contact, the sensor range to an airburst is the key-limiting factor in identifying a potential CB weapon attack. The associated sensor reporting latencies must be minimized to give sufficient preparation time to field commanders, who must assess if an attack is about to occur, has occurred, or if occurred, the type of agent that soldiers might be exposed to. The long-range propagation of acoustic blast waves from heavy artillery blasts, which are typical in a battlefield environment, introduces a feature for using acoustics and other sensor suite technologies for the early detection and identification of CB threats. Employing disparate sensor technologies implies that warning of a potential CB attack can be provided to the solider more rapidly and from a safer distance when compared to current conventional methods. Distinct characteristics arise within the different airburst signatures because High Explosive (HE) warheads emphasize concussive and shrapnel effects, while chemical/biological warheads are designed to disperse their contents over immense areas, therefore utilizing a slower burning, less intensive explosion to mix and distribute their contents. Highly reliable discrimination (100%) has been demonstrated at the Portable Area Warning Surveillance System

  16. 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...

  17. Health Outcomes of Exposure to Biological and Chemical Components of Inhalable and Respirable Particulate Matter

    OpenAIRE

    Oyewale Mayowa Morakinyo; Matlou Ingrid Mokgobu; Murembiwa Stanley Mukhola; Raymond Paul Hunter

    2016-01-01

    Particulate matter (PM) is a key indicator of air pollution and a significant risk factor for adverse health outcomes in humans. PM is not a self-contained pollutant but a mixture of different compounds including chemical and biological fractions. While several reviews have focused on the chemical components of PM and associated health effects, there is a dearth of review studies that holistically examine the role of biological and chemical components of inhalable and respirable PM in disease...

  18. Carbon Nanostructure-Based Field-Effect Transistors for Label-Free Chemical/Biological Sensors

    OpenAIRE

    PingAn Hu; Jia Zhang; Le Li; Zhenlong Wang; William O’Neill; Pedro Estrela

    2010-01-01

    Over the past decade, electrical detection of chemical and biological species using novel nanostructure-based devices has attracted significant attention for chemical, genomics, biomedical diagnostics, and drug discovery applications. The use of nanostructured devices in chemical/biological sensors in place of conventional sensing technologies has advantages of high sensitivity, low decreased energy consumption and potentially highly miniaturized integration. Owing to their particular structu...

  19. Photosynthetic system as a biological functional element

    International Nuclear Information System (INIS)

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

  20. Data driven computing for Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Samatova, Nagiza F.; Gorin, Andrey; Uberbacher, Edward; Karpinets, Tatiana V.; Park, Byung H.; Pan, Chongle; Straatsma, TP; Cannon, William R.; Resat, Haluk; Lins, Roberto D.; Oehmen, Christopher S.

    2007-11-01

    Biological breakthroughs that can lead to improved diagnosis and treatment of diseases, generation of clean energy, and solutions to other critical societal problems require high performance, data-intensive computational tools that have the ability to process, analyze and cohesively integrate massive amounts of data and information in real time. Biological computing problems are typically data-intensive and must share very large sets of data effectively across many processors. However, the various components of biological systems, composed of complex networks and pathways, must be integrated to gain a coherent understanding of the system. The more different types of data that can be integrated, the deeper the insights into the biology of the system being studied. Conventional analysis software, however, hasn’t been able to efficiently deal with such massive data set. The goal of the Data-Intensive Computing for Complex Biological Systems (BioPilot) project, a multiyear project funded by the U.S. Department of Energy’s Office of Advanced Scientific Computing Research (ASCR), is to create an integrated suite of highly flexible, highly adaptable pipelines of computational tools for analyzing large-scale data sets that will be used to address specific challenges facing the U.S. Department of Energy (DOE) and our society.

  1. Chem2Bio2RDF: A Linked Open Data Portal for Chemical Biology

    CERN Document Server

    Chen, Bin; Zhu, Qian; Ding, Ying; Dong, Xiao; Sankaranarayanan, Madhuvanthi; Wang, Huijun; Sun, Yuyin

    2010-01-01

    The Chem2Bio2RDF portal is a Linked Open Data (LOD) portal for systems chemical biology aiming for facilitating drug discovery. It converts around 25 different datasets on genes, compounds, drugs, pathways, side effects, diseases, and MEDLINE/PubMed documents into RDF triples and links them to other LOD bubbles, such as Bio2RDF, LODD and DBPedia. The portal is based on D2R server and provides a SPARQL endpoint, but adds on few unique features like RDF faceted browser, user-friendly SPARQL query generator, MEDLINE/PubMed cross validation service, and Cytoscape visualization plugin. Three use cases demonstrate the functionality and usability of this portal.

  2. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  3. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  4. Which chemicals drive biological effects in wastewater and recycled water?

    Science.gov (United States)

    Tang, Janet Y M; Busetti, Francesco; Charrois, Jeffrey W A; Escher, Beate I

    2014-09-01

    Removal of organic micropollutants from wastewater during secondary treatment followed by reverse osmosis and UV disinfection was evaluated by a combination of four in-vitro cell-based bioassays and chemical analysis of 299 organic compounds. Concentrations detected in recycled water were below the Australian Guidelines for Water Recycling. Thus the detected chemicals were considered not to pose any health risk. The detected pesticides in the wastewater treatment plant effluent and partially advanced treated water explained all observed effects on photosynthesis inhibition. In contrast, mixture toxicity experiments with designed mixtures containing all detected chemicals at their measured concentrations demonstrated that the known chemicals explained less than 3% of the observed cytotoxicity and less than 1% of the oxidative stress response. Pesticides followed by pharmaceuticals and personal care products dominated the observed mixture effects. The detected chemicals were not related to the observed genotoxicity. The large proportion of unknown toxicity calls for effect monitoring complementary to chemical monitoring. PMID:24874944

  5. Which chemicals drive biological effects in wastewater and recycled water?

    Science.gov (United States)

    Tang, Janet Y M; Busetti, Francesco; Charrois, Jeffrey W A; Escher, Beate I

    2014-09-01

    Removal of organic micropollutants from wastewater during secondary treatment followed by reverse osmosis and UV disinfection was evaluated by a combination of four in-vitro cell-based bioassays and chemical analysis of 299 organic compounds. Concentrations detected in recycled water were below the Australian Guidelines for Water Recycling. Thus the detected chemicals were considered not to pose any health risk. The detected pesticides in the wastewater treatment plant effluent and partially advanced treated water explained all observed effects on photosynthesis inhibition. In contrast, mixture toxicity experiments with designed mixtures containing all detected chemicals at their measured concentrations demonstrated that the known chemicals explained less than 3% of the observed cytotoxicity and less than 1% of the oxidative stress response. Pesticides followed by pharmaceuticals and personal care products dominated the observed mixture effects. The detected chemicals were not related to the observed genotoxicity. The large proportion of unknown toxicity calls for effect monitoring complementary to chemical monitoring.

  6. Reverse engineering and identification in systems biology: strategies, perspectives and challenges

    OpenAIRE

    Villaverde, A. F.; Banga, Julio R.

    2014-01-01

    The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among othe...

  7. Chemical Cleaning Process for Porable Water Distrubution Pipe Systems

    OpenAIRE

    ECT Team, Purdue

    2007-01-01

    Aging potable water distribution pipe systems are becoming a major concern throughout the world. Deterioration of water quality and service as a result of micro biological tuberculation and corrosion continues to increase. Major costs for replacement or rehabilitation of distribution systems are being faced by most communities. The chemical cleaning solution is an organic oxide scavenger which is mixed with a predetermined quantity of muriatic acid and circulated through an isolated section o...

  8. Stochastic Physics, Complex Systems and Biology

    CERN Document Server

    Qian, Hong

    2012-01-01

    In complex systems, the interplay between nonlinear and stochastic dynamics gives rise to an evolution process in Darwinian sense with punctuated equilibrium, random "mutations" and "adaptations". The emergent discrete states in such a system, i.e., attractors, have natural robustness against both internal and external perturbations. Epigenetic states of a biological cell, a mesoscopic nonlinear stochastic open biochemical system, could be understood through such a framework.

  9. 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.

  10. 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.

  11. Semantic annotation for biological information retrieval system.

    Science.gov (United States)

    Oshaiba, Mohamed Marouf Z; El Houby, Enas M F; Salah, Akram

    2015-01-01

    Online literatures are increasing in a tremendous rate. Biological domain is one of the fast growing domains. Biological researchers face a problem finding what they are searching for effectively and efficiently. The aim of this research is to find documents that contain any combination of biological process and/or molecular function and/or cellular component. This research proposes a framework that helps researchers to retrieve meaningful documents related to their asserted terms based on gene ontology (GO). The system utilizes GO by semantically decomposing it into three subontologies (cellular component, biological process, and molecular function). Researcher has the flexibility to choose searching terms from any combination of the three subontologies. Document annotation is taking a place in this research to create an index of biological terms in documents to speed the searching process. Query expansion is used to infer semantically related terms to asserted terms. It increases the search meaningful results using the term synonyms and term relationships. The system uses a ranking method to order the retrieved documents based on the ranking weights. The proposed system achieves researchers' needs to find documents that fit the asserted terms semantically.

  12. Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions.

    Science.gov (United States)

    Putz, Mihai V; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners' (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  13. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2016-07-01

    Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

  14. Quality fluctuation detection of an herbal injection based on biological fingerprint combined with chemical fingerprint.

    Science.gov (United States)

    Zhang, Lele; Ma, Lina; Feng, Wuwen; Zhang, Congen; Sheng, Feiya; Zhang, Yi; Xu, Chen; Dong, Gang; Dong, Xiaoping; Xiao, Xiaohe; Yan, Dan

    2014-08-01

    Herbal injection is one of the most important preparations of traditional Chinese medicine. More than 130 types of herbal injections are used clinically for 400 million patients annually with total sales of over four billion US dollars per year. However, the current quality control (QC) methods relying mainly on chemical fingerprints (CF) can hardly ensure quality and safety of the herbal injections with complex chemical composition and have resulted in an increase in serious adverse drug reactions. In this study, a comprehensive approach for the QC of a controversial herbal injection Shuang-Huang-Lian lyophilized powder (SHL) was established based on the quality fluctuation detection by a combination of CF and biological fingerprint (BF). High-performance liquid chromatography and the impedance-based xCELLigence system were applied to establish the CF and BF, respectively. In addition, multivariate analysis was performed to evaluate the discriminant ability of the two methods. The results showed that being subjected to environmental influence like oxygen/air, high temperature, and extreme illumination could lead to quality fluctuation of SHL. The combination of chemical and biological fingerprint method is a more powerful tool for the QC of SHL because it can clearly discriminate different groups of abnormal samples. This method can be used for the detection of quality fluctuation of SHL and can provide reference for the quality control of other herbal injections.

  15. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Science.gov (United States)

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  16. Occurrence of xenobiotics in gray water and removal in three biological treatment systems

    NARCIS (Netherlands)

    Hernandez Leal, L.; Vieno, N.; Temmink, B.G.; Zeeman, G.; Buisman, C.J.N.

    2010-01-01

    Eighteen selected xenobiotics related to personal care and household chemicals (UV-filters, fragrances, preservatives, biocides, surfactants) were measured in gray water from 32 houses and in effluents of three different biological treatment systems (aerobic, anaerobic, and combined anaerobic + aero

  17. A Reflection on the Fate of Chiral 1,2,4-Triazole Fungicides in Biological Systems

    Science.gov (United States)

    In biological systems, stereoisomers of chiral compounds can exhibit significantly different pharmacokinetics (absorption, distribution, metabolism, and elimination) and pharmacodynamics (physiological effects). Pharmacokinetic processes (i.e., what the body does to the chemical)...

  18. Hazardous chemical tracking system (HAZ-TRAC)

    Energy Technology Data Exchange (ETDEWEB)

    Bramlette, J D; Ewart, S M; Jones, C E

    1990-07-01

    Westinghouse Idaho Nuclear Company, Inc. (WINCO) developed and implemented a computerized hazardous chemical tracking system, referred to as Haz-Trac, for use at the Idaho Chemical Processing Plant (ICPP). Haz-Trac is designed to provide a means to improve the accuracy and reliability of chemical information, which enhances the overall quality and safety of ICPP operations. The system tracks all chemicals and chemical components from the time they enter the ICPP until the chemical changes form, is used, or becomes a waste. The system runs on a Hewlett-Packard (HP) 3000 Series 70 computer. The system is written in COBOL and uses VIEW/3000, TurboIMAGE/DBMS 3000, OMNIDEX, and SPEEDWARE. The HP 3000 may be accessed throughout the ICPP, and from remote locations, using data communication lines. Haz-Trac went into production in October, 1989. Currently, over 1910 chemicals and chemical components are tracked on the system. More than 2500 personnel hours were saved during the first six months of operation. Cost savings have been realized by reducing the time needed to collect and compile reporting information, identifying and disposing of unneeded chemicals, and eliminating duplicate inventories. Haz-Trac maintains information required by the Superfund Amendment Reauthorization Act (SARA), the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) and the Occupational Safety and Health Administration (OSHA).

  19. Modular microfluidic system for biological sample preparation

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Implications of chemical biological terrorist events for children and pregnant women.

    Science.gov (United States)

    Teran-Maciver, Maria; Larson, Kristina

    2008-01-01

    During the past decade, the world has become more aware that chemical and biological weapons could be used on civilians as terrorism and that casualties could include children. It is essential that nurses who care for children and pregnant women know how to recognize the effects of this type of weapon on the population and how to alleviate or mitigate their impact. This article reviews key aspects of chemical-biological agents, the consequences of their use, the potential impact of a chemical-biological attack on children and pregnant women, and issues to consider in the event of such a catastrophe. PMID:18664903

  1. Carcinogenesis and Chemotherapy Viewed from the Perspective of Stoichiometric Network Analysis (SNA: What Can the Biological System of the Elements Contribute to an Understanding of Tumour Induction by Elemental Chemical Noxae (e.g., Ni2+, Cd2+ and to an Understanding of Chemotherapy?

    Directory of Open Access Journals (Sweden)

    Stefan Franzle

    2003-01-01

    Full Text Available The biological application of stoichiometric network analysis (SNA permits an understanding of tumour induction, carcinogenesis, and chemotherapy. Starting from the Biological System of the Elements, which provides a comprehensive treatment of the functions and distributions of chemical (trace elements in biology, an attempt is made to interrelate the essential feature of biology and — regrettably — of tumour genesis by superimposing SNA reasoning on common features of all crucial biological processes. For this purpose, aspects, effects and drawbacks of autocatalysis (identical reproduction which can occur either under control or without control [in tumours] are linked with the known facts about element distributions in living beings and about interference of metals with tumours (in terms of both chemotherapy and carcinogenesis. The essential role of autocatalysis in biology and the drawbacks of either controlled or spontaneous cell division can be used to understand crucial aspects of carcinogenesis and chemotherapy because SNA describes and predicts effects of autocatalysis, including phase effects that may be due to some kind of intervention. The SNA-based classifications of autocatalytic networks in cell biology are outlined here to identify new approaches to chemotherapy.

  2. Estimating Escherichia coli loads in streams based on various physical, chemical, and biological factors.

    Science.gov (United States)

    Dwivedi, Dipankar; Mohanty, Binayak P; Lesikar, Bruce J

    2013-05-01

    Microbes have been identified as a major contaminant of water resources. Escherichia coli (E. coli) is a commonly used indicator organism. It is well recognized that the fate of E. coli in surface water systems is governed by multiple physical, chemical, and biological factors. The aim of this work is to provide insight into the physical, chemical, and biological factors along with their interactions that are critical in the estimation of E. coli loads in surface streams. There are various models to predict E. coli loads in streams, but they tend to be system or site specific or overly complex without enhancing our understanding of these factors. Hence, based on available data, a Bayesian Neural Network (BNN) is presented for estimating E. coli loads based on physical, chemical, and biological factors in streams. The BNN has the dual advantage of overcoming the absence of quality data (with regards to consistency in data) and determination of mechanistic model parameters by employing a probabilistic framework. This study evaluates whether the BNN model can be an effective alternative tool to mechanistic models for E. coli loads estimation in streams. For this purpose, a comparison with a traditional model (LOADEST, USGS) is conducted. The models are compared for estimated E. coli loads based on available water quality data in Plum Creek, Texas. All the model efficiency measures suggest that overall E. coli loads estimations by the BNN model are better than the E. coli loads estimations by the LOADEST model on all the three occasions (three-fold cross validation). Thirteen factors were used for estimating E. coli loads with the exhaustive feature selection technique, which indicated that six of thirteen factors are important for estimating E. coli loads. Physical factors included temperature and dissolved oxygen; chemical factors include phosphate and ammonia; biological factors include suspended solids and chlorophyll. The results highlight that the LOADEST model

  3. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

    Science.gov (United States)

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  4. Recent advances in medical device triage technologies for chemical, biological, radiological, and nuclear events.

    Science.gov (United States)

    Lansdowne, Krystal; Scully, Christopher G; Galeotti, Loriano; Schwartz, Suzanne; Marcozzi, David; Strauss, David G

    2015-06-01

    In 2010, the US Food and Drug Administration (Silver Spring, Maryland USA) created the Medical Countermeasures Initiative with the mission of development and promoting medical countermeasures that would be needed to protect the nation from identified, high-priority chemical, biological, radiological, or nuclear (CBRN) threats and emerging infectious diseases. The aim of this review was to promote regulatory science research of medical devices and to analyze how the devices can be employed in different CBRN scenarios. Triage in CBRN scenarios presents unique challenges for first responders because the effects of CBRN agents and the clinical presentations of casualties at each triage stage can vary. The uniqueness of a CBRN event can render standard patient monitoring medical device and conventional triage algorithms ineffective. Despite the challenges, there have been recent advances in CBRN triage technology that include: novel technologies; mobile medical applications ("medical apps") for CBRN disasters; electronic triage tags, such as eTriage; diagnostic field devices, such as the Joint Biological Agent Identification System; and decision support systems, such as the Chemical Hazards Emergency Medical Management Intelligent Syndromes Tool (CHEMM-IST). Further research and medical device validation can help to advance prehospital triage technology for CBRN events.

  5. STOCHSIMGPU Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    OpenAIRE

    Klingbeil, G.; Erban, R; Giles, M; Maini, P.K.

    2010-01-01

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works wi...

  6. A novel process of dye wastewater treatment by linking advanced chemical oxidation with biological oxidation

    Directory of Open Access Journals (Sweden)

    Zou Haiming

    2015-12-01

    Full Text Available Dye wastewater is one of typically non-biodegradable industrial effluents. A new process linking Fenton’s oxidation with biological oxidation proposed in this study was investigated to degrade the organic substances from real dye wastewater. During the combination process, the Fenton’s oxidation process can reduce the organic load and enhance biodegradability of dye wastewater, which is followed by biological aerated filter (BAF system to further remove organic substances in terms of discharge requirement. The results showed that 97.6% of chemical oxygen demand (COD removal by the combination process was achieved at the optimum process parameters: pH of 3.5, H2O2 of 2.0 mL/L, Fe(II of 500 mg/L, 2.0 h treatment time in the Fenton’s oxidation process and hydraulic retention time (HRT of 5 h in the BAF system. Under these conditions, COD concentration of effluent was 72.6 mg/L whereas 3020 mg/L in the influent, thus meeting the requirement of treated dye wastewater discharge performed by Chinese government (less than 100 mg/L. These results obtained here suggest that the new process combining Fenton’s oxidation with biological oxidation may provide an economical and effective alternative for treatment of non-biodegradable industrial wastewater.

  7. Analytical Applications of Nanomaterials in Monitoring Biological and Chemical Contaminants in Food.

    Science.gov (United States)

    Lim, Min-Cheol; Kim, Young-Rok

    2016-09-28

    The detection of food pathogens is an important aspect of food safety. A range of detection systems and new analytical materials have been developed to achieve fast, sensitive, and accurate monitoring of target pathogens. In this review, we summarize the characteristics of selected nanomaterials and their applications in food, and place focus on the monitoring of biological and chemical contaminants in food. The unique optical and electrical properties of nanomaterials, such as gold nanoparticles, nanorods, quantum dots, carbon nanotubes, graphenes, nanopores, and polydiacetylene nanovesicles, are closely associated with their dimensions, which are comparable in scale to those of targeted biomolecules. Furthermore, their optical and electrical properties are highly dependent on local environments, which make them promising materials for sensor development. The specificity and selectivity of analytical nanomaterials for target contaminants can be achieved by combining them with various biological entities, such as antibodies, oligonucleotides, aptamers, membrane proteins, and biological ligands. Examples of nanomaterial-based analytical systems are presented together with their limitations and associated developmental issues.

  8. Computational systems biology for aging research.

    Science.gov (United States)

    Mc Auley, Mark T; Mooney, Kathleen M

    2015-01-01

    Computational modelling is a key component of systems biology and integrates with the other techniques discussed thus far in this book by utilizing a myriad of data that are being generated to quantitatively represent and simulate biological systems. This chapter will describe what computational modelling involves; the rationale for using it, and the appropriateness of modelling for investigating the aging process. How a model is assembled and the different theoretical frameworks that can be used to build a model are also discussed. In addition, the chapter will describe several models which demonstrate the effectiveness of each computational approach for investigating the constituents of a healthy aging trajectory. Specifically, a number of models will be showcased which focus on the complex age-related disorders associated with unhealthy aging. To conclude, we discuss the future applications of computational systems modelling to aging research.

  9. Prospects for improved detection of chemical, biological, radiological, and nuclear threats

    Energy Technology Data Exchange (ETDEWEB)

    Wuest, Craig R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hart, Brad [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Slezak, Thomas R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2012-07-31

    Acquisition and use of Chemical, Biological, Radiological, and Nuclear (CBRN) weapons continue to be a major focus of concern form the security apparatus of nation states because of their potential for mass casualties when used by a determined adversary.

  10. Biological treatments affect the chemical composition of coffee pulp

    NARCIS (Netherlands)

    Ulloa Rojas, J.B.; Verreth, J.A.J.; Amato, S.; Huisman, E.A.

    2003-01-01

    Biological treatments were applied to fresh coffee pulp (CoP) to improve its nutritive value for monogastric animals by reducing its content of cellulose and antinutritional factors (ANFs) such as total phenols, tannins and caffeine. Treatments were: (1) ensiling with 0, 50 and 100 g kg¿1 molasses f

  11. Caenorhabditis elegans chemical biology: lessons from small molecules

    Science.gov (United States)

    How can we complement Caenorhabditis elegans genomics and proteomics with a comprehensive structural and functional annotation of its metabolome? Several lines of evidence indicate that small molecules of largely undetermined structure play important roles in C. elegans biology, including key pathw...

  12. Environmental parameters of the Tennessee River in Alabama. 2: Physical, chemical, and biological parameters. [biological and chemical effects of thermal pollution from nuclear power plants on water quality

    Science.gov (United States)

    Rosing, L. M.

    1976-01-01

    Physical, chemical and biological water quality data from five sites in the Tennessee River, two in Guntersville Reservoir and three in Wheeler Reservoir were correlated with climatological data for three annual cycles. Two of the annual cycles are for the years prior to the Browns Ferry Nuclear Power Plant operations and one is for the first 14 months of Plant operations. A comparison of the results of the annual cycles indicates that two distinct physical conditions in the reservoirs occur, one during the warm months when the reservoirs are at capacity and one during the colder winter months when the reservoirs have been drawn-down for water storage during the rainy months and for weed control. The wide variations of physical and chemical parameters to which the biological organisms are subjected on an annual basis control the biological organisms and their population levels. A comparison of the parameters of the site below the Power plant indicates that the heated effluent from the plant operating with two of the three reactors has not had any effect on the organisms at this site. Recommendations given include the development of prediction mathematical models (statistical analysis) for the physical and chemical parameters under specific climatological conditions which affect biological organisms. Tabulated data of chemical analysis of water and organism populations studied is given.

  13. Diversity-Oriented Synthetic Strategies Applied to Cancer Chemical Biology and Drug Discovery

    OpenAIRE

    Ian Collins; Jones, Alan M.

    2014-01-01

    How can diversity-oriented strategies for chemical synthesis provide chemical tools to help shape our understanding of complex cancer pathways and progress anti-cancer drug discovery efforts? This review (surveying the literature from 2003 to the present) considers the applications of diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS) and associated strategies to cancer biology and drug discovery, summarising the syntheses of novel and often highly complex scaffolds from p...

  14. Fourier transform infrared spectra applications to chemical systems

    CERN Document Server

    Ferraro, John R

    1978-01-01

    Fourier Transform Infrared Spectroscopy: Applications to Chemical Systems presents the chemical applications of the Fourier transform interferometry (FT-IR).The book contains discussions on the applications of FT-IR in the fields of chromatography FT-IR, polymers and biological macromolecules, emission spectroscopy, matrix isolation, high-pressure interferometry, and far infrared interferometry. The final chapter is devoted to the presentation of the use of FT-IR in solving national technical problems such as air pollution, space exploration, and energy related subjects.Researc

  15. Effects of Pesticides on Biological Systems

    Directory of Open Access Journals (Sweden)

    Ergul Belge Kurutas

    2003-06-01

    Full Text Available The use of pesticid both in Turkey and other contries is widespread in order to combat against many pests which cause economical damages. However, pesticides in human pass through skin, respiratory or digestive systems and is metabolized by monooxygenase system dependent upon cytocrome P450 in liver. They also give rise to severe decreases cytochrome P450 and amount of "hem" enzyme activites of glucose-6-phosphatase, pyrophosphatase by stimulating lipid peroxidation on hepatic microsomes. In this study effects of pesticides on biological systems will be presented in genaral terms. [Archives Medical Review Journal 2003; 12(3.000: 215-228

  16. Chaos in a chemical system

    Science.gov (United States)

    Srivastava, R.; Srivastava, P. K.; Chattopadhyay, J.

    2013-07-01

    Chaotic oscillations have been observed experimentally in dual-frequency oscillator OAP - Ce+4-BrO- 3-H2SO4 in CSTR. The system shows variation of oscillating potential and frequencies when it moves from low frequency to high frequency region and vice-versa. It was observed that system bifurcate from low frequency to chaotic regime through periode-2 and period-3 on the other hand system bifurcate from chaotic regime to high frequency oscillation through period-2. It was established that the observed oscillations are chaotic in nature on the basis of next amplitude map and bifurcation sequences.

  17. Structure and biological activity of chemically modified nisin A species

    NARCIS (Netherlands)

    Rollema, Harry S.; Metzger, Jörg W.; Both, Paula; Kuipers, Oscar P.; Siezen, Roland J.

    1996-01-01

    Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, β-methyllanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray m

  18. 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. PMID:26696234

  19. Marine Sponges and Symbionts: Chemical and Biological Studies

    OpenAIRE

    Schmidt, Eric W.

    1999-01-01

    This thesis concerns two quite different types of research that are separated into distinct sections of the thesis, but which seek to answer the same question using diametrically opposite approaches. The first part (Chapters 1-8) covers research leading to novel, bioactive compounds in marine sponges, while the second (Chapters 9-10) involves molecular biological studies of symbiosis between microbes and sponges. Although these topics seem at first glance completely separate, they are in real...

  20. Polycyclic Xanthone Natural Products: Structure, Biological Activity and Chemical Synthesis

    OpenAIRE

    Winter, Dana K.; Sloman, David L.; Porco, John A.

    2013-01-01

    Polycyclic xanthone natural products are a family of polyketides which are characterized by highly oxygenated, angular hexacyclic frameworks. In the last decade, this novel class of molecules has attracted noticeable attention from the synthetic and biological communities due to emerging reports of their potential use as antitumour agents. The aim of this article is to highlight the most recent developments of this subset of the xanthone family by detailing the innate challenges of the constr...

  1. Simaroubaceae family: botany, chemical composition and biological activities

    OpenAIRE

    Iasmine A.B.S. Alves; Henrique M. Miranda; Luiz A. L. Soares; Karina P. Randau

    2014-01-01

    The Simaroubaceae family includes 32 genera and more than 170 species of trees and brushes of pantropical distribution. The main distribution hot spots are located at tropical areas of America, extending to Africa, Madagascar and regions of Australia bathed by the Pacific. This family is characterized by the presence of quassinoids, secondary metabolites responsible of a wide spectrum of biological activities such as antitumor, antimalarial, antiviral, insecticide, feeding deterrent, amebicid...

  2. Integrated assessment of oil pollution using biological monitoring and chemical fingerprinting.

    Science.gov (United States)

    Lewis, Ceri; Guitart, Carlos; Pook, Chris; Scarlett, Alan; Readman, James W; Galloway, Tamara S

    2010-06-01

    A full assessment of the impact of oil and chemical spills at sea requires the identification of both the polluting chemicals and the biological effects they cause. Here, a combination of chemical fingerprinting of surface oils, tissue residue analysis, and biological effects measures was used to explore the relationship between spilled oil and biological impact following the grounding of the MSC Napoli container ship in Lyme Bay, England in January 2007. Initially, oil contamination remained restricted to a surface slick in the vicinity of the wreck, and there was no chemical evidence to link biological impairment of animals (the common limpet, Patella vulgata) on the shore adjacent to the oil spill. Secondary oil contamination associated with salvage activities in July 2007 was also assessed. Chemical analyses of aliphatic hydrocarbons and terpanes in shell swabs taken from limpet shells provided an unequivocal match with the fuel oil carried by the ship. Corresponding chemical analysis of limpet tissues revealed increased concentrations of polycyclic aromatic hydrocarbons (PAHs) dominated by phenanthrene and C1 to C3 phenanthrenes with smaller contributions from heavier molecular weight PAHs. Concurrent ecotoxicological tests indicated impairment of cellular viability (p oiled animals. These results illustrate the value of combining biological monitoring with chemical fingerprinting for the rapid identification of spilled oils and their sublethal impacts on biota in situ.

  3. Computer structures perspective on switching dynamics of simple biological systems

    OpenAIRE

    Moškon, Miha

    2012-01-01

    Synthetic biology is a rapidly evolving discipline that copes with the modifications of existent and with the construction of new biological systems with novel functionalities. Its interdisciplinarity arises from combining of engineering and biological sciences. Biological computing is a relatively new research field that is analyzing the possibilities of constructing a biological computer. Synthetic biology approaches can also be used in order to build biological computer. Certain levels of ...

  4. Graphical Modelling in Genetics and Systems Biology

    OpenAIRE

    Scutari, Marco

    2012-01-01

    Graphical modelling has a long history in statistics as a tool for the analysis of multivariate data, starting from Wright's path analysis and Gibbs' applications to statistical physics at the beginning of the last century. In its modern form, it was pioneered by Lauritzen and Wermuth and Pearl in the 1980s, and has since found applications in fields as diverse as bioinformatics, customer satisfaction surveys and weather forecasts. Genetics and systems biology are unique among these fields in...

  5. Systems Biology from a Yeast Omics Perspective

    OpenAIRE

    Snyder, Michael; Gallagher, Jennifer E.G.

    2009-01-01

    Systems biology represents a paradigm shift from the study of individual genes, proteins or other components to that of the analysis of entire pathways, cellular, developmental, or organismal processes. Large scale studies, primarily initiated in S. cerevisiae, have allowed the identification and characterization of components on an unprecedented level. Large scale interaction, transcription factor binding and phosphorylation data have enabled the elucidation of global regulatory networks. Th...

  6. Chemical production processes and systems

    Science.gov (United States)

    Holladay, Johnathan E.; Muzatko, Danielle S.; White, James F.; Zacher, Alan H.

    2014-06-17

    Hydrogenolysis systems are provided that can include a reactor housing an Ru-comprising hydrogenolysis catalyst and wherein the contents of the reactor is maintained at a neutral or acidic pH. Reactant reservoirs within the system can include a polyhydric alcohol compound and a base, wherein a weight ratio of the base to the compound is less than 0.05. Systems also include the product reservoir comprising a hydrogenolyzed polyhydric alcohol compound and salts of organic acids, and wherein the moles of base are substantially equivalent to the moles of salts or organic acids. Processes are provided that can include an Ru-comprising catalyst within a mixture having a neutral or acidic pH. A weight ratio of the base to the compound can be between 0.01 and 0.05 during exposing.

  7. Systems biology of cancer biomarker detection.

    Science.gov (United States)

    Mitra, Sanga; Das, Smarajit; Chakrabarti, Jayprokas

    2013-01-01

    Cancer systems-biology is an ever-growing area of research due to explosion of data; how to mine these data and extract useful information is the problem. To have an insight on carcinogenesis one need to systematically mine several resources, such as databases, microarray and next-generation sequences. This review encompasses management and analysis of cancer data, databases construction and data deposition, whole transcriptome and genome comparison, analysing results from high throughput experiments to uncover cellular pathways and molecular interactions, and the design of effective algorithms to identify potential biomarkers. Recent technical advances such as ChIP-on-chip, ChIP-seq and RNA-seq can be applied to get epigenetic information transformed into a high-throughput endeavour to which systems biology and bioinformatics are making significant inroads. The data from ENCODE and GENCODE projects available through UCSC genome browser can be considered as benchmark for comparison and meta-analysis. A pipeline for integrating next generation sequencing data, microarray data, and putting them together with the existing database is discussed. The understanding of cancer genomics is changing the way we approach cancer diagnosis and treatment. To give a better understanding of utilizing available resources' we have chosen oral cancer to show how and what kind of analysis can be done. This review is a computational genomic primer that provides a bird's eye view of computational and bioinformatics' tools currently available to perform integrated genomic and system biology analyses of several carcinoma.

  8. Tomato Derived Polysaccharides for Biotechnological Applications: Chemical and Biological Approaches

    Directory of Open Access Journals (Sweden)

    Barbara Nicolaus

    2008-06-01

    Full Text Available Recent studies concerning the isolation and purification of exopolysaccharides from suspension-cultured tomato (Lycopersicon esculentum L. var. San Marzano cells and the description of a simple, rapid and low environmental impact method with for obtaining polysaccharides from solid tomato-processing industry wastes are reported. Their chemical composition, rheological properties and partial primary structure were determined on the basis of spectroscopic analyses (UV, IR, GC-MS, 1H-, 13C-NMR. Moreover, the anticytotoxic activities of exopolysaccharides obtained from cultured tomato cells were tested in a brine shrimp bioassay and the preparation of biodegradable film by chemical processing of polysaccharides from solid tomato industry waste was also reported.

  9. Ozonation of estrogenic chemicals in biologically treated sewage

    DEFF Research Database (Denmark)

    Hansen, Kamilla Marie Speht; Andersen, Henrik Rasmus; Ledin, Anna

    2010-01-01

    The present study shows that ozonation of effluents from municipal wastewater treatment plants (WWTPs) is likely to be a future treatment solution to remove estrogens and xeno-estrogens. The required ozone dose and electrical energy for producing the ozone were determined in two WWTP effluents...... for removal of 17 estrogenic chemicals. The estrogenic compounds included parabens, industrial phenols, sunscreen chemicals, and steroid estrogens. The obtained values of Electrical Energy per Order (EEOs) for the treatment of the estrogens were in the range 0.14–1.1 kWh/m3 corresponding to 1.7–14 g O3/m3....... It is furthermore suggested that UV-absorbance is a useful parameter for online control of the ozone dose in a full scale application since the absorbance of the WWTP effluents and the remaining concentration of the estrogens and xeno-estrogens correlated well with the applied ozone dose....

  10. Sino-Dutch joint center for systematic chemical biology opens in Dalian

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ The inaugural ceremony for the Sino-Dutch Joint Research Center for Systematic Chemical Biology was held during the "Chinese-Dutch Workshop on Personalized Medicine and Preventive Diagnostics" convened on 10 July at the CAS Dalian Institute of Chemical Physics (DICP).

  11. [Advances in studies on chemical constituents and biological activities of Desmodium species].

    Science.gov (United States)

    Liu, Chao; Wu, Ying; Zhang, Qian-Jun; Kang, Wen-Yi; Zhang, Long; Zhou, Qing-Di

    2013-12-01

    The chemical constituents isolated from Desmodium species (Leguminosae) included terpenoids, flavonoids, steroids, alkaloids compounds. Modem pharmacological studies have showed that the Desmodium species have antioxidant, antibacterial, anti-inflammatory, hepatoprotective, diuretic, antipyretic, analgesic and choleretic activity. This article mainly has reviewed the research advances of chemical constituents and biological activities of Desmodium species since 2003. PMID:24791478

  12. Categorization of biologically relevant chemical signals in the medial amygdala

    OpenAIRE

    Samuelsen, Chad L.; Meredith, Michael

    2009-01-01

    Many species employ chemical signals to convey messages between members of the same species (conspecific), but chemosignals may also provide information to another species (heterospecific). Here, we found that conspecific chemosignals (male, female mouse urine) increased immediate early gene-protein (IEG) expression in both anterior and posterior medial amygdala of male mice, whereas most heterospecific chemosignals (e.g.: hamster vaginal fluid, steer urine) increased expression only in anter...

  13. Scientific Basis for a Coupled Thermal-Hydrological-Mechanical-Chemical-Biological Experimental Facility at DUSEL Homestake

    Science.gov (United States)

    Sonnenthal, E. L.; Elsworth, D.; Lowell, R. P.; Maher, K.; Mailloux, B. J.; Uzunlar, N.; Freifeld, B. M.; Keimowitz, A. R.; Wang, J. S.

    2009-12-01

    Most natural and engineered earth system processes involve strong coupling of thermal, mechanical, chemical, and sometimes biological processes in rocks that are heterogeneous at a wide range of spatial scales. One of the most pervasive processes in the Earth’s crust is that of fluids (primarily water, but also CO2, hydrocarbons, volcanic gases, etc.) flowing through fractured heated rock under stress. A preliminary design is being formulated for a large-scale subsurface experimental facility to investigate coupled Thermal-Hydrological-Mechanical-Chemical-Biological (THMCB) processes in fractured rock at depth. The experiment would be part of the proposed Deep Underground Science and Engineering Laboratory (DUSEL) in the Homestake Mine, South Dakota. Fundamental geochemical, isotopic, microbiological, laboratory THMC experiments, and numerical modeling will be used to guide the experimental design and evaluation of the time and spatial scales of the coupled THMCB processes. Although we sometimes analyze rocks and fluids for physical and chemical properties, it is difficult to create quantitative numerical models based on fundamental physics and chemistry that can capture the dynamic changes that have occurred or may yet take place. Initial conditions and history are only known roughly at best, and the boundary conditions have likely varied over time as well. Processes such as multicomponent chemical and thermal diffusion, multiphase flow, advection, and thermal expansion/contraction, are taking place simultaneously in rocks that are structurally and chemically complex—heterogeneous assemblages of mineral grains, pores, and fractures—and visually opaque. The only way to fully understand such processes is to carry out well-controlled experiments at a range of scales (grain/pore-scale to decimeter-scale) that can be interrogated and modeled. The THMCB experimental facility is also intended to be a unique laboratory for testing hypotheses regarding effects of

  14. 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.

  15. [Systems theory in medicine and biology].

    Science.gov (United States)

    Feigl, W; Bonet, E M

    1989-03-15

    We try to determinate, that systems theory has to be introduced into modern medicine. The biological roots as well as the cybernetic ones are outlined. Among various concepts about systems theory the evaluation by Riedl seems to be the most efficient to explain medical procedures. His basic informations refer to von Bertalanffy, the additional introduction of a 4-cause-principle, Aristoteles, permits the explanation of complex relations. The examples of tumor and inflammation are used to demonstrate the basic idea of the formal cause as well as the final cause. The latter should also become an important fact in the solution of other medical problems.

  16. Chemical and biological evaluation of sediments from the Wadden Sea, The Netherlands

    OpenAIRE

    Brink, van den, R.B.A.; Kater, B. J.

    2006-01-01

    We describe the results of an evaluation of marine sediments using chemical measurements and bioassays. Four groups of chemicals, i.e., heavy metals, PAHs, chlorinated aromatic compounds, and tin compounds, were measured at 16 locations in the Wadden Sea, The Netherlands. Extractions of sediments from each location also were assessed using five bioassays. Our objective was to identify chemicals likely to pose biological risks, characterize the relation between bioassay results and particular ...

  17. In-Space Chemical Propulsion System Model

    Science.gov (United States)

    Byers, David C.; Woodcock, Gordon; Benfield, Michael P. J.

    2004-01-01

    Multiple, new technologies for chemical systems are becoming available and include high temperature rockets, very light propellant tanks and structures, new bipropellant and monopropellant options, lower mass propellant control components, and zero boil off subsystems. Such technologies offer promise of increasing the performance of in-space chemical propulsion for energetic space missions. A mass model for pressure-fed, Earth and space-storable, advanced chemical propulsion systems (ACPS) was developed in support of the NASA MSFC In-Space Propulsion Program. Data from flight systems and studies defined baseline system architectures and subsystems and analyses were formulated for parametric scaling relationships for all ACPS subsystem. The paper will first provide summary descriptions of the approaches used for the systems and the subsystems and then present selected analyses to illustrate use of the model for missions with characteristics of current interest.

  18. Chemical Biology Studies on Molecular Diversity of Annonaceous Acetogenins

    Institute of Scientific and Technical Information of China (English)

    Yao Zhu-Jun

    2004-01-01

    Annonaceous acetogenins, isolated from the Annonaceae plants, have been attracting worldwide attention in recent years due to their biological activities, especially as growth inhibitors of certain tumor ceils [ 1 ]. They have been shown to function by blocking complex I in mitochondria [2] as well as ubiquinone-linked NADPH oxidase in the cells of specific tumor cell lines, including some multidrug-resistant ones [3]. These features make these acetogenins excellent leads for the new antitumor agents. In our previous work, the compounds 1a to 1d (Figure 1), which relies on structure simplification while maintaining all essential functionalities of the acetogenins, was in vitro tested against several human solid tumor cell lines and showed interesting cell selectivity [4]. All four analogues show remarkable activity against the HCT-8 and HT-29 cell lines, while compound 1c was found the best [4bi. In order to further investigate the effects of key structural features, a convergent parallel fragments assembly strategy was developed [4e]. In addition, the biological relevancies of typical annonaceous acetogenin mimetics were also studied [4f].

  19. Clustering and rule-based classifications of chemical structures evaluated in the biological activity space.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Brown, Nathan; Ertl, Peter; Jenkins, Jeremy L; Selzer, Paul; Hamon, Jacques

    2007-01-01

    Classification methods for data sets of molecules according to their chemical structure were evaluated for their biological relevance, including rule-based, scaffold-oriented classification methods and clustering based on molecular descriptors. Three data sets resulting from uniformly determined in vitro biological profiling experiments were classified according to their chemical structures, and the results were compared in a Pareto analysis with the number of classes and their average spread in the profile space as two concurrent objectives which were to be minimized. It has been found that no classification method is overall superior to all other studied methods, but there is a general trend that rule-based, scaffold-oriented methods are the better choice if classes with homogeneous biological activity are required, but a large number of clusters can be tolerated. On the other hand, clustering based on chemical fingerprints is superior if fewer and larger classes are required, and some loss of homogeneity in biological activity can be accepted.

  20. Biological and chemical removal of Cr(VI) from waste water: cost and benefit analysis.

    Science.gov (United States)

    Demir, Aynur; Arisoy, Münevver

    2007-08-17

    The objective of the present study is cost and benefit analysis of biological and chemical removal of hexavalent chromium [Cr(VI)] ions. Cost and benefit analysis were done with refer to two separate studies on removal of Cr(VI), one of heavy metals with a crucial role concerning increase in environmental pollution and disturbance of ecological balance, through biological adsorption and chemical ion-exchange. Methods of biological and chemical removal were compared with regard to their cost and percentage in chrome removal. According to the result of the comparison, cost per unit in chemical removal was calculated 0.24 euros and the ratio of chrome removal was 99.68%, whereas those of biological removal were 0.14 and 59.3% euros. Therefore, it was seen that cost per unit in chemical removal and chrome removal ratio were higher than those of biological removal method. In the current study where chrome removal is seen as immeasurable benefit in terms of human health and the environment, percentages of chrome removal were taken as measurable benefit and cost per unit of the chemicals as measurable cost.

  1. Bioluminescent bioreporter assays for targeted detection of chemical and biological agents

    Science.gov (United States)

    Ripp, Steven; Jegier, Pat; Johnson, Courtney; Moser, Scott; Islam, Syed; Sayler, Gary

    2008-04-01

    Bioluminescent bioreporters carrying the bacterial lux gene cassette have been well established for the sensing and monitoring of select chemical agents. Their ability to generate target specific visible light signals with no requirement for extraneous additions of substrate or other hands-on manipulations affords a real-time, repetitive assaying technique that is remarkable in its simplicity and accuracy. Although the predominant application of lux-based bioluminescent bioreporters has been towards chemical compound detection, novel genetic engineering schemes are yielding a variety of new bioreporter systems that extend the lux sensing mechanism beyond mere analyte discrimination. For example, the unique specificity of bacteriophage (bacterial viruses) has been exploited in lux bioluminescent assays for specific identification of foodborne bacterial pathogens such as Escherichia coli O157:H7. With the concurrent ability to interface bioluminescent bioreporter assays onto integrated circuit microluminometers (BBICs; bioluminescent bioreporter integrated circuits), the potential exists for the development of sentinel microchips that can function as environmental monitors for multiplexed recognition of chemical and biological agents in air, food, and water. The size and portability of BBIC biosensors may ultimately provide a deployable, interactive network sensing technology adaptable towards chem/bio defense.

  2. Mesophilic anaerobic co-digestion of cattle manure and corn stover with biological and chemical pretreatment.

    Science.gov (United States)

    Wei, Yufang; Li, Xiujin; Yu, Liang; Zou, Dexun; Yuan, Hairong

    2015-12-01

    Biological and chemical pretreatment methods using liquid fraction of digestate (LFD), ammonia solution (AS), and NaOH were compared in the process of mesophilic anaerobic co-digestion of cattle manure and corn stover. The results showed that LFD pretreatment could achieve the same effect as the chemical pretreatment (AS, NaOH) at the performance of anaerobic digestion (AD). Compared with the untreated corn stover, the cumulative biomethane production (CBP) and the volatile solid (VS) removal rate of three pretreatment methods were increased by 25.40-30.12% and 14.48-16.84%, respectively, in the co-digestion of cattle manure and corn stover. T80 was 20-37.14% shorter than that of the control test (35 ± 1 days). LFD pretreatment not only achieved the same effect as chemical pretreatment, but also reduced T80 and improved buffer capacity of anaerobic digestion system. Therefore, this study provides meaningful insight for exploring efficient pretreatment strategy to stabilize and enhance AD performance for practical application. PMID:26409855

  3. 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

  4. Biological and chemical decoration of peptide nanostructures via biotin-avidin interactions.

    Science.gov (United States)

    Reches, Meital; Gazit, Ehud

    2007-07-01

    Novel architectures with nanometric dimensions hold an immense promise as building blocks for future nanotechnological applications. Biological nanostructures are of special interest due to their biocompatibility and because they allow the utilization of biochemical recognition interfaces. The ability to decorate bio-nanostructures with functional groups is highly important in order to utilize them in several applications including ultrasensitive sensors, drug delivery systems, and tissue engineering. Peptide-based nanostructures have a distinct advantage over other assemblies because they can be easily modified with chemical and biological elements. Aromatic dipeptide nanotubes (ADNT) are formed by the self-assembly of a very simple building block, the diphenylalanine peptide. These nanotubes have remarkable chemical and mechanical properties and their utilization in various applications has previously been demonstrated. Here we report on the chemical modification of ADNT with biotin moieties, in order to enable the selective decoration of the tubes with avidin-labeled species. First, ADNT were prepared in aqueous solution by self-assembly of the dipeptide building blocks. Next, they were modified using N-hydroxysuccinimido-biotin. The level of biotinylation was assessed by the interaction of the tubes with gold-labeled strepavidin and ultrastructural analysis by electron microscopy. The ability of the modified assemblies to serve as a generic functional platform was demonstrated by avidin-mediated conjugation. Avidin was added as a molecular linker to allow the decoration with biotin-labeled quantum dots. The efficient decoration was again probed by the imaging of the modified tubes using laser confocal microscopy. Taken together, we demonstrated the ability to decorate ADNT using a generic avidin-biotin adaptor. This decoration should lead to the integration and utilization of the tubes in various applications. PMID:17663236

  5. 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.

  6. 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. PMID:25845304

  7. 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.

  8. Engineered Barrier System: Physical and Chemical Environment

    International Nuclear Information System (INIS)

    The conceptual and predictive models documented in this Engineered Barrier System: Physical and Chemical Environment Model report describe the evolution of the physical and chemical conditions within the waste emplacement drifts of the repository. The modeling approaches and model output data will be used in the total system performance assessment (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. These models evaluate the range of potential water compositions within the emplacement drifts, resulting from the interaction of introduced materials and minerals in dust with water seeping into the drifts and with aqueous solutions forming by deliquescence of dust (as influenced by atmospheric conditions), and from thermal-hydrological-chemical (THC) processes in the drift. These models also consider the uncertainty and variability in water chemistry inside the drift and the compositions of introduced materials within the drift. This report develops and documents a set of process- and abstraction-level models that constitute the engineered barrier system: physical and chemical environment model. Where possible, these models use information directly from other process model reports as input, which promotes integration among process models used for total system performance assessment. Specific tasks and activities of modeling the physical and chemical environment are included in the technical work plan ''Technical Work Plan for: In-Drift Geochemistry Modeling'' (BSC 2004 [DIRS 166519]). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system analysis model reports

  9. Nano-FTIR chemical mapping of minerals in biological materials

    Directory of Open Access Journals (Sweden)

    Sergiu Amarie

    2012-04-01

    Full Text Available Methods for imaging of nanocomposites based on X-ray, electron, tunneling or force microscopy provide information about the shapes of nanoparticles; however, all of these methods fail on chemical recognition. Neither do they allow local identification of mineral type. We demonstrate that infrared near-field microscopy solves these requirements at 20 nm spatial resolution, highlighting, in its first application to natural nanostructures, the mineral particles in shell and bone. "Nano-FTIR" spectral images result from Fourier-transform infrared (FTIR spectroscopy combined with scattering scanning near-field optical microscopy (s-SNOM. On polished sections of Mytilus edulis shells we observe a reproducible vibrational (phonon resonance within all biocalcite microcrystals, and distinctly different spectra on bioaragonite. Surprisingly, we discover sparse, previously unknown, 20 nm thin nanoparticles with distinctly different spectra that are characteristic of crystalline phosphate. Multicomponent phosphate bands are observed on human tooth sections. These spectra vary characteristically near tubuli in dentin, proving a chemical or structural variation of the apatite nanocrystals. The infrared band strength correlates with the mineral density determined by electron microscopy. Since nano-FTIR sensitively responds to structural disorder it is well suited for the study of biomineral formation and aging. Generally, nano-FTIR is suitable for the analysis and identification of composite materials in any discipline, from testing during nanofabrication to even the clinical investigation of osteopathies.

  10. CHEMICAL AND BIOLOGICAL EXAMINATION OF LEAVES OF MORUS INDICA

    Directory of Open Access Journals (Sweden)

    Pethakamsetty Lakshmi

    2013-06-01

    Full Text Available Mulberry belongs to the genus Morus of the family Moraceae. It is an economically important plant being used for sericulture. Studies have been reported on the chemical composition and nutritional potentials of some mulberry species worldwide. In the present study the chemical examination of Morus indica leaves on conventional extraction and various chromatographic methods, led to the isolation of five compounds- β-sitosterol-3-O-β-D-glucoside, β-sitosterol, salvigenin, cirisimaritin and quercitin. All the compounds were characterized by 2D NMR, MS spectral data and comparison with the published data for the known compounds. All the compounds were reported for the first time from the leaves of this species. The work was further extended to test the crude extracts for antibacterial and antifungal activities. The results from the present study have shown that the species have considerable activity against selected bacterial and fungal strains which can be attributed to the presence of steroidal and phenolic compounds in the crude extracts of Morus indica.

  11. Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito.

    Science.gov (United States)

    Després, Laurence; Stalinski, Renaud; Faucon, Frédéric; Navratil, Vincent; Viari, Alain; Paris, Margot; Tetreau, Guillaume; Poupardin, Rodolphe; Riaz, Muhammad Asam; Bonin, Aurélie; Reynaud, Stéphane; David, Jean-Philippe

    2014-12-01

    Worldwide evolution of mosquito resistance to chemical insecticides represents a major challenge for public health, and the future of vector control largely relies on the development of biological insecticides that can be used in combination with chemicals (integrated management), with the expectation that populations already resistant to chemicals will not become readily resistant to biological insecticides. However, little is known about the metabolic pathways affected by selection with chemical or biological insecticides. Here we show that Aedes aegypti, a laboratory mosquito strain selected with a biological insecticide (Bacillus thuringiensis israelensis, Bti) evolved increased transcription of many genes coding for endopeptidases while most genes coding for detoxification enzymes were under-expressed. By contrast, in strains selected with chemicals, genes encoding detoxification enzymes were mostly over-expressed. In all the resistant strains, genes involved in immune response were under-transcribed, suggesting that basal immunity might be a general adjustment variable to compensate metabolic costs caused by insecticide selection. Bioassays generally showed no evidence for an increased susceptibility of selected strains towards the other insecticide type, and all chemical-resistant strains were as susceptible to Bti as the unselected parent strain, which is a good premise for sustainable integrated management of mosquito populations resistant to chemicals.

  12. Capturing Biological Activity in Natural Product Fragments by Chemical Synthesis.

    Science.gov (United States)

    Crane, Erika A; Gademann, Karl

    2016-03-14

    Natural products have had an immense influence on science and have directly led to the introduction of many drugs. Organic chemistry, and its unique ability to tailor natural products through synthesis, provides an extraordinary approach to unlock the full potential of natural products. In this Review, an approach based on natural product derived fragments is presented that can successfully address some of the current challenges in drug discovery. These fragments often display significantly reduced molecular weights, reduced structural complexity, a reduced number of synthetic steps, while retaining or even improving key biological parameters such as potency or selectivity. Examples from various stages of the drug development process up to the clinic are presented. In addition, this process can be leveraged by recent developments such as genome mining, antibody-drug conjugates, and computational approaches. All these concepts have the potential to identify the next generation of drug candidates inspired by natural products.

  13. Chemical Analysis and Biological Activity of Jordanian Chamomile Extracts

    Directory of Open Access Journals (Sweden)

    Nawal Hassan Al Bahtiti

    2012-02-01

    Full Text Available The Jordanian chamomile (Matricaria chamomilla has been researched more thoroughly to evaluate its useful properties. It is investigated and found that Jordanian chamomile is rich in phenolic compounds, with beneficial biological activities. By applying the most promising HPLC method, the content of total phenolics in methanolic extract was determined according to the Folin-Clocalteu procedure, and was found (GAE>20 mg/g. The flavonoid types were found as flavones and flavonolos.The minimum inhibitory concentration values for methanolic extracts of Jordanian chamomile were determined for different kinds of bacteria. The extracts have activity against Staphylococcus aurous, candida albicans, Esherichia Coli, Betula pubescens and Pinus sylvestris. The activity has been observed to be due to the tannins and a pigenin present in the extract. To utilize these significant sources of natural compounds, further characterization of phenolic composition is needed.

  14. Fungal phytotoxins with potential herbicidal activity: chemical and biological characterization.

    Science.gov (United States)

    Cimmino, Alessio; Masi, Marco; Evidente, Marco; Superchi, Stefano; Evidente, Antonio

    2015-12-19

    Covering: 2007 to 2015 Fungal phytotoxins are secondary metabolites playing an important role in the induction of disease symptoms interfering with host plant physiological processes. Although fungal pathogens represent a heavy constraint for agrarian production and for forest and environmental heritage, they can also represent an ecofriendly alternative to manage weeds. Indeed, the phytotoxins produced by weed pathogenic fungi are an efficient tool to design natural, safe bioherbicides. Their use could avoid that of synthetic pesticides causing resistance in the host plants and the long term impact of residues in agricultural products with a risk to human and animal health. The isolation and structural and biological characterization of phytotoxins produced by pathogenic fungi for weeds, including parasitic plants, are described. Structure activity relationships and mode of action studies for some phytotoxins are also reported to elucidate the herbicide potential of these promising fungal metabolites. PMID:26443032

  15. 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.

  16. A Free Energy Principle for Biological Systems

    Directory of Open Access Journals (Sweden)

    Friston Karl

    2012-10-01

    Full Text Available This paper describes a free energy principle that tries to explain the ability of biological systems to resist a natural tendency to disorder. It appeals to circular causality of the sort found in synergetic formulations of self-organization (e.g., the slaving principle and models of coupled dynamical systems, using nonlinear Fokker Planck equations. Here, circular causality is induced by separating the states of a random dynamical system into external and internal states, where external states are subject to random fluctuations and internal states are not. This reduces the problem to finding some (deterministic dynamics of the internal states that ensure the system visits a limited number of external states; in other words, the measure of its (random attracting set, or the Shannon entropy of the external states is small. We motivate a solution using a principle of least action based on variational free energy (from statistical physics and establish the conditions under which it is formally equivalent to the information bottleneck method. This approach has proved useful in understanding the functional architecture of the brain. The generality of variational free energy minimisation and corresponding information theoretic formulations may speak to interesting applications beyond the neurosciences; e.g., in molecular or evolutionary biology.

  17. 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…

  18. 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…

  19. Silicon chip integrated photonic sensors for biological and chemical sensing

    Science.gov (United States)

    Chakravarty, Swapnajit; Zou, Yi; Yan, Hai; Tang, Naimei; Chen, Ray T.

    2016-03-01

    We experimentally demonstrate applications of photonic crystal waveguide based devices for on-chip optical absorption spectroscopy for the detection of chemical warfare simulant, triethylphosphate as well as applications with photonic crystal microcavity devices in the detection of biomarkers for pancreatic cancer in patient serum and cadmium metal ions in heavy metal pollution sensing. At mid-infrared wavelengths, we experimentally demonstrate the higher sensitivity of photonic crystal based structures compared to other nanophotonic devices such as strip and slot waveguides with detection down to 10ppm triethylphosphate. We also detected 5ppb (parts per billion) of cadmium metal ions in water at near-infrared wavelengths using established techniques for the detection of specific probe-target biomarker conjugation chemistries.

  20. Psychological casualties resulting from chemical and biological weapons.

    Science.gov (United States)

    Romano, J A; King, J M

    2001-12-01

    This symposium addresses the complications encountered by medical planners when confronted by the use or threat of the use of weapons of mass destruction. The types of chemical warfare agents (CWA), their principal target organs, and physiological effects are discussed. We have reviewed the use of CWA in 20th century warfare and otherwise with emphasis on five cases: (1) use of sulfur mustard during World War I; (2) use by Italy against Ethiopia; (3) use in the Sino-Japanese War; (4) relatively well-studied use in the Iran-Iraq conflict; and (5) the use of sarin in the Tokyo subway terrorist incident. We reviewed the additional physiological and psychological consequences of their use and threat of use. Results from training and simulation are discussed. Finally, we present our conclusions derived from the analysis of these historical situations.

  1. Functional Nanostructured Platforms for Chemical and Biological Sensing

    Energy Technology Data Exchange (ETDEWEB)

    Letant, S E

    2006-03-20

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

  2. Nanomaterial processing using self-assembly-bottom-up chemical and biological approaches

    International Nuclear Information System (INIS)

    Nanotechnology is touted as the next logical sequence in technological evolution. This has led to a substantial surge in research activities pertaining to the development and fundamental understanding of processes and assembly at the nanoscale. Both top-down and bottom-up fabrication approaches may be used to realize a range of well-defined nanostructured materials with desirable physical and chemical attributes. Among these, the bottom-up self-assembly process offers the most realistic solution toward the fabrication of next-generation functional materials and devices. Here, we present a comprehensive review on the physical basis behind self-assembly and the processes reported in recent years to direct the assembly of nanoscale functional blocks into hierarchically ordered structures. This paper emphasizes assembly in the synthetic domain as well in the biological domain, underscoring the importance of biomimetic approaches toward novel materials. In particular, two important classes of directed self-assembly, namely, (i) self-assembly among nanoparticle–polymer systems and (ii) external field-guided assembly are highlighted. The spontaneous self-assembling behavior observed in nature that leads to complex, multifunctional, hierarchical structures within biological systems is also discussed in this review. Recent research undertaken to synthesize hierarchically assembled functional materials have underscored the need as well as the benefits harvested in synergistically combining top-down fabrication methods with bottom-up self-assembly. (review article)

  3. Non-Chemical Distant Cellular Interactions as a potential confounder of Cell Biology Experiments

    Directory of Open Access Journals (Sweden)

    Ashkan eFarhadi

    2014-10-01

    Full Text Available Distant cells can communicate with each other through a variety of methods. Two such methods involve electrical and/or chemical mechanisms. Non-chemical, distant cellular interactions may be another method of communication that cells can use to modify the behavior of other cells that are mechanically separated. Moreover, non-chemical, distant cellular interactions may explain some cases of confounding effects in Cell Biology experiments. In this article, we review non-chemical, distant cellular interactions studies to try to shed light on the mechanisms in this highly unconventional field of cell biology. Despite the existence of several theories that try to explain the mechanism of non-chemical, distant cellular interactions, this phenomenon is still speculative. Among candidate mechanisms, electromagnetic waves appear to have the most experimental support. In this brief article, we try to answer a few key questions that may further clarify this mechanism.

  4. Systems Biology for Mapping Genotype-Phenotype Relations in Yeast

    KAUST Repository

    Nielsen, Jens

    2016-01-25

    The yeast Saccharomyces cerevisiae is widely used for production of fuels, chemicals, pharmaceuticals and materials. Through metabolic engineering of this yeast a number of novel new industrial processes have been developed over the last 10 years. 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 integrate with omics data and at the same time have been shown to have excellent predictive power. Despite our extensive knowledge of yeast metabolism and its regulation we are still facing challenges when we want to engineer complex traits, such as improved tolerance to toxic metabolites like butanol and elevated temperatures or when we want to engineer the highly complex protein secretory pathway. In this presentation it will be demonstrated how we can combine directed evolution with systems biology analysis to identify novel targets for rational design-build-test of yeast strains that have improved phenotypic properties. In this lecture an overview of systems biology of yeast will be presented together with examples of how genome-scale metabolic modeling can be used for prediction of cellular growth at different conditions. Examples will also be given on how adaptive laboratory evolution can be used for identifying targets for improving tolerance towards butanol, increased temperature and low pH and for improving secretion of heterologous proteins.

  5. Chemical composition and biological screening of Capsella bursa-pastoris

    Directory of Open Access Journals (Sweden)

    Clara Grosso

    2011-08-01

    Full Text Available Capsella bursa-pastoris (L. Medik. (Brassicaceae is a wild herb with high nutritional value that can be eaten raw or cooked. A metabolomic study was performed with different extracts of its aerial parts that were tested concerning their antiradical, acetylcholinesterase inhibitory and antibacterial activities. Phenolic compounds were identified and quantified by HPLC-DAD, organic acids and amino acids were determined by HPLC-UV, while free fatty acids and sterols were analysed by GC-ITMS. The vegetal material was rich in kaempferol-3-O-rutinoside (mean value 2247.09 mg/kg of dry plant, quinic acid (95628.00 mg/kg of dry plant, arginine (mean value of 1.18 mg/kg of dry plant, palmitic acid (284.48 mg/kg and β-sitosterol (28%. The extracts presented a concentration-dependent antiradical activity (against DPPH•, O2•- and LOO•, being most effective against •NO (EC25 0.20 µg/mL. In addition, the extracts were also acetylcholinesterase inhibitors and antibacterial active, revealing that, besides the plant's good nutritional value, it presents important biological properties as well.

  6. 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.

  7. 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.; Putten, van der W.H.; Ruiter, de P.C.; Struik, P.C.; Thomma, B.

    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 agricultura

  8. 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....

  9. Chemical and biological characterization of sclerosin, an antifungal lipopeptide.

    Science.gov (United States)

    Berry, Chrystal L; Brassinga, Ann Karen C; Donald, Lynda J; Fernando, W G Dilantha; Loewen, Peter C; de Kievit, Teresa R

    2012-08-01

    Pseudomonas sp. strain DF41 produces a lipopeptide, called sclerosin that inhibits the fungal pathogen Sclerotinia sclerotiorum . The aim of the current study was to deduce the chemical structure of this lipopeptide and further characterize its bioactivity. Mass spectrometry analysis determined the structure of sclerosin to be CH(3)-(CH(2))(6)-CH(OH)-CH(2)-CO-Dhb-Pro-Ala-Leu/Ile-Ala-Val-Val-Dhb-Thr-Val-Leu/Ile-Dhp-Ala-Ala-Ala-Val-Dhb-Dhb-Ala-Dab-Ser-Val-OH, similar to corpeptins A and B of the tolaasin group, differing by only 3 amino acids in the peptide chain. Subjecting sclerosin to various ring opening procedures revealed no new ions, suggesting that this molecule is linear. As such, sclerosin represents a new member of the tolaasin lipopeptide group. Incubation of S. sclerotinia ascospores and sclerotia in the presence of sclerosin inhibited the germination of both cell types. Sclerosin also exhibited antimicrobial activity against Bacillus species. Conversely, this lipopeptide demonstrated no zoosporicidal activity against the oomycete pathogen Phytophthora infestans . Next, we assessed the effect of DF41 and a lipopeptide-deficient mutant on the growth and development of Caenorhabditis elegans larvae. We discovered that sclerosin did not protect DF41 from ingestion by and degradation in the C. elegans digestive tract. However, another metabolite produced by this bacterium appeared to shorten the life-span of the nematode compared to C. elegans growing on Escherichia coli OP50. PMID:22838838

  10. Biological treatments affect the chemical composition of coffee pulp.

    Science.gov (United States)

    Ulloa Rojas, J B; Verreth, J A J; Amato, S; Huisman, E A

    2003-09-01

    Biological treatments were applied to fresh coffee pulp (CoP) to improve its nutritive value for monogastric animals by reducing its content of cellulose and antinutritional factors (ANFs) such as total phenols, tannins and caffeine. Treatments were: (1) ensiling with 0, 50 and 100 gkg(-1) molasses for 2 and 3 months, (2) aerobic decomposition for 0, 7, 14, 21, 28, 35 and 42 days, (3) aerobic bacterial inoculation (Bacillus sp.) for 0, 7, 14, 21 and 28 days. Ensiled CoP (E-CoP) showed higher fat and ash contents than oven-dried-CoP (OD-CoP; P<0.05). Similarly, true protein values tended to increase. The cellulose and total phenols levels of E-CoP were lower than OD-CoP (P<0.05). The E-CoP tannins levels tended to be lower than OD-CoP whereas caffeine levels remained unaffected. Improvement in the nutritional quality of E-CoP was associated with higher fat and protein contents and reduction of cellulose, total phenols and tannins. The aerobic decomposition treatment improved the nutritional quality of CoP by increasing true protein and fat contents. In addition, total phenols, tannins, caffeine and cellulose contents were reduced by an increase in treatment time (P<0.05). Bacterial treatment increased the protein content of CoP after 21 days (from 137 to 392 gkg(-1)) and decreased it after 28 days. Cellulose, total phenols, tannins and caffeine contents reduced with an increase in time of bacterial degradation. Bacterial treatment improved the CoP quality by increasing protein content and reducing cellulose and ANFs, especially after 21 days of treatment. Both the aerobic decomposition (after 21-28 days) and the aerobic bacterial degradation of CoP (after 21 days) appeared more suitable to improve the nutritional quality of CoP than the ensiling.

  11. Accelerated Stochastic Simulation of Large Chemical Systems

    Institute of Scientific and Technical Information of China (English)

    CHEN Xiao; AO Ling

    2007-01-01

    For efficient simulation of chemical systems with large number of reactions, we report a fast and exact algorithm for direct simulation of chemical discrete Markov processes. The approach adopts the scheme of organizing the reactions into hierarchical groups. By generating a random number, the selection of the next reaction that actually occurs is accomplished by a few successive selections in the hierarchical groups. The algorithm which is suited for simulating systems with large number of reactions is much faster than the direct method or the optimized direct method. For a demonstration of its efficiency, the accelerated algorithm is applied to simulate the reaction-diffusion Brusselator model on a discretized space.

  12. Chemical detection, identification, and analysis system

    International Nuclear Information System (INIS)

    The chemical detection, identification, and analysis system (CDIAS) has three major goals. The first is to display safety information regarding chemical environment before personnel entry. The second is to archive personnel exposure to the environment. Third, the system assists users in identifying the stage of a chemical process in progress and suggests safety precautions associated with that process. In addition to these major goals, the system must be sufficiently compact to provide transportability, and it must be extremely simple to use in order to keep user interaction at a minimum. The system created to meet these goals includes several pieces of hardware and the integration of four software packages. The hardware consists of a low-oxygen, carbon monoxide, explosives, and hydrogen sulfide detector; an ion mobility spectrometer for airborne vapor detection; and a COMPAQ 386/20 portable computer. The software modules are a graphics kernel, an expert system shell, a data-base management system, and an interface management system. A supervisory module developed using the interface management system coordinates the interaction of the other software components. The system determines the safety of the environment using conventional data acquisition and analysis techniques. The low-oxygen, carbon monoxide, hydrogen sulfide, explosives, and vapor detectors are monitored for hazardous levels, and warnings are issued accordingly

  13. 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.

  14. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    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.

  15. Biological activities and chemical composition of lichens from Serbia.

    Science.gov (United States)

    Kosanic, Marijana; Rankovic, Branislav; Stanojkovic, Tatjana; Vasiljevic, Perica; Manojlovic, Nedeljko

    2014-01-01

    The aim of this study is to investigate chemical composition of acetone extracts of the lichens Parmelia arseneana and Acarospora fuscata and in vitro antioxidant, antimicrobial, and anticancer activities of these extracts and gyrophoric acid isolated from A. fuscata. The HPLC-UV method was used for the identification of secondary metabolites. Stictic acid, norstictic acid, gyrophoric acid, usnic acid, atranorin and chloroatranorin were identified in the A. fuscata. In P. arseneana, we detected stictic acid, norstictic acid, usnic acid and atranorin, while gyrophoric acid was not identified. Antioxidant activity was evaluated by measuring the scavenging capacity of tested samples on DPPH and superoxide anion radicals, reducing the power of samples and determination of total phenolic compounds in extracts. As a result of the study, gyrophoric acid was found to have the largest DPPH radical scavenging activity with an IC50 value of 105.75 µg/ml. Moreover, the tested samples had an effective superoxide anion radical scavenging and reducing power. The total content of phenol in extracts was determined as pyrocatechol equivalent. The antimicrobial activity was estimated by determination of the minimal inhibitory concentration by the broth microdilution method. The most active was also gyrophoric acid, with minimum inhibitory concentration values ranging from 0.019 to 1.25 mg/ml. Anticancer activity was tested against LS174 (human colon carcinoma cell line), A549 (human lung carcinoma cell line), Fem-x (malignant melanoma cell line), and a chronic myelogeneous leukaemia K562 cell line using the MTT method. Extract of P. arseneana expressed the strongest anticancer activity against all cell lines with IC50 values ranging from 11.61 to 47.06 µg/ml. PMID:26417336

  16. Non-Equilibrium Quantum Entanglement in Biological Systems

    Institute of Scientific and Technical Information of China (English)

    LI Hong-Rong; ZHANG Pei; GAO Hong; BI Wen-Ting; ALAMRI M. D.; LI Fu-Li

    2012-01-01

    A non-equilibrium model of a classically driven quantum harmonic oscillator is proposed to explain persistent quantum entanglement in biological systems at ambient temperature. The conditions for periodic entanglement generation are derived. Our results support the evidence that biological systems may have quantum entanglement at biological temperatures.%A non-equilibrium model of a classically driven quantum harmonic oscillator is proposed to explain persistent quantum entanglement in biological systems at ambient temperature.The conditions for periodic entanglement generation are derived.Our results support the evidence that biological systems may have quantum entanglement at biological temperatures.

  17. 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...

  18. Biological Systems for Hydrogen Photoproduction (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Ghirardi, M. L.

    2012-05-01

    This presentation summarizes NREL biological systems for hydrogen photoproduction work for the DOE Hydrogen and Fuel Cells Program Annual Merit Review and Peer Evaluation Meeting, May 14-18, 2012. General goal is develop photobiological systems for large-scale, low cost and efficient H{sub 2} production from water (barriers AH, AI and AJ). Specific tasks are: (1) Address the O{sub 2} sensitivity of hydrogenases that prevent continuity of H{sub 2} photoproduction under aerobic, high solar-to-hydrogen (STH) light conversion efficiency conditions; and (2) Utilize a limited STH H{sub 2}-producing method (sulfur deprivation) as a platform to address or test other factors limiting commercial algal H{sub 2} photoproduction, including low rates due to biochemical and engineering mechanisms.

  19. Are Biological Systems Poised at Criticality?

    Science.gov (United States)

    Mora, Thierry; Bialek, William

    2011-07-01

    Many of life's most fascinating phenomena emerge from interactions among many elements—many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts and memories. Physicists have long hoped that these collective behaviors could be described using the ideas and methods of statistical mechanics. In the past few years, new, larger scale experiments have made it possible to construct statistical mechanics models of biological systems directly from real data. We review the surprising successes of this "inverse" approach, using examples from families of proteins, networks of neurons, and flocks of birds. Remarkably, in all these cases the models that emerge from the data are poised near a very special point in their parameter space—a critical point. This suggests there may be some deeper theoretical principle behind the behavior of these diverse systems.

  20. The effect of biological and chemical additives on the chemical composition and fermentation process of Dactylis glomerata silage

    Directory of Open Access Journals (Sweden)

    Jhonny E. Alba-Mejía

    2016-06-01

    Full Text Available This study was carried out to determine the chemical composition, silage quality and ensilability of ten cocksfoot cultivars using biological and chemical silage additives. The plant material was harvested from the first and second cut, cultivated at the Research Station of Fodder Crops in Vatín, Czech Republic. Wilted forage was chopped and ensiled in mini-silos with 3 replicates per treatment. The treatments were: 1 without additives, used as a control; 2 with bacterial inoculants; and 3 with chemical preservatives. The results indicated that the year factor (2012-2013 influenced significantly the chemical composition of the silage in both cuts. The use of biological inoculants reduced the content of crude fibre and acid detergent fibre; but it did not influence the content of neutral detergent fibre, in comparison with the control silage in both cuts. Furthermore, the application of biological inoculants reduced the concentration of lactic acid (LA and acetic acid (AA in contrast to the control silage in the first cut. Moreover, in the second cut the same values tended to be the opposite. Interestingly, ‘Amera’ was the unique variety that presented a high concentration of butyric acid (0.2% in comparison with other varieties in the first cut. In conclusion, the biological inoculants had a favourable effect on silage fermentation. Notably, only ‘Greenly’ and ‘Starly’ varieties from the first cut; and ‘Greenly’, ‘Sw-Luxor’, and ‘Otello’ varieties from the second cut were appropriate for ensiling because their pH-values; LA and AA concentrations were ideal according to the parameters of the fermentation process.

  1. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure;

    2016-01-01

    Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological fu...

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

    Science.gov (United States)

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

    2016-07-01

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

  3. Chemical characterization and biological activity of Chaga (Inonotus obliquus), a medicinal “mushroom”

    OpenAIRE

    Glamočlija, Jasmina; Ćirić, Ana; Nikolić, Miloš; Fernandes, Ângela; Barros, Lillian; Ricardo C. Calhelha; Ferreira, Isabel C.F.R.; Soković, Marina; Van Griensven, Leo J. L. D.

    2015-01-01

    Chemical composition and biological properties of aqueous and ethanolic extracts of Inonotus obliquus (Pers.:Fr.) Pilat from different origins, i.e. of Finland, Russia, and Thailand, were studied. Concerning biological activity, antimicrobial, antiqourum, antioxidative, and antitumor and cytotoxic effects were tested. Oxalic acid was found as the main organic acid, with the highest amount in Russian aqueous extract. Gallic, protocatechuic and p-hydroxybenzoic acids were detected in all sample...

  4. Characterization of PAH-contaminated soils focusing on availability, chemical composition and biological effects

    OpenAIRE

    Bergknut, Magnus

    2006-01-01

    The risks associated with a soil contaminated by polycyclic aromatic hydrocarbons (PAHs) are generally assessed by measuring individual PAHs in the soil and correlating the obtained amounts to known adverse biological effects of the PAHs. The validity of such a risk estimation is dependent on the presence of additional compounds, the availability of the compounds (including the PAHs), and the methods used to correlate the measured chemical data and biological effects. In the work underlying t...

  5. Miniaturized droplets-based microarray of chemical and biological high-throughput tests

    OpenAIRE

    Neto, Ana I.; Correia, Clara R.; Custódio, Catarina A.; Mano, J.F

    2013-01-01

    Publicado em "Journal of Tissue Engineering and Regenerative Medicine, vol. 7, supp. 1 (2013) The development of high-throughput and combinatorial technologies is helping to speed up research that is applicable in many areas of chemistry, engineering and biology. We propose a simple, versatile high-efficient and new superhydrophobic platform, which permits to arrange of quasi-spherical aqueous-based droplets with the capability to support and monitor a series of chemical/biolog...

  6. Physical, chemical and biological characterization of the sanitary landfill leachate in Limeira-SP city.

    Directory of Open Access Journals (Sweden)

    Ronaldo Teixeira Pelegrini

    2007-07-01

    Full Text Available This work presents an evaluation of the physical, chemical and biological characteristics of the waste leachate originated from solids waste mass and after permanence in average of 24 hours in the captation pond, which is located on the sanitary landfill in Limeira-SP. The points were denominated Point 0: entrance of leachate in natura in the pond and Point 1: exit of leachate from the pond. The study was accomplished through of the monitoring of physical (pH, color, turbidity, conductivity and temperature, chemical (alkalinity, acidity, phosphorus, amoniacal nitrogen, nitrite, nitrate and TOC and biological (heterotrophic bacterial parameters during a period of 50 days.

  7. Engineered Barrier System: Physical and Chemical Environment

    Energy Technology Data Exchange (ETDEWEB)

    P. Dixon

    2004-04-26

    The conceptual and predictive models documented in this Engineered Barrier System: Physical and Chemical Environment Model report describe the evolution of the physical and chemical conditions within the waste emplacement drifts of the repository. The modeling approaches and model output data will be used in the total system performance assessment (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. These models evaluate the range of potential water compositions within the emplacement drifts, resulting from the interaction of introduced materials and minerals in dust with water seeping into the drifts and with aqueous solutions forming by deliquescence of dust (as influenced by atmospheric conditions), and from thermal-hydrological-chemical (THC) processes in the drift. These models also consider the uncertainty and variability in water chemistry inside the drift and the compositions of introduced materials within the drift. This report develops and documents a set of process- and abstraction-level models that constitute the engineered barrier system: physical and chemical environment model. Where possible, these models use information directly from other process model reports as input, which promotes integration among process models used for total system performance assessment. Specific tasks and activities of modeling the physical and chemical environment are included in the technical work plan ''Technical Work Plan for: In-Drift Geochemistry Modeling'' (BSC 2004 [DIRS 166519]). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system analysis model reports.

  8. Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Laura R. Jarboe

    2010-01-01

    Full Text Available Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.

  9. Chemical reactions in reverse micelle systems

    Science.gov (United States)

    Matson, Dean W.; Fulton, John L.; Smith, Richard D.; Consani, Keith A.

    1993-08-24

    This invention is directed to conducting chemical reactions in reverse micelle or microemulsion systems comprising a substantially discontinuous phase including a polar fluid, typically an aqueous fluid, and a microemulsion promoter, typically a surfactant, for facilitating the formation of reverse micelles in the system. The system further includes a substantially continuous phase including a non-polar or low-polarity fluid material which is a gas under standard temperature and pressure and has a critical density, and which is generally a water-insoluble fluid in a near critical or supercritical state. Thus, the microemulsion system is maintained at a pressure and temperature such that the density of the non-polar or low-polarity fluid exceeds the critical density thereof. The method of carrying out chemical reactions generally comprises forming a first reverse micelle system including an aqueous fluid including reverse micelles in a water-insoluble fluid in the supercritical state. Then, a first reactant is introduced into the first reverse micelle system, and a chemical reaction is carried out with the first reactant to form a reaction product. In general, the first reactant can be incorporated into, and the product formed in, the reverse micelles. A second reactant can also be incorporated in the first reverse micelle system which is capable of reacting with the first reactant to form a product.

  10. Coupled chemical oscillators and emergent system properties.

    Science.gov (United States)

    Epstein, Irving R

    2014-09-25

    We review recent work on a variety of systems, from the nanometre to the centimetre scale, including microemulsions, microfluidic droplet arrays, gels and flow reactors, in which chemical oscillators interact to generate novel spatiotemporal patterns and/or mechanical motion. PMID:24835430

  11. Technologies and devices for micro chemical systems

    NARCIS (Netherlands)

    Gardeniers, Han; Schasfoort, Richard; Berg, van den Albert

    2000-01-01

    This article describes recent developments at MESA+ in the field of miniaturised systems for chemical synthesis and analysis, also frequently referred to as "Lab-on-a-Chip". Several examples of siliconbased devices will be discussed, like micro pipettes for DNA studies, chips for cation analysis in

  12. Optimization of integrated chemical-biological degradation of a reactive azo dye using response surface methodology

    Energy Technology Data Exchange (ETDEWEB)

    Sudarjanto, Gatut [Advanced Wastewater Management Centre, The University of Queensland, Qld 4072 (Australia); Keller-Lehmann, Beatrice [Advanced Wastewater Management Centre, The University of Queensland, Qld 4072 (Australia); Keller, Jurg [Advanced Wastewater Management Centre, The University of Queensland, Qld 4072 (Australia)]. E-mail: j.keller@awmc.uq.edu.au

    2006-11-02

    The integrated chemical-biological degradation combining advanced oxidation by UV/H{sub 2}O{sub 2} followed by aerobic biodegradation was used to degrade C.I. Reactive Azo Red 195A, commonly used in the textile industry in Australia. An experimental design based on the response surface method was applied to evaluate the interactive effects of influencing factors (UV irradiation time, initial hydrogen peroxide dosage and recirculation ratio of the system) on decolourisation efficiency and optimizing the operating conditions of the treatment process. The effects were determined by the measurement of dye concentration and soluble chemical oxygen demand (S-COD). The results showed that the dye and S-COD removal were affected by all factors individually and interactively. Maximal colour degradation performance was predicted, and experimentally validated, with no recirculation, 30 min UV irradiation and 500 mg H{sub 2}O{sub 2}/L. The model predictions for colour removal, based on a three-factor/five-level Box-Wilson central composite design and the response surface method analysis, were found to be very close to additional experimental results obtained under near optimal conditions. This demonstrates the benefits of this approach in achieving good predictions while minimising the number of experiments required.

  13. Five Decades with Polyunsaturated Fatty Acids: Chemical Synthesis, Enzymatic Formation, Lipid Peroxidation and Its Biological Effects

    Science.gov (United States)

    Catalá, Angel

    2013-01-01

    I have been involved in research on polyunsaturated fatty acids since 1964 and this review is intended to cover some of the most important aspects of this work. Polyunsaturated fatty acids have followed me during my whole scientific career and I have published a number of studies concerned with different aspects of them such as chemical synthesis, enzymatic formation, metabolism, transport, physical, chemical, and catalytic properties of a reconstructed desaturase system in liposomes, lipid peroxidation, and their effects. The first project I became involved in was the organic synthesis of [1-14C] eicosa-11,14-dienoic acid, with the aim of demonstrating the participation of that compound as a possible intermediary in the biosynthesis of arachidonic acid “in vivo.” From 1966 to 1982, I was involved in several projects that study the metabolism of polyunsaturated fatty acids. In the eighties, we studied fatty acid binding protein. From 1990 up to now, our laboratory has been interested in the lipid peroxidation of biological membranes from various tissues and different species as well as liposomes prepared with phospholipids rich in PUFAs. We tested the effect of many antioxidants such as alpha tocopherol, vitamin A, melatonin and its structural analogues, and conjugated linoleic acid, among others. PMID:24490074

  14. Optimization of integrated chemical-biological degradation of a reactive azo dye using response surface methodology

    International Nuclear Information System (INIS)

    The integrated chemical-biological degradation combining advanced oxidation by UV/H2O2 followed by aerobic biodegradation was used to degrade C.I. Reactive Azo Red 195A, commonly used in the textile industry in Australia. An experimental design based on the response surface method was applied to evaluate the interactive effects of influencing factors (UV irradiation time, initial hydrogen peroxide dosage and recirculation ratio of the system) on decolourisation efficiency and optimizing the operating conditions of the treatment process. The effects were determined by the measurement of dye concentration and soluble chemical oxygen demand (S-COD). The results showed that the dye and S-COD removal were affected by all factors individually and interactively. Maximal colour degradation performance was predicted, and experimentally validated, with no recirculation, 30 min UV irradiation and 500 mg H2O2/L. The model predictions for colour removal, based on a three-factor/five-level Box-Wilson central composite design and the response surface method analysis, were found to be very close to additional experimental results obtained under near optimal conditions. This demonstrates the benefits of this approach in achieving good predictions while minimising the number of experiments required

  15. Vacuum Ultraviolet Photoionization of Complex Chemical Systems

    Science.gov (United States)

    Kostko, Oleg; Bandyopadhyay, Biswajit; Ahmed, Musahid

    2016-05-01

    Tunable vacuum ultraviolet (VUV) radiation coupled to mass spectrometry is applied to the study of complex chemical systems. The identification of novel reactive intermediates and radicals is revealed in flame, pulsed photolysis, and pyrolysis reactors, leading to the elucidation of spectroscopy, reaction mechanisms, and kinetics. Mass-resolved threshold photoelectron photoion coincidence measurements provide unprecedented access to vibrationally resolved spectra of free radicals present in high-temperature reactors. Photoionization measurements in water clusters, nucleic acid base dimers, and their complexes with water provide signatures of proton transfer in hydrogen-bonded and π-stacked systems. Experimental and theoretical methods to track ion-molecule reactions and fragmentation pathways in intermolecular and intramolecular hydrogen-bonded systems in sugars and alcohols are described. Photoionization of laser-ablated molecules, clusters, and their reaction products inform thermodynamics and spectroscopy that are relevant to astrochemistry and catalysis. New directions in coupling VUV radiation to interrogate complex chemical systems are discussed.

  16. Integrated Design of Antibodies for Systems Biology Using Ab Designer

    OpenAIRE

    Pisitkun, Trairak; Dummer, Patrick; Somparn, Poorichaya; Hirankarn, Nattiya; Kopp, Jeffrey B.; Knepper, Mark A.

    2014-01-01

    In the current era of large-scale biology, systems biology has evolved as a powerful approach to identify complex interactions within biological systems. In addition to high throughput identification and quantification techniques, methods based on high-quality mono-specific antibodies remain an essential element of the approach. To assist the large-scale design and production of peptide-directed antibodies for systems biology studies, we developed a fully integrated online application, AbDesi...

  17. Compound Activity Mapping: Integrating Chemical and Biological Profiling for the Functional Annotation of Natural Product Libraries

    OpenAIRE

    Kurita, Kenji Long

    2015-01-01

    Natural products research has had a significant impact on human-health and our understanding of the natural world as a pillar of pharmacognosy, organic chemistry, ecology, and chemical biology. But while this science has yielded countless discoveries such as penicillin, taxol, and artimesinin and will continue to improve quality of life around the world, the idea that natural products is a panacea of chemical diversity has been challenged by problems including the endless rediscovery of known...

  18. Integrated biological chemical approach for the identification of polyaromatic mutagens in surface waters

    OpenAIRE

    GALLAMPOIS Christine

    2012-01-01

    Surface waters are essential for human life, to supply of drinking water and as an important resource for agricultural, industrial and recreational activities. However, tonnes of pollutants enter these surface waters every year. Amongst the substances discharged into the environment, a large number are known to be mutagenic. Effect-directed analysis (EDA) is a tool to identify chemicals responsible for the observed toxic effects. It is based on a combination of chemical and biological analysi...

  19. [Biological, chemical, and radiation factors in the classification of medical waste].

    Science.gov (United States)

    Rusakov, N V; Korotkova, G I; Orlov, A Iu; Kadyrov, D E

    2011-01-01

    The current classification of medical waste does not consider the sanitary-and-chemical hazard of epidemiologically dangerous and extremely dangerous medical waste (classes B and C). According to the results of the studies performed, the authors propose the improved classification of medical waste, which makes it possible to take into account not only infectious, radiation, and toxicological, but also sanitary-and-chemical hazards (toxicity, carcinogenicity, mutagenicity, and biological activity) of medical waste. PMID:21901883

  20. SYSTEM PERFORMANCE SPECIFICATION FOR A NATIONAL CHEMICAL INFORMATION SYSTEM.

    Science.gov (United States)

    Information Management, Inc., Burlington, MA.

    THIS DOCUMENT CONTAINS A SET OF STATEMENTS ABOUT INFORMATION NEEDS, SYSTEM GOALS, SYSTEM REQUIREMENTS, AND SYSTEM SPECIFICATIONS FOR THE DEVELOPMENT OF A NATIONAL CHEMICAL INFORMATION SYSTEM. IN ITS PRESENT FORM, THE DOCUMENT CONSTITUTES A BASIS FOR FUTURE PLANNING. AS POLICY DECISIONS ARE MADE, TECHNICAL PROBLEMS SOLVED AND PLANS ARE ALTERED, THE…

  1. 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.

  2. Methods of 15N tracer research in biological systems

    International Nuclear Information System (INIS)

    The application of the stable isotope 15N is of increasing importance in different scientific disciplines, especially in medicine, agriculture, and the biosciences. The close correlation between the growing interest and improvements of analytical procedures resulted in remarkable advances in the 15N tracer technique. On the basis of the latest results of 15N tracer research in life sciences and agriculture methods of 15N tracer research in biological systems are compiled. The 15N methodology is considered under three headings: Chemical analysis with a description of methods of sample preparation (including different separation and isolation methods for N-containing substances of biological and agricultural origin) and special procedures converting ammonia to molecular nitrogen. Isotopic analysis with a review on the most important methods of isotopic analysis of nitrogen: mass spectrometry (including the GC-MS technique), emission spectrometry, NMR spectroscopy, and other analytical procedures. 15N-tracer techniques with a consideration of the role of the isotope dilution analysis as well as different labelling techniques and the mathematical interpretation of tracer data (modelling, N turnover experiments). In these chapters also sources of errors in chemical and isotopic analysis, the accuracy of the different methods and its importance on tracer experiments are discussed. Procedures for micro scale 15N analysis and aspects of 15N analysis on the level of natural abundance are considered. Furthermore some remarks on isotope effects in 15N tracer experiments are made. (author)

  3. Quantum integrable systems. Quantitative methods in biology

    CERN Document Server

    Feverati, Giovanni

    2011-01-01

    Quantum integrable systems have very strong mathematical properties that allow an exact description of their energetic spectrum. From the Bethe equations, I formulate the Baxter "T-Q" relation, that is the starting point of two complementary approaches based on nonlinear integral equations. The first one is known as thermodynamic Bethe ansatz, the second one as Kl\\"umper-Batchelor-Pearce-Destri- de Vega. I show the steps toward the derivation of the equations for some of the models concerned. I study the infrared and ultraviolet limits and discuss the numerical approach. Higher rank integrals of motion can be obtained, so gaining some control on the eigenvectors. After, I discuss the Hubbard model in relation to the N = 4 supersymmetric gauge theory. The Hubbard model describes hopping electrons on a lattice. In the second part, I present an evolutionary model based on Turing machines. The goal is to describe aspects of the real biological evolution, or Darwinism, by letting evolve populations of algorithms. ...

  4. The start of systems biology in Ukraine

    Directory of Open Access Journals (Sweden)

    Obolenskaya M. Yu.

    2014-01-01

    Full Text Available The first laboratory of Systems Biology in Ukraine (IMBIG NASU represents a track record of its scientific results. They include the pioneered development of a web-based tool for genome-wide surveys of eukaryotic promoters for the presence of transcription factors binding sites (COTRASIF; the deciphered mechanisms of the fine-tuned and balanced response of primary hepatocytes to interferon alpha levels recorded after partial hepatectomy; the elaboration of a novel method of gene regulatory network inference compatible with GRID environment and the development of a stoichiometric model of folate-related one carbon unit metabolism in human placenta and its application for the characteristics of the system’s behavior as a whole at different human pathologies.

  5. Nutritional Systems Biology: Definitions and Approaches

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Nielsen, Jens

    2009-01-01

    Nutrigenetics and nutrigenomics are nascent areas that are evolving quickly and riding on the wave of “personalized medicine” that is providing opportunities in the discovery and development of nutraceutical compounds. The human genome sequence and sequences of model organisms provide...... will benefit most from, or be placed at risk by, intervention strategies. More accurate assessment of the inputs to human health and the consequences of those inputs measured as accurate transcriptomic, proteomic, and metabolomic analyses would bring personalized health/diet to practice far faster than would...... waiting for a predictive knowledge of genetic variation. It is widely recognized that systems and network biology has the potential to increase our understanding of how nutrition influences metabolic pathways and homeostasis, how this regulation is disturbed in a diet-related disease, and to what extent...

  6. Protecting buildings from a biological or chemical attack: Actions to take before or during a release

    Energy Technology Data Exchange (ETDEWEB)

    Price, Phillip N.; Sohn, Michael D.; Gadgil, Ashok J.; Delp, William W.; Lorenzetti, David M.; Finlayson, Elizabeth U.; Thatcher, Tracy L.; Sextro, Richard G.; Derby, Elisabeth A.; Jarvis, Sondra A.

    2003-01-29

    This report presents advice on how to operate a building to reduce casualties from a biological or chemical attack, as well as potential changes to the building (e.g. the design of the ventilation system) that could make it more secure. It also documents the assumptions and reasoning behind the advice. The particular circumstances of any attack, such as the ventilation system design, building occupancy, agent type, source strength and location, and so on, may differ from the assumptions made here, in which case actions other than our recommendations may be required; we hope that by understanding the rationale behind the advice, building operators can modify it as required for their circumstances. The advice was prepared by members of the Airflow and Pollutant Transport Group, which is part of the Indoor Environment Department at the Lawrence Berkeley National Laboratory. The group's expertise in this area includes: tracer-gas measurements of airflows in buildings (Sextro, Thatcher); design and operation of commercial building ventilation systems (Delp); modeling and analysis of airflow and tracer gas transport in large indoor spaces (Finlayson, Gadgil, Price); modeling of gas releases in multi-zone buildings (Sohn, Lorenzetti, Finlayson, Sextro); and occupational health and safety experience related to building design and operation (Sextro, Delp). This report is concerned only with building design and operation; it is not a how-to manual for emergency response. Many important emergency response topics are not covered here, including crowd control, medical treatment, evidence gathering, decontamination methods, and rescue gear.

  7. Microbial systems biology: New frontiers open to predictive microbiology

    NARCIS (Netherlands)

    S. Brul; F.I.C. Mensonides; K.J. Hellingwerf; M.J. Teixeira De Mattos

    2008-01-01

    The field of Systems Biology is a rapidly evolving area of research. It follows on from the previous experimental and theoretical ‘omics’ revolution in biology. Now that we have through the use of these tools many ‘indices’ of biological systems available the next step is to actually start composing

  8. 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...

  9. Expert systems guide biological phosphorus removal

    Energy Technology Data Exchange (ETDEWEB)

    Krichten, D.J.; Wilson, K.D.; Tracy, K.D. (Air Products and Chemicals, Inc., Allentown, PA (United States))

    1991-10-01

    There is a large body of knowledge regarding optimum control strategies for new secondary wastewater treatment technology using an anaerobic selector to provide biological phosphorus removal. However, because the selector technology is new and the concepts differ somewhat from those used in conventional activated sludge wastewater treatment, a method of communicating this knowledge to plant operators is needed. Traditional methods such as classroom training and operating manuals are of limited effectiveness. The commonplace availability and low cost of the personal computer (PC) makes it practical to use a computer program to communicate the type of information required to control a wastewater treatment plant. Knowledge-based systems technology, commonly referred to as expert systems (ES) technology, is easy to use, provides useful information regarding a consistent control strategy, relieves the anxiety associated with learning a new process,' and provides instruction for inexperienced personnel. ES technology does not require special formatted input and is therefore easily accessible. All information required by the program is readily available through routine laboratory analysis, common plant instrumentation, or direct user observation. The program was designed for all levels of computer users and will run on all IBM-compatible or Apple MacIntosh systems.

  10. Biological robustness: paradigms, mechanisms, and systems principles.

    Science.gov (United States)

    Whitacre, James Michael

    2012-01-01

    Robustness has been studied through the analysis of data sets, simulations, and a variety of experimental techniques that each have their own limitations but together confirm the ubiquity of biological robustness. Recent trends suggest that different types of perturbation (e.g., mutational, environmental) are commonly stabilized by similar mechanisms, and system sensitivities often display a long-tailed distribution with relatively few perturbations representing the majority of sensitivities. Conceptual paradigms from network theory, control theory, complexity science, and natural selection have been used to understand robustness, however each paradigm has a limited scope of applicability and there has been little discussion of the conditions that determine this scope or the relationships between paradigms. Systems properties such as modularity, bow-tie architectures, degeneracy, and other topological features are often positively associated with robust traits, however common underlying mechanisms are rarely mentioned. For instance, many system properties support robustness through functional redundancy or through response diversity with responses regulated by competitive exclusion and cooperative facilitation. Moreover, few studies compare and contrast alternative strategies for achieving robustness such as homeostasis, adaptive plasticity, environment shaping, and environment tracking. These strategies share similarities in their utilization of adaptive and self-organization processes that are not well appreciated yet might be suggestive of reusable building blocks for generating robust behavior. PMID:22593762

  11. Biological Robustness: Paradigms, Mechanisms, and Systems Principles

    Directory of Open Access Journals (Sweden)

    James Michael Whitacre

    2012-05-01

    Full Text Available Robustness has been studied through the analysis of data sets, simulations, and a variety of experimental techniques that each have their own limitations but together confirm the ubiquity of biological robustness. Recent trends suggest that different types of perturbation (e.g. mutational, environmental are commonly stabilized by similar mechanisms, and system sensitivities often display a long-tailed distribution with relatively few perturbations representing the majority of sensitivities. Conceptual paradigms from network theory, control theory, complexity science, and natural selection have been used to understand robustness, however each paradigm has a limited scope of applicability and there has been little discussion of the conditions that determine this scope or the relationships between paradigms. Systems properties such as modularity, bow-tie architectures, degeneracy, and other topological features are often positively associated with robust traits, however common underlying mechanisms are rarely mentioned. For instance, many system properties support robustness through functional redundancy or through response diversity with responses regulated by competitive exclusion and cooperative facilitation. Moreover, few studies compare and contrast alternative strategies for achieving robustness such as homeostasis, adaptive plasticity, environment shaping, and environment tracking. These strategies share similarities in their utilization of adaptive and self-organization processes that are not well appreciated yet might be suggestive of reusable building blocks for generating robust behavior.

  12. Genetic Resources of Energy Crops: Biological Systems to Combat Climate Change

    Science.gov (United States)

    Biological systems are expected to contribute to renewable energy production, help stabilize rising levels of green house gases (GHG), and mitigate the risk of global climate change (GCC). Bioenergy crop plants that function as solar energy collectors and thermo-chemical energy storage systems are t...

  13. Comparison of biological and chemical phosphorus removals in continuous and sequencing batch reactors

    Energy Technology Data Exchange (ETDEWEB)

    Ketchum, L.H.; Irvine, R.L. Jr.; Breyfogle, R.E.; Manning, J.F. Jr.

    1987-01-01

    A full-scale study of phosphorus removal has been conducted at Culver using continuous-flow operation, SBR operation, and several different chemical treatment schemes. A full-scale demonstration of SBR biological phosphorus removal also has been shown to be effective. Four contributing groups of organisms and their roles in biological SBR phosphorus removal have been described: denitrifying organisms, fermentation product-manufacturing organisms, phosphorus- accumulating organisms, and aerobic autotrophs and heterotrophs. The SBR can provide the proper balance of anoxic, anaerobic, and aerobic conditions to allow these group of organisms to successfully remove phosphorus biologically, without chemical addition. Treatment results using various chemicals for phosphorus removal, both during conventional, continuous-flow operation and after the plant was converted for SBR operation, have also been provided for comparison. Effluent phosphorus concentrations were almost identical for each period, except for the period when phosphorus was removed biologically and without any chemical addition when effluent phosphorus concentrations were the lowest. These removals were made as a result of settling alone; no tertiary rapid stand filter was used or required.

  14. 78 FR 38782 - Lifting of Chemical and Biological Weapons (CBW) Proliferation Sanctions Against Chinese Entities

    Science.gov (United States)

    2013-06-27

    ... These restrictions were imposed on July 9, 2002 (see Volume 67 FR Public Notice 4071). Dated: June 21... of Chemical and Biological Weapons (CBW) Proliferation Sanctions Against Chinese Entities AGENCY... lift nonproliferation measures on Chinese entities. DATES: Effective Date: Upon publication in...

  15. The search for life's origins: Progress and future directions in planetary biology and chemical evolution

    Science.gov (United States)

    1990-01-01

    The current state is reviewed of the study of chemical evolution and planetary biology and the probable future is discussed of the field, at least for the near term. To this end, the report lists the goals and objectives of future research and makes detailed, comprehensive recommendations for accomplishing them, emphasizing those issues that were inadequately discussed in earlier Space Studies Board reports.

  16. Natural product diversity and its role in chemical biology and drug discovery

    OpenAIRE

    Hong, Jiyong

    2011-01-01

    Through the natural selection process, natural products possess a unique and vast chemical diversity and have been evolved for optimal interactions with biological macromolecules. Owing to their diversity, target affinity, and specificity, natural products have demonstrated enormous potential as modulators of biomolecular function, been an essential source for drug discovery, and provided design principles for combinatorial library development.

  17. PERFORMANCE OF NORTH AMERICAN BIOREACTOR LANDFILLS: II. CHEMICAL AND BIOLOGICAL CHARACTERISTICS

    Science.gov (United States)

    The objective of this research was to examine the performance of five North American bioreactor landfills. This paper represents the second of a two part series and addresses biological and chemical aspects of bioreactor performance including gas production and management, and l...

  18. Combined biological and physico-chemical treatment of filtered pig manure wastewater : pilot investigations

    NARCIS (Netherlands)

    Kalyuzhnyi, S.; Sklyar, V.; Epov, A.; Archipchenko, I.; Barboulina, I.; Orlova, O.; Klapwijk, A.

    2002-01-01

    Combined biological and physico-chemical treatment of filtered pig manure wastewater has been investigated on the pilot installation operated under ambient temperatures (15-20°C) and included: i) UASB-reactor for elimination of major part of COD from the filtrate; (ii) stripper of CO2 fluidised bed

  19. Chemical and biological extraction of metals present in E waste: A hybrid technology

    International Nuclear Information System (INIS)

    Highlights: ► Hybrid methodology for E waste management. ► Efficient extraction of metals. ► Trace metal extraction is possible. - Abstract: Management of metal pollution associated with E-waste is widespread across the globe. Currently used techniques for the extraction of metals from E-waste by using either chemical or biological leaching have their own limitations. Chemical leaching is much rapid and efficient but has its own environmental consequences, even the future prospects of associated nanoremediation are also uncertain. Biological leaching on the other hand is comparatively a cost effective technique but at the same moment it is time consuming and the complete recovery of the metal, alone by biological leaching is not possible in most of the cases. The current review addresses the individual issues related to chemical and biological extraction techniques and proposes a hybrid-methodology which incorporates both, along with safer chemicals and compatible microbes for better and efficient extraction of metals from the E-waste.

  20. ENGINEERED BARRIER SYSTEM: PHYSICAL AND CHEMICAL ENVIRONMENT

    Energy Technology Data Exchange (ETDEWEB)

    R. Jarek

    2004-11-23

    The purpose of this report is to describe the evolution of the physical and chemical environmental conditions within the waste emplacement drifts of the repository, including the drip shield and waste package surfaces. The abstraction model is used in the total system performance assessment for the license application (TSPA LA) to assess the performance of the engineered barrier system and the waste form. This report develops and documents a set of these abstraction-level models that describe the engineered barrier system physical and chemical environment. Where possible, these models use information directly from other reports as input, which promotes integration among process models used for TSPA-LA. Specific tasks and activities of modeling the physical and chemical environment are included in ''Technical Work Plan for: Near-Field Environment and Transport In-Drift Geochemistry Model Report Integration'' (BSC 2004 [DIRS 171156], Section 1.2.2). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system reports.

  1. ENGINEERED BARRIER SYSTEM: PHYSICAL AND CHEMICAL ENVIRONMENT

    International Nuclear Information System (INIS)

    The purpose of this report is to describe the evolution of the physical and chemical environmental conditions within the waste emplacement drifts of the repository, including the drip shield and waste package surfaces. The abstraction model is used in the total system performance assessment for the license application (TSPA LA) to assess the performance of the engineered barrier system and the waste form. This report develops and documents a set of these abstraction-level models that describe the engineered barrier system physical and chemical environment. Where possible, these models use information directly from other reports as input, which promotes integration among process models used for TSPA-LA. Specific tasks and activities of modeling the physical and chemical environment are included in ''Technical Work Plan for: Near-Field Environment and Transport In-Drift Geochemistry Model Report Integration'' (BSC 2004 [DIRS 171156], Section 1.2.2). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system reports

  2. 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 ...

  3. Multiparametric imaging of biological systems by force-distance curve-based AFM.

    Science.gov (United States)

    Dufrêne, Yves F; Martínez-Martín, David; Medalsy, Izhar; Alsteens, David; Müller, Daniel J

    2013-09-01

    A current challenge in the life sciences is to understand how biological systems change their structural, biophysical and chemical properties to adjust functionality. Addressing this issue has been severely hampered by the lack of methods capable of imaging biosystems at high resolution while simultaneously mapping their multiple properties. Recent developments in force-distance (FD) curve-based atomic force microscopy (AFM) now enable researchers to combine (sub)molecular imaging with quantitative mapping of physical, chemical and biological interactions. Here we discuss the principles and applications of advanced FD-based AFM tools for the quantitative multiparametric characterization of complex cellular and biomolecular systems under physiological conditions. PMID:23985731

  4. Physical, chemical, and biological data for selected streams in Chester County, Pennsylvania, 1981-94

    Science.gov (United States)

    Reif, Andrew G.

    1999-01-01

    Physical, chemical, and biological data were collected at 51 sampling sites in Chester County, Pa., from 1970 through 1994 as part of the Stream Conditions of Chester County Program. This report presents data collected from 1981 through 1994. Physical data include water temperature, instantaneous stream discharge, pH, alkalinity, specific conductance, and dissolved oxygen. Chemical data include laboratory determinations of nutrients, major ions, and selected metals in whole water samples and selected metals, pesticides, gross polychlorinated biphenyls (PCB?s), gross polychlorinated napthalenes (PCN?s), and total carbon in stream-bottom sediment samples. The biological data consists of benthic macroinvertebrate population analyses and diversity indices. Chester County is undergoing rapid urbanization as agricultural lands are converted to residential, commercial, and industrial areas. The purpose of the Stream Conditions of Chester County Program is to further the understanding of stream habitat and chemical changes in response to this urbanization.

  5. Comparison on decolorization of palm oil mill effluent by biological, chemical and physical methods

    Directory of Open Access Journals (Sweden)

    Chantaphaso, S.

    2001-11-01

    Full Text Available Decolorization of palm oil mill effluent pretreated by enzyme from Aspergillus niger ATCC 6275 was investigated. The culture filtrate after separation of suspended solids was used for decolorization by biological, chemical and physical methods. Results indicated that the chemical method (using coagulant was more effective than the biological method (using commercial peroxidase, two strains of white-rot fungi Phanerochaete chrysosporium and Coriolus versicolor and physical method (using activated carbon, pararubber seed and sand filter. Studies on the effect of coagulant concentrations on decolorization revealed that using the combination of 10 ml/l polyferric sulphate and 10 g/l calcium oxide gave the highest color removal of 84.5% and organic matter (in term of chemical oxygen demand, COD removal of 86.5%.

  6. Surface-enhanced Raman scattering (SERS) detection for chemical and biological agents

    Science.gov (United States)

    Yan, Fei; Stokes, David L.; Wabuyele, Musundi B.; Griffin, Guy D.; Vass, Arpad A.; Vo-Dinh, Tuan

    2004-07-01

    Surface-enhanced Raman scattering (SERS) spectra of chemical agent simulants such as dimethyl methylphonate (DMMP), pinacolyl methylphosphonate (PMP), diethyl phosphoramidate (DEPA), and 2-chloroethyl ethylsulfide (CEES), and biological agent simulants such as bacillus globigii (BG), erwinia herbicola (EH), and bacillus thuringiensis (BT) were obtained from silver oxide film-deposited substrates. Thin AgO films ranging in thickness from 50 nm to 250 nm were produced by chemical bath deposition onto glass slides. Further Raman intensity enhancements were noticed in UV irradiated surfaces due to photo-induced Ag nanocluster formation, which may provide a possible route to producing highly useful plasmonic sensors for the detection of chemical and biological agents upon visible light illumination.

  7. PINS: A field PGNAA chemical identification system

    Energy Technology Data Exchange (ETDEWEB)

    Gehrke, R.J.; Caffrey, A.J.; Krebs, K.M.; Watts, K.D.; Oates, M.A.; McLaughlin, G.D. (Idaho National Engineering Lab., Idaho Falls (United States))

    1993-01-01

    Prompt gamma neutron activation analysis (PGNAA) has long been employed for chemical analysis in process streams and laboratories. Recent improvements in the design of germanium gamma-ray spectrometers, the miniaturization of their associated components, and the development of [open quotes]powerful[close quotes] notebook personal computers (PCs) permit the design of PGNAA systems for truly portable in-field use. Portable isotopic neutron spectrometry (PINS) (of gamma rays) was developed at the Idaho National Engineering Laboratory for in-field inspection and verification of chemical weapon inventories where a system that can be carried into an area inaccessible by wheeled transport (rough terrain, confined spaces, etc.) and that is capable of operating on battery power is required. PINS is now also finding use outside of military applications.

  8. Systems Biology in Aging: Linking the Old and the Young

    OpenAIRE

    HOU, LEI; Huang, Jialiang; Green, Christopher D.; Boyd-Kirkup, Jerome; Zhang, Wei; Yu, Xiaoming; Gong, Wenxuan; Zhou, Bing; Jing-Dong J Han

    2012-01-01

    Aging can be defined as a process of progressive decline in the physiological capacity of an organism, manifested by accumulated alteration and destabilization at the whole system level. Systems biology approaches offer a promising new perspective to examine the old problem of aging. We begin this review by introducing the concepts of systems biology, and then illustrate the application of systems biology approaches to aging research, from gene expression profiling to network analysis. We the...

  9. Fusion of chemical, biological, and meteorological observations for agent source term estimation and hazard refinement

    Science.gov (United States)

    Bieringer, Paul E.; Rodriguez, Luna M.; Sykes, Ian; Hurst, Jonathan; Vandenberghe, Francois; Weil, Jeffrey; Bieberbach, George, Jr.; Parker, Steve; Cabell, Ryan

    2011-05-01

    Chemical and biological (CB) agent detection and effective use of these observations in hazard assessment models are key elements of our nation's CB defense program that seeks to ensure that Department of Defense (DoD) operations are minimally affected by a CB attack. Accurate hazard assessments rely heavily on the source term parameters necessary to characterize the release in the transport and dispersion (T&D) simulation. Unfortunately, these source parameters are often not known and based on rudimentary assumptions. In this presentation we describe an algorithm that utilizes variational data assimilation techniques to fuse CB and meteorological observations to characterize agent release source parameters and provide a refined hazard assessment. The underlying algorithm consists of a combination of modeling systems, including the Second order Closure Integrated PUFF model (SCIPUFF), its corresponding Source Term Estimation (STE) model, a hybrid Lagrangian-Eulerian Plume Model (LEPM), its formal adjoint, and the software infrastructure necessary to link them. SCIPUFF and its STE model are used to calculate a "first guess" source estimate. The LEPM and corresponding adjoint are then used to iteratively refine this release source estimate using variational data assimilation techniques. This algorithm has undergone preliminary testing using virtual "single realization" plume release data sets from the Virtual THreat Response Emulation and Analysis Testbed (VTHREAT) and data from the FUSION Field Trials 2007 (FFT07). The end-to-end prototype of this system that has been developed to illustrate its use within the United States (US) Joint Effects Model (JEM) will be demonstrated.

  10. The implications of non-linear biological oscillations on human electrophysiology for electrohypersensitivity (EHS) and multiple chemical sensitivity (MCS).

    Science.gov (United States)

    Sage, Cindy

    2015-01-01

    The 'informational content' of Earth's electromagnetic signaling is like a set of operating instructions for human life. These environmental cues are dynamic and involve exquisitely low inputs (intensities) of critical frequencies with which all life on Earth evolved. Circadian and other temporal biological rhythms depend on these fluctuating electromagnetic inputs to direct gene expression, cell communication and metabolism, neural development, brainwave activity, neural synchrony, a diversity of immune functions, sleep and wake cycles, behavior and cognition. Oscillation is also a universal phenomenon, and biological systems of the heart, brain and gut are dependent on the cooperative actions of cells that function according to principles of non-linear, coupled biological oscillations for their synchrony. They are dependent on exquisitely timed cues from the environment at vanishingly small levels. Altered 'informational content' of environmental cues can swamp natural electromagnetic cues and result in dysregulation of normal biological rhythms that direct growth, development, metabolism and repair mechanisms. Pulsed electromagnetic fields (PEMF) and radiofrequency radiation (RFR) can have the devastating biological effects of disrupting homeostasis and desynchronizing normal biological rhythms that maintain health. Non-linear, weak field biological oscillations govern body electrophysiology, organize cell and tissue functions and maintain organ systems. Artificial bioelectrical interference can give false information (disruptive signaling) sufficient to affect critical pacemaker cells (of the heart, gut and brain) and desynchronize functions of these important cells that orchestrate function and maintain health. Chronic physiological stress undermines homeostasis whether it is chemically induced or electromagnetically induced (or both exposures are simultaneous contributors). This can eventually break down adaptive biological responses critical to health

  11. Solar System chemical abundances corrected for systematics

    OpenAIRE

    Gonzalez, Guillermo

    2014-01-01

    The relative chemical abundances between CI meteorites and the solar photosphere exhibit a significant trend with condensation temperature. A trend with condensation temperature is also seen when the solar photospheric abundances are compared to those of nearby solar twins. We use both these trends to determine the alteration of the elemental abundances of the meteorties and the photosphere by fractionation and calculate a new set of primordial Solar System abundances.

  12. Apparatus and Methods for Manipulation and Optimization of Biological Systems

    Science.gov (United States)

    Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Sun, Ren (Inventor); Yu, Fuqu (Inventor)

    2014-01-01

    The invention provides systems and methods for manipulating biological systems, for example to elicit a more desired biological response from a biological sample, such as a tissue, organ, and/or a cell. In one aspect, the invention operates by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The invention can be used, e.g., to optimize any biological system, e.g., bioreactors for proteins, and the like, small molecules, polysaccharides, lipids, and the like. Another use of the apparatus and methods includes is for the discovery of key parameters in complex biological systems.

  13. Modeling and Simulation Tools: From Systems Biology to Systems Medicine.

    Science.gov (United States)

    Olivier, Brett G; Swat, Maciej J; Moné, Martijn J

    2016-01-01

    Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of "Software as a Medical Device" and what this may imply for the migration of research-oriented, simulation software into the domain of human health.In our second perspective, we see how in practice hundreds of computational tools already accompany drug discovery and development at every stage of the process. Standardized exchange formats are required to streamline the model exchange between tools, which would minimize translation errors and reduce the required time. With the emergence, almost 15 years ago, of the SBML standard, a large part of the domain of interest is already covered and models can be shared and passed from software to software without recoding them. Until recently the last stage of the process, the pharmacometric analysis used in clinical studies carried out on subject populations, lacked such an exchange medium. We describe a new emerging exchange format in Pharmacometrics which covers the non-linear mixed effects models, the standard statistical model type used in this area. By interfacing these two formats the entire domain can be covered by complementary standards and subsequently the according tools.

  14. The effect of nanoparticle size, shape, and surface chemistry on biological systems.

    Science.gov (United States)

    Albanese, Alexandre; Tang, Peter S; Chan, Warren C W

    2012-01-01

    An understanding of the interactions between nanoparticles and biological systems is of significant interest. Studies aimed at correlating the properties of nanomaterials such as size, shape, chemical functionality, surface charge, and composition with biomolecular signaling, biological kinetics, transportation, and toxicity in both cell culture and animal experiments are under way. These fundamental studies will provide a foundation for engineering the next generation of nanoscale devices. Here, we provide rationales for these studies, review the current progress in studies of the interactions of nanomaterials with biological systems, and provide a perspective on the long-term implications of these findings.

  15. On the study of nonlinear dynamics of complex chemical reaction systems

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical processes in the life system, and to crosslinking the scientific study of chemistry, physics and biology.

  16. Strategies for the reduction of Legionella in biological treatment systems.

    Science.gov (United States)

    Nogueira, R; Utecht, K-U; Exner, M; Verstraete, W; Rosenwinkel, K-H

    2016-01-01

    A community-wide outbreak of Legionnaire's disease occurred in Warstein, Germany, in August 2013. The epidemic strain, Legionella pneumophila Serogruppe 1, was isolated from an industrial wastewater stream entering the municipal wastewater treatment plant (WWTP) in Wartein, the WWTP itself, the river Wäster and air/water samples from an industrial cooling system 3 km downstream of the WWTP. The present study investigated the effect of physical-chemical disinfection methods on the reduction of the concentration of Legionella in the biological treatment and in the treated effluent entering the river Wäster. Additionally, to gain insight into the factors that promote the growth of Legionella in biological systems, growth experiments were made with different substrates and temperatures. The dosage rates of silver micro-particles, hydrogen peroxide, chlorine dioxide and ozone and pH stress to the activated sludge were not able to decrease the number of culturable Legionella spp. in the effluent. Nevertheless, the UV treatment of secondary treated effluent reduced Legionella spp. on average by 1.6-3.4 log units. Laboratory-scale experiments and full-scale measurements suggested that the aerobic treatment of warm wastewater (30-35 °C) rich in organic nitrogen (protein) is a possible source of Legionella infection. PMID:27533856

  17. Abstract Interpretation for Probabilistic Termination of Biological Systems

    CERN Document Server

    Gori, Roberta; 10.4204/EPTCS.11.9

    2009-01-01

    In a previous paper the authors applied the Abstract Interpretation approach for approximating the probabilistic semantics of biological systems, modeled specifically using the Chemical Ground Form calculus. The methodology is based on the idea of representing a set of experiments, which differ only for the initial concentrations, by abstracting the multiplicity of reagents present in a solution, using intervals. In this paper, we refine the approach in order to address probabilistic termination properties. More in details, we introduce a refinement of the abstract LTS semantics and we abstract the probabilistic semantics using a variant of Interval Markov Chains. The abstract probabilistic model safely approximates a set of concrete experiments and reports conservative lower and upper bounds for probabilistic termination.

  18. 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.

  19. 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...

  20. Chemical or Biological Terrorist Attacks: An Analysis of the Preparedness of Hospitals for Managing Victims Affected by Chemical or Biological Weapons of Mass Destruction

    Directory of Open Access Journals (Sweden)

    Russell L. Bennett

    2006-03-01

    Full Text Available The possibility of a terrorist attack employing the use of chemical or biological weapons of mass destruction (WMD on American soil is no longer an empty threat, it has become a reality. A WMD is defined as any weapon with the capacity to inflict death and destruction on such a massive scale that its very presence in the hands of hostile forces is a grievous threat. Events of the past few years including the bombing of the World Trade Center in 1993, the Murrah Federal Building in Oklahoma City in 1995 and the use of planes as guided missiles directed into the Pentagon and New York’s Twin Towers in 2001 (9/11 and the tragic incidents involving twentythree people who were infected and five who died as a result of contact with anthrax-laced mail in the Fall of 2001, have well established that the United States can be attacked by both domestic and international terrorists without warning or provocation. In light of these actions, hospitals have been working vigorously to ensure that they would be “ready” in the event of another terrorist attack to provide appropriate medical care to victims. However, according to a recent United States General Accounting Office (GAO nationwide survey, our nation’s hospitals still are not prepared to manage mass causalities resulting from chemical or biological WMD. Therefore, there is a clear need for information about current hospital preparedness in order to provide a foundation for systematic planning and broader discussions about relative cost, probable effectiveness, environmental impact and overall societal priorities. Hence, the aim of this research was to examine the current preparedness of hospitals in the State of Mississippi to manage victims of terrorist attacks involving chemical or biological WMD. All acute care hospitals in the State were selected for inclusion in this study. Both quantitative and qualitative methods were utilized for data collection

  1. A coupled physical-biological-chemical model for the Indian Ocean

    Indian Academy of Sciences (India)

    P S Swathi; M K Sharada; K S Yajnik

    2000-12-01

    A coupled physical-biological-chemical model has been developed at C-MMACS. for studying the time- variation of primary productivity and air-sea carbon-dioxide exchange in the Indian Ocean. The physical model is based on the Modular Ocean Model, Version 2 (MOM2) and the biological model describes the nonlinear dynamics of a 7-component marine ecosystem. The chemical model includes dynamical equation for the evolution of dissolved inorganic carbon and total alkalinity. The interaction between the biological and chemical model is through the Redfield ratio. The partial pressure of carbon dioxide pCO2 of the surface layer is obtained from the chemical equilibrium equations of Peng et al 1987. Transfer coefficients for air-sea exchange of CO2 are computed dynamically based on the wind speeds. The coupled model reproduces the high productivity observed in the Arabian Sea off the Somali and Omani coasts during the Southwest (SW) monsoon. The entire Arabian Sea is an outgassing region for CO2 in spite of high productivity with transfer rates as high as 80 m-mol C/m2/day during SW monsoon near the Somali Coast on account of strong winds.

  2. Chemical analysis and biological testing of materials from the EDS coal liquefaction process: a status report

    Energy Technology Data Exchange (ETDEWEB)

    Later, D.W.; Pelroy, R.A.; Wilson, B.W.

    1984-05-01

    Representative process materials were obtained from the EDS pilot plant for chemical and biological analyses. These materials were characterized for biological activity and chemical composition using a microbial mutagenicity assay and chromatographic and mass spectrometric analytical techniques. The two highest boiling distillation cuts, as well as process solvent (PS) obtained from the bottoms recycle mode operation, were tested for initiation of mouse skin tumorigenicity. All three materials were active; the crude 800/sup 0 +/F cut was substantially more potent than the crude bottoms recycle PS or 750 to 800/sup 0/F distillate cut. Results from chemical analyses showed the EDS materials, in general, to be more highly alkylated and have higher hydroaromatic content than analogous SRC II process materials (no in-line process hydrogenation) used for comparison. In the microbial mutagenicity assays the N-PAC fractions showed greater activity than did the aliphatic hydrocarbon, hydroxy-PAH, or PAH fractions, although mutagenicity was detected in certain PAH fractions by a modified version of the standard microbial mutagenicity assay. Mutagenic activities for the EDS materials were lower, overall, than those for the corresponding materials from the SRC II process. The EDS materials produced under different operational modes had distinguishable differences in both their chemical constituency and biological activity. The primary differences between the EDS materials studied here and their SRC II counterparts used for comparison are most likely attributable to the incorporation of catalytic hydrogenation in the EDS process. 27 references, 28 figures, 27 tables.

  3. Mapping the patent landscape of synthetic biology for fine chemical production pathways.

    Science.gov (United States)

    Carbonell, Pablo; Gök, Abdullah; Shapira, Philip; Faulon, Jean-Loup

    2016-09-01

    A goal of synthetic biology bio-foundries is to innovate through an iterative design/build/test/learn pipeline. In assessing the value of new chemical production routes, the intellectual property (IP) novelty of the pathway is important. Exploratory studies can be carried using knowledge of the patent/IP landscape for synthetic biology and metabolic engineering. In this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable chemicals in the extended metabolic space of chassis organisms, as computed by the retrosynthesis-based algorithm RetroPath. Our database for reactions processed by sequences in heterologous pathways was screened against the PatSeq database, a comprehensive collection of more than 150M sequences present in patent grants and applications. We also examine related patent families using Derwent Innovations. This large-scale computational study provides useful insights into the IP landscape of synthetic biology for fine and specialty chemicals production. PMID:27489206

  4. Commentary: Systems Biology and Its Relevance to Alcohol Research

    OpenAIRE

    Guo, Q. Max; Zakhari, Sam

    2008-01-01

    Systems biology, a new scientific discipline, aims to study the behavior of a biological organization or process in order to understand the function of a dynamic system. This commentary will put into perspective topics discussed in this issue of Alcohol Research & Health, provide insight into why alcohol-induced disorders exemplify the kinds of conditions for which a systems biological approach would be fruitful, and discuss the opportunities and challenges facing alcohol researchers.

  5. Interactive analysis of systems biology molecular expression data

    OpenAIRE

    Prabhakar Sunil; Salt David E; Kane Michael D; Stephenson Alan; Ouyang Qi; Zhang Mingwu; Burgner John; Buck Charles; Zhang Xiang

    2008-01-01

    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 preferr...

  6. Influence of low intensity laser radiation on different biological systems

    OpenAIRE

    Tsivunchyk, Olga S.

    2004-01-01

    Abstract There are a lot of examples and contradictory results concerning influence of low intensity laser irradiation (LILI) on biological objects. In this work with a number of experiments the influence of LILI on different biological systems was investigated. For the carried out experiments the following biological objects and systems were used: * different enzymes of anti-oxidant system of animals (i.e. catalase, superoxide-di...

  7. Advanced Systems Biology Methods in Drug Discovery and Translational Biomedicine

    OpenAIRE

    Jun Zou; Ming-Wu Zheng; Gen Li; Zhi-Guang Su

    2013-01-01

    Systems biology is in an exponential development stage in recent years and has been widely utilized in biomedicine to better understand the molecular basis of human disease and the mechanism of drug action. Here, we discuss the fundamental concept of systems biology and its two computational methods that have been commonly used, that is, network analysis and dynamical modeling. The applications of systems biology in elucidating human disease are highlighted, consisting of human disease networ...

  8. Chemical and biological tracers to determine groundwater flow in karstic aquifer, Yucatan Peninsula

    Science.gov (United States)

    Lenczewski, M.; Leal-Bautista, R. M.; McLain, J. E.

    2013-05-01

    Little is known about the extent of pollution in groundwater in the Yucatan Peninsula; however current population growth, both from international tourism and Mexican nationals increases the potential for wastewater release of a vast array of contaminants including personal care products, pharmaceuticals (Rx), and pathogenic microorganisms. Pathogens and Rx in groundwater can persist and can be particularly acute in this region where high permeability of the karst bedrock and the lack of top soil permit the rapid transport of contaminants into groundwater aquifers. The objective of this research is to develop and utilize novel biological and chemical source tracking methods to distinguish between different sources of anthropogenic pollution in degraded groundwater. Although several methods have been used successfully to track fecal contamination sources in small scale studies, little is known about their spatial limitations, as source tracking studies rarely include sample collection over a wide geographical area and with different sources of water. In addition, although source tracking methods to distinguish human from animal fecal contamination are widely available, this work has developed source tracking distinguish between separate human populations is highly unique. To achieve this objective, we collected water samples from a series of drinking wells, cenotes (sinkholes), wastewater treatment plants, and injection wells across the Yucatan Peninsula and examine potential source tracers within the collected water samples. The result suggests that groundwater sources impacted by tourist vs. local populations contain different chemical stressors. This work has developed a more detailed understanding of the presence and persistence of personal care products, pharmaceuticals, and fecal indicators in a karstic system; such understanding will be a vital component for the protection Mexican groundwater and human health. Quantification of different pollution sources

  9. Zanthoxylum caribaeum (Rutaceae) essential oil: chemical investigation and biological effects on Rhodnius prolixus nymph.

    Science.gov (United States)

    Nogueira, J; Mourão, S C; Dolabela, I B; Santos, M G; Mello, C B; Kelecom, A; Mexas, R; Feder, D; Fernandes, C P; Gonzalez, M S; Rocha, L

    2014-11-01

    A chemical investigation and bioassays against fifth-instar nymphae of the hematophagous insect Rhodnius prolixus, vector of Chagas disease, were conducted with the essential oil from Zanthoxylum caribaeum. The main results may be summarized as follows: (i) 54 components were identified, corresponding to 90.4% of the relative composition; sesquiterpenes (47.3%) and monoterpenes (41.2%) are the major constituents; (ii) muurola-4,5-trans-diene and isodaucene are described for the first time as chemical constituents of the essential oil from leaves of this species; (iii) topical treatment with the crude essential oil induced high levels of paralysis (from 18.88 to 33.33%) and mortality (from 80 to 98.9%) depending on the dose applied (0.5 to 5.0 μl per insect); (iv) feeding treatment with the crude essential oil also induced high levels of mortality (from 48.8 to 100%) but low levels of paralysis (from 2.22 to 7.77%) depending on the dose applied (0.5 to 5.0 μl/ml of blood); (v) in the continuous treatment, only the dose of 5.0 μl/cm(2) was able to promote statistical significant levels of mortality (63.3%) but no paralysis were detected. However in this group, occasionally, only few insects displayed malformations of legs and wings after treatment; and (vi) any treatment was able to disrupt the metamorphosis process since the low adult stage emergence observed to all groups was due the high insect mortality. These observations suggest the interference of Z. caribaeum compounds on the triatomine neuroendocrine system. The significance of these results in relation to the relevant biological events in R. prolixus as well as the possible use of insect growth regulators present in Z. caribaeum oil in integrated vector control programs against hematophagous triatomine species is herein discussed. PMID:25224729

  10. Measurement of 100 B. anthracis Ames spores within 15 minutes by SERS at the US Army Edgewood Chemical Biological Ctr.

    Science.gov (United States)

    Farquharson, Stuart; Shende, Chetan; Smith, Wayne; Huang, Hermes; Sperry, Jay; Sickler, Todd; Prugh, Amber; Guicheteau, Jason

    2014-05-01

    Since the distribution of Bacillus anthracis-Ames spores through the US Postal System, there has been a persistent fear that biological warfare agents will be used by terrorists against our military abroad and our civilians at home. While there has been substantial effort since the anthrax attack of 2001 to develop analyzers to detect this and other biological warfare agents, the analyzers remain either too slow, lack sensitivity, produce high false-positive rates, or cannot be fielded. In an effort to overcome these limitations we have been developing a surface-enhanced Raman spectroscopy system. Here we describe the use of silver nanoparticles functionalized with a short peptide to selectively capture Bacillus anthracis spores and produce SER scattering. Specifically, measurements of 100 B. anthracis-Ames spores/mL in ~25 minutes performed at the US Army's Edgewood Chemical Biological Center are presented. The measurements provide a basis for the development of systems that can detect spores collected from the air or water supplies with the potential of saving lives during a biological warfare attack.

  11. MEMBRANE COMPUTING AS THE PARADIGM FOR MODELING SYSTEMS BIOLOGY

    Directory of Open Access Journals (Sweden)

    Ravie Chandren Muniyandi

    2013-01-01

    Full Text Available Membrane computing is a field in computer science that is inspired from the structure and the processes of living cells and is being considered as an alternative in solving the limitations in conventional mathematical approaches by taking into consideration its essential features that are of interest for research in systems biology. Advancements in computability make it feasible to handle huge volumes of data in biology and propose a new and better approach using a discreet computer science model, such as membrane computing. In this respect, membrane-computing abilities, to enhance the understanding of the system level of biological systems, have been explored. This study discusses experiences in applying membrane computing in modeling biological systems as well as possibilities of incorporating membrane computing into other computer science paradigms to enhance the use of membrane computing in systems biology. Experiences in modeling aspects of systems biology with membrane computing demonstrate additional advantages and possibilities compared with conventional methods. However, they are not yet used widely to model or simulate biological processes or systems. A general framework of modeling and verifying biological systems using membrane computing is essential as a guideline for biologists in their research in systems biology.

  12. Peroxisystem: harnessing systems cell biology to study peroxisomes.

    Science.gov (United States)

    Schuldiner, Maya; Zalckvar, Einat

    2015-04-01

    In recent years, high-throughput experimentation with quantitative analysis and modelling of cells, recently dubbed systems cell biology, has been harnessed to study the organisation and dynamics of simple biological systems. Here, we suggest that the peroxisome, a fascinating dynamic organelle, can be used as a good candidate for studying a complete biological system. We discuss several aspects of peroxisomes that can be studied using high-throughput systematic approaches and be integrated into a predictive model. Such approaches can be used in the future to study and understand how a more complex biological system, like a cell and maybe even ultimately a whole organism, works.

  13. At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code.

    Science.gov (United States)

    Xiao, Han; Schultz, Peter G

    2016-01-01

    The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted. PMID:27413101

  14. A guide to numerical modelling in systems biology

    CERN Document Server

    Deuflhard, Peter

    2015-01-01

    This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks, and identification of model parameters by means of comparisons...

  15. Diagnosis of water pollution caused by chemical effluents using hydro biological methods

    International Nuclear Information System (INIS)

    Industrial plants which discharge chemical effluents into rivers are faced with a double problem. 1 - To avoid excessive pollution which leads to an important modification of the medium and to a poisoning of the aquatic fauna, and in particular to the killing of fish. These disadvantages are avoided by a treatment of the effluents, by calculating the minimum fatal doses and the limiting dilutions for fish, and by carrying out biological analyses and tests on the residual waters. 2 - To avoid provoking continuous, slow and insidious pollutions which are more difficult to detect and which would result in the gradual sterilization of receptive media. In order to estimate this possible influence, the authors have listed the aquatic fauna and flora found in the canal which was the object of the experiment, and have modified the Saprobies system due to Kolwickz. They have tried to detect the presence or absence of pollution by estimating the density of the phyto-plankton formed on submerged laminae (periphyton) and the specific variations in the alga of which these populations are made up. In this report are given details of the tests and of the first results obtained. (authors)

  16. Chemical and biological attributes of a lowland soil affected by land leveling

    Directory of Open Access Journals (Sweden)

    José Maria Barbat Parfitt

    2013-11-01

    Full Text Available The objective of this work was to evaluate the relationship between soil chemical and biological attributes and the magnitude of cuts and fills after the land leveling process of a lowland soil. Soil samples were collected from the 0 - 0.20 m layer, before and after leveling, on a 100 point grid established in the experimental area, to evaluate chemical attributes and soil microbial biomass carbon (MBC. Leveling operations altered the magnitude of soil chemical and biological attributes. Values of Ca, Mg, S, cation exchange capacity, Mn, P, Zn, and soil organic matter (SOM decreased in the soil profile, whereas Al, K, and MBC increased after leveling. Land leveling decreased in 20% SOM average content in the 0 - 0.20 m layer. The great majority of the chemical attributes did not show relations between their values and the magnitude of cuts and fills. The relation was quadratic for SOM, P, and total N, and was linear for K, showing a positive slope and indicating increase in the magnitude of these attributes in cut areas and stability in fill areas. The relationships between these chemical attributes and the magnitude of cuts and fills indicate that the land leveling map may be a useful tool for degraded soil recuperation through amendments and organic fertilizers.

  17. Chemical and biological toxicity assessment of simulated Hanford site low-level waste grouts

    International Nuclear Information System (INIS)

    Defining the potential damage to the biosphere associated with exposure to low-level waste grouting operations at the Hanford Site near Richland, Washington, is difficult and controversial. Combined chemical and biological assessment of grout toxicity is needed to provide information on the potential risks of animal and plant exposure to the grouts. This paper will identify and predict the chemical components of the grout that will have the greatest potential of causing deleterious effects on fish and wildlife indigenous to the Hanford Site. This paper will also determine whether the current grout technology is adequate in controlling toxicant and pollutant releases for regulatory compliance

  18. The Chemical Composition and Biological Properties of Coconut (Cocos nucifera L. Water

    Directory of Open Access Journals (Sweden)

    Yan Fei Ng

    2009-12-01

    Full Text Available Coconut water (coconut liquid endosperm, with its many applications, is one of the world’s most versatile natural product. This refreshing beverage is consumed worldwide as it is nutritious and beneficial for health. There is increasing scientific evidence that supports the role of coconut water in health and medicinal applications. Coconut water is traditionally used as a growth supplement in plant tissue culture/micropropagation. The wide applications of coconut water can be justified by its unique chemical composition of sugars, vitamins, minerals, amino acids and phytohormones. This review attempts to summarise and evaluate the chemical composition and biological properties of coconut water.

  19. Integrated Assessment Systems for Chemical Warfare Material

    Energy Technology Data Exchange (ETDEWEB)

    A. M. Snyder; D. A. Verrill; G. L. Thinnes; K. D. Watts; R. J. McMorland

    1999-05-27

    The US Army must respond to a variety of situations involving suspect discovered, recovered, stored, and buried chemical warfare materiel (CWM). In some cases, the identity of the fill materiel and the status of the fusing and firing train cannot be visually determined due to aging of the container, or because the item is contained in an over-pack. In these cases, non-intrusive assessments are required to provide information to allow safe handling, storage, and disposal of the materiel. This paper will provide an overview of the integrated mobile and facility-based CWM assessment system prototypes that have been, and are being developed, at the Idaho National Engineering and Environmental Laboratory (INEEL) for the US Army Non-Stockpile Chemical Materiel Project. In addition, this paper will discuss advanced sensors being developed to enhance the capability of the existing and future assessment systems. The Phase I Mobile Munitions Assessment System (MMAS) is currently being used by the Army's Technical Escort Unit (TEU) at Dugway Proving Ground, Utah. This system includes equipment for non-intrusively identifying the munitions fill materiel and for assessing the condition and stability of the fuzes, firing trains, and other potential safety hazards. The system provides a self-contained, integrated command post including an on-board computer system, communications equipment, video and photographic equipment, weather monitoring equipment, and miscellaneous safety-related equipment. The Phase II MMAS is currently being tested and qualified for use by the INEEL and the US Army. The Phase II system contains several new assessment systems that significantly enhance the ability to assess CWM. A facility-based munitions assessment system prototype is being developed for the assessment of CWM stored in igloos at Pine Bluff Arsenal, Arkansas. This system is currently in the design and fabrication stages. Numerous CWM advanced sensors are being developed and tested, and

  20. A unified biological modeling and simulation system for analyzing biological reaction networks

    Science.gov (United States)

    Yu, Seok Jong; Tung, Thai Quang; Park, Junho; Lim, Jongtae; Yoo, Jaesoo

    2013-12-01

    In order to understand the biological response in a cell, a researcher has to create a biological network and design an experiment to prove it. Although biological knowledge has been accumulated, we still don't have enough biological models to explain complex biological phenomena. If a new biological network is to be created, integrated modeling software supporting various biological models is required. In this research, we design and implement a unified biological modeling and simulation system, called ezBioNet, for analyzing biological reaction networks. ezBioNet designs kinetic and Boolean network models and simulates the biological networks using a server-side simulation system with Object Oriented Parallel Accelerator Library framework. The main advantage of ezBioNet is that a user can create a biological network by using unified modeling canvas of kinetic and Boolean models and perform massive simulations, including Ordinary Differential Equation analyses, sensitivity analyses, parameter estimates and Boolean network analysis. ezBioNet integrates useful biological databases, including the BioModels database, by connecting European Bioinformatics Institute servers through Web services Application Programming Interfaces. In addition, we employ Eclipse Rich Client Platform, which is a powerful modularity framework to allow various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool and a simulation system for understanding the control mechanism by monitoring the change of each component in a biological network. The simulation result can be managed and visualized on ezBioNet, which is available free of charge at http://ezbionet.sourceforge.net or http://ezbionet.cbnu.ac.kr.

  1. An Introduction to the Biological and Chemical Oceanography Data Management Office (BCO- DMO)

    Science.gov (United States)

    Chandler, C.; Glover, D.; Groman, R.; Wiebe, P.

    2007-12-01

    The BCO-DMO (http://www.bco-dmo.org) was created to serve PIs funded by the NSF Biological and Chemical Oceanography Sections as a facility where marine biogeochemical and ecological data and information developed in the course of scientific research can easily be disseminated, protected, and stored on short and intermediate time-frames. The Data Management Office also strives to provide research scientists and others with the tools and systems necessary to work with marine biogeochemical and ecological data from heterogeneous sources with increased efficacy. To accomplish this, two data management offices (former- U.S. JGOFS and U.S. GLOBEC) have been united and enhanced to provide a venue for contribution of electronic data/metadata and other information for open distribution via the World Wide Web. The JGOFS/GLOBEC Client/Server distributed data management system software is used to serve data and information to every investigator, regardless of computing platform. In addition, Web services are provided for data discovery, and development has begun on a machine-to-machine application programming interface (API) to allow interoperability between Web-based data systems. The BCO-DMO will manage existing and new data sets from individual scientific investigators, collaborative groups of investigators, and data management offices of larger multi-institutional projects via any standard Web browser. The office will work with principal investigators on data quality control; maintain an inventory and program thesaurus of strictly defined field names; generate metadata (e.g. Directory Interchange Format (DIF) ) records required by Federal agencies; ensure submission of data to national data centers; support and encourage data synthesis by providing new, online, Web-based display tools; facilitate interoperability among different data portals; and facilitate regional, national, and international data and information exchange.

  2. Secondary metabolites as potential cancer therapeutic leads : : synthesis and chemical biology of Englerin A and Fusarisetin A

    OpenAIRE

    Caro-Diaz, Eduardo J.E.

    2014-01-01

    Secondary metabolites generated from natural sources such as microbes, fungi, marine fauna and other microorganism have proven to represent a microcosm of chemical diversity and therefore a great source of novel phamacophoric structures. It is without question that nature in its long biological and chemical evolution has gifted us with beautiful molecular architectures with equally important biological function to provide leads into new and potentially useful biologically active molecules. As...

  3. Chemical and Biological Aspects of Marine Sponges from the Family Mycalidae.

    Science.gov (United States)

    Habener, Leesa J; Hooper, John N A; Carroll, Anthony R

    2016-06-01

    Sponges are a useful source of bioactive natural products. Members of the family Mycalidae, in particular, have provided a variety of chemical structures including alkaloids, polyketides, terpene endoperoxides, peptides, and lipids. This review highlights the compounds isolated from Mycalid sponges and their associated biological activities. A diverse group of 190 compounds have been reported from over 40 specimens contained in 49 references. Over half of the studies have reported on the biological activities for the compounds isolated. The polyketides, in particular the macrolides, displayed potent cytotoxic activities (< 1 µM), and the alkaloids, in particular the 2,5-disubstituted pyrrole derivatives, were associated with moderate cytotoxic activities (1-20 µM). The pyrrole alkaloids and the cyclic peroxides appear to be phylogenetically restricted to sponges and thus might prove useful when applied to sponge taxonomy. The observed diversity of chemical structures suggests this family makes a good target for targeted biodiscovery projects. PMID:27002400

  4. Physical, chemical, and biological data for selected streams in Chester County, Pennsylvania, 1995-97

    Science.gov (United States)

    Reif, Andrew G.

    2000-01-01

    Physical, chemical, and biological data were collected at 51 sampling sites in Chester County, Pa., from 1970 through 1997 as part of the Stream Conditions of Chester County Program. This report presents data collected from 43 sites from 1995 through 1997 that constitute a continuation of the program. Physical data include water temperature, instantaneous stream discharge, pH, alkalinity, specific conductance, and dissolved oxygen. Chemical data collected include laboratory determinations of nutrients and major ions in whole water samples and selected metals, pesticides, gross polychlorinated biphenyls (PCB's), gross polychlorinated napthalenes (PCN's), and total carbon in stream-sediment samples. The biological data include benthic-macroinvertebrate populations. The data are presented without interpretation. Chester County is undergoing urbanization as agricultural land is converted to residential developments, commercial areas, and industrial and corporate parks. The major goal of the Stream Conditions of Chester County Program is to further the understanding of stream changes in response to urbanization.

  5. HRI catalytic two-stage liquefaction (CTSL) process materials: chemical analysis and biological testing

    Energy Technology Data Exchange (ETDEWEB)

    Wright, C.W.; Later, D.W.

    1985-12-01

    This report presents data from the chemical analysis and biological testing of coal liquefaction materials obtained from the Hydrocarbon Research, Incorporated (HRI) catalytic two-stage liquefaction (CTSL) process. Materials from both an experimental run and a 25-day demonstration run were analyzed. Chemical methods of analysis included adsorption column chromatography, high-resolution gas chromatography, gas chromatography/mass spectrometry, low-voltage probe-inlet mass spectrometry, and proton nuclear magnetic resonance spectroscopy. The biological activity was evaluated using the standard microbial mutagenicity assay and an initiation/promotion assay for mouse-skin tumorigenicity. Where applicable, the results obtained from the analyses of the CTSL materials have been compared to those obtained from the integrated and nonintegrated two-stage coal liquefaction processes. 18 refs., 26 figs., 22 tabs.

  6. Particle size distribution and removal in the chemical-biological flocculation process

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhi-bin; ZHAO Jian-fu; XIA Si-qing; LIU Chang-qing; KANG Xing-sheng

    2007-01-01

    The particle characterization from the influent and effluent of a chemical-biological flocculation (CBF) process was studied with a laser diffraction device. Water samples from a chemically enhanced primary treatment (CEPT) process and a primary sediment tank process were also analyzed for comparison. The results showed that CBF process was not only effective for both the big size particles and small size particles removal, but also the best particle removal process in the three processes. The results also indicated that CBF process was superior to CEPT process in the heavy metals removal. The high and non-selective removal for heavy metals might be closely related to its strong ability to eliminate small particles. Samples from different locations in CBF reactors showed that small particles were easier to aggregate into big ones and those disrupted flocs could properly flocculate again along CBF reactor because of the biological flocculation.

  7. Identification of a thienopyrimidine derivatives target by a kinome and chemical biology approach.

    Science.gov (United States)

    Lee, Chulho; Yang, Jee Sun; Han, Gyoonhee

    2015-09-01

    Target identification through chemical biology has been considered one of the most efficient approaches for drug discovery. Thienopyrimidine derivatives were designed to discover potent IκB kinase β (IKKβ) inhibitors based on a known IKKβ inhibitor library. Most of the thienopyrimidine derivatives inhibited nitric oxide and tumor necrosis factor alpha, which are downstream of the NF-κB signaling pathway, but not IKKβ. To identify the appropriate targets of thienopyrimidine analogues, chemical biology approaches, including text mining and a subsequent kinase panel assay from the kinome profiling were used. Based on the results, Fms-like tyrosine kinase 3 was found to be the target for thienopyrimidine derivatives, and was confirmed to be a potent inhibitor for acute myeloid leukemia. PMID:26186885

  8. Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

    Science.gov (United States)

    Villaverde, Alejandro F; Banga, Julio R

    2014-02-01

    The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?

  9. Survey and discussion of models applicable to the transport and fate thrust area of the Department of Energy Chemical and Biological Nonproliferation Program

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    The availability and easy production of toxic chemical and biological agents by domestic and international terrorists pose a serious threat to US national security, especially to civilian populations in and around urban areas. To address this threat, the Department of Energy (DOE) has established the Chemical and Biological Nonproliferation Program (CBNP) with the goal of focusing the DOE`s technical resources and expertise on capabilities to deny, deter, mitigate and respond to clandestine releases of chemical and biological agents. With the intent to build on DOE core competencies, the DOE has established six technology thrust areas within the CBNP Program: Biological Information Resources; Point Sensor Systems; Stand-off Detection; Transport and Fate; Decontamination; and Systems Analysis and Integration. The purpose of the Transport and Fate Thrust is to accurately predict the dispersion, concentration and ultimate fate of chemical and biological agents released into the urban and suburban environments and has two major goals: (1) to develop an integrated and validated state-of-the-art atmospheric transport and fate modeling capability for chemical and biological agent releases within the complex urban environment from the regional scale down to building and subway interiors, and (2) to apply this modeling capability in a broad range of simulation case studies of chemical and biological agent release scenarios in suburban, urban and confined (buildings and subways) environments and provide analysis for the incident response user community. Sections of this report discuss subway transport and fate models; buildings interior transport and fate modeling; models for flow and transport around buildings; and local-regional meteorology and dispersion models.

  10. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

    OpenAIRE

    Jun Hong; Litao Yang; Dabing Zhang; Jianxin Shi

    2016-01-01

    As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plan...

  11. Predictive modeling of nanomaterial exposure effects in biological systems

    OpenAIRE

    Liu X; Tang K.; Harper S.; Harper B; Steevens JA; Xu R

    2013-01-01

    Xiong Liu,1 Kaizhi Tang,1 Stacey Harper,2 Bryan Harper,2 Jeffery A Steevens,3 Roger Xu1 1Intelligent Automation, Inc., Rockville, MD, USA; 2Department of Environmental and Molecular Toxicology, School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR, USA; 3ERDC Environmental Laboratory, Vicksburg, MS, USA Background: Predictive modeling of the biological effects of nanomaterials is critical for industry and policymakers to assess the potential ha...

  12. Determining the Chemical and Biological Availability of Zinc in Urban Stormwater Retention Ponds

    Science.gov (United States)

    Camponelli, K.; Casey, R.; Lev, S. M.; Landa, E. R.; Snodgrass, J.

    2005-12-01

    Highway runoff has the potential to negatively impact receiving systems due to transport of contaminants that accumulate on road surfaces. Metals such as copper and zinc are major components of automobile brake pads and tires, respectively. As these automobile parts are degraded, these metal containing particulates are deposited on the roadway and are washed into storm water retention ponds and surface water bodies during precipitation events. It has been estimated that 15 to 60% of the Zn in urban stormwater runoff comes from tire wear and that tire wear is a significant source of Zn to the environment with release inventories comparable to waste incineration sources. In urban and sub-urban systems, this large source of Zn can accumulate in stormwater retention ponds which serve as habitat for a variety of species. Understanding the chemical and biological availability of Zn to biota is integral to assessing the habitat quality of retention ponds. This study is a first effort to relate the amount and speciation of Zn in a retention pond to Zn inputs through highway-derived runoff events. In addition, results suggest that the chemical speciation and availability of particulate Zn can be related to the bioavailability and toxicity of Zn to pond organisms (i.e. larval amphibians). The study site in Owings Mills, MD is located next to a four-lane highway from which it receives runoff through a single culvert. Five species of anurans are known to utilize the pond as a breeding site and Zn in amphibian tissues and retention pond sediments were highly elevated at this site in 2001 and 2002. A recent analysis of pond sediments, soils, roadway dust and storm water collected at this site suggests that roadway particulate matter transported during runoff events is the dominant source of Zn in this system. Overall, Zn and other trace metals were found to be most abundant in the clay sized faction of pond sediments and soils. The pond cores were found to have higher Zn and Cu

  13. Chemical Composition and Biological Activities of Fragrant Mexican Copal (Bursera spp.).

    Science.gov (United States)

    Gigliarelli, Giulia; Becerra, Judith X; Curini, Massimo; Marcotullio, Maria Carla

    2015-12-12

    Copal is the Spanish word used to describe aromatic resins from several genera of plants. Mexican copal derives from several Bursera spp., Protium copal, some Pinus spp. (e.g., P. pseudostrobus) and a few Fabaceae spp. It has been used for centuries as incense for religious ceremonies, as a food preservative, and as a treatment for several illnesses. The aim of this review is to analyze the chemical composition and biological activity of commercial Mexican Bursera copal.

  14. Application of chemical oxidation processes for the removal of pharmaceuticals in biologically treated wastewater

    OpenAIRE

    Hey, Gerly

    2013-01-01

    The discharge of effluents from wastewater treatment plants (WWTPs) is considered to be the major source of residual pharmaceuticals frequently found in aquatic environments. The complex nature of such compounds tends to make conventional biological treatments aimed at their removal ineffective. The present thesis concerns the removal of 62 different active pharmaceutical ingredients commonly detected in Swedish wastewater effluents by means of chemical oxidation techniques. Techniques wit...

  15. Editorial : special Issue contributed by the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008

    OpenAIRE

    Ferreira, E. C.; Mota, M.

    2009-01-01

    The 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008, was held in Braga, Portugal, from the 4th to the 6th of September, 2008. The conference was jointly organized by the University of Minho, the “Ordem dos Engenheiros,” and the Institute for Biotechnology and Bioengineeing, with the support of “Sociedade Portuguesa de Qu´ımica” and “Sociedade Portuguesa de Biotecnologia”. The CHEMPOR series traditionally brings together both young and establishe...

  16. Chemical Composition and Biological Activities of Fragrant Mexican Copal (Bursera spp.

    Directory of Open Access Journals (Sweden)

    Giulia Gigliarelli

    2015-12-01

    Full Text Available Copal is the Spanish word used to describe aromatic resins from several genera of plants. Mexican copal derives from several Bursera spp., Protium copal, some Pinus spp. (e.g., P. pseudostrobus and a few Fabaceae spp. It has been used for centuries as incense for religious ceremonies, as a food preservative, and as a treatment for several illnesses. The aim of this review is to analyze the chemical composition and biological activity of commercial Mexican Bursera copal.

  17. STUDY OF PHYSIO-CHEMICAL CHARACTERISTICS AND BIOLOGICAL TREATMENT OF MOLASSES-BASED DISTILLERY EFFLUENT

    OpenAIRE

    Anupama Chaudhary* AK Sharma and Birbal Singh

    2013-01-01

    Molasses based distilleries are recognized as of major polluting industries with a large amount of annual effluent production. Modi Distillery, located at Modi Nagar in western Uttar Pradesh, is a molasses-based distillery with a capacity of 26 KLPD. Being an alcohol-processing unit, we estimated capacity and efficiency of Modi distillery that discharges highly polluted effluent to small drainage with a very high biological oxygen demand (BOD) (42,000-51,000mg/ltr) and chemical oxygen demand ...

  18. Nuclear, biological, and chemical combined injuries and countermeasures on the battlefield.

    Science.gov (United States)

    Knudson, Gregory B; Elliott, Thomas B; Brook, Itzhak; Shoemaker, Michael O; Pastel, Ross H; Lowy, Robert J; King, Gregory L; Herzig, Thomas C; Landauer, Michael R; Wilson, Scott A; Peacock, Susan J; Bouhaouala, S Samy; Jackson, William E; Ledney, G David

    2002-02-01

    The Armed Forces Radiobiological Research Institute (AFRRI) has developed a research program to determine the major health risks from exposure to ionizing radiation in combination with biological and chemical warfare agents and to assess the extent to which exposure to ionizing radiation compromises the effectiveness of protective drugs, vaccines, and other biological and chemical warfare prophylactic and treatment strategies. AFRRI's Defense Technology Objective MD22 supports the development of treatment modalities and studies to assess the mortality rates for combined injuries from exposure to ionizing radiation and Bacillus anthracis, and research to provide data for casualty prediction models that assess the health consequences of combined exposures. In conjunction with the Defense Threat Reduction Agency, our research data are contributing to the development of casualty prediction models that estimate mortality and incapacitation in an environment of radiation exposure plus other weapons of mass destruction. Specifically, the AFFRI research program assesses the effects of ionizing radiation exposure in combination with B. anthracis, Venezuelan equine encephalomyelitis virus, Shigella sonnei, nerve agents, and mustard as well as their associated treatments and vaccines. In addition, the long-term psychological effects of radiation combined with nuclear, biological, and chemical (NBC) injuries are being evaluated. We are also assessing the effectiveness of gamma photons and high-speed neutrons and electrons for neutralizing biological and chemical warfare agents. New protocols based on our NBC bioeffects experiments will enable U.S. armed forces to accomplish military operations in NBC environments while optimizing both survival and military performance. Preserving combatants' health in an NBC environment will improve warfighting operations and mission capabilities.

  19. Influence of physical and chemical factors on biological leaching process of copper from printed circuit boards

    OpenAIRE

    Willner, J

    2013-01-01

    The article presents the results of the research regarding the biological leaching of this metal from electronic wastes components in the form of printed circuit boards. The purpose of the study was to evaluate the influence of some physical and chemical factors (e.g. pH, oxidation-reduction potential) on bioleaching process and efficiency of copper transfer from solid phase into solution. Bioleaching experiments were carried out with pure cultures of Acidithiobacillus ferrooxidans. The obtai...

  20. Chemical and biological metal nanoparticles as antimycobacterial agents: A comparative study.

    Science.gov (United States)

    Singh, Richa; Nawale, Laxman U; Arkile, Manisha; Shedbalkar, Utkarsha U; Wadhwani, Sweety A; Sarkar, Dhiman; Chopade, Balu A

    2015-08-01

    Resistance among mycobacteria leading to multidrug-resistant and extensively drug-resistant tuberculosis is a major threat. However, nanotechnology has provided new insights in drug delivery and medicine development. This is the first comparative report to determine the activity of chemically and biologically synthesised silver nanoparticles (AgNPs) and gold nanoparticles (AuNPs) against mycobacteria. Screening data revealed the high mycobactericidal efficiency of AgNPs, with minimum inhibitory concentrations (MICs) of therapeutics for tuberculosis.

  1. Safe management of mass fatalities following chemical, biological, and radiological incidents.

    Science.gov (United States)

    Baker, David J; Jones, Kelly A; Mobbs, Shelly F; Sepai, Ovnair; Morgan, Dilys; Murray, Virginia S G

    2009-01-01

    Contaminated mass fatalities following the release of chemical, biological, or radiological agents pose a potential major health hazard. A United Kingdom government investigation has identified a number of areas of risk. This paper presents an outline of the findings of the study and describes specific pathways for the management of contaminated and non-contaminated fatalities. Factors determining the choice between cremation and burial are discussed. Effective decontamination remains a neglected area of study for both fatalities and casualties.

  2. Physico-Chemical and Biological Parameters of the Three Rural Ponds of Sasaram of Bihar

    Directory of Open Access Journals (Sweden)

    Jyoti Choudhary

    2014-06-01

    Full Text Available Physico chemical and biological parameters of the three rural pond of Sasaram,Bihar has been studied to see the present condition for its better utilization. The study revealed that parameters are within permissible limit for fish culture and the stocking should be done as per the productivity of the water. As per the BOD estimation the ponds falls under moderately polluted category.

  3. 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

  4. Dynamics and kinetics of model biological systems

    Science.gov (United States)

    Mirigian, Stephen

    In this work we study three systems of biological interest: the translocation of a heterogeneously charged polymer through an infinitely thin pore, the wrapped of a rigid particle by a soft vesicle and the modification of the dynamical properties of a gel due to the presence of rigid inclusions. We study the kinetics of translocation for a heterogeneously charged polyelectrolyte through an infinitely narrow pore using the Fokker-Planck formalism to compute mean first passage times, the probability of successful translocation, and the mean successful translocation time for a diblock copolymer. We find, in contrast to the homopolymer result, that details of the boundary conditions lead to qualitatively different behavior. Under experimentally relevant conditions for a diblock copolymer we find that there is a threshold length of the charged block, beyond which the probability of successful translocation is independent of charge fraction. Additionally, we find that mean successful translocation time exhibits non-monotonic behavior with increasing length of the charged fraction; there is an optimum length of the charged block where the mean successful translocation time is slowest and there can be a substantial range of charge fraction where it is slower than a minimally charged chain. For a fixed total charge on the chain, we find that finer distributions of the charge along the chain leads to a significant reduction in mean translocation time compared to the diblock distribution. Endocytosis is modeled using a simple geometrical model from the literature. We map the process of wrapping a rigid spherical bead onto a one-dimensional stochastic process described by the Fokker-Planck equation to compute uptake rates as a function of membrane properties and system geometry. We find that simple geometrical considerations pick an optimal particle size for uptake and a corresponding maximal uptake rate, which can be controlled by altering the material properties of the

  5. Synthetic biology outside the cell: linking computational tools to cell-free systems.

    Science.gov (United States)

    Lewis, Daniel D; Villarreal, Fernando D; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems. PMID:25538941

  6. Synthetic biology outside the cell: linking computational tools to cell-free systems.

    Science.gov (United States)

    Lewis, Daniel D; Villarreal, Fernando D; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  7. 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.

  8. 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.

  9. Approximate bayesian parameter inference for dynamical systems in systems biology

    International Nuclear Information System (INIS)

    This paper proposes to use approximate instead of exact stochastic simulation algorithms for approximate Bayesian parameter inference of dynamical systems in systems biology. It first presents the mathematical framework for the description of systems biology models, especially from the aspect of a stochastic formulation as opposed to deterministic model formulations based on the law of mass action. In contrast to maximum likelihood methods for parameter inference, approximate inference method- share presented which are based on sampling parameters from a known prior probability distribution, which gradually evolves toward a posterior distribution, through the comparison of simulated data from the model to a given data set of measurements. The paper then discusses the simulation process, where an over- view is given of the different exact and approximate methods for stochastic simulation and their improvements that we propose. The exact and approximate simulators are implemented and used within approximate Bayesian parameter inference methods. Our evaluation of these methods on two tasks of parameter estimation in two different models shows that equally good results are obtained much faster when using approximate simulation as compared to using exact simulation. (Author)

  10. Building momentum for systems and synthetic biology in India

    OpenAIRE

    Krishnan, Remya; Manjaly-Antony, Lijo Anto; Dhar, Pawan K.

    2010-01-01

    Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out) and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computat...

  11. Global optimization in systems biology: stochastic methods and their applications

    OpenAIRE

    Balsa-Canto, Eva; Banga, Julio R.; Egea, José A.; Villaverde, A. F.; Hijas-Liste, G. M.

    2012-01-01

    Mathematical optimization is at the core of many problems in systems biology: (1) as the underlying hypothesis for model development, (2) in model identification, or (3) in the computation of optimal stimulation procedures to synthetically achieve a desired biological behavior. These problems are usually formulated as nonlinear programing problems (NLPs) with dynamic and algebraic constraints. However the nonlinear and highly constrained nature of systems biology models, together with the usu...

  12. Leukemia, an effective model for chemical biology and target therapy1

    Institute of Scientific and Technical Information of China (English)

    Guo-qiang CHEN; Li-shun WANG; Ying-li WU; Yun YU

    2007-01-01

    The rapid rise of chemical biology aimed at studying signaling networks for basic cellular activities using specific, active small molecules as probes has greatly accelerated research on pathological mechanisms and target therapy of diseases.This research is especially important for malignant tumors such as leukemia, a heterogeneous group of hematopoietic malignancies that occurs worldwide. With the use of a chemical approach combined with genetic manipulation, great progresshas been achieved over the past few decades on the biological, molecular and cytogenetic aspects of leukemia, and in its diagnosis and therapy. In particular,discoveries of the clinical effectiveness of all-trans rctinoic acid and arsenic trioxide in the treatment of acute promyelocytic leukemia and the kinase inhibitorsImatinib and Dasatinib in the treatment of chronic myelogenous leukemia not only make target therapy of leukemia a reality, but also push mechanisms of leukemo-genesis and leukemic cell activities forward. This review will outline advances in chemical biology that help our understanding of the molecular mechanisms of cell differentiation and apoptosis induction and target therapy of leukemia.

  13. Enhanced Removal of Lead by Chemically and Biologically Treated Carbonaceous Materials

    Directory of Open Access Journals (Sweden)

    Mohamed E. Mahmoud

    2012-01-01

    Full Text Available Hybrid sorbents and biosorbents were synthesized via chemical and biological treatment of active carbon by simple and direct redox reaction followed by surface loading of baker’s yeast. Surface functionality and morphology of chemically and biologically modified sorbents and biosorbents were studied by Fourier Transform Infrared analysis and scanning electron microscope imaging. Hybrid carbonaceous sorbents and biosorbents were characterized by excellent efficiency and superiority toward lead(II sorption compared to blank active carbon providing a maximum sorption capacity of lead(II ion as 500 μmol g−1. Sorption processes of lead(II by these hybrid materials were investigated under the influence of several controlling parameters such as pH, contact time, mass of sorbent and biosorbent, lead(II concentration, and foreign ions. Lead(II sorption mechanisms were found to obey the Langmuir and BET isotherm models. The potential applications of chemically and biologically modified-active carbonaceous materials for removal and extraction of lead from real water matrices were also studied via a double-stage microcolumn technique. The results of this study were found to denote to superior recovery values of lead (95.0–99.0±3.0–5.0% by various carbonaceous-modified-bakers yeast biosorbents.

  14. Green Jobs: Definition and Method of Appraisal of Chemical and Biological Risks.

    Science.gov (United States)

    Cheneval, Erwan; Busque, Marc-Antoine; Ostiguy, Claude; Lavoie, Jacques; Bourbonnais, Robert; Labrèche, France; Bakhiyi, Bouchra; Zayed, Joseph

    2016-04-01

    In the wake of sustainable development, green jobs are developing rapidly, changing the work environment. However a green job is not automatically a safe job. The aim of the study was to define green jobs, and to establish a preliminary risk assessment of chemical substances and biological agents for workers in Quebec. An operational definition was developed, along with criteria and sustainable development principles to discriminate green jobs from regular jobs. The potential toxicity or hazard associated with their chemical and biological exposures was assessed, and the workers' exposure appraised using an expert assessment method. A control banding approach was then used to assess risks for workers in selected green jobs. A double entry model allowed us to set priorities in terms of chemical or biological risk. Among jobs that present the highest risk potential, several are related to waste management. The developed method is flexible and could be adapted to better appraise the risks that workers are facing or to propose control measures. PMID:26718400

  15. Chemical and biological characterization of residential oil burner emission. A literature survey

    International Nuclear Information System (INIS)

    This literature study covers the time period 1980 to 1993 and is concerned with oil burners used for residential heating with a nominal heating power of less than 20 kW, which are normally used in one-family houses. Emission samples from domestic heaters using organic fuels consists of a very complex matrix of pollutants ranging from aggregate states solid to gaseous. Biological effects elicited by exhaust emissions have been detected and determined. It has been shown for diesel vehicles that selection of fuel properties has an impact on combustion reaction paths which results in different exhaust chemical compositions. It was also determined that diesel fuel properties have an impact on the biological activity of diesel exhaust emissions, which is to be expected from their chemical characterization. As a result of this, Sweden has an environmental classification of diesel fuels which has been in force since 1991. Analogously, the Swedish Environmental Protection Agency has asked whether detrimental environmental and health effects from residential heating can be reduced by selection of fuel properties, and if so by how much? In addition, which properties are most important to control in a future environmental classification of heating oils? As a first step in this process, a literature survey was performed. Major topics were: Sampling technology, chemical composition, biological activity, and risk assessment of emissions. 33 refs, 11 tabs

  16. Systems biology in aging: linking the old and the young.

    Science.gov (United States)

    Hou, Lei; Huang, Jialiang; Green, Christopher D; Boyd-Kirkup, Jerome; Zhang, Wei; Yu, Xiaoming; Gong, Wenxuan; Zhou, Bing; Han, Jing-Dong J

    2012-11-01

    Aging can be defined as a process of progressive decline in the physiological capacity of an organism, manifested by accumulated alteration and destabilization at the whole system level. Systems biology approaches offer a promising new perspective to examine the old problem of aging. We begin this review by introducing the concepts of systems biology, and then illustrate the application of systems biology approaches to aging research, from gene expression profiling to network analysis. We then introduce the network that can be constructed using known lifespan and aging regulators, and conclude with a look forward to the future of systems biology in aging research. In summary, systems biology is not only a young field that may help us understand aging at a higher level, but also an important platform that can link different levels of knowledge on aging, moving us closer to a more comprehensive control of systematic decline during aging. PMID:23633915

  17. Artificial Cell Research as a Field that Connects Chemical, Biological and Philosophical Questions.

    Science.gov (United States)

    Deplazes-Zemp, Anna

    2016-01-01

    This review article discusses the interdisciplinary nature and implications of artificial cell research. It starts from two historical theories: Gánti's chemoton model and the autopoiesis theory by Maturana and Varela. They both explain the transition from chemical molecules to biological cells. These models exemplify two different ways in which disciplines of chemistry, biology and philosophy can profit from each other. In the chemoton model, conclusions from one disciplinary approach are relevant for the other disciplines. In contrast, the autopoiesis model itself (rather than its conclusions) is transferred from one discipline to the other. The article closes by underpinning the relevance of artificial cell research for philosophy with reference to the on-going philosophical debates on emergence, biological functions and biocentrism. PMID:27363375

  18. An optimized, chemically regulated gene expression system for Chlamydomonas.

    Directory of Open Access Journals (Sweden)

    Paola Ferrante

    Full Text Available BACKGROUND: Chlamydomonas reinhardtii is a model system for algal and cell biology and is used for biotechnological applications, such as molecular farming or biological hydrogen production. The Chlamydomonas metal-responsive CYC6 promoter is repressed by copper and induced by nickel ions. However, induction by nickel is weak in some strains, poorly reversible by chelating agents like EDTA, and causes, at high concentrations, toxicity side effects on Chlamydomonas growth. Removal of these bottlenecks will encourage the wide use of this promoter as a chemically regulated gene expression system. METHODOLOGY: Using a codon-optimized Renilla luciferase as a reporter gene, we explored several strategies to improve the strength and reversibility of CYC6 promoter induction. Use of the first intron of the RBCS2 gene or of a modified TAP medium increases the strength of CYC6 induction up to 20-fold. In the modified medium, induction is also obtained after addition of specific copper chelators, like TETA. At low concentrations (up to 10 microM TETA is a more efficient inducer than Ni, which becomes a very efficient inducer at higher concentrations (50 microM. Neither TETA nor Ni show toxicity effects at the concentrations used. Unlike induction by Ni, induction by TETA is completely reversible by micromolar copper concentrations, thus resulting in a transient "wave" in luciferase activity, which can be repeated in subsequent growth cycles. CONCLUSIONS: We have worked out a chemically regulated gene expression system that can be finely tuned to produce temporally controlled "waves" in gene expression. The use of cassettes containing the CYC6 promoter, and of modified growth media, is a reliable and economically sustainable system for the temporally controlled expression of foreign genes in Chlamydomonas.

  19. 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...

  20. Microbial metabolism fuels ecosystem-scale organic matter transformations: an integrated biological and chemical perspective

    Science.gov (United States)

    Wrighton, K. C.; Narrowe, A. B.; Angle, J.; Stefanik, K. S.; Daly, R. A.; Johnston, M.; Miller, C. S.

    2014-12-01

    Freshwater saturated sediments and soils represent vital ecosystems due to their nutrient cycling capacities and their prominent contribution to global greenhouse gas emissions. However, the diversity of microorganisms and metabolic pathways involved in carbon cycling, and the impacts of these processes on other biogeochemical cycles remain poorly understood. Major advances in DNA sequencing have helped forge linkages between the previously disconnected biological and chemical components of these systems. Here, we present data on the use of assembly-based metagenomics to generate hypotheses on microbial carbon degradation and biogeochemical cycling in waterlogged sediments and soils. DNA sequencing from a fresh water aquifer adjacent to the Colorado River in Rifle, CO yielded extensive genome recovery from multiple previously unknown bacterial lineages. Fermentative metabolisms encoded by these genomes drive nitrogen, hydrogen, and sulfur cycling in this subsurface system. We are also applying a similar approach to identify microbial processes in a freshwater wetland on Lake Erie, OH. Given the increased diversity (increased richness, decreased evenness, and strain variation) of wetland sediment microbial communities, we modified methods for specialized assembly of long taxonomic marker gene amplicons (EMIRGE) to create a biogeographical map of Fungi, Archaea, and Bacteria along depth and hydrological transects. This map reveals that the microbial community associated with the top two depths (>7 cm) is significantly different from bottom depths (7-40 cm). Dissolved organic matter (DOM) molecular weight and the presence of oxidized terminal electron acceptors best predict differences in microbial community structure. Laboratory mesocosms amended with pore-water DOM, in situ soil communities, and variable oxygen conditions link DOM composition and redox to microbial metabolic networks, biogeochemical cycles, and green house gas emission. Organism identities from

  1. Chemical and biological indicators of water quality in three agricultural watersheds of the Po valley, Italy

    Directory of Open Access Journals (Sweden)

    Linda Pieri

    2011-12-01

    Full Text Available Agriculture has both direct and indirect effects on quality of surface water and is one of the key activities causing water quality degradation. Its environmental impact can be evaluated by the determination of indicators of the quality of water bodies that collect drainage and runoff waters from agricultural watersheds. For this research, the water quality draining from three watersheds, totally or partially cultivated, all within the Po river valley (Italy, was determined, using chemical indicators (N-NO3 and N-NH4 concentration, N balance, trophic status (chlorophyll-a concentration and benthic population indexes. Together, they should provide an overview of the water status, which is supposed to be strictly related to the land use and the management. Results show that the chemical parameters are well related to land use and farming management: intensive agricultural activity leads to high N-NO3 concentration in water and N surplus and vice versa. The chlorophyll-a concentration follows the same trend, being linked to nitrogen loads and land use. Not always there is accordance between chemical and biological indicators: no direct correspondence is evident between the N-NO3 concentration in waters and benthic community. Its presence and abundance seems to be mostly correlated with the geomorphology, hydrology, riparian strips, etc. of the habitat than to the land use. Only the integration of chemical and biological parameters allows a correct understanding of the state of health of water body and benthic communities.

  2. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

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

  3. The Current State and Perspectives of Systems Biology

    Institute of Scientific and Technical Information of China (English)

    Tielui Shi; Yixue Li

    2006-01-01

    Emerging as a new field in biology recently, Systems Biology provides a branch new way to study the biological activities in organisms. In order to decode the complexity of life systematically,systems biology integrates the "-omics" and uses the high throughput methods from transcriptomics,protomics and metabonomics to detect the dynamic activities in cell; and then, it incorporates bioinformatics methods to integrate and analyze those data, and simulate the biological processes based on the model built from those integrated data. In this paper, the current state, the research field and the methods for the Systems Biology are introduced briefly, and then, several ideas about future development in this field are also proposed.

  4. Cell reprogramming: a new chemical approach to stem cell biology and tissue regeneration.

    Science.gov (United States)

    Anastasia, L; Piccoli, M; Garatti, A; Conforti, E; Scaringi, R; Bergante, S; Castelvecchio, S; Venerando, B; Menicanti, L; Tettamanti, G

    2011-02-01

    Generation of pluripotent stem cells (iPSCs) from adult fibroblasts starts a "new era" in stem cell biology, as it overcomes several key issues associated with previous approaches, including the ethical concerns associated with human embryonic stem cells. However, as the genetic approach for cell reprogramming has already shown potential safety issues, a chemical approach may be a safer and easier alternative. Moreover, a chemical approach could be advantageous not only for the de-differentiation phase, but also for inducing reprogrammed cells into the desired cell type with higher efficiency than current methodologies. Finally, a chemical approach may be envisioned to activate resident adult stem cells to proliferate and regenerate damaged tissues in situ, without the need for exogenous cell injections.

  5. Chemical, biological, radiological, and nuclear decontamination: Recent trends and future perspective

    Directory of Open Access Journals (Sweden)

    Vinod Kumar

    2010-01-01

    Full Text Available Chemical, biological, radiological, and nuclear (CBRN decontamination is the removal of CBRN material from equipment or humans. The objective of the decontamination is to reduce radiation burden, salvage equipment, and materials, remove loose CBRN contaminants, and fix the remaining in place in preparation for protective storage or permanent disposal work activities. Decontamination may be carried out using chemical, electrochemical, and mechanical means. Like materials, humans may also be contaminated with CBRN contamination. Changes in cellular function can occur at lower radiation doses and exposure to chemicals. At high dose, cell death may take place. Therefore, decontamination of humans at the time of emergency while generating bare minimum waste is an enormous task requiring dedication of large number of personnel and large amount of time. General principles of CBRN decontamination are discussed in this review with emphasis on radiodecontamination.

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

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

    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...... 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...

  7. Mathematical modeling of the evolution of a simple biological system

    Digital Repository Service at National Institute of Oceanography (India)

    Gonsalves, M.J.B.D.; Neetu, S.; Krishnan, K.P.; Attri, K.; LokaBharathi, P.A.

    physical system, where a model usually can be developed from well established fundamental principles, in case of biological systems such principles are not always available offering an opportunity for innovation. The success of the innovation, of course...

  8. Using ANN to predict E. coli accumulation in coves based on interaction amongst various physical, chemical and biological factors

    Science.gov (United States)

    Dwivedi, D.; Mohanty, B. P.; Lesikar, B. J.

    2008-12-01

    The accumulation of Escherichia Coli (E. coli) in canals, coves and streams is the result of a number of interacting processes operating at multiple spatial and temporal scales. Fate and transport of E. coli in surface water systems is governed by different physical, chemical, and biological processes. Various models developed to quantify each of these processes occurring at different scales are not so far pooled into a single predictive model. At present, very little is known about the fate and transport of E. coli in the environment. We hypothesize that E. coli population heterogeneity in canals and coves is affected by physical factors (average stream width and/ depth, secchi depth, flow and flow severity, day since precipitation, aquatic vegetation, solar radiation, dissolved and total suspended solids etc.); chemical factors (basic water quality, nutrients, organic compounds, pH, and toxicity etc.); and biological factors (type of bacterial strain, predation, and antagonism etc.). The specific objectives of this study are to: (1) examine the interactions between E. coli and various coupled physical, chemical and biological factors; (2) examine the interactions between E. coli and toxic organic pollutants and other pathogens (viruses); and (3) evaluate qualitatively the removal efficiency of E. coli. We suggest that artificial neural networks (ANN) may be used to provide a possible solution to this problem. To demonstrate the application of the approach, we develop an ANN representing E. coli accumulation in two polluted sites at Lake Granbury in the upper part of the Brazos River in North Central Texas. The graphical structure of ANN explicitly represents cause- and-effect relationship between system variables. Each of these relationships can then be quantified independently using an approach suitable for the type and scale of information available. Preliminary results revealed that E. coli concentrations in canals show seasonal variations regardless of change

  9. ENGINEERED BARRIER SYSTEM: PHYSICAL AND CHEMICAL ENVIRONMENT

    International Nuclear Information System (INIS)

    The purpose of this model report is to describe the evolution of the physical and chemical environmental conditions within the waste emplacement drifts of the repository, including the drip shield and waste package surfaces. The resulting seepage evaporation and gas abstraction models are used in the total system performance assessment for the license application (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. This report develops and documents a set of abstraction-level models that describe the engineered barrier system physical and chemical environment. Where possible, these models use information directly from other reports as input, which promotes integration among process models used for TSPA-LA. Specific tasks and activities of modeling the physical and chemical environment are included in ''Technical Work Plan for: Near-Field Environment and Transport In-Drift Geochemistry Model Report Integration'' (BSC 2005 [DIRS 173782], Section 1.2.2). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system reports. To be consistent with other project documents that address features, events, and processes (FEPs), Table 6.14.1 of the current report includes updates to FEP numbers and FEP subjects for two FEPs identified in the technical work plan (TWP) governing this report (BSC 2005 [DIRS 173782]). FEP 2.1.09.06.0A (Reduction-oxidation potential in EBS), as listed in Table 2 of the TWP (BSC 2005 [DIRS 173782]), has been updated in the current report to FEP 2.1.09.06.0B (Reduction-oxidation potential in Drifts; see Table 6.14-1). FEP 2.1.09.07.0A (Reaction kinetics in EBS), as listed in Table 2 of the TWP (BSC 2005 [DIRS 173782]), has been updated in the current report to FEP 2.1.09.07.0B (Reaction kinetics in Drifts; see Table 6.14-1). These deviations from the TWP are justified because they improve integration with FEPs documents. The updates

  10. ENGINEERED BARRIER SYSTEM: PHYSICAL AND CHEMICAL ENVIRONMENT

    Energy Technology Data Exchange (ETDEWEB)

    R. Jarek

    2005-08-29

    The purpose of this model report is to describe the evolution of the physical and chemical environmental conditions within the waste emplacement drifts of the repository, including the drip shield and waste package surfaces. The resulting seepage evaporation and gas abstraction models are used in the total system performance assessment for the license application (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. This report develops and documents a set of abstraction-level models that describe the engineered barrier system physical and chemical environment. Where possible, these models use information directly from other reports as input, which promotes integration among process models used for TSPA-LA. Specific tasks and activities of modeling the physical and chemical environment are included in ''Technical Work Plan for: Near-Field Environment and Transport In-Drift Geochemistry Model Report Integration'' (BSC 2005 [DIRS 173782], Section 1.2.2). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system reports. To be consistent with other project documents that address features, events, and processes (FEPs), Table 6.14.1 of the current report includes updates to FEP numbers and FEP subjects for two FEPs identified in the technical work plan (TWP) governing this report (BSC 2005 [DIRS 173782]). FEP 2.1.09.06.0A (Reduction-oxidation potential in EBS), as listed in Table 2 of the TWP (BSC 2005 [DIRS 173782]), has been updated in the current report to FEP 2.1.09.06.0B (Reduction-oxidation potential in Drifts; see Table 6.14-1). FEP 2.1.09.07.0A (Reaction kinetics in EBS), as listed in Table 2 of the TWP (BSC 2005 [DIRS 173782]), has been updated in the current report to FEP 2.1.09.07.0B (Reaction kinetics in Drifts; see Table 6.14-1). These deviations from the TWP are justified because they improve integration with FEPs

  11. Interactions of physical, chemical, and biological weather calling for an integrated approach to assessment, forecasting, and communication of air quality.

    Science.gov (United States)

    Klein, Thomas; Kukkonen, Jaakko; Dahl, Aslög; Bossioli, Elissavet; Baklanov, Alexander; Vik, Aasmund Fahre; Agnew, Paul; Karatzas, Kostas D; Sofiev, Mikhail

    2012-12-01

    This article reviews interactions and health impacts of physical, chemical, and biological weather. Interactions and synergistic effects between the three types of weather call for integrated assessment, forecasting, and communication of air quality. Today's air quality legislation falls short of addressing air quality degradation by biological weather, despite increasing evidence for the feasibility of both mitigation and adaptation policy options. In comparison with the existing capabilities for physical and chemical weather, the monitoring of biological weather is lacking stable operational agreements and resources. Furthermore, integrated effects of physical, chemical, and biological weather suggest a critical review of air quality management practices. Additional research is required to improve the coupled modeling of physical, chemical, and biological weather as well as the assessment and communication of integrated air quality. Findings from several recent COST Actions underline the importance of an increased dialog between scientists from the fields of meteorology, air quality, aerobiology, health, and policy makers.

  12. 29 CFR 1910.161 - Fixed extinguishing systems, dry chemical.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 5 2010-07-01 2010-07-01 false Fixed extinguishing systems, dry chemical. 1910.161 Section... § 1910.161 Fixed extinguishing systems, dry chemical. (a) Scope and application. This section applies to all fixed extinguishing systems, using dry chemical as the extinguishing agent, installed to meet...

  13. A novel process of dye wastewater treatment by linking advanced chemical oxidation with biological oxidation

    OpenAIRE

    Zou Haiming; Ma Wanzheng; Wang Yan

    2015-01-01

    Dye wastewater is one of typically non-biodegradable industrial effluents. A new process linking Fenton’s oxidation with biological oxidation proposed in this study was investigated to degrade the organic substances from real dye wastewater. During the combination process, the Fenton’s oxidation process can reduce the organic load and enhance biodegradability of dye wastewater, which is followed by biological aerated filter (BAF) system to further remove organic substances in terms of dischar...

  14. A suggested approach to the selection of chemical and biological protective clothing--meeting industry and emergency response needs for protection against a variety of hazards.

    Science.gov (United States)

    Stull, Jeffrey O

    2004-01-01

    The paper describes the development of a comprehensive decision logic for selection and use of biological and chemical protective clothing (BCPC). The decision logic recognizes the separate areas of BCPC use among emergency, biological, and chemical hazards. The proposed decision logic provides a system for type classifying BCPC in terms of its compliance with existing standards (for emergency applications), the overall clothing integrity, and the material barrier performance. Type classification is offered for garments, gloves, footwear, and eye/face protection devices. On the basis of multiple, but simply designed flowcharts, the type of BCPC appropriate for specific biological and chemical hazards can be selected. The decision logic also provides supplemental considerations for choosing appropriate BCPC features. PMID:15377412

  15. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.

    2011-02-25

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.

  16. 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.

  17. Machine learning in systems biology at different scales : from molecular biology to ecology

    OpenAIRE

    Aderhold, Andrej

    2015-01-01

    Machine learning has been a source for continuous methodological advances in the field of computational learning from data. Systems biology has profited in various ways from machine learning techniques but in particular from network inference, i.e. the learning of interactions given observed quantities of the involved components or data that stem from interventional experiments. Originally this domain of system biology was confined to the inference of gene regulation networks but ...

  18. Cycles and the qualitative evolution of chemical systems.

    Directory of Open Access Journals (Sweden)

    Peter Kreyssig

    Full Text Available Cycles are abundant in most kinds of networks, especially in biological ones. Here, we investigate their role in the evolution of a chemical reaction system from one self-sustaining composition of molecular species to another and their influence on the stability of these compositions. While it is accepted that, from a topological standpoint, they enhance network robustness, the consequence of cycles to the dynamics are not well understood. In a former study, we developed a necessary criterion for the existence of a fixed point, which is purely based on topological properties of the network. The structures of interest we identified were a generalization of closed autocatalytic sets, called chemical organizations. Here, we show that the existence of these chemical organizations and therefore steady states is linked to the existence of cycles. Importantly, we provide a criterion for a qualitative transition, namely a transition from one self-sustaining set of molecular species to another via the introduction of a cycle. Because results purely based on topology do not yield sufficient conditions for dynamic properties, e.g. stability, other tools must be employed, such as analysis via ordinary differential equations. Hence, we study a special case, namely a particular type of reflexive autocatalytic network. Applications for this can be found in nature, and we give a detailed account of the mitotic spindle assembly and spindle position checkpoints. From our analysis, we conclude that the positive feedback provided by these networks' cycles ensures the existence of a stable positive fixed point. Additionally, we use a genome-scale network model of the Escherichia coli sugar metabolism to illustrate our findings. In summary, our results suggest that the qualitative evolution of chemical systems requires the addition and elimination of cycles.

  19. Using PBPK guided “Body-on-a-Chip” Systems to Predict Mammalian Response to Drug and Chemical Exposure

    OpenAIRE

    Sung, Jong Hwan; Srinivasan, Balaji; Esch, Mandy Brigitte; McLamb, William T.; Bernabini, Catia; Shuler, Michael L.; Hickman, James J.

    2014-01-01

    The continued development of in vitro systems that accurately emulate human response to drugs or chemical agents will impact drug development, our understanding of chemical toxicity, and enhance our ability to respond to threats from chemical or biological agents. A promising technology is to build microscale replicas of humans that capture essential elements of physiology, pharmacology and/or toxicology (microphysiological systems). Here, we review progress on systems for microscale models o...

  20. Computational modeling of chemo-bio-mechanical coupling: a systems-biology approach toward wound healing.

    Science.gov (United States)

    Buganza Tepole, A; Kuhl, E

    2016-01-01

    Wound healing is a synchronized cascade of chemical, biological, and mechanical phenomena, which act in concert to restore the damaged tissue. An imbalance between these events can induce painful scarring. Despite intense efforts to decipher the mechanisms of wound healing, the role of mechanics remains poorly understood. Here, we establish a computational systems biology model to identify the chemical, biological, and mechanical mechanisms of scar formation. First, we introduce the generic problem of coupled chemo-bio-mechanics. Then, we introduce the model problem of wound healing in terms of a particular chemical signal, inflammation, a particular biological cell type, fibroblasts, and a particular mechanical model, isotropic hyperelasticity. We explore the cross-talk between chemical, biological, and mechanical signals and show that all three fields have a significant impact on scar formation. Our model is the first step toward rigorous multiscale, multifield modeling in wound healing. Our formulation has the potential to improve effective wound management and optimize treatment on an individualized patient-specific basis.