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Sample records for biosequestration integrating biology

  1. Carbon Cycling and Biosequestration Integrating Biology and Climate Through Systems Science Report from the March 2008 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Graber, J.; Amthor, J.; Dahlman, R.; Drell, D.; Weatherwax, S.

    2008-12-01

    One of the most daunting challenges facing science in the 21st Century is to predict how Earth's ecosystems will respond to global climate change. The global carbon cycle plays a central role in regulating atmospheric carbon dioxide (CO{sub 2}) levels and thus Earth's climate, but our basic understanding of the myriad of tightly interlinked biological processes that drive the global carbon cycle remains limited at best. Whether terrestrial and ocean ecosystems will capture, store, or release carbon is highly dependent on how changing climate conditions affect processes performed by the organisms that form Earth's biosphere. Advancing our knowledge of biological components of the global carbon cycle is thus crucial to predicting potential climate change impacts, assessing the viability of climate change adaptation and mitigation strategies, and informing relevant policy decisions. Global carbon cycling is dominated by the paired biological processes of photosynthesis and respiration. Photosynthetic plants and microbes of Earth's land-masses and oceans use solar energy to transform atmospheric CO{sub 2} into organic carbon. The majority of this organic carbon is rapidly consumed by plants or microbial decomposers for respiration and returned to the atmosphere as CO{sub 2}. Coupling between the two processes results in a near equilibrium between photosynthesis and respiration at the global scale, but some fraction of organic carbon also remains in stabilized forms such as biomass, soil, and deep ocean sediments. This process, known as carbon biosequestration, temporarily removes carbon from active cycling and has thus far absorbed a substantial fraction of anthropogenic carbon emissions.

  2. 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.

  3. Raise Test Scores: Integrate Biology and Calculus.

    Science.gov (United States)

    Lukens, Jeffrey D.; Feinstein, Sheryl

    This paper presents the results of research that compared the academic achievement of high school students enrolled in an integrated Advanced Placement Biology/Advanced Placement Calculus course with students enrolled in traditional Advanced Placement Biology and Advanced Placement Calculus courses. Study subjects included high school students…

  4. Biosequestration of atmospheric CO2 and flue gas-containing CO2 by microalgae.

    Science.gov (United States)

    Cheah, Wai Yan; Show, Pau Loke; Chang, Jo-Shu; Ling, Tau Chuan; Juan, Joon Ching

    2015-05-01

    The unceasing rise of greenhouse gas emission has led to global warming and climate change. Global concern on this phenomenon has put forward the microalgal-based CO2 sequestration aiming to sequester carbon back to the biosphere, ultimately reducing greenhouse effects. Microalgae have recently gained enormous attention worldwide, to be the valuable feedstock for renewable energy production, due to their high growth rates, high lipid productivities and the ability to sequester carbon. The photosynthetic process of microalgae uses atmospheric CO2 and CO2 from flue gases, to synthesize nutrients for their growth. In this review article, we will primarily discuss the efficiency of CO2 biosequestration by microalgae species, factors influencing microalgal biomass productions, microalgal cultivation systems, the potential and limitations of using flue gas for microalgal cultivation as well as the bio-refinery approach of microalgal biomass.

  5. Integrative Biology: A Capstone Course for an Introductory Biology Core

    Science.gov (United States)

    Chaplin, Susan B.; Hartung, Nancy Z.

    2012-01-01

    A capstone to the biology introductory curriculum was developed with the specific goals of enhancing integration of course content, promoting development of oral presentation skills and critical reading and thinking skills, and introducing ecological principles omitted from the rest of the core. Classes of 12 to 16 students were team taught by…

  6. Integrative Systems Biology: Elucidating Complex Traits

    DEFF Research Database (Denmark)

    Pers, Tune Hannes

    product itself. My doctoral studies have been focused on the development of integrative approaches to identify systemic risk-modifying and disease-causing patterns. ey have been rooted in the hypothesis that data integration of complementary data sets may yield additional etiologic insights compared...... traits and disease. e esis is structured as follows. Chapter  presents a few introductory remarks to integrative systems biology, and Chapter  gives a brief description of human genetic variation and GWA analysis. Chapters - present the main topics in the esis (integrative methodologies...... to analyses conducted within a single type of data. e first line of research presented here outlines two integrative methodologies designed to identify etiological pathways and susceptibility genes. In Paper I, my coworkers and I present an integrative approach that interrogates protein complexes...

  7. Network biology methods integrating biological data for translational science.

    Science.gov (United States)

    Bebek, Gurkan; Koyutürk, Mehmet; Price, Nathan D; Chance, Mark R

    2012-07-01

    The explosion of biomedical data, both on the genomic and proteomic side as well as clinical data, will require complex integration and analysis to provide new molecular variables to better understand the molecular basis of phenotype. Currently, much data exist in silos and is not analyzed in frameworks where all data are brought to bear in the development of biomarkers and novel functional targets. This is beginning to change. Network biology approaches, which emphasize the interactions between genes, proteins and metabolites provide a framework for data integration such that genome, proteome, metabolome and other -omics data can be jointly analyzed to understand and predict disease phenotypes. In this review, recent advances in network biology approaches and results are identified. A common theme is the potential for network analysis to provide multiplexed and functionally connected biomarkers for analyzing the molecular basis of disease, thus changing our approaches to analyzing and modeling genome- and proteome-wide data.

  8. WISB: Warwick Integrative Synthetic Biology Centre.

    Science.gov (United States)

    McCarthy, John

    2016-06-15

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia.

  9. 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. ...

  10. Biochips: The Integrated Circuit of Biology

    DEFF Research Database (Denmark)

    Madsen, Jan

    2012-01-01

    Microfluidic biochips integrate different biochemical analysis functionalities (e.g., dispensers, filters, mixers, separators, detectors) on-chip, miniaturizing the macroscopic chemical and biological processes often processed by lab-robots, to a sub-millimeter scale. These microsystems offer...... several advantages over the conventional biochemical analyzers, e.g., reduced sample and reagent volumes, speeded up biochemical reactions, ultra-sensitive detection and higher system throughput, with several assays being integrated on the same chip. Hence, microfluidic biochips are replacing...... the conventional biochemical analyzers, and areable to integrate on-chip all the necessary functions for biochemical analysis. Microfluidic biochips have an immense potential in multiple application areas, such as clinical diagnostics, advanced sequencing, drug discovery, and environmental monitoring, to name...

  11. A linguistic integration of a biological database

    Energy Technology Data Exchange (ETDEWEB)

    Collado-Vides, J. [Univ. Nacional Autonoma de Mexico, Morelos (Mexico)

    1993-12-31

    One of the major theoretical concerns associated with the Human Genome Project is that of the methodology to decipher ``raw`` sequences of DNA. This work is concerned with a subsequent problem, the one of how huge amounts of already deciphered information that will emerge in the near future can be integrated in order to enhance their biological understanding. The formal foundations for a linguistic theory of the regulation of gene expression will be discussed. The linguistic analysis presented here is restricted to sequences with known biological function since: (1) there is no way to obtain, from DNA sequences alone, a regulatory representation of transcription units, and (2) the elements of substitution -- methodologically equivalent to phonemes -- are complete sequences of the binding sites of proteins. The authors have recently collected and analyzed the regulatory regions of a large number of E. coli promoters. The number of sigma 70 promoters studied may well represent the largest homogeneous body of knowledge of gene regulation at present. This collection is a data set for the construction of a grammar of the sigma 70 system of transcription and regulation. This grammatical model generates all the arrays of the collection, as well as novel combinations predicted to be consistent with the principles of the data set. This Grammar is testable, as well as expandable if the analysis of emerging data requires it. The elaboration of a linguistic methodology capable of integrating prokaryotic data constitutes a preliminary step towards the analysis and integration of the more complex eukaryotic systems of regulation.

  12. Data mining and data integration in biology

    DEFF Research Database (Denmark)

    Ólason, Páll Ísólfur

    2008-01-01

    between molecules, the essence of systems biology. Internet technologies are very important in this respect as bioinformatics labs around the world generate staggering amounts of novel annotations, increasing the importance of on-line processing and distributed systems. One of the most important new data...... types in proteomics is protein-protein interactions. Interactions between the functional elements in the cell are a natural place to start when integrating protein annotations with the aim of gaining a systems view of the cell. Interaction data, however, are notoriously biased, erroneous and incomplete....... They also necessitate new ways of data preparation as established methods for sequence sets are often useless when dealing with sets of sequence pairs. Therefore careful analysis on the sequence level as well as the integrated network level is needed to benchmark these data prior to use. The networks, which...

  13. The Virtual Institute for Integrative Biology (VIIB)

    Energy Technology Data Exchange (ETDEWEB)

    Rivera, G.; Gonzalez-Nieto, F.; Perez-Acle, T.; Isea, R.; Holmes, D. S.

    2007-07-01

    The Virtual Institute for Integrative Biology (VII B) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, Metagenomic, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomic, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: inter operability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible work flows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions. (Author)

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

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

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

  15. Integrative Biological Analysis of the APOE*3-Leiden Transgenic Mouse

    NARCIS (Netherlands)

    Clish, C.B.; Davidov, E.; Oresic, M.; Plasterer, T.N.; Lavine, G.; Londo, T.; Meys, M.; Snell, P.; Stochaj, W.; Adourian, A.; Zhang, X.; Morel, N.; Neumann, E.; Verheij, E.; Vogels, J.T.W.E.; Havekes, L.M.; Afeyan, N.; Regnier, F.; Greef, J. van der; Naylor, S.

    2004-01-01

    Integrative (or systems biology) is a new approach to analyzing biological entities as integrated systems of genetic, genomic, protein, metabolite, cellular, and pathway events that are in flux and interdependent. Here, we demonstrate the application of intregrative biological analysis to a mammalia

  16. Reconstruction of biological networks based on life science data integration

    OpenAIRE

    Kormeier, Benjamin; Hippe, Klaus; Arrigo, Patrizio; Töpel, Thoralf; Janowski, Sebastian; Hofestädt, Ralf

    2010-01-01

    For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and V...

  17. Integration of culture and biology in human development.

    Science.gov (United States)

    Mistry, Jayanthi

    2013-01-01

    The challenge of integrating biology and culture is addressed in this chapter by emphasizing human development as involving mutually constitutive, embodied, and epigenetic processes. Heuristically rich constructs extrapolated from cultural psychology and developmental science, such as embodiment, action, and activity, are presented as promising approaches to the integration of cultural and biology in human development. These theoretical notions are applied to frame the nascent field of cultural neuroscience as representing this integration of culture and biology. Current empirical research in cultural neuroscience is then synthesized to illustrate emerging trends in this body of literature that examine the integration of biology and culture.

  18. Interdisciplinary problem-solving: emerging modes in integrative systems biology

    NARCIS (Netherlands)

    MacLeod, Miles; Nersessian, Nancy J.

    2016-01-01

    Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an interd

  19. Integrated Modular Teaching of Human Biology for Primary Care Practitioners

    Science.gov (United States)

    Glasgow, Michael S.

    1977-01-01

    Describes the use of integrated modular teaching of the human biology component of the Health Associate Program at Johns Hopkins University, where the goal is to develop an understanding of the sciences as applied to primary care. Discussion covers the module sequence, the human biology faculty, goals of the human biology faculty, laboratory…

  20. Integrating Quantitative Thinking into an Introductory Biology Course Improves Students’ Mathematical Reasoning in Biological Contexts

    OpenAIRE

    Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

    2014-01-01

    Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students’ apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In ...

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

    Science.gov (United States)

    Haave, Neil

    2012-01-01

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

  2. Integrating quantitative thinking into an introductory biology course improves students' mathematical reasoning in biological contexts.

    Science.gov (United States)

    Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

    2014-01-01

    Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students' apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students' understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students' inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students' biology learning.

  3. Integrating interactive computational modeling in biology curricula.

    Directory of Open Access Journals (Sweden)

    Tomáš Helikar

    2015-03-01

    Full Text Available While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  4. Integrating interactive computational modeling in biology curricula.

    Science.gov (United States)

    Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

    2015-03-01

    While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  5. Integration of microfluidics into the synthetic biology design flow.

    Science.gov (United States)

    Huang, Haiyao; Densmore, Douglas

    2014-09-21

    One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Major challenges in these efforts include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of specification-design-assembly-verification. We present here a summary of the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. The integration of microfluidics and synthetic biology has the capability to produce rapid prototyping platforms for characterization of genetic devices, testing of biotherapeutics, and development of biosensors.

  6. Integrative systems biology for data-driven knowledge discovery.

    Science.gov (United States)

    Greene, Casey S; Troyanskaya, Olga G

    2010-09-01

    Integrative systems biology is an approach that brings together diverse high-throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost-effective manner. By using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of as yet unknown components of a system of interest and how its malfunction leads to disease.

  7. Implementation of integral feedback control in biological systems.

    Science.gov (United States)

    Somvanshi, Pramod R; Patel, Anilkumar K; Bhartiya, Sharad; Venkatesh, K V

    2015-01-01

    Integral control design ensures that a key variable in a system is tightly maintained within acceptable levels. This approach has been widely used in engineering systems to ensure offset free operation in the presence of perturbations. Several biological systems employ such an integral control design to regulate cellular processes. An integral control design motif requires a negative feedback and an integrating process in the network loop. This review describes several biological systems, ranging from bacteria to higher organisms in which the presence of integral control principle has been hypothesized. The review highlights that in addition to the negative feedback, occurrence of zero-order kinetics in the process is a key element to realize the integral control strategy. Although the integral control motif is common to these systems, the mechanisms involved in achieving it are highly specific and can be incorporated at the level of signaling, metabolism, or at the phenotypic levels.

  8. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  9. Integrated Chemistry and Biology for First-Year College Students

    Science.gov (United States)

    Abdella, Beth R. J.; Walczak, Mary M.; Kandl, Kim A.; Schwinefus, Jeffrey J.

    2011-01-01

    A three-course sequence for first-year students that integrates beginning concepts in biology and chemistry has been designed. The first two courses that emphasize chemistry and its capacity to inform biological applications are described here. The content of the first course moves from small to large particles with an emphasis on membrane…

  10. Integrating computer technology in the teaching of Biology

    OpenAIRE

    GarrawayLashley, Yassanne

    2014-01-01

    Over the past decade, the number of students who gained satisfactory passes at the Caribbean Secondary Education Certificate (CSEC) in Biology in Guyana has been few. This poor performance may be attributed to the traditional method of teaching that was used to teach Biology. This study therefore ascertained if the integration of computer technology into the teaching of Biology would enhance students’ academic performance. The study was guided by a null research hypothesis. Hence, the related...

  11. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

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

  12. Mass Spec Studio for Integrative Structural Biology

    NARCIS (Netherlands)

    Rey, Martial; Sarpe, Vladimir; Burns, Kyle M.; Buse, Joshua; Baker, Charles A. H.; van Dijk, Marc; Wordeman, Linda; Bonvin, Alexandre M. J. J.; Schriemer, David C.

    2014-01-01

    The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and

  13. Integration of proteomics into systems biology of cancer.

    Science.gov (United States)

    Hanash, S; Schliekelman, M; Zhang, Q; Taguchi, A

    2012-01-01

    Deciphering the complexity and heterogeneity of cancer, benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date, and the challenges involved in integrating diverse datasets are addressed in this review.

  14. Integrated physiology and systems biology of PPARα.

    Science.gov (United States)

    Kersten, Sander

    2014-07-01

    The Peroxisome Proliferator Activated Receptor alpha (PPARα) is a transcription factor that plays a major role in metabolic regulation. This review addresses the functional role of PPARα in intermediary metabolism and provides a detailed overview of metabolic genes targeted by PPARα, with a focus on liver. A distinction is made between the impact of PPARα on metabolism upon physiological, pharmacological, and nutritional activation. Low and high throughput gene expression analyses have allowed the creation of a comprehensive map illustrating the role of PPARα as master regulator of lipid metabolism via regulation of numerous genes. The map puts PPARα at the center of a regulatory hub impacting fatty acid uptake, fatty acid activation, intracellular fatty acid binding, mitochondrial and peroxisomal fatty acid oxidation, ketogenesis, triglyceride turnover, lipid droplet biology, gluconeogenesis, and bile synthesis/secretion. In addition, PPARα governs the expression of several secreted proteins that exert local and endocrine functions.

  15. Defining the biological integrity of coral reefs using a biological condition gradient framework

    Science.gov (United States)

    Under authority of the Clean Water Act (CWA), the US EPA is committed to protecting the biological integrity of tropical ecosystems, including mangroves, seagrasses and coral reefs that lie within the 3-mile limit of the territorial seas. The biological condition gradient (BCG) w...

  16. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-10-11

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

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

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

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

  18. Integration in biology: Philosophical perspectives on the dynamics of interdisciplinarity.

    Science.gov (United States)

    Brigandt, Ingo

    2013-12-01

    This introduction to the special section on integration in biology provides an overview of the different contributions. In addition to motivating the philosophical significance of analyzing integration and interdisciplinary research, I lay out common themes and novel insights found among the special section contributions, and indicate how they exhibit current trends in the philosophical study of integration. One upshot of the contributed papers is that there are different aspects to and kinds of integration, so that rather than attempting to offer a universal construal of what integrations is, philosophers have to analyze in concrete cases in what respects particular aspects of scientific theorizing and/or practice are 'integrative' and how this instance of integration works and was achieved.

  19. Software for systems biology: from tools to integrated platforms.

    Science.gov (United States)

    Ghosh, Samik; Matsuoka, Yukiko; Asai, Yoshiyuki; Hsin, Kun-Yi; Kitano, Hiroaki

    2011-11-03

    Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review describes the types of software tools that are required at different stages of systems biology research and the current options that are available for systems biology researchers. We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform.

  20. Toward an integration of evolutionary biology and ecosystem science.

    Science.gov (United States)

    Matthews, Blake; Narwani, Anita; Hausch, Stephen; Nonaka, Etsuko; Peter, Hannes; Yamamichi, Masato; Sullam, Karen E; Bird, Kali C; Thomas, Mridul K; Hanley, Torrance C; Turner, Caroline B

    2011-07-01

    At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes.

  1. Genetic Robots: An Integrated Art and Biology Curriculum.

    Science.gov (United States)

    Schramm, Susan L.

    2000-01-01

    Describes the design and implementation of an integrated art and science curriculum "Genetic Robotics: A Three-Dimensional Scientific Inquiry" for high school art and biology students at Madeira Junior/Senior High School in Cincinnati, Ohio. States that the project aimed at recognizing individual differences while enabling students to become…

  2. Milkweed Seed Dispersal: A Means for Integrating Biology and Physics.

    Science.gov (United States)

    Bisbee, Gregory D.; Kaiser, Cheryl A.

    1997-01-01

    Describes an activity that integrates biology and physics concepts by experimenting with the seed dispersal of common milkweed or similar wind-dispersed seeds. Student teams collect seeds and measure several parameters, review principles of trajectory motion, perform experiments, and graph data. Students examine the ideas of…

  3. Integrated Network Analysis and Effective Tools in Plant Systems Biology

    Directory of Open Access Journals (Sweden)

    Atsushi eFukushima

    2014-11-01

    Full Text Available One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1 network visualization tools, (2 pathway analyses, (3 genome-scale metabolic reconstruction, and (4 the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms.

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

    Science.gov (United States)

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

    2014-03-24

    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, AbDesigner (http://helixweb.nih.gov/AbDesigner/), to help researchers select optimal peptide immunogens for antibody generation against relatively disordered regions of target proteins. Here we describe AbDesigner in terms of its features, comparing it to other software tools, and use it to design three antibodies against kidney disease-related proteins in human, viz. nephrin, podocin, and apolipoprotein L1.

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

    Directory of Open Access Journals (Sweden)

    Taishin eNomura

    2010-12-01

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

  6. Integrated pathway clusters with coherent biological themes for target prioritisation.

    Directory of Open Access Journals (Sweden)

    Yi-An Chen

    Full Text Available Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.

  7. Systematic integration of experimental data and models in systems biology

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    Simeonidis Evangelos

    2010-11-01

    Full Text Available Abstract Background The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Results Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML. A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Conclusions Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

  8. Sympodial bamboo species differ in carbon bio-sequestration and stocks within phytoliths of leaf litters and living leaves.

    Science.gov (United States)

    Xiang, Tingting; Ying, Yuqi; Teng, Jiangnan; Huang, Zhangting; Wu, Jiasen; Meng, Cifu; Jiang, Peikun; Tang, Caixian; Li, Jianmin; Zheng, Rong

    2016-10-01

    Phytolith-occluded carbon (PhytOC) with high resistance against decomposition is an important carbon (C) sink in many ecosystems. This study compared concentrations of phytolith in plants and the PhytOC production of seven sympodial bamboo species in southern China, aiming to provide the information for the managed bamboo plantation and selection of bamboo species to maximize phytolith C sequestration. Leaf litters and living leaves of seven sympodial bamboo species were collected from the field sites. Concentrations of phytoliths, silicon (Si), and PhytOC in leaf litters and living leaves were measured. Carbon sequestration as PhytOC was estimated. There was a considerable variation in the PhytOC concentrations in the leaf litters and living leaves among the seven bamboo species. The mean concentrations of PhytOC ranged from 3.4 to 6.9 g kg(-1) in leaf litters and from 1.6 to 5.9 g kg(-1) in living leaves, with the PhytOC production rates ranging from 5.7 to 52.3 kg e-CO2 ha(-1) year(-1) as leaf litters. Dendrocalamopsis oldhami (Munro) Keng f. had the highest PhytOC production rate. Based on a bio-sequestration rate of 52.3 kg e-CO2 ha(-1) year(-1), we estimated that the current 8 × 10(5) ha of sympodial bamboo stands in China could potentially acquire 4.2 × 10(4) t e-CO2 yearly via phytolith carbon. Furthermore, the seven sympodial bamboo species stored 5.38 × 10(5) t e-CO2 as PhytOC in living leaves and leaf litters in China. It is concluded that sympodial bamboos make a significant contribution to C sequestration and that to maximize the PhytOC accumulation, the bamboo species with the highest PhytOC production rate should be selected for plantation.

  9. Semiconductor Devices Inspired By and Integrated With Biology

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, John [University of Illinois

    2012-04-25

    Biology is curved, soft and elastic; silicon wafers are not. Semiconductor technologies that can bridge this gap in form and mechanics will create new opportunities in devices that adopt biologically inspired designs or require intimate integration with the human body. This talk describes the development of ideas for electronics that offer the performance of state-of-the-art, wafer- based systems but with the mechanical properties of a rubber band. We explain the underlying materials science and mechanics of these approaches, and illustrate their use in (1) bio- integrated, ‘tissue-like’ electronics with unique capabilities for mapping cardiac and neural electrophysiology, and (2) bio-inspired, ‘eyeball’ cameras with exceptional imaging properties enabled by curvilinear, Petzval designs.

  10. Phytosequestration: Carbon biosequestration by plants and the prospects of genetic engineering

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, C.; Wullschleger, S.D.; Kalluri, U.C.; Tuskan, G.A.

    2010-07-15

    Photosynthetic assimilation of atmospheric carbon dioxide by land plants offers the underpinnings for terrestrial carbon (C) sequestration. A proportion of the C captured in plant biomass is partitioned to roots, where it enters the pools of soil organic C and soil inorganic C and can be sequestered for millennia. Bioenergy crops serve the dual role of providing biofuel that offsets fossil-fuel greenhouse gas (GHG) emissions and sequestering C in the soil through extensive root systems. Carbon captured in plant biomass can also contribute to C sequestration through the deliberate addition of biochar to soil, wood burial, or the use of durable plant products. Increasing our understanding of plant, microbial, and soil biology, and harnessing the benefits of traditional genetics and genetic engineering, will help us fully realize the GHG mitigation potential of phytosequestration.

  11. The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

    Science.gov (United States)

    Faini, Marco; Stengel, Florian; Aebersold, Ruedi

    2016-06-01

    Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

  12. Teaching the fundamentals of biological data integration using classroom games.

    Directory of Open Access Journals (Sweden)

    Maria Victoria Schneider

    Full Text Available This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems as a method for data integration.

  13. Teaching the fundamentals of biological data integration using classroom games.

    Science.gov (United States)

    Schneider, Maria Victoria; Jimenez, Rafael C

    2012-01-01

    This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers) will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems) as a method for data integration.

  14. The roles of integration in molecular systems biology.

    Science.gov (United States)

    O'Malley, Maureen A; Soyer, Orkun S

    2012-03-01

    A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.

  15. Integrative biological systems modeling:challenges and opportunities

    Institute of Scientific and Technical Information of China (English)

    Jialiang WU; Eberhard VOIT

    2009-01-01

    Most biological systems are by nature hybrids consist of interacting discrete and continuous components,which may even operate on different time scales. Therefore," it is desirable to establish modeling frameworks that are capable of combining deterministic and stochastic, discrete and continuous, as well as multi-timescale features. In the context of molecular systems biology, an example for the need of such a combination is the investigation of integrated biological pathways that contain gene regulatory, metabolic and signaling components, which may operate on different time scales and involve on-off switches as well as stochastic effects. The implementation of integrated hybrid systems is not trivial because most software is limited to one or the other of the dichotomies above. In this study, we first review the motivation for hybrid modeling. Secondly, by using the example of a toggle switch model, we illustrate a recently developed modeling framework that is based on the combination of biochemical systems theory (BST) and hybrid functional Petri nets (HFPN). Finally, we discuss remaining challenges and future opportunities.

  16. Toward efficient riparian restoration: integrating economic, physical, and biological models.

    Science.gov (United States)

    Watanabe, Michio; Adams, Richard M; Wu, Junjie; Bolte, John P; Cox, Matt M; Johnson, Sherri L; Liss, William J; Boggess, William G; Ebersole, Joseph L

    2005-04-01

    This paper integrates economic, biological, and physical models to explore the efficient combination and spatial allocation of conservation efforts to protect water quality and increase salmonid populations in the Grande Ronde basin, Oregon. We focus on the effects of shade on water temperatures and the subsequent impacts on endangered juvenile salmonid populations. The integrated modeling system consists of a physical model that links riparian conditions and hydrological characteristics to water temperature; a biological model that links water temperature and riparian conditions to salmonid abundance, and an economic model that incorporates both physical and biological models to estimate minimum cost allocations of conservation efforts. Our findings indicate that conservation alternatives such as passive and active riparian restoration, the width of riparian restoration zones, and the types of vegetation used in restoration activities should be selected based on the spatial distribution of riparian characteristics in the basin. The relative effectiveness of passive and active restoration plays an important role in determining the efficient allocations of conservation efforts. The time frame considered in the restoration efforts and the magnitude of desired temperature reductions also affect the efficient combinations of restoration activities. If the objective of conservation efforts is to maximize fish populations, then fishery benefits should be directly targeted. Targeting other criterion such as water temperatures would result in different allocations of conservation efforts, and therefore are not generally efficient.

  17. Bayesian integration of position and orientation cues in perception of biological and non-biological forms.

    Science.gov (United States)

    Thurman, Steven M; Lu, Hongjing

    2014-01-01

    Visual form analysis is fundamental to shape perception and likely plays a central role in perception of more complex dynamic shapes, such as moving objects or biological motion. Two primary form-based cues serve to represent the overall shape of an object: the spatial position and the orientation of locations along the boundary of the object. However, it is unclear how the visual system integrates these two sources of information in dynamic form analysis, and in particular how the brain resolves ambiguities due to sensory uncertainty and/or cue conflict. In the current study, we created animations of sparsely-sampled dynamic objects (human walkers or rotating squares) comprised of oriented Gabor patches in which orientation could either coincide or conflict with information provided by position cues. When the cues were incongruent, we found a characteristic trade-off between position and orientation information whereby position cues increasingly dominated perception as the relative uncertainty of orientation increased and vice versa. Furthermore, we found no evidence for differences in the visual processing of biological and non-biological objects, casting doubt on the claim that biological motion may be specialized in the human brain, at least in specific terms of form analysis. To explain these behavioral results quantitatively, we adopt a probabilistic template-matching model that uses Bayesian inference within local modules to estimate object shape separately from either spatial position or orientation signals. The outputs of the two modules are integrated with weights that reflect individual estimates of subjective cue reliability, and integrated over time to produce a decision about the perceived dynamics of the input data. Results of this model provided a close fit to the behavioral data, suggesting a mechanism in the human visual system that approximates rational Bayesian inference to integrate position and orientation signals in dynamic form analysis.

  18. Characteristics of integrated biological aerated filter in municipal wastewater treatment

    Institute of Scientific and Technical Information of China (English)

    HE Qiang; ZHANG Yu-ping; XU Jian-bin

    2005-01-01

    In this paper, the characteristics of integrated biological aerated filter (IBAF) applied to municipal wastewater treatment were studied in a pilot scale experiment. The experimental results showed that IBAF has high efficiencies in removing organic pollutants, such as CODCr and SS, in municipal wastewater. The removal rates of CODCr and SS can reach over 90% and 80%, respectively, when COD and SS in the influent are 234 mg L-1 and 112 mg L-1, hydraulic retention time (HRT) is 8 h, and the aerated intensity is in the range of (0.5 to 0.6) L m-2 s-1.

  19. Integrated MEMS/NEMS Resonant Cantilevers for Ultrasensitive Biological Detection

    Directory of Open Access Journals (Sweden)

    Xinxin Li

    2009-01-01

    Full Text Available The paper reviews the recent researches implemented in Chinese Academy of Sciences, with achievements on integrated resonant microcantilever sensors. In the resonant cantilevers, the self-sensing elements and resonance exciting elements are both top-down integrated with silicon micromachining techniques. Quite a lot of effort is focused on optimization of the resonance mode and sensing structure for improvement of sensitivity. On the other hand, to enable the micro-cantilevers specifically sensitive to bio/chemical molecules, sensing materials are developed and modified on the cantilever surface with a self-assembled monolayer (SAM based bottom-up construction and surface functionalization. To improve the selectivity of the sensors and depress environmental noise, multiple and localized surface modifications are developed. The achieved volume production capability and satisfactory detecting resolution to trace-level biological antigen of alpha-fetoprotein (AFP give the micro-cantilever sensors a great promise for rapid and high-resoluble detection.

  20. Towards improving the integration of undergraduate biology and mathematics education.

    Science.gov (United States)

    Bergevin, Christopher

    2010-01-01

    Arguments have recently asserted the need for change in undergraduate biology education, particularly with regard to the role of mathematics. The crux of these protests is that rapidly developing technology is expanding the types of measurements and subsequent data available to biologists. Thus future generations of biologists will require a set of quantitative and analytic skills that will allow them to handle these types of data in order to tackle relevant questions of interest. In this spirit, we describe here strategies (or lessons learned) for undergraduate educators with regard to better preparing undergraduate biology majors for the new types of challenges that lay ahead. The topics covered here span a broad range, from classroom approaches to the administrative level (e.g., fostering inter-departmental communication, student advising) and beyond. A key theme here is the need for an attitude shift with regard to mathematics education by both students and faculty alike. Such a shift will facilitate the development and implementation of new teaching strategies with regard to improving integration of mathematics and biology pedagogy.

  1. Assessment of Constructed Wetland Biological Integrity Using Aquatic Macroinvertebrates

    Directory of Open Access Journals (Sweden)

    C. Galbrand

    2007-01-01

    Full Text Available A surface flow constructed wetland consisting of seven cells was used to treat the leachates from a decommissioned landfill. Wetland monitoring was performed by evaluating the treatment efficiency of the landfill leachate and the wetland biological integrity of the wetland. The water quality samples were analyzed for iron, manganese, phosphorus (orthophosphate, pH, dissolved oxygen (DO, nitrogen (ammonia, nitrate, nitrite and TKN, chemical oxygen demand (COD, total suspended solids (TSS and total dissolved solids (TDS. Aquatic macroinvertebrates were examined using Average Score per Taxon (ASPT via the Biological Monitoring Working Party (BMWP biotic index, the Ephemeroptera, Trichoptera, Sphaeriidae and Odonata (ETSD biotic index, abundance of mayflies and trophic structure. Reductions of 49.66, 66.66, 1.91, 46.37 and 8.33% were obtained for manganese, orthophosphate, TSS, TDS and COD, respectively. The nitrite, dissolved oxygen and iron concentrations were not in accordance with the water quality guidelines for aquatic life. ASPT, ETSD, percent abundance of mayflies and trophic structure represented moderate to moderately-poor water quality in comparison to a high quality reference site. Iron had most adverse effect on the biological system of the wetland.

  2. Integrating paleobiology, archeology, and history to inform biological conservation.

    Science.gov (United States)

    Rick, Torben C; Lockwood, Rowan

    2013-02-01

    The search for novel approaches to establishing ecological baselines (reference conditions) is constrained by the fact that most ecological studies span the past few decades, at most, and investigate ecosystems that have been substantially altered by human activities for decades, centuries, or more. Paleobiology, archeology, and history provide historical ecological context for biological conservation, remediation, and restoration. We argue that linking historical ecology explicitly with conservation can help unify related disciplines of conservation paleobiology, conservation archeobiology, and environmental history. Differences in the spatial and temporal resolution and extent (scale) of prehistoric, historic, and modern ecological data remain obstacles to integrating historical ecology and conservation biology, but the prolonged temporal extents of historical ecological data can help establish more complete baselines for restoration, document a historical range of ecological variability, and assist in determining desired future conditions. We used the eastern oyster (Crassostrea virginica) fishery of the Chesapeake Bay (U.S.A.) to demonstrate the utility of historical ecological data for elucidating oyster conservation and the need for an approach to conservation that transcends disciplinary boundaries. Historical ecological studies from the Chesapeake have documented dramatic declines (as much as 99%) in oyster abundance since the early to mid-1800 s, changes in oyster size in response to different nutrient levels from the sixteenth to nineteenth centuries, and substantial reductions in oyster accretion rates (from 10 mm/year to effectively 0 mm/year) from the Late Holocene to modern times. Better integration of different historical ecological data sets and increased collaboration between paleobiologists, geologists, archeologists, environmental historians, and ecologists to create standardized research designs and methodologies will help unify prehistoric

  3. Meat science: From proteomics to integrated omics towards system biology.

    Science.gov (United States)

    D'Alessandro, Angelo; Zolla, Lello

    2013-01-14

    Since the main ultimate goal of farm animal raising is the production of proteins for human consumption, research tools to investigate proteins play a major role in farm animal and meat science. Indeed, proteomics has been applied to the field of farm animal science to monitor in vivo performances of livestock animals (growth performances, fertility, milk quality etc.), but also to further our understanding of the molecular processes at the basis of meat quality, which are largely dependent on the post mortem biochemistry of the muscle, often in a species-specific way. Post mortem alterations to the muscle proteome reflect the biological complexity of the process of "muscle to meat conversion," a process that, despite decades of advancements, is all but fully understood. This is mainly due to the enormous amounts of variables affecting meat tenderness per se, including biological factors, such as animal species, breed specific-characteristic, muscle under investigation. However, it is rapidly emerging that the tender meat phenotype is not only tied to genetics (livestock breeding selection), but also to extrinsic factors, such as the rearing environment, feeding conditions, physical activity, administration of hormonal growth promotants, pre-slaughter handling and stress, post mortem handling. From this intricate scenario, biochemical approaches and systems-wide integrated investigations (metabolomics, transcriptomics, interactomics, phosphoproteomics, mathematical modeling), which have emerged as complementary tools to proteomics, have helped establishing a few milestones in our understanding of the events leading from muscle to meat conversion. The growing integration of omics disciplines in the field of systems biology will soon contribute to take further steps forward.

  4. Integration and macroevolutionary patterns in the pollination biology of conifers.

    Science.gov (United States)

    Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Knopf, Patrick; Donoghue, Michael J

    2015-06-01

    Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology.

  5. Integrated Ecological River Health Assessments, Based on Water Chemistry, Physical Habitat Quality and Biological Integrity

    Directory of Open Access Journals (Sweden)

    Ji Yoon Kim

    2015-11-01

    Full Text Available This study evaluated integrative river ecosystem health using stressor-based models of physical habitat health, chemical water health, and biological health of fish and identified multiple-stressor indicators influencing the ecosystem health. Integrated health responses (IHRs, based on star-plot approach, were calculated from qualitative habitat evaluation index (QHEI, nutrient pollution index (NPI, and index of biological integrity (IBI in four different longitudinal regions (Groups I–IV. For the calculations of IHRs values, multi-metric QHEI, NPI, and IBI models were developed and their criteria for the diagnosis of the health were determined. The longitudinal patterns of the river were analyzed by a self-organizing map (SOM model and the key major stressors in the river were identified by principal component analysis (PCA. Our model scores of integrated health responses (IHRs suggested that mid-stream and downstream regions were impaired, and the key stressors were closely associated with nutrient enrichment (N and P and organic matter pollutions from domestic wastewater disposal plants and urban sewage. This modeling approach of IHRs may be used as an effective tool for evaluations of integrative ecological river health..

  6. Integrative biology identifies shared transcriptional networks in CKD.

    Science.gov (United States)

    Martini, Sebastian; Nair, Viji; Keller, Benjamin J; Eichinger, Felix; Hawkins, Jennifer J; Randolph, Ann; Böger, Carsten A; Gadegbeku, Crystal A; Fox, Caroline S; Cohen, Clemens D; Kretzler, Matthias

    2014-11-01

    A previous meta-analysis of genome-wide association data by the Cohorts for Heart and Aging Research in Genomic Epidemiology and CKDGen consortia identified 16 loci associated with eGFR. To define how each of these single-nucleotide polymorphisms (SNPs) could affect renal function, we integrated GFR-associated loci with regulatory pathways, producing a molecular map of CKD. In kidney biopsy specimens from 157 European subjects representing nine different CKDs, renal transcript levels for 18 genes in proximity to the SNPs significantly correlated with GFR. These 18 genes were mapped into their biologic context by testing coregulated transcripts for enriched pathways. A network of 97 pathways linked by shared genes was constructed and characterized. Of these pathways, 56 pathways were reported previously to be associated with CKD; 41 pathways without prior association with CKD were ranked on the basis of the number of candidate genes connected to the respective pathways. All pathways aggregated into a network of two main clusters comprising inflammation- and metabolism-related pathways, with the NRF2-mediated oxidative stress response pathway serving as the hub between the two clusters. In all, 78 pathways and 95% of the connections among those pathways were verified in an independent North American biopsy cohort. Disease-specific analyses showed that most pathways are shared between sets of three diseases, with closest interconnection between lupus nephritis, IgA nephritis, and diabetic nephropathy. Taken together, the network integrates candidate genes from genome-wide association studies into their functional context, revealing interactions and defining established and novel biologic mechanisms of renal impairment in renal diseases.

  7. Competency-based reforms of the undergraduate biology curriculum: integrating the physical and biological sciences.

    Science.gov (United States)

    Thompson, Katerina V; Chmielewski, Jean; Gaines, Michael S; Hrycyna, Christine A; LaCourse, William R

    2013-06-01

    The National Experiment in Undergraduate Science Education project funded by the Howard Hughes Medical Institute is a direct response to the Scientific Foundations for Future Physicians report, which urged a shift in premedical student preparation from a narrow list of specific course work to a more flexible curriculum that helps students develop broad scientific competencies. A consortium of four universities is working to create, pilot, and assess modular, competency-based curricular units that require students to use higher-order cognitive skills and reason across traditional disciplinary boundaries. Purdue University; the University of Maryland, Baltimore County; and the University of Miami are each developing modules and case studies that integrate the biological, chemical, physical, and mathematical sciences. The University of Maryland, College Park, is leading the effort to create an introductory physics for life sciences course that is reformed in both content and pedagogy. This course has prerequisites of biology, chemistry, and calculus, allowing students to apply strategies from the physical sciences to solving authentic biological problems. A comprehensive assessment plan is examining students' conceptual knowledge of physics, their attitudes toward interdisciplinary approaches, and the development of specific scientific competencies. Teaching modules developed during this initial phase will be tested on multiple partner campuses in preparation for eventual broad dissemination.

  8. Selfishness, warfare, and economics; or integration, cooperation, and biology.

    Science.gov (United States)

    Salvucci, Emiliano

    2012-01-01

    The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. It is necessary to discuss the explaining power of the dominant paradigm. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. In addition to the discussion on the validity of natural selection, modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related to the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: viruses are recognized as a macroorganism with a huge collection of genes, most unknown that constitute the major planet's gene pool. They play a fundamental role in evolution since their sequences are capable of integrating into the genomes in an "infective" way and become an essential part of multicellular organisms. They have content with "biological sense" i.e., they appear as part of normal life processes and have a serious role as carrier elements of complex genetic information. Antibiotics are cell signals with main effects on general metabolism and transcription on bacterial cells and communities. The hologenome theory considers an organism and all of its associated symbiotic microbes (parasites, mutualists, synergists, amensalists) as a result of symbiopoiesis. Microbes, helmints, that are normally understood as parasites are cohabitants and they have cohabited with their host and drive the evolution and existence of the partners. Each organism is the result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial

  9. Pegasys: software for executing and integrating analyses of biological sequences

    Directory of Open Access Journals (Sweden)

    Lett Drew

    2004-04-01

    Full Text Available Abstract Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

  10. The potential for carbon bio-sequestration in China’s paddy rice (Oryza sativa L.) as impacted by slag-based silicate fertilizer

    Science.gov (United States)

    Song, Alin; Ning, Dongfeng; Fan, Fenliang; Li, Zhaojun; Provance-Bowley, Mary; Liang, Yongchao

    2015-12-01

    Rice is a typical silicon-accumulating plant. Silicon (Si), deposited as phytoliths during plant growth, has been shown to occlude organic carbon, which may prove to have significant effects on the biogeochemical sequestration of atmospheric CO2. This study evaluated the effects of silicate fertilization on plant Si uptake and carbon bio-sequestration in field trials on China’s paddy soils. The results showed (1) Increased Si concentrations in rice straw with increasing application rates of silicate fertilizer; (2) Strong positive correlations between phytolith contents and straw SiO2 contents and between phytolith contents and phytolith-occluded carbon (PhytOC) contents in rice straw; (3) Positive correlations between the phytolith production flux and either the above-ground net primary productivity (ANPP) or the PhytOC production rates; (4) Increased plant PhytOC storage with increasing application rates of silicate fertilizer. The average above-ground PhytOC production rates during China’s rice production are estimated at 0.94 × 106 tonnes CO2 yr-1 without silicate fertilizer additions. However, the potential exists to increase PhytOC levels to 1.16-2.17 × 106 tonnes CO2 yr-1 with silicate fertilizer additions. Therefore, providing silicate fertilizer during rice production may serve as an effective tool in improving atmospheric CO2 sequestration in global rice production areas.

  11. The potential for carbon bio-sequestration in China's paddy rice (Oryza sativa L.) as impacted by slag-based silicate fertilizer.

    Science.gov (United States)

    Song, Alin; Ning, Dongfeng; Fan, Fenliang; Li, Zhaojun; Provance-Bowley, Mary; Liang, Yongchao

    2015-12-01

    Rice is a typical silicon-accumulating plant. Silicon (Si), deposited as phytoliths during plant growth, has been shown to occlude organic carbon, which may prove to have significant effects on the biogeochemical sequestration of atmospheric CO2. This study evaluated the effects of silicate fertilization on plant Si uptake and carbon bio-sequestration in field trials on China's paddy soils. The results showed (1) Increased Si concentrations in rice straw with increasing application rates of silicate fertilizer; (2) Strong positive correlations between phytolith contents and straw SiO2 contents and between phytolith contents and phytolith-occluded carbon (PhytOC) contents in rice straw; (3) Positive correlations between the phytolith production flux and either the above-ground net primary productivity (ANPP) or the PhytOC production rates; (4) Increased plant PhytOC storage with increasing application rates of silicate fertilizer. The average above-ground PhytOC production rates during China's rice production are estimated at 0.94 × 10(6) tonnes CO2 yr(-1) without silicate fertilizer additions. However, the potential exists to increase PhytOC levels to 1.16-2.17 × 10(6) tonnes CO2 yr(-1) with silicate fertilizer additions. Therefore, providing silicate fertilizer during rice production may serve as an effective tool in improving atmospheric CO2 sequestration in global rice production areas.

  12. Models for integrated pest control and their biological implications.

    Science.gov (United States)

    Tang, Sanyi; Cheke, Robert A

    2008-09-01

    Successful integrated pest management (IPM) control programmes depend on many factors which include host-parasitoid ratios, starting densities, timings of parasitoid releases, dosages and timings of insecticide applications and levels of host-feeding and parasitism. Mathematical models can help us to clarify and predict the effects of such factors on the stability of host-parasitoid systems, which we illustrate here by extending the classical continuous and discrete host-parasitoid models to include an IPM control programme. The results indicate that one of three control methods can maintain the host level below the economic threshold (ET) in relation to different ET levels, initial densities of host and parasitoid populations and host-parasitoid ratios. The effects of host intrinsic growth rate and parasitoid searching efficiency on host mean outbreak period can be calculated numerically from the models presented. The instantaneous pest killing rate of an insecticide application is also estimated from the models. The results imply that the modelling methods described can help in the design of appropriate control strategies and assist management decision-making. The results also indicate that a high initial density of parasitoids (such as in inundative releases) and high parasitoid inter-generational survival rates will lead to more frequent host outbreaks and, therefore, greater economic damage. The biological implications of this counter intuitive result are discussed.

  13. Integrated photocatalytic-biological reactor for accelerated phenol mineralization.

    Science.gov (United States)

    Zhang, Yongming; Wang, Lei; Rittmann, Bruce E

    2010-05-01

    An integrated photocatalytic-biological reactor (IPBR) was developed for accelerated phenol degradation and mineralization. In the IPBR, photodegradation and biodegradation occurred simultaneously, but in two separated zones: a piece of mat-glass plate coated with TiO(2) film and illuminated by UV light was connected by internal circulation to a honeycomb ceramic that was the biofilm carrier for biodegradation. This arrangement was designed to give intimate coupling of photocatalysis and biodegradation. Phenol degradation was investigated by following three protocols: photocatlysis with TiO(2) film under ultraviolet light, but no biofilm (photodegradation); biofilm biodegradation with no UV light (biodegradation); and simultaneous photodegradation and biodegradation (intimately coupled photobiodegradation). Photodegradation alone could partly degrade phenol, but was not able to achieve significant mineralization, even with an HRT of 10 h. Biodegradation alone could completely degrade phenol, but it did not mineralize the COD by more than 74%. Photobiodegradation allowed continuous rapid degradation of phenol, but it also led to more complete mineralization of phenol (up to 92%) than the other protocols. The results demonstrate that intimate coupling was achieved by protecting the biofilm from UV and free-radical inhibition. With phenol as the target compound, the main advantage of intimate coupling in the IPBR was increased mineralization, presumably because photocatalysis made soluble microbial products more rapidly biodegradable.

  14. Inspiring Integration in College Students Reading Multiple Biology Texts

    Science.gov (United States)

    Firetto, Carla

    2013-01-01

    Introductory biology courses typically present topics on related biological systems across separate chapters and lectures. A complete foundational understanding requires that students understand how these biological systems are related. Unfortunately, spontaneous generation of these connections is rare for novice learners. These experiments focus…

  15. Future of Chemical Engineering: Integrating Biology into the Undergraduate ChE Curriculum

    Science.gov (United States)

    Mosto, Patricia; Savelski, Mariano; Farrell, Stephanie H.; Hecht, Gregory B.

    2007-01-01

    Integrating biology in the chemical engineering curriculum seems to be the future for chemical engineering programs nation and worldwide. Rowan University's efforts to address this need include a unique chemical engineering curriculum with an intensive biology component integrated throughout from freshman to senior years. Freshman and Sophomore…

  16. SYSTOMONAS — an integrated database for systems biology analysis of Pseudomonas

    OpenAIRE

    Choi, Claudia; Münch, Richard; Leupold, Stefan; Klein, Johannes; Siegel, Inga; Thielen, Bernhard; Benkert, Beatrice; Kucklick, Martin; Schobert, Max; Barthelmes, Jens; Ebeling, Christian; Haddad, Isam; Scheer, Maurice; Grote, Andreas; Hiller, Karsten

    2007-01-01

    To provide an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology the database SYSTOMONAS (SYSTems biology of pseudOMONAS) was established. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as gene-regulatory networks were stored. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integr...

  17. Toward an interactive article: integrating journals and biological databases

    Directory of Open Access Journals (Sweden)

    Marygold Steven J

    2011-05-01

    Full Text Available Abstract Background Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. Results We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD and FlyBase, and has been implemented in marking up a paper with links to multiple databases. Conclusions Our semi-automated pipeline hyperlinks articles published in GENETICS to

  18. On the Edge of Mathematics and Biology Integration: Improving Quantitative Skills in Undergraduate Biology Education

    Science.gov (United States)

    Feser, Jason; Vasaly, Helen; Herrera, Jose

    2013-01-01

    In this paper, the authors describe how two institutions are helping their undergraduate biology students build quantitative competencies. Incorporation of quantitative skills and reasoning in biology are framed through a discussion of two cases that both concern introductory biology courses, but differ in the complexity of the mathematics and the…

  19. Teaching the Fundamentals of Biological Data Integration Using Classroom Games

    OpenAIRE

    Maria Victoria Schneider; Jimenez, Rafael C.

    2012-01-01

    This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers) will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, t...

  20. Economic value of biological control in integrated pest management of managed plant systems.

    Science.gov (United States)

    Naranjo, Steven E; Ellsworth, Peter C; Frisvold, George B

    2015-01-07

    Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.

  1. KinomeXplorer: an integrated platform for kinome biology studies

    DEFF Research Database (Denmark)

    Horn, Heiko; Schoof, Erwin; Kim, Jinho;

    2014-01-01

    A letter to the editor is presented related to the KinomeXplorer, an integrated platform providing workflows to efficiently analyze phosphorylation dependent interaction networks or kinase signaling networks.......A letter to the editor is presented related to the KinomeXplorer, an integrated platform providing workflows to efficiently analyze phosphorylation dependent interaction networks or kinase signaling networks....

  2. Integrating biological redesign: where synthetic biology came from and where it needs to go.

    Science.gov (United States)

    Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

    2014-03-27

    Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering.

  3. Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous catalytic ozonation and biological process.

    Science.gov (United States)

    Zhuang, Haifeng; Han, Hongjun; Jia, Shengyong; Hou, Baolin; Zhao, Qian

    2014-08-01

    Advanced treatment of biologically pretreated coal gasification wastewater (CGW) was investigated employing heterogeneous catalytic ozonation integrated with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process. The results indicated that catalytic ozonation with the prepared catalyst (i.e. MnOx/SBAC, sewage sludge was converted into sludge based activated carbon (SBAC) which loaded manganese oxides) significantly enhanced performance of pollutants removal by generated hydroxyl radicals. The effluent of catalytic ozonation process was more biodegradable and less toxic than that in ozonation alone. Meanwhile, ANMBBR-BAF showed efficient capacity of pollutants removal in treatment of the effluent of catalytic ozonation at a shorter reaction time, allowing the discharge limits to be met. Therefore, the integrated process with efficient, economical and sustainable advantages was suitable for advanced treatment of real biologically pretreated CGW.

  4. Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous Fenton oxidation and biological process.

    Science.gov (United States)

    Xu, Peng; Han, Hongjun; Zhuang, Haifeng; Hou, Baolin; Jia, Shengyong; Xu, Chunyan; Wang, Dexin

    2015-04-01

    Laboratorial scale experiments were conducted in order to investigate a novel system integrating heterogeneous Fenton oxidation (HFO) with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process on advanced treatment of biologically pretreated coal gasification wastewater (CGW). The results indicated that HFO with the prepared catalyst (FeOx/SBAC, sewage sludge based activated carbon (SBAC) which loaded Fe oxides) played a key role in eliminating COD and COLOR as well as in improving the biodegradability of raw wastewater. The surface reaction and hydroxyl radicals (OH) oxidation were the mechanisms for FeOx/SBAC catalytic reaction. Compared with ANMBBR-BAF process, the integrated system was more effective in abating COD, BOD5, total phenols (TPs), total nitrogen (TN) and COLOR and could shorten the retention time. Therefore, the integrated system was a promising technology for engineering applications.

  5. Biological data - Integrated acoustic and trawl survey of Pacific hake off the Pacific Coast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Integrated acoustic and trawl surveys are used to assess the distribution, biomass, and biology of Pacific hake along the Pacific coasts of the United States and...

  6. Evaluating Biology Achievement Scores in an ICT Integrated PBL Environment

    Science.gov (United States)

    Osman, Kamisah; Kaur, Simranjeet Judge

    2014-01-01

    Students' achievement in Biology is often looked up as a benchmark to evaluate the mode of teaching and learning in higher education. Problem-based learning (PBL) is an approach that focuses on students' solving a problem through collaborative groups. There were eighty samples involved in this study. The samples were divided into three groups: ICT…

  7. Integrating Biological Systems in the Process Dynamics and Control Curriculum

    Science.gov (United States)

    Parker, Robert S.; Doyle, Francis J.; Henson, Michael A.

    2006-01-01

    The evolution of the chemical engineering discipline motivates a re-evaluation of the process dynamics and control curriculum. A key requirement of future courses will be the introduction of theoretical concepts and application examples relevant to emerging areas, notably complex biological systems. We outline the critical concepts required to…

  8. Biological soil crusts as an integral component of desert environments

    Science.gov (United States)

    Belnap, Jayne; Weber, Bettina

    2013-01-01

    The biology and ecology of biological soil crusts, a soil surface community of mosses, lichens, cyanobacteria, green algae, fungi, and bacteria, have only recently been a topic of research. Most efforts began in the western U.S. (Cameron, Harper, Rushforth, and St. Clair), Australia (Rogers), and Israel (Friedmann, Evenari, and Lange) in the late 1960s and 1970s (e.g., Friedmann et al. 1967; Evenari 1985reviewed in Harper and Marble 1988). However, these groups worked independently of each other and, in fact, were often not aware of each other’s work. In addition, biological soil crust communities were seen as more a novelty than a critical component of dryland ecosystems. Since then, researchers have investigated many different aspects of these communities and have shown that although small to microscopic, biological soil crusts are critical in many ecological processes of deserts. They often cover most of desert soil surfaces and substantially mediate inputs and outputs from desert soils (Belnap et al. 2003). They can be a large source of biodiversity for deserts, as they can contain more species than the surrounding vascular plant community (Rosentreter 1986). These communities are important in reducing soil erosion and increasing soil fertility through the capture of dust and the fixation of atmospheric nitrogen and carbon into forms available to other life forms (Elbert et al. 2012). Because of their many effects on soil characteristics, such as external and internal morphological characteristics, aggregate stability, soil moisture, and permeability, they also affect seed germination and establishment and local hydrological cycles. Covering up to 70% of the surface area in many arid and semi-arid regions around the world (Belnap and Lange 2003), biological soil crusts are a key component within desert environments.

  9. 'Systems biology' in human exercise physiology: is it something different from integrative physiology?

    Science.gov (United States)

    Greenhaff, Paul L; Hargreaves, Mark

    2011-03-01

    On first impression the 'whole-istic approach to understanding biology' that has been used to describe Systems Biology bears a striking resemblance to what many of us know as Integrative Physiology. However, closer scrutiny reveals that at the present time Systems Biology is rooted in processes operating at a cellular level ('the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life ultimately responsible for an organism's form and functions'; http://www.systemsbiology.org), and appears to have evolved as a direct result of advances in high throughput molecular biology platforms (and associated bioinformatics) over the past decade. The Systems Biology approach is in many ways laudable, but it will be immediately apparent to most exercise or integrative physiologists that the challenge of understanding the whole-animal response to exercise as a network of integrated and interacting genes, proteins and biochemical reactions is unlikely to be realized in the near future. This short review will attempt to clarify conceptual inconsistencies between the fields of Systems Biology and Integrative Physiology in the context of exercise science, and will attempt to identify the challenges to whole-body physiologists wishing to harness the tools of Systems Biology.

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

    OpenAIRE

    Narayanasamy, Shaman; Muller, Emilie; Sheik, Abdul; Wilmes, Paul

    2015-01-01

    Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalitie...

  11. Lean Big Data integration in systems biology and systems pharmacology.

    Science.gov (United States)

    Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, Yan

    2014-09-01

    Data sets from recent large-scale projects can be integrated into one unified puzzle that can provide new insights into how drugs and genetic perturbations applied to human cells are linked to whole-organism phenotypes. Data that report how drugs affect the phenotype of human cell lines and how drugs induce changes in gene and protein expression in human cell lines can be combined with knowledge about human disease, side effects induced by drugs, and mouse phenotypes. Such data integration efforts can be achieved through the conversion of data from the various resources into single-node-type networks, gene-set libraries, or multipartite graphs. This approach can lead us to the identification of more relationships between genes, drugs, and phenotypes as well as benchmark computational and experimental methods. Overall, this lean 'Big Data' integration strategy will bring us closer toward the goal of realizing personalized medicine.

  12. Membrane curvature in cell biology: An integration of molecular mechanisms.

    Science.gov (United States)

    Jarsch, Iris K; Daste, Frederic; Gallop, Jennifer L

    2016-08-15

    Curving biological membranes establishes the complex architecture of the cell and mediates membrane traffic to control flux through subcellular compartments. Common molecular mechanisms for bending membranes are evident in different cell biological contexts across eukaryotic phyla. These mechanisms can be intrinsic to the membrane bilayer (either the lipid or protein components) or can be brought about by extrinsic factors, including the cytoskeleton. Here, we review examples of membrane curvature generation in animals, fungi, and plants. We showcase the molecular mechanisms involved and how they collaborate and go on to highlight contexts of curvature that are exciting areas of future research. Lessons from how membranes are bent in yeast and mammals give hints as to the molecular mechanisms we expect to see used by plants and protists.

  13. Integrating ethical analysis "into the DNA" of synthetic biology.

    Science.gov (United States)

    Heavey, Patrick

    2015-02-01

    Current ethical analysis tends to evaluate synthetic biology at an overview level. Synthetic biology, however, is an umbrella term that covers a variety of areas of research. These areas contain, in turn, a hierarchy of different research fields. This abstraction hierarchy-the term is borrowed from engineering-permits synthetic biologists to specialise to a very high degree. Though synthetic biology per se may create profound ethical challenges, much of the day-to-day research does not. Yet seemingly innocuous research could lead to ethically problematic results. For example, Dolly the sheep resulted from a long series of research steps, none of which presented any ethical problems. The atomic bomb was developed as a result of Einstein's uncontentions theoretical research that proved the equivalence of matter and energy. Therefore it would seem wise for ethicists to evaluate synbio research across its subfields and through its abstraction hierarchies, comparing and inter-relating the various areas of research. In addition, it would be useful if journals that publish synbio papers require an ethical statement from authors, as standard practice, so as to encourage scientists to constantly engage with ethical issues in their work. Also, this would allow an ethical snapshot of the state of the research at any given time to exist, allowing for accurate evaluation by scientists and ethicists, regulators and policymakers.

  14. [Systems biology is a bridge of integrated traditional Chinese and Western medicine].

    Science.gov (United States)

    Chen, Hai-Bin; Cheng, Hai-Bo; Lu, Wei; Zhou, Hong-Guang; Wu, Mian-Hua

    2013-01-01

    The integration of Chinese medicine (CM) and Western medicine (WM) is the only way for the development of medicine, and it is the best form for unifying systems theory and reductionism. In this paper, systems biology and its application in medical research were discussed. The authors put forward that systems biology may possibly interpret the scientific connotation of the complex theoretic systems of CM, which will make WM to well know the human body and disease. We hold that systems biology is a bridge of integrated CM and WM.

  15. Deducing protein function by forensic integrative cell biology.

    Directory of Open Access Journals (Sweden)

    William C Earnshaw

    2013-12-01

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

  16. Deducing protein function by forensic integrative cell biology.

    Science.gov (United States)

    Earnshaw, William C

    2013-12-01

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

  17. Physical constraints on biological integral control design for homeostasis and sensory adaptation.

    Science.gov (United States)

    Ang, Jordan; McMillen, David R

    2013-01-22

    Synthetic biology includes an effort to use design-based approaches to create novel controllers, biological systems aimed at regulating the output of other biological processes. The design of such controllers can be guided by results from control theory, including the strategy of integral feedback control, which is central to regulation, sensory adaptation, and long-term robustness. Realization of integral control in a synthetic network is an attractive prospect, but the nature of biochemical networks can make the implementation of even basic control structures challenging. Here we present a study of the general challenges and important constraints that will arise in efforts to engineer biological integral feedback controllers or to analyze existing natural systems. Constraints arise from the need to identify target output values that the combined process-plus-controller system can reach, and to ensure that the controller implements a good approximation of integral feedback control. These constraints depend on mild assumptions about the shape of input-output relationships in the biological components, and thus will apply to a variety of biochemical systems. We summarize our results as a set of variable constraints intended to provide guidance for the design or analysis of a working biological integral feedback controller.

  18. From Statistical to Biological Interactions via Omics Integration

    OpenAIRE

    Bessonov, Kyrylo

    2016-01-01

    The XXI century opened a new ‘Big Data’ era in which, thanks to rapid technological advancements and appearance of high throughput technologies, vast amounts of unstructured omics data (e.g., transcriptomic, genomic, etc.) are generated every day. This thesis mainly focuses on solving the problems related diverse omics data integration and interaction identification tasks. Particular attention is given to useful knowledge extraction in the context of complex diseases including pathological me...

  19. Ion transport through biological membranes an integrated theoretical approach

    CERN Document Server

    Mackey, Michael C

    1975-01-01

    This book illustrates some of the ways physics and mathematics have been, and are being, used to elucidate the underlying mechan­ isms of passive ion movement through biological membranes in general, and the membranes of excltable cells in particular. I have made no effort to be comprehensive in my introduction of biological material and the reader interested in a brief account of single cell electro­ physlology from a physically-oriented biologists viewpoint will find the chapters by Woodbury (1965) an excellent introduction. Part I is introductory in nature, exploring the basic electrical properties of inexcitable and excitable cell plasma membranes. Cable theory is utilized to illustrate the function of the non-decrementing action potential as a signaling mechanism for the long range trans­ mission of information in the nervous system, and to gain some in­ sight into the gross behaviour of neurons. The detailed analysis of Hodgkin and Huxley on the squid giant axon membrane ionic conductance properties...

  20. INTEGRATED MANAGEMENT OF CHROMOLAENA ODORATA EMPHASIZING THE CLASSICAL BIOLOGICAL CONTROL

    Directory of Open Access Journals (Sweden)

    SOEKISMAN TJITROSEMITO

    1998-01-01

    Full Text Available Chromolaena odorata, Siam weed, a very important weed of Java Island (Indonesia is native to Central and South America. In the laboratory it showed rapid growth (1.15 g/g/week in the first 8 weeks of its growth. The biomass was mainly as leaves (LAR : 317.50 cm'/g total weight. It slowed down in the following month as the biomass was utilized for stem and branch formation. This behavior supported the growth of C. odorata into a very dense stand. It flowered, fruited during the dry season, and senesced following maturation of seeds from inflorescence branches. These branches dried out, but soon the stem resumed aggressive growth following the wet season. Leaf biomass was affected by the size of the stem in its early phase of regrowth, but later on it was more affected by the number of branches. The introduction of Pareuchaetes pseudoinsulata to Indonesia, was successful only in North Sumatera. In Java it has not been reported to establish succesfully. The introduction of another biological control agent, Procecidochares conneca to Indonesia was shown to be sp ecific and upon release in West Java it established immediately. It spread exponentia lly in the first 6 months of its release. Field monitoring continues to eval uate the impact of the agents. Other biocontrol agents (Actmole anteas and Conotrachelus wilt be introduced to Indonesia in 1997 through ACIAR Project on the Biological Control of Chromolaena odorata in Indonesia and Papua New Guinea.

  1. BioInt: an integrative biological object-oriented application framework and interpreter.

    Science.gov (United States)

    Desai, Sanket; Burra, Prasad

    2015-01-01

    BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

  2. Probabilistic Inference of Biological Networks via Data Integration

    Directory of Open Access Journals (Sweden)

    Mark F. Rogers

    2015-01-01

    Full Text Available There is significant interest in inferring the structure of subcellular networks of interaction. Here we consider supervised interactive network inference in which a reference set of known network links and nonlinks is used to train a classifier for predicting new links. Many types of data are relevant to inferring functional links between genes, motivating the use of data integration. We use pairwise kernels to predict novel links, along with multiple kernel learning to integrate distinct sources of data into a decision function. We evaluate various pairwise kernels to establish which are most informative and compare individual kernel accuracies with accuracies for weighted combinations. By associating a probability measure with classifier predictions, we enable cautious classification, which can increase accuracy by restricting predictions to high-confidence instances, and data cleaning that can mitigate the influence of mislabeled training instances. Although one pairwise kernel (the tensor product pairwise kernel appears to work best, different kernels may contribute complimentary information about interactions: experiments in S. cerevisiae (yeast reveal that a weighted combination of pairwise kernels applied to different types of data yields the highest predictive accuracy. Combined with cautious classification and data cleaning, we can achieve predictive accuracies of up to 99.6%.

  3. Making United States Integrated Ocean Observing System (U.S. IOOS) inclusive of marine biological resources

    Science.gov (United States)

    Moustahfid, H.; Potemra, J.; Goldstein, P.; Mendelssohn, R.; Desrochers, A.

    2011-01-01

    An important Data Management and Communication (DMAC) goal is to enable a multi-disciplinary view of the ocean environment by facilitating discovery and integration of data from various sources, projects and scientific domains. United States Integrated Ocean Observing System (U.S. IOOS) DMAC functional requirements are based upon guidelines for standardized data access services, data formats, metadata, controlled vocabularies, and other conventions. So far, the data integration effort has focused on geophysical U.S. IOOS core variables such as temperature, salinity, ocean currents, etc. The IOOS Biological Observations Project is addressing the DMAC requirements that pertain to biological observations standards and interoperability applicable to U.S. IOOS and to various observing systems. Biological observations are highly heterogeneous and the variety of formats, logical structures, and sampling methods create significant challenges. Here we describe an informatics framework for biological observing data (e.g. species presence/absence and abundance data) that will expand information content and reconcile standards for the representation and integration of these biological observations for users to maximize the value of these observing data. We further propose that the approach described can be applied to other datasets generated in scientific observing surveys and will provide a vehicle for wider dissemination of biological observing data. We propose to employ data definition conventions that are well understood in U.S. IOOS and to combine these with ratified terminologies, policies and guidelines. ?? 2011 MTS.

  4. Integrated Raman and angular scattering of single biological cells

    Science.gov (United States)

    Smith, Zachary J.

    2009-12-01

    Raman, or inelastic, scattering and angle-resolved elastic scattering are two optical processes that have found wide use in the study of biological systems. Raman scattering quantitatively reports on the chemical composition of a sample by probing molecular vibrations, while elastic scattering reports on the morphology of a sample by detecting structure-induced coherent interference between incident and scattered light. We present the construction of a multimodal microscope platform capable of gathering both elastically and inelastically scattered light from a 38 mum2 region in both epi- and trans-illumination geometries. Simultaneous monitoring of elastic and inelastic scattering from a microscopic region allows noninvasive characterization of a living sample without the need for exogenous dyes or labels. A sample is illuminated either from above or below with a focused 785 nm TEM00 mode laser beam, with elastic and inelastic scattering collected by two separate measurement arms. The measurements may be made either simultaneously, if identical illumination geometries are used, or sequentially, if the two modalities utilize opposing illumination paths. In the inelastic arm, Stokes-shifted light is dispersed by a spectrograph onto a CCD array. In the elastic scattering collection arm, a relay system images the microscope's back aperture onto a CCD detector array to yield an angle-resolved elastic scattering pattern. Post-processing of the inelastic scattering to remove fluorescence signals yields high quality Raman spectra that report on the sample's chemical makeup. Comparison of the elastically scattered pupil images to generalized Lorenz-Mie theory yields estimated size distributions of scatterers within the sample. In this thesis we will present validations of the IRAM instrument through measurements performed on single beads of a few microns in size, as well as on ensembles of sub-micron particles of known size distributions. The benefits and drawbacks of the

  5. Treatment of atrazine by integrating photocatalytic and biological processes.

    Science.gov (United States)

    Chan, C Y; Tao, S; Dawson, R; Wong, P K

    2004-09-01

    This research examines the degradation of atrazine by photocatalytic oxidation (PCO) under different experimental conditions. Deisopropylatrazine, deethylatrazine and deethyldeisopropylatrazine were formed as major intermediates based on gas chromatography-mass spectrometry. The reaction mixture was found to be toxic towards two bioassays, i.e. the Microtox and amphipods survival tests even when atrazine was completely degraded by PCO within 2 h under optimized conditions. The results indicate that adding H2O2 could significantly enhance the degradation of atrazine by PCO. Ammeline, ammelide and cyanuric acid (CA) became the major intermediates/products as detected by high performance liquid chromatography from 6th to the 40th h of PCO treatment. After 72 h PCO treatment, only CA was detectable in the reaction mixture. Further degradation of CA was carried out by a newly isolated CA-degrading bacterium, Sphingomonas capsulata. The photochemical pretreatment integrated with microbial degradation lead to the complete degradation and detoxification of atrazine.

  6. Human evolution. Evolution of early Homo: an integrated biological perspective.

    Science.gov (United States)

    Antón, Susan C; Potts, Richard; Aiello, Leslie C

    2014-07-04

    Integration of evidence over the past decade has revised understandings about the major adaptations underlying the origin and early evolution of the genus Homo. Many features associated with Homo sapiens, including our large linear bodies, elongated hind limbs, large energy-expensive brains, reduced sexual dimorphism, increased carnivory, and unique life history traits, were once thought to have evolved near the origin of the genus in response to heightened aridity and open habitats in Africa. However, recent analyses of fossil, archaeological, and environmental data indicate that such traits did not arise as a single package. Instead, some arose substantially earlier and some later than previously thought. From ~2.5 to 1.5 million years ago, three lineages of early Homo evolved in a context of habitat instability and fragmentation on seasonal, intergenerational, and evolutionary time scales. These contexts gave a selective advantage to traits, such as dietary flexibility and larger body size, that facilitated survival in shifting environments.

  7. An integrated platform for assessing biologics (Conference Presentation)

    Science.gov (United States)

    Schein, Perry; O'Dell, Dakota; Erickson, David

    2016-04-01

    Protein therapeutics are a rapidly growing portion of the pharmaceuticals market and have many significant advantages over traditional small molecule drugs. As this market expands, however, critical regulatory and quality control issues remain, most notably the problem of protein aggregation. Individual target proteins often aggregate into larger masses which trigger an immune response in the body, which can reduce the efficacy of the drug for its intended purpose, or cause serious anaphylactic side-effects. Although detecting and minimizing aggregate formation is critical to ensure an effective product, aggregation dynamics are often highly complicated and there is little hope of reliable prediction and prevention from first principles. This problem is compounded for aggregates in the subvisible range of 100 nm to 10 micrometers where traditional techniques for detecting aggregates have significant limitations. Here, we present an integrated optofluidic platform for detecting nanoscale protein aggregates and characterizing interactions between these aggregates and a reference surface. By delivering light to a solution of proteins with an optical waveguide, scattered light from individual protein aggregates can be detected and analyzed to determine the force profile between each particle and the waveguide surface. Unlike existing methods which only determine size or charge, our label-free screening technique can directly measure the surface interaction forces between single aggregates and the glass substrate. This direct measurement capability may allow for better empirical predictions of the stability of protein aggregates during drug manufacturing and storage.

  8. Mapping biological ideas: Concept maps as knowledge integration tools for evolution education

    OpenAIRE

    Schwendimann, Beat Adrian

    2011-01-01

    Many students leave school with a fragmented understanding of biology that does not allow them to connect their ideas to their everyday lives (Wandersee, 1989; Mintzes, Wandersee, & Novak, 1998; Mintzes, Wandersee, & Novak, 2000a). Understanding evolution ideas is seen as central to building an integrated knowledge of biology (Blackwell, Powell, & Dukes, 2003; Thagard & Findlay, 2010). However, the theory of evolution has been found difficult to understand as it incorporates a wide range of i...

  9. The biology of lysine acetylation integrates transcriptional programming and metabolism

    Directory of Open Access Journals (Sweden)

    Mujtaba Shiraz

    2011-03-01

    Full Text Available Abstract The biochemical landscape of lysine acetylation has expanded from a small number of proteins in the nucleus to a multitude of proteins in the cytoplasm. Since the first report confirming acetylation of the tumor suppressor protein p53 by a lysine acetyltransferase (KAT, there has been a surge in the identification of new, non-histone targets of KATs. Added to the known substrates of KATs are metabolic enzymes, cytoskeletal proteins, molecular chaperones, ribosomal proteins and nuclear import factors. Emerging studies demonstrate that no fewer than 2000 proteins in any particular cell type may undergo lysine acetylation. As described in this review, our analyses of cellular acetylated proteins using DAVID 6.7 bioinformatics resources have facilitated organization of acetylated proteins into functional clusters integral to cell signaling, the stress response, proteolysis, apoptosis, metabolism, and neuronal development. In addition, these clusters also depict association of acetylated proteins with human diseases. These findings not only support lysine acetylation as a widespread cellular phenomenon, but also impel questions to clarify the underlying molecular and cellular mechanisms governing target selectivity by KATs. Present challenges are to understand the molecular basis for the overlapping roles of KAT-containing co-activators, to differentiate between global versus dynamic acetylation marks, and to elucidate the physiological roles of acetylated proteins in biochemical pathways. In addition to discussing the cellular 'acetylome', a focus of this work is to present the widespread and dynamic nature of lysine acetylation and highlight the nexus that exists between epigenetic-directed transcriptional regulation and metabolism.

  10. Selfishness, warfare and economics; or integration, cooperation and biology

    Directory of Open Access Journals (Sweden)

    Emiliano Jesus Salvucci

    2012-05-01

    Full Text Available The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. Modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related with the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: Viruses are recognized as a macroorganism with a huge collection of genes, most unknown, that constitute the major planet's gene pool with a fundamental role in evolution. The hologenome theory considers an organism and all of its associated symbiotic microbes as a result of symbiopoiesis. Microbes, helmints, that normally are understood as parasites, are cohabitants and they have cohabited with their host and drives the evolution and existence of the partners. Each organism is a result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus and eukaryotic DNA and the interaction of its own genome with the genome of its microbiota resulting in an intertwined metabolism (a superorganism along evolution. These new interpretations are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.

  11. Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

    Science.gov (United States)

    Currin, Andrew; Jervis, Adrian J.; Rattray, Nicholas J. W.; Swainston, Neil; Yan, Cunyu; Breitling, Rainer

    2016-01-01

    Covering: 2000 to 2016 Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted. PMID:27185383

  12. Network-based drug discovery by integrating systems biology and computational technologies.

    Science.gov (United States)

    Leung, Elaine L; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua; Liu, Liang

    2013-07-01

    Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple '-omics' databases. The newly developed algorithm- or network-based computational models can tightly integrate '-omics' databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various '-omics' platforms and computational tools would accelerate development of network-based drug discovery and network medicine.

  13. Gold nanoparticle wire and integrated wire array for electronic detection of chemical and biological molecules

    Directory of Open Access Journals (Sweden)

    J. J. Diao

    2011-03-01

    Full Text Available Nanoparticle wire and integrated nanoparticle wire array have been prepared through a green technique: discontinuous vertical evaporation-driven colloidal deposition. The conducting gold nanoparticle wire made by this technique shows ability for the sensitive electronic detection of chemical and biological molecules due to its high surface to volume ratio. Furthermore, we also demonstrate a potential usage of integrated gold nanoparticle wire array for the localized detection.

  14. Emphasizing the "Literacy" in "Scientific Literacy": A Concise Blueprint for Integrating Writing into Biology Classes

    Science.gov (United States)

    Yule, Jeffrey V.; Wolf, William C.; Young, Nolan L.

    2010-01-01

    Effectively integrating writing into biology classes gives students the opportunity to develop a better understanding of and engagement with course content. Yet many instructors remain reluctant to emphasize writing. Some are concerned about the time commitment writing assessment requires. Others shy away from emphasizing writing in their classes…

  15. Problem-Solving Inquiry-Oriented Biology Tasks Integrating Practical Laboratory and Computer.

    Science.gov (United States)

    Friedler, Yael; And Others

    1992-01-01

    Presents results of a study that examines the development and use of computer simulations for high school science instruction and for integrated laboratory and computerized tests that are part of the biology matriculation examination in Israel. Eleven implications for teaching are presented. (MDH)

  16. Personalized Genetic Testing as a Tool for Integrating Ethics Instruction into Biology Courses

    Directory of Open Access Journals (Sweden)

    Tenny R. Zhang

    2014-09-01

    Full Text Available Personalized genetic testing (PGT has been used by some educational institutions as a pedagogical tool for teaching human genetics. While work has been done that examines the potential for PGT to improve students’ interest and understanding of the science involved in genetic testing, there has been less dialogue about how this method might be useful for integrating ethical and societal issues surrounding genetic testing into classroom discussions. Citing the importance of integrating ethics into the biology classroom, we argue that PGT can be an effective educational tool for integrating ethics and science education, and discuss relevant ethical considerations for instructors using this approach. 

  17. Functionalization and microfluidic integration of silicon nanowire biologically gated field effect transistors

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

    with nanowire sensors functionalized using different modification schemes. To facilitate functionalization and measurement and as a first step towards integration into a point-of-care device, several microfluidic tools were developed for sample delivery to the sensor surface and as a modular platform......This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project...

  18. An integrated, low noise patch-clamp amplifier for biological nanopore applications.

    Science.gov (United States)

    Wang, Gang; Dunbar, William B

    2010-01-01

    We present an integrated, low noise patch-clamp amplifier for biological nanopore applications. Our amplifier consists of an integrator-differentiator architecture coupled with a novel opamp design in the CMOS 0.35 µm process. The post-layout full-chip simulation shows the input referred noise of the amplifier is 0.49 pA RMS over a 5 kHz bandwidth using a verified electrical model for the biological nanopore system. In our biological nanopore experiments studying protein-DNA interactions, we encounter capacitive transients with a nominal settling time of 5 ms. Our amplifier design reduces the settling time to 0.2 ms, without requiring any compensation circuitry.

  19. Integrated Graduate Program in Physical and Engineering Biology at Yale University

    Science.gov (United States)

    Caballero, Diego; Noble, Dorottya; Pollard, Thomas; Mochrie, Simon; O'Hern, Corey; Regan, Lynne

    2014-03-01

    Quantitative, integrated approaches are necessary to solve biology's grand challenges. Yale's Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) prepares students to excel at applying physics and engineering approaches, whilst also ensuring that they are sufficiently biologically sophisticated that they can readily identify and tackle cutting-edge problems. Students enter the program through a ``home'' department but also take a set of IGPPEB core courses with students from other departments. The IGPPEB curriculum is co-taught by faculty from a wide array of departments and motivates students to work together and learn from each other. The curriculum complements those of the home departments and includes primer courses to rapidly bring all students to a level where they ``speak each others language.'' The program is a member of the NSF's Physics of Living Systems: Student Research Network, which connects graduate students from different institutions that are engaged in research at the interface of physics and biology. Convergent research thrusts at Yale include Cellular Shape and Motion; Mechanical Force Generation and Sensing; Biomaterials and Bioinspired Design; Systems and Synthetic Biology; Modeling Biological Processes and Methods Development.

  20. Camels, Cormorants, and Kangaroo Rats: Integration and Synthesis in Organismal Biology After World War II.

    Science.gov (United States)

    Hagen, Joel B

    2015-01-01

    During the decades following World War II diverse groups of American biologists established a variety of distinctive approaches to organismal biology. Rhetorically, organismal biology could be used defensively to distinguish established research traditions from perceived threats from newly emerging fields such as molecular biology. But, organismal biologists were also interested in integrating biological disciplines and using a focus on organisms to synthesize levels of organization from molecules and cells to populations and communities. Part of this broad movement was the development of an area of research variously referred to as physiological ecology, environmental physiology, or ecophysiology. This area of research was distinctive in its self-conscious blend of field and laboratory practices and its explicit integration with other areas of biology such as ecology, animal behavior, and evolution in order to study adaptation. Comparing the intersecting careers of Knut Schmidt-Nielsen and George Bartholomew highlights two strikingly different approaches to physiological ecology. These alternative approaches to studying the interactions of organisms and environments also differed in important ways from the organismal biology championed by leading figures in the modern synthesis.

  1. A data integration approach for cell cycle analysis oriented to model simulation in systems biology

    Directory of Open Access Journals (Sweden)

    Mosca Ettore

    2007-08-01

    Full Text Available Abstract Background The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies. Description In this work, we present a resource, the Cell Cycle Database, intended to support systems biology analysis on the Cell Cycle process, based on two organisms, yeast and mammalian. The database integrates information about genes and proteins involved in the cell cycle process, stores complete models of the interaction networks and allows the mathematical simulation over time of the quantitative behaviour of each component. To accomplish this task, we developed, a web interface for browsing information related to cell cycle genes, proteins and mathematical models. In this framework, we have implemented a pipeline which allows users to deal with the mathematical part of the models, in order to solve, using different variables, the ordinary differential equation systems that describe the biological process. Conclusion This integrated system is freely available in order to support systems biology research on the cell cycle and

  2. The role of bacillus-based biological control agents in integrated pest management systems: plant diseases.

    Science.gov (United States)

    Jacobsen, B J; Zidack, N K; Larson, B J

    2004-11-01

    ABSTRACT Bacillus-based biological control agents (BCAs) have great potential in integrated pest management (IPM) systems; however, relatively little work has been published on integration with other IPM management tools. Unfortunately, most research has focused on BCAs as alternatives to synthetic chemical fungicides or bactericides and not as part of an integrated management system. IPM has had many definitions and this review will use the national coalition for IPM definition: "A sustainable approach to managing pests by combining biological, cultural, physical and chemical tools in a way that minimizes economic, health and environmental risks." This review will examine the integrated use of Bacillus-based BCAs with disease management tools, including resistant cultivars, fungicides or bactericides, or other BCAs. This integration is important because the consistency and degree of disease control by Bacillus-based BCAs is rarely equal to the control afforded by the best fungicides or bactericides. In theory, integration of several tools brings stability to disease management programs. Integration of BCAs with other disease management tools often provides broader crop adaptation and both more efficacious and consistent levels of disease control. This review will also discuss the use of Bacillus-based BCAs in fungicide resistance management. Work with Bacillus thuringiensis and insect pest management is the exception to the relative paucity of reports but will not be the focus of this review.

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

    Science.gov (United States)

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

    2015-05-01

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

  4. Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

    Directory of Open Access Journals (Sweden)

    Christley Scott

    2010-08-01

    Full Text Available Abstract Background Simulation of sophisticated biological models requires considerable computational power. These models typically integrate together numerous biological phenomena such as spatially-explicit heterogeneous cells, cell-cell interactions, cell-environment interactions and intracellular gene networks. The recent advent of programming for graphical processing units (GPU opens up the possibility of developing more integrative, detailed and predictive biological models while at the same time decreasing the computational cost to simulate those models. Results We construct a 3D model of epidermal development and provide a set of GPU algorithms that executes significantly faster than sequential central processing unit (CPU code. We provide a parallel implementation of the subcellular element method for individual cells residing in a lattice-free spatial environment. Each cell in our epidermal model includes an internal gene network, which integrates cellular interaction of Notch signaling together with environmental interaction of basement membrane adhesion, to specify cellular state and behaviors such as growth and division. We take a pedagogical approach to describing how modeling methods are efficiently implemented on the GPU including memory layout of data structures and functional decomposition. We discuss various programmatic issues and provide a set of design guidelines for GPU programming that are instructive to avoid common pitfalls as well as to extract performance from the GPU architecture. Conclusions We demonstrate that GPU algorithms represent a significant technological advance for the simulation of complex biological models. We further demonstrate with our epidermal model that the integration of multiple complex modeling methods for heterogeneous multicellular biological processes is both feasible and computationally tractable using this new technology. We hope that the provided algorithms and source code will be a

  5. Integration of advanced oxidation technologies and biological processes: recent developments, trends, and advances.

    Science.gov (United States)

    Tabrizi, Gelareh Bankian; Mehrvar, Mehrab

    2004-01-01

    The greatest challenge of today's wastewater treatment technology is to optimize the use of biological and chemical wastewater treatment processes. The choice of the process and/or integration of the processes depend strongly on the wastewater characteristics, concentrations, and the desired efficiencies. It has been observed by many investigators that the coupling of a bioreactor and advanced oxidation processes (AOPs) could reduce the final concentrations of the effluent to the desired values. However, optimizing the total cost of the treatment is a challenge, as AOPs are much more expensive than biological processes alone. Therefore, an appropriate design should not only consider the ability of this coupling to reduce the concentration of organic pollutants, but also try to obtain the desired results in a cost effective process. To consider the total cost of the treatment, the residence time in biological and photochemical reactors, the kinetic rates, and the capital and operating costs of the reactors play significant roles. In this study, recent developments and trends (1996-2003) on the integration of photochemical and biological processes for the degradation of problematic pollutants in wastewater have been reviewed. The conditions to get the optimum results from this integration have also been considered. In most of the studies, it has been shown that the integrated processes were more efficient than individual processes. However, slight changes in the configuration of the reactors, temperature, pH, treatment time, concentration of the oxidants, and microorganism's colonies could lead to a great deviation in results. It has also been demonstrated that the treatment cost in both reactors is a function of time, which changes by the flow rate. The minimum cost in the coupling of the processes cannot be achieved unless considering the best treatment time in chemical and biological reactors individually.

  6. Tav4SB: integrating tools for analysis of kinetic models of biological systems

    Directory of Open Access Journals (Sweden)

    Rybiński Mikołaj

    2012-04-01

    Full Text Available Abstract Background Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology. Results The Taverna services for Systems Biology (Tav4SB project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project’s Web page: http://bioputer.mimuw.edu.pl/tav4sb/. Conclusions The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.

  7. Measurement of the Ecological Integrity of Cerrado Streams Using Biological Metrics and the Index of Habitat Integrity

    Science.gov (United States)

    dos Reis, Deusiano Florêncio; Salazar, Ayala Eduardo; Machado, Mayana Mendes Dias; Couceiro, Sheyla Regina Marques; de Morais, Paula Benevides

    2017-01-01

    Generally, aquatic communities reflect the effects of anthropogenic changes such as deforestation or organic pollution. The Cerrado stands among the most threatened ecosystems by human activities in Brazil. In order to evaluate the ecological integrity of the streams in a preserved watershed in the Northern Cerrado biome corresponding to a mosaic of ecosystems in transition to the Amazonia biome in Brazil, biological metrics related to diversity, structure, and sensitivity of aquatic macroinvertebrates were calculated. Sampling included collections along stretches of 200 m of nine streams and measurements of abiotic variables (temperature, electrical conductivity, pH, total dissolved solids, dissolved oxygen, and discharge) and the Index of Habitat Integrity (HII). The values of the abiotic variables and the HII indicated that most of the streams have good ecological integrity, due to high oxygen levels and low concentrations of dissolved solids and electric conductivity. Two streams showed altered HII scores mainly related to small dams for recreational and domestic use, use of Cerrado natural pasture for cattle raising, and spot deforestation in bathing areas. However, this finding is not reflected in the biological metrics that were used. Considering all nine streams, only two showed satisfactory ecological quality (measured by Biological Monitoring Working Party (BMWP), total richness, and EPT (Ephemeroptera, Plecoptera, and Trichoptera) richness), only one of which had a low HII score. These results indicate that punctual measures of abiotic parameters do not reveal the long-term impacts of anthropic activities in these streams, including related fire management of pasture that annually alters the vegetation matrix and may act as a disturbance for the macroinvertebrate communities. Due to this, biomonitoring of low order streams in Cerrado ecosystems of the Northern Central Brazil by different biotic metrics and also physical attributes of the riparian zone

  8. A reproducible approach to high-throughput biological data acquisition and integration

    Directory of Open Access Journals (Sweden)

    Daniela Börnigen

    2015-03-01

    Full Text Available Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories. Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa.

  9. Research on models of biological systems that can be integrated into mechatronic systems

    Science.gov (United States)

    Pop, P. P.; Pop-Vadean, A.; Barz, C.; Latinovic, T.; Chiver, O.

    2016-02-01

    The models of biological systems that we find on Earth can be the subject of research to develop a few mechatronic systems. Such models are offered by bees, ants, crows, cranes, etc. Article aims to investigate these models and their manifestations. Imitating this behavior and studied him offer ideas for develop models that can be integrated into mechatronic systems. They can be integrated into mechatronic system as algorithms for finding local optimum, to search, to detect an optimal way travel on a network, to find best decision, etc.

  10. A biological plausible Generalized Leaky Integrate-and-Fire neuron model.

    Science.gov (United States)

    Wang, Zhenzhong; Guo, Lilin; Adjouadi, Malek

    2014-01-01

    This study introduces a new Generalized Leaky Integrate-and-Fire (GLIF) neuron model. Unlike Normal Leaky Integrate-and-Fire (NLIF) models, the leaking resistor in the GLIF model equation is assumed to be variable, and an additional term would have the bias current added to the model equation in order to improve the accuracy. Adjusting the parameters defined for the leaking resistor and bias current, a GLIF model could be accurately matched to any Hodgkin-Huxley (HH) model and be able to reproduce plausible biological neuron behaviors.

  11. Teacher Perceptions of the Integration of Laptop Computers in Their High School Biology Classrooms

    Science.gov (United States)

    Gundy, Morag S.

    2011-12-01

    Studies indicate that teachers, and in particular science teachers in the senior high school grades, do not integrate laptop computers into their instruction to the extent anticipated by researchers. This technology has not spread easily to other teachers even with improved access to hardware and software, increased support, and a paradigm shift from teacher-centred to student-centred education. Although a number of studies have focused on the issues and problems related to the integration of laptops in classroom instruction, these studies, largely quantitative in nature, have tended to bypass the role teachers play in integrating laptop computers into their instruction. This thesis documents and describes the role of Ontario high school science teachers in the integration of laptop computers in the classroom. Ten teachers who have successfully integrated laptop computers into their biology courses participated in this descriptive study. Their perceptions of implementing laptops into their biology courses, key factors about the implementation process, and how the implementation was accomplished are examined. The study also identifies the conditions which they feel would allow this innovation to be implemented by other teachers. Key findings of the study indicate that teachers must initiate, implement and sustain an emergent and still evolving innovation; teacher perceptions change and continue to change with increased experience using laptops in the science classroom; changes in teaching approaches are significant as a result of the introduction of laptop technology; and, the teachers considered the acquisition and use of new teaching materials to be an important aspect of integrating laptop computers into instruction. Ongoing challenges for appropriate professional development, sharing of knowledge, skills and teaching materials are identified. The study provides a body of practical knowledge for biology teachers who are considering the integration of laptops into

  12. Integration of biological control and botanical pesticides : evaluation in a tritrophic context

    OpenAIRE

    Charleston, D.S.; Dicke, M.; Vet, L.E.M.; Kfir, R.

    2001-01-01

    The plant kingdom is by far the most efficient producer of chemical compounds, synthesising many products that are used in defence against herbivores. Extracts made from some plants, particularly extracts from plants within the Meliaceae (mahogany) family, have been shown to have insecticidal properties. We investigated the potential of these extracts and the possibility of integrating botanical pesticides with biological control of the diamondback moth, Plutella xylostella. Sub-lethal doses ...

  13. SU 8 used as optical waveguide in integrated optical microsensor for biological applications

    Science.gov (United States)

    Műller, Raluca; Obreja, P.; Kusko, M.; Esinenco, D.; Tibeica, C.; Conache, G.; Buia, L.; Apostol, D.; Damian, V.; Mateescu, M.; Diaconu, Mirela; Moldovan, Lucia

    2005-08-01

    We present preliminary experiments for an integrated optical sensor based on a Mach-Zehnder interferometer for biological applications. The sensor is sensitive to refractive index change produced by the presence of a biological species in the cladding of the optical waveguide. A "window" can be patterned in the upper cladding, so that the evanescent wave can be in direct contact with the environmental (the sensitive layer). We investigated as optical waveguides a new material, SU-8, a negative photoresist well known from the development of 3D micromachmed structures. We structured, by photolithographic techniques, rib and channel optical waveguides. We studied the influence of the silicon substrate on propagation losses and the possibility to use these losses for the selective attenuation of the higher order modes on the vertical direction. As biological materials we experimented collagen, which is a bio-polymer which can bind different enzymes or antibodies.

  14. Biologic and clinical aspects of integration of different bone substitutes in oral surgery: a literature review.

    Science.gov (United States)

    Zizzari, Vincenzo Luca; Zara, Susi; Tetè, Giulia; Vinci, Raffaele; Gherlone, Enrico; Cataldi, Amelia

    2016-10-01

    Many bone substitutes have been proposed for bone regeneration, and researchers have focused on the interactions occurring between grafts and host tissue, as the biologic response of host tissue is related to the origin of the biomaterial. Bone substitutes used in oral and maxillofacial surgery could be categorized according to their biologic origin and source as autologous bone graft when obtained from the same individual receiving the graft; homologous bone graft, or allograft, when harvested from an individual other than the one receiving the graft; animal-derived heterologous bone graft, or xenograft, when derived from a species other than human; and alloplastic graft, made of bone substitute of synthetic origin. The aim of this review is to describe the most commonly used bone substitutes, according to their origin, and to focus on the biologic events that ultimately lead to the integration of a biomaterial with the host tissue.

  15. NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology.

    Science.gov (United States)

    Romano, Paolo; Cordero, Francesca

    2016-03-02

    The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, and systems biology.43 scientific contributions were presented at NETTAB 2014, including keynote, special guest and tutorial talks, oral communications, and posters. Full papers from some of the best contributions presented at the workshop were later submitted to a special Call for this Supplement.Here, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement.

  16. 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.

  17. Conservation Biology and Traditional Ecological Knowledge: Integrating Academic Disciplines for Better Conservation Practice

    Directory of Open Access Journals (Sweden)

    Joshua A. Drew

    2006-12-01

    Full Text Available Conservation biology and environmental anthropology are disciplines that are both concerned with the identification and preservation of diversity, in one case biological and in the other cultural. Both conservation biology and the study of traditional ecoloigcal knowledge function at the nexus of the social and natural worlds, yet historically there have been major impediments to integrating the two. Here we identify linguistic, cultural, and epistemological barriers between the two disciplines. We argue that the two disciplines are uniquely positioned to inform each other and to provide critical insights and new perspectives on the way these sciences are practiced. We conclude by synthesizing common themes found in conservation success stories, and by making several suggestions on integration. These include cross-disciplinary publication, expanding memberships in professional societies and conducting multidisciplinary research based on similar interests in ecological process, taxonomy, or geography. Finally, we argue that extinction threats, be they biological or cultural/linguistic are imminent, and that by bringing these disciplines together we may be able to forge synergistic conservation programs capable of protecting the vivid splendor of life on Earth.

  18. Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses.

    Science.gov (United States)

    Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

    2016-01-01

    Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning.

  19. Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

    Science.gov (United States)

    Li, Le; Yip, Kevin Y.

    2016-01-01

    Currently most terms and term-term relationships in Gene Ontology (GO) are defined manually, which creates cost, consistency and completeness issues. Recent studies have demonstrated the feasibility of inferring GO automatically from biological networks, which represents an important complementary approach to GO construction. These methods (NeXO and CliXO) are unsupervised, which means 1) they cannot use the information contained in existing GO, 2) the way they integrate biological networks may not optimize the accuracy, and 3) they are not customized to infer the three different sub-ontologies of GO. Here we present a semi-supervised method called Unicorn that extends these previous methods to tackle the three problems. Unicorn uses a sub-tree of an existing GO sub-ontology as training part to learn parameters in integrating multiple networks. Cross-validation results show that Unicorn reliably inferred the left-out parts of each specific GO sub-ontology. In addition, by training Unicorn with an old version of GO together with biological networks, it successfully re-discovered some terms and term-term relationships present only in a new version of GO. Unicorn also successfully inferred some novel terms that were not contained in GO but have biological meanings well-supported by the literature.Availability: Source code of Unicorn is available at http://yiplab.cse.cuhk.edu.hk/unicorn/. PMID:27976738

  20. A biomimetic functionalization approach to integration of carbon nanoutbes into biological systems

    Science.gov (United States)

    Chen, Xing; Tam, Un Chong; Bertozzi, Carolyn; Zettl, Alex

    2006-03-01

    Due to their remarkable structural, electrical, and mechanical properties, carbon nanotubes (CNTs) have potential applications in biology ranging from imaging and tissue engineering. To realize these applications, however, new strategies for controlling the interaction between CNTs and biological systems such as proteins and cells are required. Here we describe a biomimetic approach to functionalize CNTs and therefore render them biocompatibility in order to facilitate their integration into biological systems. CNTs were coated with synthetic gycopolymers that mimic cell surface mucin gycoproteins. The functionalized CNTs were soluble in water, resisted non-specific protein binding and bound specifically to biomolecules. The coated CNTs could then be integrated onto mammalian cell surface by virtue of glycan-receptor interactions. Furthermore, the functionalized CNTs are non-toxic to cells. This strategy offers new opportunities for development of biosensor to probe biological processes. References: 1. X. Chen, G. S. Lee, A. Zettl, C. R. Bertozzi, Angewandte Chemie-International Edition 43, 6111 (2004). 2. X. Chen, U. C. Tam, J. L. Czlapanski, G. S. Lee, D. Rabuka, A. Zettl, C. R. Bertozzi, submitted.

  1. Biological and psychological rhythms: an integrative approach to rhythm disturbances in autistic disorder.

    Science.gov (United States)

    Botbol, Michel; Cabon, Philippe; Kermarrec, Solenn; Tordjman, Sylvie

    2013-09-01

    Biological rhythms are crucial phenomena that are perfect examples of the adaptation of organisms to their environment. A considerable amount of work has described different types of biological rhythms (from circadian to ultradian), individual differences in their patterns and the complexity of their regulation. In particular, the regulation and maturation of the sleep-wake cycle have been thoroughly studied. Its desynchronization, both endogenous and exogenous, is now well understood, as are its consequences for cognitive impairments and health problems. From a completely different perspective, psychoanalysts have shown a growing interest in the rhythms of psychic life. This interest extends beyond the original focus of psychoanalysis on dreams and the sleep-wake cycle, incorporating central theoretical and practical psychoanalytic issues related to the core functioning of the psychic life: the rhythmic structures of drive dynamics, intersubjective developmental processes and psychic containment functions. Psychopathological and biological approaches to the study of infantile autism reveal the importance of specific biological and psychological rhythmic disturbances in this disorder. Considering data and hypotheses from both perspectives, this paper proposes an integrative approach to the study of these rhythmic disturbances and offers an etiopathogenic hypothesis based on this integrative approach.

  2. Integrated biological-behavioural surveillance in pandemic-threat warning systems.

    Science.gov (United States)

    Miller, Maureen; Hagan, Emily

    2017-01-01

    Economically and politically disruptive disease outbreaks are a hallmark of the 21st century. Although pandemics are driven by human behaviours, current surveillance systems for identifying pandemic threats are largely reliant on the monitoring of disease outcomes in clinical settings. Standardized integrated biological-behavioural surveillance could, and should, be used in community settings to complement such clinical monitoring. The usefulness of such an approach has already been demonstrated in studies on human immunodeficiency virus, where integrated surveillance contributed to a biologically based and quantifiable understanding of the behavioural risk factors associated with the transmission dynamics of the virus. When designed according to Strengthening the Reporting of Observational Studies in Epidemiology criteria, integrated surveillance requires that both behavioural risk factors - i.e. exposure variables - and disease-indicator outcome variables be measured in behavioural surveys. In the field of pandemic threats, biological outcome data could address the weaknesses of self-reported data collected in behavioural surveys. Data from serosurveys of viruses with pandemic potential, collected under non-outbreak conditions, indicate that serosurveillance could be used to predict future outbreaks. When conducted together, behavioural surveys and serosurveys could warn of future pandemics, potentially before the disease appears in clinical settings. Traditional disease-outcome surveillance must be frequent and ongoing to remain useful but behavioural surveillance remains informative even if conducted much less often, since behaviour change occurs slowly over time. Only through knowledge of specific behavioural risk factors can interventions and policies that can prevent the next pandemic be developed.

  3. Systems Biology of cancer: Moving toward the Integrative Study of the metabolic alterations in cancer cells.

    Directory of Open Access Journals (Sweden)

    Claudia Erika Hernández Patiño

    2013-01-01

    Full Text Available One of the main objectives in systems biology is to understand the biological mechanisms that give rise to the phenotype of a microorganism by using high-throughput technologies and genome-scale mathematical modeling. The computational modeling of genome-scale metabolic reconstructions is one systemic and quantitative strategy for characterizing the metabolic phenotype associated with human diseases and potentially for designing drugs with optimal clinical effects. The purpose of this short review is to describe how computational modeling, including the specific case of constraint-based modeling, can be used to explore, characterize and predict the metabolic capacities that distinguish the metabolic phenotype of cancer cell lines. As we show herein, this computational framework is far from a pure theoretical description, and to ensure proper biological interpretation, it is necessary to integrate high-throughput data and generate predictions for later experimental assessment. Hence, genome-scale modeling serves as a platform for the following: 1 the integration of data from high-throughput technologies, 2 the assessment of how metabolic activity is related to phenotype in cancer cell lines and 3 the design of new experiments to evaluate the outcomes of the in silico analysis. By combining the functions described above, we show that computational modeling is a useful methodology to construct an integrative, systemic and quantitative scheme for understanding the metabolic profiles of cancer cell lines, a first step to determine the metabolic mechanism by which cancer cells maintain and support their malignant phenotype in human tissues.

  4. Systems biology of cancer: moving toward the integrative study of the metabolic alterations in cancer cells.

    Science.gov (United States)

    Hernández Patiño, Claudia E; Jaime-Muñoz, Gustavo; Resendis-Antonio, Osbaldo

    2012-01-01

    One of the main objectives in systems biology is to understand the biological mechanisms that give rise to the phenotype of a microorganism by using high-throughput technologies (HTs) and genome-scale mathematical modeling. The computational modeling of genome-scale metabolic reconstructions is one systemic and quantitative strategy for characterizing the metabolic phenotype associated with human diseases and potentially for designing drugs with optimal clinical effects. The purpose of this short review is to describe how computational modeling, including the specific case of constraint-based modeling, can be used to explore, characterize, and predict the metabolic capacities that distinguish the metabolic phenotype of cancer cell lines. As we show herein, this computational framework is far from a pure theoretical description, and to ensure proper biological interpretation, it is necessary to integrate high-throughput data and generate predictions for later experimental assessment. Hence, genome-scale modeling serves as a platform for the following: (1) the integration of data from HTs, (2) the assessment of how metabolic activity is related to phenotype in cancer cell lines, and (3) the design of new experiments to evaluate the outcomes of the in silico analysis. By combining the functions described above, we show that computational modeling is a useful methodology to construct an integrative, systemic, and quantitative scheme for understanding the metabolic profiles of cancer cell lines, a first step to determine the metabolic mechanism by which cancer cells maintain and support their malignant phenotype in human tissues.

  5. IS IT POSSIBLE TO INTEGRATE BASIC BIOLOGICAL DISCIPLINES IN A PRIVATE INSTITUTION?

    Directory of Open Access Journals (Sweden)

    L.A. Azzalis

    2008-05-01

    Full Text Available Basic biological disciplines as biochemistry, genetic and molecular biology have grown faster than any of other sciences. Moreover, those disciplines contribute to the understanding and treatment of an elevated number of illnesses. On the other hand, teachers cannot assure the graduating students that each particular discipline  is essential.  Furthermore,  those disciplines are often studied separately without any interdisciplinary integration between them.  The new curriculum proposed at Anhembi Morumbi University  - a private institution placed at São Paulo city  - incorporates learning blocks that  have been designed to integrate basic biological disciplines and clinical contents from the beginning in order to provide the stimulation and motivation to guide the  student through his learning.  The educational trend has concentrated on the following steps: 1 Biochemistry, genetic, cellular and molecular biology teachers´ from that institution have elaborated a new discipline  that was named Biologic Process. The aim of this new discipline was integrate basic biological sciences in a single content;  2  Selecting problems that could be discussed in the light of biochemistry, genetic and molecular contents; e.g. sickle cell anemia; 3 Developing  an innovative instructional method that challenges students “learn to learn” different from problem-based learning , economically unavailable at any particular university,  and  4 Assessments that measure knowledge, skills, attitudes and beliefs.  We believe that the future pedagogical system in  private health university will be a combination of “classical”  presentation of contents combined with actively involved students in the educational process and instruction based on either hypothetical  or real clinical cases in order to create  the stimulus for  the student continues to  integrate basic and clinical investigation.

  6. Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML.

    Science.gov (United States)

    Yan, Qing

    2010-01-01

    Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields.

  7. Multi-omic data integration enables discovery of hidden biological regularities

    DEFF Research Database (Denmark)

    Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin

    2016-01-01

    Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi- level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration...... of primary omics data reveals regularities that tie cellular processes together in Escherichia coli: the number of protein molecules made per mRNA transcript and the number of ribosomes required per translated protein molecule. Second, we show that genome- scale models, based on genomic and bibliomic data......, enable quantitative synchronization of disparate data types. Integrating omics data with models enabled the discovery of two novel regularities: condition invariant in vivo turnover rates of enzymes and the correlation of protein structural motifs and translational pausing. These regularities can...

  8. iTools: a framework for classification, categorization and integration of computational biology resources.

    Directory of Open Access Journals (Sweden)

    Ivo D Dinov

    Full Text Available The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long

  9. iTools: a framework for classification, categorization and integration of computational biology resources.

    Science.gov (United States)

    Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

    2008-05-28

    The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management

  10. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

    Directory of Open Access Journals (Sweden)

    Gregorio Sergio E

    2009-05-01

    Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

  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. Adaptation of sensor morphology: an integrative view of perception from biologically inspired robotics perspective.

    Science.gov (United States)

    Iida, Fumiya; Nurzaman, Surya G

    2016-08-01

    Sensor morphology, the morphology of a sensing mechanism which plays a role of shaping the desired response from physical stimuli from surroundings to generate signals usable as sensory information, is one of the key common aspects of sensing processes. This paper presents a structured review of researches on bioinspired sensor morphology implemented in robotic systems, and discusses the fundamental design principles. Based on literature review, we propose two key arguments: first, owing to its synthetic nature, biologically inspired robotics approach is a unique and powerful methodology to understand the role of sensor morphology and how it can evolve and adapt to its task and environment. Second, a consideration of an integrative view of perception by looking into multidisciplinary and overarching mechanisms of sensor morphology adaptation across biology and engineering enables us to extract relevant design principles that are important to extend our understanding of the unfinished concepts in sensing and perception.

  13. Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy.

    Directory of Open Access Journals (Sweden)

    Aleixandre Beltrà

    Full Text Available Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa, sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain.

  14. Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy

    Science.gov (United States)

    Beltrà, Aleixandre; Addison, Pia; Ávalos, Juan Antonio; Crochard, Didier; Garcia-Marí, Ferran; Guerrieri, Emilio; Giliomee, Jan H.; Malausa, Thibaut; Navarro-Campos, Cristina; Palero, Ferran; Soto, Antonia

    2015-01-01

    Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae) is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy) a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa), sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain. PMID:26047349

  15. A Neural Systems-Based Neurobiology and Neuropsychiatry Course: Integrating Biology, Psychodynamics, and Psychology in the Psychiatric Curriculum

    Science.gov (United States)

    Lacy, Timothy; Hughes, John D.

    2006-01-01

    Objective: Psychotherapy and biological psychiatry remain divided in psychiatry residency curricula. Behavioral neurobiology and neuropsychiatry provide a systems-level framework that allows teachers to integrate biology, psychodynamics, and psychology. Method: The authors detail the underlying assumptions and outline of a neural systems-based…

  16. INTEGRATING BIOLOGICAL PRINCIPLES WITH INSTRUCTION IN VOCATIONAL AGRICULTURE, A RESEARCH REPORT OF A GRADUATE STUDY. RESEARCH SERIES IN AGRICULTURAL EDUCATION.

    Science.gov (United States)

    BENDER, RALPH E.; STARLING, JOHN T.

    TO DETERMINE THE FEASIBILITY OF INTEGRATING BIOLOGICAL PRINCIPLES WITH INSTRUCTION IN VOCATIONAL AGRICULTURE IN OHIO HIGH SCHOOLS, 15 PILOT SCHOOLS AND 8 CONTROL SCHOOLS WERE STUDIED. PRETESTS ADMINISTERED TO STUDENTS IN OCTOBER 1963 WERE AN AGRICULTURAL ACHIEVEMENT TEST, A BIOLOGICAL PRINCIPLES TEST, THE CALIFORNIA SHORT-FORM TEST OF MENTAL…

  17. [Validation of two indices of biological integrity (IBI) for the Angulo River subbasin in Central Mexico].

    Science.gov (United States)

    Ramírez-Herrejón, Juan Pablo; Mercado-Silva, Norman; Medina-Nava, Martina; Domínguez-Domínguez, Omar

    2012-12-01

    Efforts to halt freshwater ecosystem degradation in central Mexico can benefit from using bio-monitoring tools that reflect the condition of their biotic integrity. We analyzed the applicability of two fish-based indices of biotic integrity using data from lotic and lentic systems in the Angulo River subbasin (Lerma-Chapala basin). Both independent data from our own collections during two consecutive years, and existing information detailing the ecological attributes of each species, were used to calculate indices of biological integrity for 16 sites in lotic and lentic habitats. We assessed environmental quality by combining independent evaluations water and habitat quality for each site. We found sites with poor, regular and good biotic integrity. Our study did not find sites with good environmental quality. Fish-based IBI scores were strongly and significantly correlated with scores from independent environmental assessment techniques. IBI scores were adequate at representing environmental conditions in most study sites. These results expand the area where a lotic system fish-based IBI can be used, and constitute an initial validation of a lentic system fish-based IBI. Our results suggest that these bio-monitoring tools can be used in future conservation efforts in freshwater ecosystems in the Middle Lerma Basin.

  18. The Role of Model Integration in Complex Systems Modelling An Example from Cancer Biology

    CERN Document Server

    Patel, Manish

    2010-01-01

    Model integration – the process by which different modelling efforts can be brought together to simulate the target system – is a core technology in the field of Systems Biology. In the work presented here model integration was addressed directly taking cancer systems as an example. An in-depth literature review was carried out to survey the model forms and types currently being utilised. This was used to formalise the main challenges that model integration poses, namely that of paradigm (the formalism on which a model is based), focus (the real-world system the model represents) and scale. A two-tier model integration strategy, including a knowledge-driven approach to address model semantics, was developed to tackle these challenges. In the first step a novel description of models at the level of behaviour, rather than the precise mathematical or computational basis of the model, is developed by distilling a set of abstract classes and properties. These can accurately describe model behaviour and hence d...

  19. Interactive exploration of integrated biological datasets using context-sensitive workflows

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2014-02-01

    Full Text Available Network inference utilises experimental high-throughput data for the reconstruction of molecular interaction networks where new relationships between the network entities can be predicted. Despite the increasing amount of experimental data, the parameters of each modelling technique cannot be optimised based on the experimental data alone, but needs to be qualitatively assessed if the components of the resulting network describe the experimental setting. Candidate list prioritisation and validation builds upon data integration and data visualisation. The application of tools supporting this procedure is limited to the exploration of smaller information networks because the display and interpretation of large amounts of information is challenging regarding the computational effort and the users’ experience.The Ondex software framework was extended with customisable context-sensitive menus which allow additional integration and data analysis options for a selected set of candidates during interactive data exploration. We provide new functionalities for on-the-fly data integration using InterProScan, PubMed Central literature search, and sequence-based homology search. We applied the Ondex system to the integration of publicly available data for Aspergillus nidulans and analysed transcriptome data. We demonstrate the advantages of our approach by proposing new hypotheses for the functional annotation of specific genes of differentially expressed fungal gene clusters. Our extension of the Ondex framework makes it possible to overcome the separation between data integration and interactive analysis. More specifically, computationally demanding calculations can be performed on selected sub-networks without losing any information from the whole network. Furthermore, our extensions allow for direct access to online biological databases which helps to keep the integrated information up-to-date.

  20. New Challenges Facing Integrative Biological Science in the Post-Genomic Era

    Energy Technology Data Exchange (ETDEWEB)

    Oehmen, Chris S.; Straatsma, TP; Anderson, Gordon A.; Orr, Galya; Webb-Robertson, Bobbie-Jo M.; Taylor, Ronald C.; Mooney, Ryan W.; Baxter, Douglas J.; Jones, Donald R.; Dixon, David A.

    2006-06-01

    The future of biology will be increasingly driven by the fundamental paradigm shift from hypothesis-driven research to data-driven discovery research employing the massive amounts of available biological data. We identify key technological developments needed to enable this paradigm shift involving (1) the ability to store and manage extremely large datasets which are dispersed over a wide geographical area, (2) development of novel analysis and visualization tools which are capable of operating on enormous data resources without overwhelming researchers with unusable information, and (3) formalisms for integrating mathematical models of biosystems from the molecular level to the organism population level. This will require the development of tools which efficiently utilize high-performance compute power, large storage infrastructures and large aggregate memory architectures. The end result will be the ability of a researcher to integrate complex data from many different sources with simulations to analyze a given system at a wide range of temporal and spatial scales in a single conceptual model.

  1. An integrated data-warehouse-concept for clinical and biological information.

    Science.gov (United States)

    Brammen, Dominik; Katzer, Christian; Röhrig, Rainer; Weismüller, Katja; Maier, Michael; Hossain, Hamid; Menges, Thilo; Hempelmann, Gunter; Chakraborty, Trinad

    2005-01-01

    The development of medical research networks within the framework of translational research has fostered interest in the integration of clinical and biological research data in a common database. The building of one single database integrating clinical data and biological research data requires a concept which enables scientists to retrieve information and to connect known facts to new findings. Clinical parameters are collected by a Patient Data Management System and viewed in a database which also includes genomic data. This database is designed as an Entity Attribute Value model, which implicates the development of a data warehouse concept. For the realization of this project, various requirements have to be taken into account which has to be fulfilled sufficiently in order to align with international standards. Data security and protection of data privacy are most important parts of the data warehouse concept. It has to be clear how patient pseudonymization has to be carried out in order to be within the scope of data security law. To be able to evaluate the data stored in a database consisting of clinical data collected by a Patient Data Management System and genomic research data easily, a data warehouse concept based on an Entity Attribute Value datamodel has been developed.

  2. Telomeric repeat-containing RNA TERRA: a noncoding RNA connecting telomere biology to genome integrity.

    Science.gov (United States)

    Cusanelli, Emilio; Chartrand, Pascal

    2015-01-01

    Telomeres are dynamic nucleoprotein structures that protect the ends of chromosomes from degradation and activation of DNA damage response. For this reason, telomeres are essential to genome integrity. Chromosome ends are enriched in heterochromatic marks and proper organization of telomeric chromatin is important to telomere stability. Despite their heterochromatic state, telomeres are transcribed giving rise to long noncoding RNAs (lncRNA) called TERRA (telomeric repeat-containing RNA). TERRA molecules play critical roles in telomere biology, including regulation of telomerase activity and heterochromatin formation at chromosome ends. Emerging evidence indicate that TERRA transcripts form DNA-RNA hybrids at chromosome ends which can promote homologous recombination among telomeres, delaying cellular senescence and sustaining genome instability. Intriguingly, TERRA RNA-telomeric DNA hybrids are involved in telomere length homeostasis of telomerase-negative cancer cells. Furthermore, TERRA transcripts play a role in the DNA damage response (DDR) triggered by dysfunctional telomeres. We discuss here recent developments on TERRA's role in telomere biology and genome integrity, and its implication in cancer.

  3. Scale relativity theory and integrative systems biology: 1. Founding principles and scale laws.

    Science.gov (United States)

    Auffray, Charles; Nottale, Laurent

    2008-05-01

    In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, and discuss how scale laws of increasing complexity can be used to model and understand the behaviour of complex biological systems. In scale relativity theory, the geometry of space is considered to be continuous but non-differentiable, therefore fractal (i.e., explicitly scale-dependent). One writes the equations of motion in such a space as geodesics equations, under the constraint of the principle of relativity of all scales in nature. To this purpose, covariant derivatives are constructed that implement the various effects of the non-differentiable and fractal geometry. In this first review paper, the scale laws that describe the new dependence on resolutions of physical quantities are obtained as solutions of differential equations acting in the scale space. This leads to several possible levels of description for these laws, from the simplest scale invariant laws to generalized laws with variable fractal dimensions. Initial applications of these laws to the study of species evolution, embryogenesis and cell confinement are discussed.

  4. BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects.

    Science.gov (United States)

    He, Xin; Li, Yanen; Khetani, Radhika; Sanders, Barry; Lu, Yue; Ling, Xu; Zhai, Chengxiang; Schatz, Bruce

    2010-07-01

    Text mining is one promising way of extracting information automatically from the vast biological literature. To maximize its potential, the knowledge encoded in the text should be translated to some semantic representation such as entities and relations, which could be analyzed by machines. But large-scale practical systems for this purpose are rare. We present BeeSpace question/answering (BSQA) system that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster. For any text query, BSQA exploits entity annotation of retrieved documents to identify important concepts in different categories. By utilizing the extracted relations, BSQA is also able to answer many biologically motivated questions, from simple ones such as, which anatomical part is a gene expressed in, to more complex ones involving multiple types of relations. BSQA is freely available at http://www.beespace.uiuc.edu/QuestionAnswer.

  5. Developing integrated TOF-SIMS/MALDI IMS system in studying biological systems

    Science.gov (United States)

    Wu, Ligang

    Using imaging mass spectrometry (IMS) techniques (including TOF-SIMS and MALDI IMS) to study biological systems is a relatively new concept and quickly gained popularity in recent years. Imaging mass spectrometry is a discovery technology that utilizes a focused ion beam or laser beam to desorb ions from sample surface. By detecting the desorbed ions, the chemical distributions and biological changes of a sample surface can be analyzed. These techniques offer a new analytical imaging approach to investigate biological processes at the cellular and tissue level. In this research, a novel integrated TOF-SIMS/MALDI IMS system as well as IMS based biological-sample-preparation techniques and data-reduction methods are developed. We then demonstrate the power of these techniques in studying different biological systems, including monosaccharides isomers, human breast cancer cell lines, mouse embryo tissues and mouse kidney sections. Using TOF-SIMS and statistical analysis methods, seven monosaccharide isomers are fully differentiated by analyzing their characteristic spectral pattern. In addition, a deep understanding of the fragmentation pathway of these isomers under ion bombardment is gained. In an application of TOF-SIMS to the differentiation of three human breast cancer cell lines, MCF-7, T47D, and MDA-MB-231, we show that principal component analysis (PCA) data reduction of TOF-SIMS spectra can differentiate cellular compartments (cytosol, nuclear and particulate) within the cell types, as well as homogenates from among the three cell lines. In a tissue-specific application, we extend the analytical capabilities of TOF-SIMS and PCA by imaging and differentiating Formalin-fixed paraffin-embedded (FFPE) mouse embryo tissues. We demonstrate reproducible differentiation of six tissue types based on the remaining small molecules after paraffin-embedding and the fragments of the cellular proteins. In a unique study of fresh frozen mouse kidney tissues, both TOF

  6. Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics.

    Science.gov (United States)

    Nottale, Laurent; Auffray, Charles

    2008-05-01

    In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space-time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space-time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential

  7. Meteorological Integration for the Biological Warning and Incident Characterization (BWIC) System: General Guidance for BWIC Cities

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, William J.; Wang, Weiguo; Rutz, Frederick C.; Chapman, Elaine G.; Rishel, Jeremy P.; Xie, YuLong; Seiple, Timothy E.; Allwine, K Jerry

    2007-02-16

    The U.S. Department of Homeland Security (DHS) is responsible for developing systems to detect the release of aerosolized bioagents in urban environments. The system that accomplishes this, known as BioWatch, is a robust first-generation monitoring system. In conjunction with the BioWatch detection network, DHS has also developed a software tool for cities to use to assist in their response when a bioagent is detected. This tool, the Biological Warning and Incident Characterization (BWIC) System, will eventually be deployed to all BioWatch cities to aid in the interpretation of the public health significance of indicators from the BioWatch networks. BWIC consists of a set of integrated modules, including meteorological models, that estimate the effect of a biological agent on a city’s population once it has been detected. For the meteorological models in BWIC to successfully calculate the distribution of biological material, they must have as input accurate meteorological data, and wind fields in particular. The purpose of this document is to provide guidance for cities to use in identifying sources of good-quality local meteorological data that BWIC needs to function properly. This process of finding sources of local meteorological data, evaluating the data quality and gaps in coverage, and getting the data into BWIC, referred to as meteorological integration, is described. The good news for many cities is that meteorological measurement networks are becoming increasingly common. Most of these networks allow their data to be distributed in real time via the internet. Thus, cities will often only need to evaluate the quality of available measurements and perhaps add a modest number of stations where coverage is poor.

  8. Mitochondrial Flash: Integrative Reactive Oxygen Species and pH Signals in Cell and Organelle Biology

    Science.gov (United States)

    Gong, Guohua; Wang, Xianhua; Wei-LaPierre, Lan; Cheng, Heping; Dirksen, Robert

    2016-01-01

    Abstract Significance: Recent breakthroughs in mitochondrial research have advanced, reshaped, and revolutionized our view of the role of mitochondria in health and disease. These discoveries include the development of novel tools to probe mitochondrial biology, the molecular identification of mitochondrial functional proteins, and the emergence of new concepts and mechanisms in mitochondrial function regulation. The discovery of “mitochondrial flash” activity has provided unique insights not only into real-time visualization of individual mitochondrial redox and pH dynamics in live cells but has also advanced understanding of the excitability, autonomy, and integration of mitochondrial function in vivo. Recent Advances: The mitochondrial flash is a transient and stochastic event confined within an individual mitochondrion and is observed in a wide range of organisms from plants to Caenorhabditis elegans to mammals. As flash events involve multiple transient concurrent changes within the mitochondrion (e.g., superoxide, pH, and membrane potential), a number of different mitochondrial targeted fluorescent indicators can detect flash activity. Accumulating evidence indicates that flash events reflect integrated snapshots of an intermittent mitochondrial process arising from mitochondrial respiration chain activity associated with the transient opening of the mitochondrial permeability transition pore. Critical Issues: We review the history of flash discovery, summarize current understanding of flash biology, highlight controversies regarding the relative roles of superoxide and pH signals during a flash event, and bring forth the integration of both signals in flash genesis. Future Directions: Investigations using flash as a biomarker and establishing its role in cell signaling pathway will move the field forward. Antioxid. Redox Signal. 25, 534–549. PMID:27245241

  9. Integration of plant defense traits with biological control of arthropod pests: challenges and opportunities

    Directory of Open Access Journals (Sweden)

    Julie A Peterson

    2016-11-01

    Full Text Available Crop plants exhibit a wide diversity of defensive traits and strategies to protect themselves from damage by herbivorous pests and disease. These defensive traits may be naturally occurring or artificially selected through crop breeding, including introduction via genetic engineering. While these traits can have obvious and direct impacts on herbivorous pests, many have profound effects on higher trophic levels, including the natural enemies of herbivores. Multi-trophic effects of host plant resistance have the potential to influence, both positively and negatively, biological control. Plant defense traits can influence both the numerical and functional responses of natural enemies; these interactions can be semiochemically-, plant toxin-, plant nutrient-, and/or physically-mediated. Case studies involving predators, parasitoids, and pathogens of crop pests will be presented and discussed. These diverse groups of natural enemies may respond differently to crop plant traits based on their own unique biology and the ecological niches they fill. Genetically modified crop plants that have been engineered to express transgenic products affecting herbivorous pests are an additional consideration. For the most part, transgenic plant incorporated protectant (PIP traits are compatible with biological control due to their selective toxicity to targeted pests and relatively low non-target impacts, although transgenic crops may have indirect effects on higher trophic levels and arthropod communities mediated by lower host or prey number and/or quality. Host plant resistance and biological control are two of the key pillars of integrated pest management; their potential interactions, whether they are synergistic, complementary, or disruptive, are key in understanding and achieving sustainable and effective pest management.

  10. Mapping biological ideas: Concept maps as knowledge integration tools for evolution education

    Science.gov (United States)

    Schwendimann, Beat Adrian

    Many students leave school with a fragmented understanding of biology that does not allow them to connect their ideas to their everyday lives (Wandersee, 1989; Mintzes, Wandersee, & Novak, 1998; Mintzes, Wandersee, & Novak, 2000a). Understanding evolution ideas is seen as central to building an integrated knowledge of biology (Blackwell, Powell, & Dukes, 2003; Thagard & Findlay, 2010). However, the theory of evolution has been found difficult to understand as it incorporates a wide range of ideas from different areas (Bahar et al., 1999; Tsui & Treagust, 2003) and multiple interacting levels (Wilensky & Resnick, 1999; Duncan & Reiser, 2007; Hmelo-Silver et al., 2007). Research suggests that learners can hold a rich repertoire of co-existing alternative ideas of evolution (for example, Bishop & Anderson, 1990; Demastes, Good, & Peebles, 1996; Evans, 2008), especially of human evolution (for example, Nelson, 1986; Sinatra et al., 2003; Poling & Evans, 2004). Evolution ideas are difficult to understand because they often contradict existing alternative ideas (Mayr, 1982; Wolpert, 1994; Evans, 2008). Research suggests that understanding human evolution is a key to evolution education (for example, Blackwell et al., 2003; Besterman & Baggott la Velle, 2007). This dissertation research investigates how different concept mapping forms embedded in a collaborative technology-enhanced learning environment can support students' integration of evolution ideas using case studies of human evolution. Knowledge Integration (KI) (Linn et al., 2000; Linn et al., 2004) is used as the operational framework to explore concept maps as knowledge integration tools to elicit, add, critically distinguish, group, connect, and sort out alternative evolution ideas. Concept maps are a form of node-link diagram for organizing and representing connections between ideas as a semantic network (Novak & Gowin, 1984). This dissertation research describes the iterative development of a novel biology

  11. Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

    Science.gov (United States)

    He, Yongqun

    2014-07-01

    While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

  12. Assessing Vermont's stream health and biological integrity using artificial neural networks and Bayesian methods

    Science.gov (United States)

    Rizzo, D. M.; Fytilis, N.; Stevens, L.

    2012-12-01

    Environmental managers are increasingly required to monitor and forecast long-term effects and vulnerability of biophysical systems to human-generated stresses. Ideally, a study involving both physical and biological assessments conducted concurrently (in space and time) could provide a better understanding of the mechanisms and complex relationships. However, costs and resources associated with monitoring the complex linkages between the physical, geomorphic and habitat conditions and the biological integrity of stream reaches are prohibitive. Researchers have used classification techniques to place individual streams and rivers into a broader spatial context (hydrologic or health condition). Such efforts require environmental managers to gather multiple forms of information - quantitative, qualitative and subjective. We research and develop a novel classification tool that combines self-organizing maps with a Naïve Bayesian classifier to direct resources to stream reaches most in need. The Vermont Agency of Natural Resources has developed and adopted protocols for physical stream geomorphic and habitat assessments throughout the state of Vermont. Separate from these assessments, the Vermont Department of Environmental Conservation monitors the biological communities and the water quality in streams. Our initial hypothesis is that the geomorphic reach assessments and water quality data may be leveraged to reduce error and uncertainty associated with predictions of biological integrity and stream health. We test our hypothesis using over 2500 Vermont stream reaches (~1371 stream miles) assessed by the two agencies. In the development of this work, we combine a Naïve Bayesian classifier with a modified Kohonen Self-Organizing Map (SOM). The SOM is an unsupervised artificial neural network that autonomously analyzes inherent dataset properties using input data only. It is typically used to cluster data into similar categories when a priori classes do not exist. The

  13. OpenStructure: an integrated software framework for computational structural biology.

    Science.gov (United States)

    Biasini, M; Schmidt, T; Bienert, S; Mariani, V; Studer, G; Haas, J; Johner, N; Schenk, A D; Philippsen, A; Schwede, T

    2013-05-01

    Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.

  14. Affects as central organising and integrating factors. A new psychosocial/biological model of the psyche.

    Science.gov (United States)

    Ciompi, L

    1991-07-01

    A new psychosocial/biological model of the psyche is proposed, in which the affects play a central role in organising and integrating cognition. The psyche is understood here as a complex hierarchical structure of affective/cognitive systems of reference (or 'programmes for feeling, thinking, and behaviour'), generated by repetitive concrete action. These systems store past experience in their structure, and provide the functional basis for further cognition and communication. Affects endow these programmes with a specific qualitative value (such as motivation), connect cognitive elements synchronically and diachronically, and contribute to their storage and mobilisation according to context. They also participate in differentiating cognitive systems at higher levels of abstraction. These assumptions are supported by recent findings on the role of the limbic and hypothalamic system for the regulation of emotion, on neuronal plasticity, and on the phenomenon of state-dependent learning and memory. Refutable hypotheses are formulated for further research on the interaction of emotion and cognition.

  15. OpenStructure: an integrated software framework for computational structural biology

    Science.gov (United States)

    Biasini, M.; Schmidt, T.; Bienert, S.; Mariani, V.; Studer, G.; Haas, J.; Johner, N.; Schenk, A. D.; Philippsen, A.; Schwede, T.

    2013-01-01

    Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org. PMID:23633579

  16. 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.

  17. Scientific drilling projects in ancient lakes: Integrating geological and biological histories

    Science.gov (United States)

    Wilke, Thomas; Wagner, Bernd; Van Bocxlaer, Bert; Albrecht, Christian; Ariztegui, Daniel; Delicado, Diana; Francke, Alexander; Harzhauser, Mathias; Hauffe, Torsten; Holtvoeth, Jens; Just, Janna; Leng, Melanie J.; Levkov, Zlatko; Penkman, Kirsty; Sadori, Laura; Skinner, Alister; Stelbrink, Björn; Vogel, Hendrik; Wesselingh, Frank; Wonik, Thomas

    2016-08-01

    Sedimentary sequences in ancient or long-lived lakes can reach several thousands of meters in thickness and often provide an unrivalled perspective of the lake's regional climatic, environmental, and biological history. Over the last few years, deep-drilling projects in ancient lakes became increasingly multi- and interdisciplinary, as, among others, seismological, sedimentological, biogeochemical, climatic, environmental, paleontological, and evolutionary information can be obtained from sediment cores. However, these multi- and interdisciplinary projects pose several challenges. The scientists involved typically approach problems from different scientific perspectives and backgrounds, and setting up the program requires clear communication and the alignment of interests. One of the most challenging tasks, besides the actual drilling operation, is to link diverse datasets with varying resolution, data quality, and age uncertainties to answer interdisciplinary questions synthetically and coherently. These problems are especially relevant when secondary data, i.e., datasets obtained independently of the drilling operation, are incorporated in analyses. Nonetheless, the inclusion of secondary information, such as isotopic data from fossils found in outcrops or genetic data from extant species, may help to achieve synthetic answers. Recent technological and methodological advances in paleolimnology are likely to increase the possibilities of integrating secondary information. Some of the new approaches have started to revolutionize scientific drilling in ancient lakes, but at the same time, they also add a new layer of complexity to the generation and analysis of sediment-core data. The enhanced opportunities presented by new scientific approaches to study the paleolimnological history of these lakes, therefore, come at the expense of higher logistic, communication, and analytical efforts. Here we review types of data that can be obtained in ancient lake drilling

  18. Bringing together an ocean of information: An extensible data integration framework for biological oceanography

    Science.gov (United States)

    Stocks, Karen I.; Condit, Chris; Qian, Xufei; Brewin, Paul E.; Gupta, Amarnath

    2009-09-01

    As increasing volumes and varieties of data are becoming available online, the challenges of accessing and using heterogeneous data resources are growing. We have developed a mediator-based data integration system called Cartel for biological oceanography data. A mediation approach is appropriate in cases where a single central warehouse is not desirable, such as when the needed data sources change frequently through time, or when there are advantages for holding heterogeneous data in their native formats. Through Cartel, data sources of a variety of types can be registered to the system, and users can query against simplified virtual schemas, without needing to know the underlying schema and computational capabilities of each data source. The system can operate on a variety of relational and geospatial data formats, and can perform joins between formats. We tested the performance of the Cartel mediator in two biological oceanography application areas, and found that the system was able to support the variety of data types needed in a typical ecology study, but that the response times were unacceptably slow when very large databases (i.e. Ocean Biogeographic Information System and the World Ocean Atlas) were used. Indexing and caching are currently being added to the system to improve response times. The mediator is an open-source product, and was developed to be a generic, extensible component available to projects developing oceanography data systems.

  19. Integration of photocatalysis and biological treatment for azo dye removal--application to AR183.

    Science.gov (United States)

    Chebli, Derradji; Fourcade, Florence; Brosillon, Stephan; Nacef, Saci; Amrane, Abdeltif

    2011-04-01

    The feasibility of coupling photocatalysis with biological treatment to treat effluents containing azo dyes was examined in this work. With this aim, the degradation of Acid Red 183 was investigated. The very low biodegradability of AR183 was confirmed beforehand by measuring the biological oxygen demand (BOD5). Photocatalysis experiments were carried out in a closed-loop step photoreactor. The reactor walls were covered by TiO2 catalyst coated on non-woven paper, and the effluent flowed over the photocatalyst as a thin falling film. The removal of the dye was 82.7% after 4 h, and a quasi-complete decolorization (98.5%) was obtained for 10 h of irradiation (initial concentration 100 mg L(-1)). The decrease in concentration followed pseudo-first-order kinetics, with a constant k of 0.47 h(-1). Mineralization and oxidation yields were 80% and 75%, respectively, after 10 h of pretreatment. Therefore, even if target compound oxidation occurs (COD removal), indicating a modification to the chemical structure, the concomitant high mineralization was not in favour of subsequent microbial growth. The BOD5 measurement confirmed the non-biodegradability of the irradiated solution, which remained toxic since the EC50 decreased from 35 to 3 mg L(-1). The proposed integrated process appeared, therefore, to be not relevant for the treatment of AR183. However, this result should be confirmed for other azo dyes.

  20. Integration of 3D structure from disparity into biological motion perception independent of depth awareness.

    Science.gov (United States)

    Wang, Ying; Jiang, Yi

    2014-01-01

    Images projected onto the retinas of our two eyes come from slightly different directions in the real world, constituting binocular disparity that serves as an important source for depth perception - the ability to see the world in three dimensions. It remains unclear whether the integration of disparity cues into visual perception depends on the conscious representation of stereoscopic depth. Here we report evidence that, even without inducing discernible perceptual representations, the disparity-defined depth information could still modulate the visual processing of 3D objects in depth-irrelevant aspects. Specifically, observers who could not discriminate disparity-defined in-depth facing orientations of biological motions (i.e., approaching vs. receding) due to an excessive perceptual bias nevertheless exhibited a robust perceptual asymmetry in response to the indistinguishable facing orientations, similar to those who could consciously discriminate such 3D information. These results clearly demonstrate that the visual processing of biological motion engages the disparity cues independent of observers' depth awareness. The extraction and utilization of binocular depth signals thus can be dissociable from the conscious representation of 3D structure in high-level visual perception.

  1. Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

    Science.gov (United States)

    Roever, Stefan

    2012-01-01

    A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

  2. An assessment of aquatic ecosystem health in a temperate watershed using the index of biological integrity.

    Science.gov (United States)

    An, Kwang-Guk; Choi, Shin-Sok

    2003-06-01

    The health effect of an aquatic ecosystem on habitat modifications were evaluated in the Keum river watershed, Korea during 1977-1996 using the Index of Biological Integrity (IBI) based on fish assemblages. Values of IBI, based on overall sites, averaged 35 (range: 26-45, n = 38) before dam construction, indicating a "fair health condition" based on the modified criteria of Karr and Chu (Karr, J.R.; Chu, E.W. Restoring Life in Running Waters: Better Biological Monitoring; Inland Press: Washington, DC, 1999; 206 pp.), while the values averaged 33 (range: 18-48, n = 15) after dam construction, indicating a similar ecosystem health condition in the IBI between the two periods. Marked modifications in the IBI, however, were partially observed along the longitudinal gradients from the headwaters to downstream along with variations of trophic compositions and habitat guilds. Annual mean of IBI showed significant decreases (p 20% decreases of insectivores and >25% increases of omnivores. Comparisons of habitat guilds indicated that the proportion of riffle benthic species declined linearly from 1977 to 1996 and had inverse relations (r = -0.78, p health was mainly affected by the habitat modifications.

  3. ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics.

    Science.gov (United States)

    Chung, Hee-Joon; Kim, Mingoo; Park, Chan Hee; Kim, Jihoon; Kim, Ju Han

    2004-07-01

    Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integrating major bio-databases and searching pathway resources, ArrayXPath automatically maps different types of identifiers from microarray probes and pathway elements. When one inputs gene-expression clusters, ArrayXPath produces a list of the best matching pathways for each cluster. We applied Fisher's exact test and the false discovery rate (FDR) to evaluate the statistical significance of the association between a cluster and a pathway while correcting the multiple-comparison problem. ArrayXPath produces Javascript-enabled SVGs for web-enabled interactive visualization of pathways integrated with gene-expression profiles.

  4. MetNet Online: a novel integrated resource for plant systems biology

    Directory of Open Access Journals (Sweden)

    Sucaet Yves

    2012-10-01

    Full Text Available Abstract Background Plants are important as foods, pharmaceuticals, biorenewable chemicals, fuel resources, bioremediation tools and general tools for recombinant technology. The study of plant biological pathways is advanced by easy access to integrated data sources. Today, various plant data sources are scattered throughout the web, making it increasingly complicated to build comprehensive datasets. Results MetNet Online is a web-based portal that provides access to a regulatory and metabolic plant pathway database. The database and portal integrate Arabidopsis, soybean (Glycine max and grapevine (Vitis vinifera data. Pathways are enriched with known or predicted information on sub cellular location. MetNet Online enables pathways, interactions and entities to be browsed or searched by multiple categories such as sub cellular compartment, pathway ontology, and GO term. In addition to this, the “My MetNet” feature allows registered users to bookmark content and track, import and export customized lists of entities. Users can also construct custom networks using existing pathways and/or interactions as building blocks. Conclusion The site can be reached at http://www.metnetonline.org. Extensive video tutorials on how to use the site are available through http://www.metnetonline.org/tutorial/.

  5. Removal of Furfural From Wastewater Using Integrated Catalytic Ozonation and Biological Approaches

    Directory of Open Access Journals (Sweden)

    Mostafa Leili

    2014-12-01

    Full Text Available Furfural with a chemical formula of C5H4O2 is a toxic compound which has several health problems for both humans and environment. It has a few exposure routes for entering the human body such as oral, dermal or nasal. In the present study, the efficacies of an integrated catalytic ozonation process (COP and novel cyclic biological reactor (CBR were explored for the removal of furfural from aqueous solutions. Activated carbon was purchased from Merck Company. It had a Brunauer, Emmett, and Teller (BET specific surface area of 1100 m2/g, with an average micropore volume and size of 0.385 cm3/g and 595 µm, respectively. The results indicated that 30% pretreatment with COP could increase furfural and chemical oxygen demand (COD removal efficiency with CBR 5.56% and 27.01%, respectively. With 70% pretreatment by COP, 98.57% furfural and 95.34% COD removal efficiencies happen in CBR. Generally, batch and continuous experiments showed that the integrated COP/CBR could be efficient in eliminating furfural from wastewater and thus may be a promising technique for treating furfural-containing wastewater.

  6. Integrated photocatalytic-biological reactor for accelerated 2,4,6-trichlorophenol degradation and mineralization.

    Science.gov (United States)

    Zhang, Yongming; Sun, Xia; Chen, Lujun; Rittmann, Bruce E

    2012-02-01

    An integrated photocatalytic-biological reactor (IPBR) was used for accelerated degradation and mineralization of 2,4,6-trichlorophenol (TCP) through simultaneous, intimate coupling of photocatalysis and biodegradation in one reactor. Intimate coupling was realized by circulating the IPBR's liquid contents between a TiO(2) film on mat glass illuminated by UV light and honeycomb ceramics as biofilm carriers. Three protocols-photocatalysis alone (P), biodegradation alone (B), and integrated photocatalysis and biodegradation (photobiodegradation, P&B)-were used for degradation of different initial TCP concentrations. Intimately coupled P&B also was compared with sequential P and B. TCP removal by intimately coupled P&B was faster than that by P and B alone or sequentially coupled P and B. Because photocatalysis relieved TCP inhibition to biodegradation by decreasing its concentration, TCP biodegradation could become more important over the full batch P&B experiments. When phenol, an easy biodegradable compounds, was added to TCP in order to promote TCP mineralization by means of secondary utilization, P&B was superior to P and B in terms of mineralization of TCP, giving 95% removal of chemical oxygen demand. Cl(-) was only partially released during P experiments (24%), and this corresponded to its poor mineralization in P experiments (32%). Thus, intimately coupled P&B in the IPBR made it possible obtain the best features of each: rapid photocatalytic transformation in parallel with mineralization of photocatalytic products.

  7. Problem-based learning on cell biology and ecophysiology using integrated laboratory and computational activities

    Directory of Open Access Journals (Sweden)

    C. Sousa

    2016-03-01

    Full Text Available Since all the known biological systems require water for their basic biochemical processes, one can find several osmoregulation mechanisms on living organisms for adaptation to related environmental challenges. Osmosis is a cellular mechanism of water movement across membranes which is known to be present throughout the tree of life and occurs by either diffusion across the membrane bilayer or by a faster movement mediated by transmembrane channel proteins, called aquaporins. The expression of aquaporins is regulated at, the cellular level, by environment conditions such as hydric stress, therefore allowing the adaptation of organisms to increase salinity in soils, water deprivation and increase beverage intake.  Osmosis and diffusion concepts have been described to be difficult to learn, so, in order to promote meaningfull learning, we used a problem-based learning approach that integrates a laboratory activity and a computer simulation model of osmosis and a two phase conceptual mapping. We observed that high school students developed adequate laboratory skills and were able to communicate their results as text and using scientific drawings; and the learning environment was adequate. Therefore we presented a successful implementation case of integrated PBL, in a public portuguese school, that may constitute an example to facilitate the implementation of active inquiry strategies by other teachers, as well as the basis for future research.

  8. GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

    Science.gov (United States)

    Tran, P. B.; Berrios, D. C.; Gurram, M. M.; Hashim, J. C. M.; Raghunandan, S.; Lin, S. Y.; Le, T. Q.; Heher, D. M.; Thai, H. T.; Welch, J. D.; Caldwell, S. M.; Stotzky, O. G.; Skidmore, M. G.

    2016-01-01

    The GeneLab project is a science initiative to maximize the scientific return of omics data collected from spaceflight and from ground simulations of microgravity and radiation experiments, supported by a data system for a public bioinformatics repository and collaborative analysis tools for these data. The mission of GeneLab is to maximize the utilization of the valuable biological research resources aboard the ISS by collecting genomic, transcriptomic, proteomic and metabolomic (so-called omics) data to enable the exploration of the molecular network responses of terrestrial biology to space environments using a systems biology approach. All GeneLab data are made available to a worldwide network of researchers through its open-access data system. GeneLab is currently being developed by NASA to support Open Science biomedical research in order to enable the human exploration of space and improve life on earth. Open access to Phase 1 of the GeneLab Data Systems (GLDS) was implemented in April 2015. Download volumes have grown steadily, mirroring the growth in curated space biology research data sets (61 as of June 2016), now exceeding 10 TB/month, with over 10,000 file downloads since the start of Phase 1. For the period April 2015 to May 2016, most frequently downloaded were data from studies of Mus musculus (39) followed closely by Arabidopsis thaliana (30), with the remaining downloads roughly equally split across 12 other organisms (each 10 of total downloads). GLDS Phase 2 is focusing on interoperability, supporting data federation, including integrated search capabilities, of GLDS-housed data sets with external data sources, such as gene expression data from NIHNCBIs Gene Expression Omnibus (GEO), proteomic data from EBIs PRIDE system, and metagenomic data from Argonne National Laboratory's MG-RAST. GEO and MG-RAST employ specifications for investigation metadata that are different from those used by the GLDS and PRIDE (e.g., ISA-Tab). The GLDS Phase 2 system

  9. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    Science.gov (United States)

    Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

    2016-06-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  10. An informatics-based analysis of developments to date and prospects for the application of microalgae in the biological sequestration of industrial flue gas.

    Science.gov (United States)

    Zhu, Xi; Rong, Junfeng; Chen, Hui; He, Chenliu; Hu, Wensheng; Wang, Qiang

    2016-03-01

    The excessive emission of flue gas contributes to air pollution, abnormal climate change, global warming, and sea level rises associated with glacial melting. With the ability to utilize NOx as a nitrogen source and to convert solar energy into chemical energy via CO2 fixation, microalgae can potentially reduce air pollution and relax global warming, while also enhancing biomass and biofuel production as well as the production of high-value-added products. This informatics-based review analyzes the trends in the related literature and in patent activity to draw conclusions and to offer a prospective view on the developments of microalgae for industrial flue gas biosequestration. It is revealed that in recent years, microalgal research for industrial flue gas biosequestration has started to attract increasing attention and has now developed into a hot research topic, although it is still at a relatively early stage, and needs more financial and policy support in order to better understand microalgae and to develop an economically viable process. In comparison with onsite microalgal CO2 capture, microalgae-based biological DeNOx appears to be a more realistic and attractive alternative that could be applied to NOx treatment.

  11. A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks

    Directory of Open Access Journals (Sweden)

    Thomas eEissing

    2011-02-01

    Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

  12. A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks.

    Science.gov (United States)

    Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

    2011-01-01

    Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim(®) and MoBi(®) capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug, or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

  13. 'Integrative Physiology 2.0': Integration of systems biology into physiology and its application to cardiovascular homeostasis

    NARCIS (Netherlands)

    D.W.D. Kuster (Diederik); D. Merkus (Daphne); J. van der Velden (Jolanda); A.J.M. Verhoeven (Adrie); D.J.G.M. Duncker (Dirk)

    2011-01-01

    textabstractSince the completion of the Human Genome Project and the advent of the large scaled unbiased '-omics' techniques, the field of systems biology has emerged. Systems biology aims to move away from the traditional reductionist molecular approach, which focused on understanding the role of s

  14. Integrating writing into an introductory environmental science curriculum: Perspectives from biology and physics

    Science.gov (United States)

    Selkin, P. A.; Cline, E. T.; Beaufort, A.

    2008-12-01

    In the University of Washington, Tacoma's Environmental Science program, we are implementing a curriculum-wide, scaffolded strategy to teach scientific writing. Writing in an introductory science course is a powerful means to make students feel part of the scientific community, an important goal in our environmental science curriculum. Writing is already an important component of the UW Tacoma environmental science program at the upper levels: our approach is designed to prepare students for the writing-intensive junior- and senior-level seminars. The approach is currently being tested in introductory biology and physics before it is incorporated in the rest of the introductory environmental science curriculum. The centerpiece of our approach is a set of research and writing assignments woven throughout the biology and physics course sequences. The assignments progress in their degree of complexity and freedom through the sequence of introductory science courses. Each assignment is supported by a number of worksheets and short written exercises designed to teach writing and critical thought skills. The worksheets are focused on skills identified both by research in science writing and the instructors' experience with student writing. Students see the assignments as a way to personalize their understanding of basic science concepts, and to think critically about ideas that interest them. We find that these assignments provide a good way to assess student comprehension of some of the more difficult ideas in the basic sciences, as well as a means to engage students with the challenging concepts of introductory science courses. Our experience designing these courses can inform efforts to integrate writing throughout a geoscience or environmental science curriculum, as opposed to on a course-by-course basis.

  15. Fungal biological control agents for integrated management of Culicoides spp. (Diptera: Ceratopogonidae of livestock

    Directory of Open Access Journals (Sweden)

    B. W. Narladkar

    2015-02-01

    Full Text Available Aim: Entomopathogenic fungi Metarhizium anisopliae and Beauveria bassiana had wide host range against insects and hence these are being exploited as fungal bio-pesticide on a large scale. Both fungi are proved pesticides against many crop pests and farmers are well acquainted with their use on the field. Thus, research was aimed to explore the potency of these fungal spores against larval and adult Culicoides midges, a pest of livestock. Materials and Methods: In-vitro testing of both fungal biological control agents was undertaken in Petri dishes against field collected Culicoides larvae, while in plastic beakers against field collected blood-engorged female Culicoides midges. In-vivo testing was undertaken by spraying requisite concentration of fungal spores on the drainage channel against larvae and resting sites of adult Culicoides midges in the cattle shed. Lethal concentration 50 (LC50 values and regression equations were drawn by following probit analysis using SPSS statistical computerized program. Results: The results of this study revealed LC50 values of 2692 mg and 3837 mg (108 cfu/g for B. bassiana and M. anisopliae, respectively, against Culicoides spp. larvae. Death of Culicoides larvae due to B. bassiana showed greenish coloration in the middle of the body with head and tail showed intense blackish changes, while infection of M. anisopliae resulted in death of Culicoides larvae with greenish and blackish coloration of body along with total destruction, followed by desquamation of intestinal channel. The death of adult Culicoides midges were caused by both the fungi and after death growth of fungus were very well observed on the dead cadavers proving the efficacy of the fungus. Conclusion: Preliminary trials with both funguses (M. anisopliae, B. bassiana showed encouraging results against larvae and adults of Culicoides spp. Hence, it was ascertained that, these two fungal molecules can form a part of biological control and

  16. BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies

    Directory of Open Access Journals (Sweden)

    Ponomarenko Julia

    2011-01-01

    Full Text Available Abstract Background Understanding of immune response mechanisms of pathogen-infected host requires multi-scale analysis of genome-wide data. Data integration methods have proved useful to the study of biological processes in model organisms, but their systematic application to the study of host immune system response to a pathogen and human disease is still in the initial stage. Results To study host-pathogen interaction on the systems biology level, an extension to the previously described BiologicalNetworks system is proposed. The developed methods and data integration and querying tools allow simplifying and streamlining the process of integration of diverse experimental data types, including molecular interactions and phylogenetic classifications, genomic sequences and protein structure information, gene expression and virulence data for pathogen-related studies. The data can be integrated from the databases and user's files for both public and private use. Conclusions The developed system can be used for the systems-level analysis of host-pathogen interactions, including host molecular pathways that are induced/repressed during the infections, co-expressed genes, and conserved transcription factor binding sites. Previously unknown to be associated with the influenza infection genes were identified and suggested for further investigation as potential drug targets. Developed methods and data are available through the Java application (from BiologicalNetworks program at http://www.biologicalnetworks.org and web interface (at http://flu.sdsc.edu.

  17. Water as Life, Death, and Power: Building an Integrated Interdisciplinary Course Combining Perspectives from Anthropology, Biology, and Chemistry

    Science.gov (United States)

    Willermet, Cathy; Mueller, Anja; Juris, Stephen J.; Drake, Eron; Upadhaya, Samik; Chhetri, Pratik

    2013-01-01

    In response to a request from a campus student organization, faculty from three fields came together to develop and teach an integrated interdisciplinary course on water issues and social activism. This course, "Water as Life, Death, and Power", brought together topics from the fields of anthropology, biology and chemistry to explore…

  18. Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA (ACS Fall meeting)

    Science.gov (United States)

    Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intent...

  19. Integrating the Agents of Bioterrorism into the General Biology Curriculum: II. Mode of Action of the Biological Agents.

    Science.gov (United States)

    Pommerville, Jeffrey C.

    2003-01-01

    Integrates bioterrorism into the science curriculum and explains actions against serious agents such as anthrax, plague, smallpox, botulinum toxin, and ricin toxin. Uses the learning cycle as the instructional tool which is student-centered and has three phases that include exploring, explaining, and extending. (Contains 24 references.) (YDS)

  20. Single beam optical trapping integrated in a confocal microscope for biological applications.

    Science.gov (United States)

    Visscher, K; Brakenhoff, G J

    1991-01-01

    Confocal microscopy is very useful in biology because of its three dimensional imaging capacities and has proven to be an excellent tool to study the 3D organization of, for instance, cell structures. This property of confocal microscopy makes it also very suitable for observation during guidance of the three dimensional manipulation of single cells or cell elements. Therefore we decided to integrate a confocal microscope and a single beam optical manipulator into a single instrument. The advantage of optical manipulation over mechanical techniques is that it is non-invasive and therefore may be applied on living (micro-) organisms and cells. The creation of an effective single beam optical trap requires the use of a high numerical aperture (N.A.) objective to focus the laser beam. In this paper we briefly discuss the vertical or axial force exerted on a sphere in a single beam trap. The axial force on a sphere placed on the optical axis, caused by reflection and refraction, is calculated applying a electromagnetic vector diffraction theory to determine the field distribution in the focal region. One of the results is that the particle also experiences a vertical trapping force towards the focusing lens when it is in the strongly convergent part of the field in addition to the known negative signed trapping force in the divergent part of the field. Further we describe an instrumental approach to realize optical trapping in which the optical trap position is controlled by moving the focusing objective only.(ABSTRACT TRUNCATED AT 250 WORDS)

  1. 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.

  2. Application of integrated ozone biological aerated filters and membrane filtration in water reuse of textile effluents.

    Science.gov (United States)

    He, Yaozhong; Wang, Xiaojun; Xu, Jinling; Yan, Jinli; Ge, Qilong; Gu, Xiaoyang; Jian, Lei

    2013-04-01

    A combined process including integrated ozone-BAFs (ozone biological aerated filters) and membrane filtration was first applied for recycling textile effluents in a cotton textile mill with capacity of 5000 m(3)/d. Influent COD (chemical oxygen demand) in the range of 82-120 mg/L, BOD5 (5-day biochemical oxygen demand) of 12.6-23.1 mg/L, suspended solids (SSs) of 38-52 mg/L and color of 32-64° were observed during operation. Outflows with COD≤45 mg/L, BOD5≤7.6 mg/L, SS≤15 mg/L, color≤8° were obtained after being decontaminated by ozone-BAF with ozone dosage of 20-25 mg/L. Besides, the average removal rates of PVA (polyvinyl alcohol) and UV254 were 100% and 73.4% respectively. Permeate water produced by RO (reverse osmosis) could be reused in dyeing and finishing processes, while the RO concentrates could be discharged directly under local regulations with COD≤100 mg/L, BOD5≤21 mg/L, SS≤52 mg/L, color≤32°. Results showed that the combined process could guarantee water reuse with high quality, and solve the problem of RO concentrate disposal.

  3. Evolution of epithelial morphogenesis: phenotypic integration across multiple levels of biological organization

    Directory of Open Access Journals (Sweden)

    Thorsten eHorn

    2015-09-01

    Full Text Available Morphogenesis involves the dynamic reorganization of cell and tissue shapes to create the three-dimensional body. Intriguingly, different species have evolved different morphogenetic processes to achieve the same general outcomes during embryonic development. How are meaningful comparisons between species made, and where do the differences lie? In this Perspective, we argue that examining the evolution of embryonic morphogenesis requires the simultaneous consideration of different levels of biological organization: (1 genes, (2 cells, (3 tissues, and (4 the entire egg. To illustrate the importance of integrating these levels, we use the extraembryonic epithelia of insects – a lineage-specific innovation and evolutionary hotspot – as an exemplary case study. We discuss how recent functional data, primarily from RNAi experiments targeting the Hox3/ Zen and U-shaped group transcription factors, provide insights into developmental processes at all four levels. Comparisons of these data from several species both challenge and inform our understanding of homology, in assessing how the process of epithelial morphogenesis has itself evolved.

  4. Semantic data integration and knowledge management to represent biological network associations.

    Science.gov (United States)

    Losko, Sascha; Heumann, Klaus

    2009-01-01

    The vast quantities of information generated by academic and industrial research groups are reflected in a rapidly growing body of scientific literature and exponentially expanding resources of formalized data including experimental data from "-omics" platforms, phenotype information, and clinical data. For bioinformatics, several challenges remain: to structure this information as biological networks enabling scientists to identify relevant information; to integrate this information as specific "knowledge bases"; and to formalize this knowledge across multiple scientific domains to facilitate hypothesis generation and validation and, thus, the generation of new knowledge. Risk management in drug discovery and clinical research is used as a typical example to illustrate this approach. In this chapter we will introduce techniques and concepts (such as ontologies, semantic objects, typed relationships, contexts, graphs, and information layers) that are used to represent complex biomedical networks. The BioXM Knowledge Management Environment is used as an example to demonstrate how a domain such as oncology is represented and how this representation is utilized for research.

  5. Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.

    Science.gov (United States)

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology.

  6. A metatheory integrating social, biological and technological factors in information behavior research

    Directory of Open Access Journals (Sweden)

    Leon James

    2014-06-01

    Full Text Available A metatheory is presented and diagrammed as an integrated conceptual framework for information seeking and use. It represents the symbiotic relationship between users and the technological environment. Receiving and adapting to information is achieved through each user’s biological satisficing procedures defined by group information practices, namely, noticing information, appraising it and evaluating it. Information use is achieved through optimizing procedures, namely, activating goal-setting intentions, constructing a plan and executing it through acting upon the technological environment to attain one’s goals. Evidence is given by listing a variety of information seeking behaviors that others have identified in their review of the literature, then showing how each element fits within the model, as well as by analyzing the interpretive discourse of college students while engaged in carrying out assigned information tasks. Each discourse segment in the samples was categorized as either an affective, cognitive or sensorimotor procedure carried out by the user, and transcribed as a string or sequence. This code sequence was then compared with the sequence produced when the model’s mapping is followed. Every discourse sample inspected contained the six categories specified by the model. The metatheory is suitable for providing a common framework for discussing various areas of information behavior research.

  7. A Biophysicochemical Model for NO Removal by the Chemical Absorption-Biological Reduction Integrated Process.

    Science.gov (United States)

    Zhao, Jingkai; Xia, Yinfeng; Li, Meifang; Li, Sujing; Li, Wei; Zhang, Shihan

    2016-08-16

    The chemical absorption-biological reduction (CABR) integrated process is regarded as a promising technology for NOx removal from flue gas. To advance the scale-up of the CABR process, a mathematic model based on mass transfer with reaction in the gas, liquid, and biofilm was developed to simulate and predict the NOx removal by the CABR system in a biotrickling filter. The developed model was validated by the experimental results and subsequently was used to predict the system performance under different operating conditions, such as NO and O2 concentration and gas and liquid flow rate. NO distribution in the gas phase along the biotrickling filter was also modeled and predicted. On the basis of the modeling results, the liquid flow rate and total iron concentration were optimized to achieve >90% NO removal efficiency. Furthermore, sensitivity analysis of the model revealed that the performance of the CABR process was controlled by the bioreduction activity of Fe(III)EDTA. This work will provide the guideline for the design and operation of the CABR process in the industrial application.

  8. An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates.

    Science.gov (United States)

    Hawley, Robert G; Chen, Yuzhong; Riz, Irene; Zeng, Chen

    2012-05-04

    In this study, we utilized an integrated bioinformatics and computational biology approach in search of new BH3-only proteins belonging to the BCL2 family of apoptotic regulators. The BH3 (BCL2 homology 3) domain mediates specific binding interactions among various BCL2 family members. It is composed of an amphipathic α-helical region of approximately 13 residues that has only a few amino acids that are highly conserved across all members. Using a generalized motif, we performed a genome-wide search for novel BH3-containing proteins in the NCBI Consensus Coding Sequence (CCDS) database. In addition to known pro-apoptotic BH3-only proteins, 197 proteins were recovered that satisfied the search criteria. These were categorized according to α-helical content and predictive binding to BCL-xL (encoded by BCL2L1) and MCL-1, two representative anti-apoptotic BCL2 family members, using position-specific scoring matrix models. Notably, the list is enriched for proteins associated with autophagy as well as a broad spectrum of cellular stress responses such as endoplasmic reticulum stress, oxidative stress, antiviral defense, and the DNA damage response. Several potential novel BH3-containing proteins are highlighted. In particular, the analysis strongly suggests that the apoptosis inhibitor and DNA damage response regulator, AVEN, which was originally isolated as a BCL-xL-interacting protein, is a functional BH3-only protein representing a distinct subclass of BCL2 family members.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hazen, Terry C.

    2008-08-12

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

  10. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics.

    Science.gov (United States)

    Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F X

    2004-01-01

    Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db.

  11. Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach

    Science.gov (United States)

    Wright, Megan H.; Clough, Barbara; Rackham, Mark D.; Rangachari, Kaveri; Brannigan, James A.; Grainger, Munira; Moss, David K.; Bottrill, Andrew R.; Heal, William P.; Broncel, Malgorzata; Serwa, Remigiusz A.; Brady, Declan; Mann, David J.; Leatherbarrow, Robin J.; Tewari, Rita; Wilkinson, Anthony J.; Holder, Anthony A.; Tate, Edward W.

    2014-02-01

    Malaria is an infectious disease caused by parasites of the genus Plasmodium, which leads to approximately one million deaths per annum worldwide. Chemical validation of new antimalarial targets is urgently required in view of rising resistance to current drugs. One such putative target is the enzyme N-myristoyltransferase, which catalyses the attachment of the fatty acid myristate to protein substrates (N-myristoylation). Here, we report an integrated chemical biology approach to explore protein myristoylation in the major human parasite P. falciparum, combining chemical proteomic tools for identification of the myristoylated and glycosylphosphatidylinositol-anchored proteome with selective small-molecule N-myristoyltransferase inhibitors. We demonstrate that N-myristoyltransferase is an essential and chemically tractable target in malaria parasites both in vitro and in vivo, and show that selective inhibition of N-myristoylation leads to catastrophic and irreversible failure to assemble the inner membrane complex, a critical subcellular organelle in the parasite life cycle. Our studies provide the basis for the development of new antimalarials targeting N-myristoyltransferase.

  12. Biospheric Life Support - integrating biological regeneration into protection of humans in space.

    Science.gov (United States)

    Rocha, Mauricio; Iha, Koshun

    2016-07-01

    A biosphere stands for a set of biomes (regional biological communities) interacting in a materially closed (though energetically open) ecological system (CES). Earth's biosphere, the thin layer of life on the planet's surface, can be seen as a natural CES- where life "consumables" are regenerated/restored via biological, geological and chemical processes. In Life Sciences, artificial CESs- local ecosystems extracts with varying scales and degrees of closure, are considered convenient/representatives objects of study. For outer space, these concepts have been applied to the issue of life support- a significant consideration as long as distance from Earth increases. In the nineties, growing on the Russian expertise on biological life support, backed by a multidisciplinary science team, the famous Biosphere 2 appeared. That private project innovated, by assembling a set of Earth biomes samples- plus an organic ag one, inside a closed Mars base-like structure, next to 1.5 ha under glass, in Arizona, US. The crew of 8 inside completed their two years contract, though facing setbacks- the system failed, e.g., to produce enough food/air supplies. But their "failures"- if this word can be fairly applied to science endeavors, were as meaningful as their achievements for the future of life support systems (LSS) research. By this period, the Russians had accumulated experience in extended orbital stays, achieving biological outcomes inside their stations- e.g. complete wheat cycles. After reaching the Moon, the US administration decided to change national priorities, putting the space program as part of a "détente" policy, to relieve international tensions. Alongside the US space shuttle program, the Russians were invited to join the new International Space Station (ISS), bringing to that pragmatic project, also their physical/chemical LSS- top air/water regenerative technology at the time. Present US policy keeps the ISS operational, extending its service past its planned

  13. Multilevel integrative analyses of human behavior: social neuroscience and the complementing nature of social and biological approaches.

    Science.gov (United States)

    Cacioppo, J T; Berntson, G G; Sheridan, J F; McClintock, M K

    2000-11-01

    Social and biological explanations traditionally have been cast as incompatible, but advances in recent years have revealed a new view synthesized from these 2 very different levels of analysis. The authors review evidence underscoring the complementing nature of social and biological levels of analysis and how the 2 together can foster understanding of the mechanisms underlying complex behavior and the mind. Specifically, they review the utility of considering social influences on biological processes that are often viewed as outside the social domain including genetic constitution, gene expression, disease, and autonomic, neuroendocrine, and immune activity. This research underscores the unity of psychology and the importance of retaining multilevel integrative research that spans molar and molecular levels of analysis. Especially needed in the coming years is more research on the mechanisms linking social and biological events and processes.

  14. A novel integration of three-dimensional electro-Fenton and biological activated carbon and its application in the advanced treatment of biologically pretreated Lurgi coal gasification wastewater.

    Science.gov (United States)

    Hou, Baolin; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Jia, Shengyong; Li, Kun

    2015-11-01

    A novel integrated process with three-dimensional electro-Fenton (3D EF) and biological activated carbon (BAC) was employed in advanced treatment of biologically pretreated Lurgi coal gasification wastewater. SAC-Fe (sludge deserved activated carbon from sewage and iron sludge) and SAC (sludge deserved activated carbon) were used in 3D EF as catalytic particle electrodes (CPEs) and in BAC as carriers respectively. Results indicated that 3D EF with SAC-Fe as CPEs represented excellent pollutants and COLOR removals as well as biodegradability improvement. The efficiency enhancement attributed to generating more H2O2 and OH. The integrated process exhibited efficient performance of COD, BOD5, total phenols, TOC, TN and COLOR removals at a much shorter retention time, with the corresponding concentrations in effluent of 31.18, 6.69, 4.29, 17.82, 13.88mg/L and <20 times, allowing discharge criteria to be met. The integrated system was efficient, cost-effective and ecological sustainable and could be a promising technology for engineering applications.

  15. Integration of an innovative biological treatment with physical or chemical disinfection for wastewater reuse

    Energy Technology Data Exchange (ETDEWEB)

    De Sanctis, Marco, E-mail: marco.desanctis@ba.irsa.cnr.it [Water Research Institute, CNR, Via F. De Blasio 5, 70123 Bari (Italy); Del Moro, Guido [Water Research Institute, CNR, Via F. De Blasio 5, 70123 Bari (Italy); Levantesi, Caterina; Luprano, Maria Laura [Water Research Institute, CNR, Via Salaria Km 29.600, 00015 Monterotondo, RM (Italy); Di Iaconi, Claudio [Water Research Institute, CNR, Via F. De Blasio 5, 70123 Bari (Italy)

    2016-02-01

    In the present paper, the effectiveness of a Sequencing Batch Biofilter Granular Reactor (SBBGR) and its integration with different disinfection strategies (UV irradiation, peracetic acid) for producing an effluent suitable for agricultural use was evaluated. The plant treated raw domestic sewage, and its performances were evaluated in terms of the removal efficiency of a wide group of physical, chemical and microbiological parameters. The SBBGR resulted really efficient in removing suspended solids, COD and nitrogen with an average effluent concentration of 5, 32 and 10 mg/L, respectively. Lower removal efficiency was observed for phosphorus with an average concentration in the effluent of 3 mg/L. Plant effluent was also characterized by an average electrical conductivity and sodium adsorption ratio of 680 μS/cm and 2.9, respectively. Therefore, according to these gross parameters, the SBBGR effluent was conformed to the national standards required in Italy for agricultural reuse. Moreover, disinfection performances of the SBBGR was higher than that of conventional municipal wastewater treatment plants and met the quality criteria suggested by WHO (Escherichia coli < 1000 CFU/100 mL) for agricultural reuse. In particular, the biological treatment by SBBGR removed 3.8 ± 0.4 log units of Giardia lamblia, 2.8 ± 0.8 log units of E. coli, 2.5 ± 0.7 log units of total coliforms, 2.0 ± 0.3 log units of Clostridium perfringens, 2.0 ± 0.4 log units of Cryptosporidium parvum and 1.7 ± 0.7 log units of Somatic coliphages. The investigated disinfection processes (UV and peracetic acid) resulted very effective for total coliforms, E. coli and somatic coliphages. In particular, a UV radiation and peracetic acid doses of 40 mJ/cm{sup 2} and 1 mg/L respectively reduced E. coli content in the effluent below the limit for agricultural reuse in Italy (10 CFU/100 mL). Conversely, they were both ineffective on C.perfringens spores. - Highlights: • SBBGR system showed high

  16. Development of Two Color Fluorescent Imager and Integrated Fluidic System for Nanosatellite Biology Applications

    Science.gov (United States)

    Wu, Diana Terri; Ricco, Antonio Joseph; Lera, Matthew P.; Timucin, Linda R.; Parra, Macarena P.

    2012-01-01

    Nanosatellites offer frequent, low-cost space access as secondary payloads on launches of larger conventional satellites. We summarize the payload science and technology of the Microsatellite in-situ Space Technologies (MisST) nanosatellite for conducting automated biological experiments. The payload (two fused 10-cm cubes) includes 1) an integrated fluidics system that maintains organism viability and supports growth and 2) a fixed-focus imager with fluorescence and scattered-light imaging capabilities. The payload monitors temperature, pressure and relative humidity, and actively controls temperature. C. elegans (nematode, 50 m diameter x 1 mm long) was selected as a model organism due to previous space science experience, its completely sequenced genome, size, hardiness, and the variety of strains available. Three strains were chosen: two green GFP-tagged strains and one red tdTomato-tagged strain that label intestinal, nerve, and pharyngeal cells, respectively. The integrated fluidics system includes bioanalytical and reservoir modules. The former consists of four 150 L culture wells and a 4x5 mm imaging zone the latter includes two 8 mL fluid reservoirs for reagent and waste storage. The fluidic system is fabricated using multilayer polymer rapid prototyping: laser cutting, precision machining, die cutting, and pressure-sensitive adhesives it also includes eight solenoid-operated valves and one mini peristaltic pump. Young larval-state (L2) nematodes are loaded in C. elegans Maintenance Media (CeMM) in the bioanalytical module during pre-launch assembly. By the time orbit is established, the worms have grown to sufficient density to be imaged and are fed fresh CeMM. The strains are pumped sequentially into the imaging area, imaged, then pumped into waste. Reagent storage utilizes polymer bags under slight pressure to prevent bubble formation in wells or channels. The optical system images green and red fluorescence bands by excitation with blue (473 nm peak

  17. Reviews and synthesis: Carbon capture and storage monitoring - an integrated biological, biophysical and chemical approach

    Science.gov (United States)

    Hicks, N.; Vik, U.; Taylor, P.; Ladoukakis, E.; Park, J.; Kolisis, F.; Stahl, H.; Jakobsen, K. S.

    2015-06-01

    Carbon capture and storage (CCS) is a developing technology that seeks to mitigate against the impact of increasing anthropogenic carbon dioxide (CO2) production by capturing CO2 from large point source emitters. After capture the CO2 is compressed and transported to a reservoir where it is stored for geological time scales. Potential leakages from CCS projects, where stored CO2 migrates through the overlaying sediments, are likely to have severe implications on benthic and marine ecosystems. Nonetheless, prokaryotic response to elevated CO2 concentrations has been suggested as one of the first detectable warnings if a CO2 leakage should occur. Applying properties of prokaryotic communities (i.e. community composition and metabolic status) as a novel CO2 monitoring application is highly reliable within a multidisciplinary framework, where deviations from the baseline can easily be identified. In this paper we review current knowledge about the impact of CO2 leakages on marine sediments from a multidisciplinary-based monitoring perspective. We focus on aspects from the fields of biology, geophysics, and chemistry, and discuss a case study example. We argue the importance of an integrative multidisciplinary approach, incorporating biogeochemistry, geophysics, microbial ecology and modelling, with a particular emphasis on metagenomic techniques and novel bioinformatics, for future CCS monitoring. Within this framework, we consider that an effective CCS monitoring programme will ensure that large-scale leakages with potentially devastating effects for the overlaying ecosystem are avoided. Furthermore, the multidisciplinary approach suggested here for CCS monitoring is generic, and can be adapted to other systems of interest.

  18. Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of catalytic ultrasound oxidation and membrane bioreactor.

    Science.gov (United States)

    Jia, Shengyong; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Hou, Baolin

    2015-01-01

    Laboratorial scale experiments were conducted to investigate a novel system integrating catalytic ultrasound oxidation (CUO) with membrane bioreactor (CUO-MBR) on advanced treatment of biologically pretreated coal gasification wastewater. Results indicated that CUO with catalyst of FeOx/SBAC (sewage sludge based activated carbon (SBAC) which loaded Fe oxides) represented high efficiencies in eliminating TOC as well as improving the biodegradability. The integrated CUO-MBR system with low energy intensity and high frequency was more effective in eliminating COD, BOD5, TOC and reducing transmembrane pressure than either conventional MBR or ultrasound oxidation integrated MBR. The enhanced hydroxyl radical oxidation, facilitation of substrate diffusion and improvement of cell enzyme secretion were the mechanisms for CUO-MBR performance. Therefore, the integrated CUO-MBR was the promising technology for advanced treatment in engineering applications.

  19. Assessment of The Biological Integrity of The Native Vegetative Community In A Surface Flow Constructed Wetland Treating Industrial Park Contaminants

    Directory of Open Access Journals (Sweden)

    C. C. Galbrand

    2007-01-01

    Full Text Available A study was conducted to evaluate the biological integrity of a constructed wetland receiving landfill leachate and stormwater runoff from the Burnside Industrial Park, Dartmouth, Nova Scotia. The biological integrity of the constructed wetland was tested in the second growing season using vegetative community monitoring. The metrics analyzed were species diversity, species heterogeneity (dominance and exotic/invasive species abundance. There was no significant difference in the plant species diversity between the constructed wetland and the reference site. However, the constructed wetland supported a higher plant species richness than the reference site. The top three species in the constructed wetland were tweedy’s rush (Juncus brevicaudatus, soft rush (Juncus effusus and fowl mannagrass (Glyceria striata. In total, these three species occupied 46.4% of the sampled population. The top three species in the reference site were soft rush (Juncus effusus, sweetgale (Myrica gale and woolgrass (Scirpus cyperinus. In total, these three species occupied a more reasonable 32.6% of the sampled population. The reference site supported greater biological integrity as it had greater heterogeneity and a smaller abundance of exotic and invasive species compared to the constructed wetland (3.8% versus 10.7%. Although poor heterogeneity and the presence of weedy, exotic species can be a sign of degraded biological health and future problems, these are also common indicators of a system simply undergoing early succession. As the constructed wetland matures, its plant biodiversity may actually decrease, but its integrity, as measured by exotic and invasive species abundance as well as heterogeneity, is expected to increase, so long as invasive species present in the constructed wetland remain controlled through weeding during the first few growing seasons.

  20. ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web

    OpenAIRE

    Geoffrey Fucile; David Di Biase; Hardeep Nahal; Garon La; Shokoufeh Khodabandeh; Yani Chen; Kante Easley; Dinesh Christendat; Lawrence Kelley; Provart, Nicholas J.

    2011-01-01

    Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide we...

  1. Finding Clarity by Fostering Confusion: Reflections on Teaching an Undergraduate Integrated Biological Systems Course

    Science.gov (United States)

    Martin, Kirsten H.

    2015-01-01

    Undergraduate biology programs in smaller liberal arts colleges are increasingly becoming focused on health science fields. This narrowing of focus potentially decreases opportunities for these students to explore other sub-fields of biology. This perspectives article highlights how one small university in Connecticut decided to institute a…

  2. A Course in Biophysics: An Integration of Physics, Chemistry, and Biology

    Science.gov (United States)

    Giancoli, Douglas C.

    1971-01-01

    Describes an interdisciplinary course for advanced undergraduates in the physical and biological sciences. The goal is to understand a living cell from the most basic standpoint possible. The ideas of physics, chemistry, and molecular biology are all essential to the course, which leads to a unified view of the sciences. (PR)

  3. Using dual classifications in the development of avian wetland indices of biological integrity for wetlands in West Virginia, USA.

    Science.gov (United States)

    Veselka, Walter; Anderson, James T; Kordek, Walter S

    2010-05-01

    Considerable resources are being used to develop and implement bioassessment methods for wetlands to ensure that "biological integrity" is maintained under the United States Clean Water Act. Previous research has demonstrated that avian composition is susceptible to human impairments at multiple spatial scales. Using a site-specific disturbance gradient, we built avian wetland indices of biological integrity (AW-IBI) specific to two wetland classification schemes, one based on vegetative structure and the other based on the wetland's position in the landscape and sources of water. The resulting class-specific AW-IBI was comprised of one to four metrics that varied in their sensitivity to the disturbance gradient. Some of these metrics were specific to only one of the classification schemes, whereas others could discriminate varying levels of disturbance regardless of classification scheme. Overall, all of the derived biological indices specific to the vegetative structure-based classes of wetlands had a significant relation with the disturbance gradient; however, the biological index derived for floodplain wetlands exhibited a more consistent response to a local disturbance gradient. We suspect that the consistency of this response is due to the inherent nature of the connectivity of available habitat in floodplain wetlands.

  4. Evaluating the informatics for integrating biology and the bedside system for clinical research

    Directory of Open Access Journals (Sweden)

    Meystre Stéphane M

    2009-10-01

    Full Text Available Abstract Background Selecting patient cohorts is a critical, iterative, and often time-consuming aspect of studies involving human subjects; informatics tools for helping streamline the process have been identified as important infrastructure components for enabling clinical and translational research. We describe the evaluation of a free and open source cohort selection tool from the Informatics for Integrating Biology and the Bedside (i2b2 group: the i2b2 hive. Methods Our evaluation included the usability and functionality of the i2b2 hive using several real world examples of research data requests received electronically at the University of Utah Health Sciences Center between 2006 - 2008. The hive server component and the visual query tool application were evaluated for their suitability as a cohort selection tool on the basis of the types of data elements requested, as well as the effort required to fulfill each research data request using the i2b2 hive alone. Results We found the i2b2 hive to be suitable for obtaining estimates of cohort sizes and generating research cohorts based on simple inclusion/exclusion criteria, which consisted of about 44% of the clinical research data requests sampled at our institution. Data requests that relied on post-coordinated clinical concepts, aggregate values of clinical findings, or temporal conditions in their inclusion/exclusion criteria could not be fulfilled using the i2b2 hive alone, and required one or more intermediate data steps in the form of pre- or post-processing, modifications to the hive metadata, etc. Conclusion The i2b2 hive was found to be a useful cohort-selection tool for fulfilling common types of requests for research data, and especially in the estimation of initial cohort sizes. For another institution that might want to use the i2b2 hive for clinical research, we recommend that the institution would need to have structured, coded clinical data and metadata available that can be

  5. Integrating the Agents of Bioterrorism into the General Biology Curriculum: 1. A Primer on Bioterrorism.

    Science.gov (United States)

    Pommerville, Jeffrey

    2002-01-01

    Reviews the history of and describes what biology educators should know about the topic of bioterrorism. Suggests materials that can be used to communicate more effectively with students and the community and prepare a classroom discussion on bioterrorism. (KHR)

  6. YeastMed: an XML-Based System for Biological Data Integration of Yeast

    CERN Document Server

    Briache, Abdelaali; Kerzazi, Amine; Navas-Delgado, Ismael; Montes, Jose F Aldana; Hassani, Badr D Rossi; Lairini, Khalid

    2010-01-01

    A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of biological data. SGD, Yeastract, CYGD-MIPS, BioGrid and PhosphoGrid are five of the most visited databases by the yeast community. These sources provide complementary data on biological entities. Biologists are brought systematically to query these data sources in order to analyse the results of their experiments. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned result is a complex and laborious task. To provide transparent and simultaneous access to these sources, we have developed a mediator-based system called YeastMed. In this paper, we present YeastMed focusing on its architecture.

  7. The functionality of biological knowledge in the workplace. Integrating school and workplace learning about reproduction

    NARCIS (Netherlands)

    Mazereeuw, M.

    2013-01-01

    This thesis reports on a design research project about a learning, supervising and teaching strategy to enable students in agricultural preparatory vocational secondary education (VMBO) to recognize the functionality of biological knowledge of reproduction in work placement sites. Although biologica

  8. A tale of two basins: An integrated physical and biological perspective of the deep Arctic Ocean

    Science.gov (United States)

    Bluhm, B. A.; Kosobokova, K. N.; Carmack, E. C.

    2015-12-01

    This review paper integrates the current knowledge, based on available literature, on the physical and biological conditions of the Amerasian and Eurasian basins (AB, EB) of the deep Arctic Ocean (AO) in a comparative fashion. The present day (Holocene) AO is a mediterranean sea that is roughly half continental shelf and half basin and ridge complex. Even more recently it is roughly two thirds seasonally and one third perennially ice-covered, thus now exposing a portion of basin waters to sunlight and wind. Basin boundaries and submarine ridges steer circulation pathways in overlying waters and limit free exchange in deeper waters. The AO is made integral to the global ocean by the Northern Hemisphere Thermohaline Circulation (NHTC) which drives Pacific-origin water (PW) through Bering Strait into the Canada Basin, and counter-flowing Atlantic-origin water (AW) through Fram Strait and across the Barents Sea into the Nansen Basin. As a framework for biogeography within the AO, four basic, large-scale circulation systems (with L > 1000 km) are noted; these are: (1) the large scale wind-driven circulation which forces the cyclonic Trans-Polar Drift from Siberia to the Fram Strait and the anticyclonic Beaufort Gyre in the southern Canada Basin; (2) the circulation of waters that comprise the halocline complex, composed largely of waters of Pacific and Atlantic origin that are modified during passage over the Bering/Chukchi and Barents/Siberian shelves, respectively; (3) the topographically-trapped Arctic Circumpolar Boundary Current (ACBC) which carries AW cyclonically around the boundaries of the entire suite of basins, and (4) the very slow exchange of Arctic Ocean Deep Waters. Within the basin domain two basic water mass assemblies are observed, the difference between them being the absence or presence of PW sandwiched between Arctic Surface Waters (ASW) above and the AW complex below; the boundary between these domains is the Atlantic/Pacific halocline front. Both

  9. Fort Collins Science Center- Policy Analysis and Science Assistance Branch : Integrating social, behavioral, economic and biological sciences

    Science.gov (United States)

    2010-01-01

    The Fort Collins Science Center's Policy Analysis and Science Assistance (PASA) Branch is a team of approximately 22 scientists, technicians, and graduate student researchers. PASA provides unique capabilities in the U.S. Geological Survey by leading projects that integrate social, behavioral, economic, and biological analyses in the context of human-natural resource interactions. Resource planners, managers, and policymakers in the U.S. Departments of the Interior (DOI) and Agriculture (USDA), State and local agencies, as well as international agencies use information from PASA studies to make informed natural resource management and policy decisions. PASA scientists' primary functions are to conduct both theoretical and applied social science research, provide technical assistance, and offer training to advance performance in policy relevant research areas. Management and research issues associated with human-resource interactions typically occur in a unique context, involve difficult to access populations, require knowledge of both natural/biological science in addition to social science, and require the skill to integrate multiple science disciplines. In response to these difficult contexts, PASA researchers apply traditional and state-of-the-art social science methods drawing from the fields of sociology, demography, economics, political science, communications, social-psychology, and applied industrial organization psychology. Social science methods work in concert with our rangeland/agricultural management, wildlife, ecology, and biology capabilities. The goal of PASA's research is to enhance natural resource management, agency functions, policies, and decision-making. Our research is organized into four broad areas of study.

  10. Workshop Report on the European Bone Sarcoma Networking Meeting: Integration of Clinical Trials with Tumor Biology.

    Science.gov (United States)

    Thomas, David M; Wilhelm, Miriam; Cleton-Jansen, Anne-Marie; Dirksen, Uta; Entz-Werlé, Natacha; Gelderblom, Hans; Hassan, Bass; Jürgens, Heribert; Koster, Jan; Kovar, Heinrich; Lankester, Arjan C; Lewis, Ian J; Myklebost, Ola; Nathrath, Michaela H M; Picci, Piero; Whelan, Jeremy S; Hogendoorn, Pancras C W; Bielack, Stefan S

    2011-09-01

    A key workshop was held in The Netherlands in June 2011, hosted by several European bone sarcoma networks and with a broad range of stakeholders from Europe and Australia. The purpose of the meeting was to identify the strengths and weaknesses in current clinical trials for bone sarcomas and to make recommendations as to how to accelerate progress in this field. Two areas of particular interest were discussed. First, all participants agreed upon the importance of tumor biology to understanding clinical responses for all types of bone sarcoma. Various barriers to biobanking tumor and germline specimens were canvassed and are outlined in this paper. Second, there was consideration of the particular challenges of dealing with adolescent and young adult cancers, exemplified by bone sarcomas. Participants recommended greater engagement of both pediatric and adult sarcoma trial organizations to address this issue. Specific opportunities were identified to develop biological sub-studies within osteosarcoma, focused on understanding germ line risk and pharmacogenomics defining toxicity and biological responses. In Ewing sarcoma, it was harder to define opportunities for biological insights. There was agreement that the results for insulin-like growth factor pathway inhibition in Ewing family tumors were disappointing, but represented a clear indication of the need for companion biologic studies to develop predictive biomarkers. The meeting ended with broad commitment to working together to make progress in this rare but important subgroup of cancers.

  11. Integration of Proteomics, Bioinformatics and Systems biology in Brain Injury Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    Joy eGuingab-Cagmat

    2013-05-01

    Full Text Available Traumatic brain injury (TBI is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed.

  12. 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.

  13. Design and control strategies for CELSS - Integrating mechanistic paradigms and biological complexities

    Science.gov (United States)

    Moore, B., III; Kaufmann, R.; Reinhold, C.

    1981-01-01

    Systems analysis and control theory consideration are given to simulations of both individual components and total systems, in order to develop a reliable control strategy for a Controlled Ecological Life Support System (CELSS) which includes complex biological components. Because of the numerous nonlinearities and tight coupling within the biological component, classical control theory may be inadequate and the statistical analysis of factorial experiments more useful. The range in control characteristics of particular species may simplify the overall task by providing an appropriate balance of stability and controllability to match species function in the overall design. The ultimate goal of this research is the coordination of biological and mechanical subsystems in order to achieve a self-supporting environment.

  14. A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

    Science.gov (United States)

    Price, S A; Schmitz, L

    2016-04-05

    Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart.

  15. Evolution of natural history information in the 21st century – developing an integrated framework for biological and geographical data

    Science.gov (United States)

    Reusser, Deborah A.; Lee, Henry

    2011-01-01

    Threats to marine and estuarine species operate over many spatial scales, from nutrient enrichment at the watershed/estuarine scale to invasive species and climate change at regional and global scales. To help address research questions across these scales, we provide here a standardized framework for a biogeographical information system containing queriable biological data that allows extraction of information on multiple species, across a variety of spatial scales based on species distributions, natural history attributes and habitat requirements. As scientists shift from research on localized impacts on individual species to regional and global scale threats, macroecological approaches of studying multiple species over broad geographical areas are becoming increasingly important. The standardized framework described here for capturing and integrating biological and geographical data is a critical first step towards addressing these macroecological questions and we urge organizations capturing biogeoinformatics data to consider adopting this framework.

  16. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

    DEFF Research Database (Denmark)

    Canelas, Andre B.; Harrison, Nicola; Fazio, Alessandro

    2010-01-01

    The field of systems biology is often held back by difficulties in obtaining comprehensive, high-quality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae,...

  17. Using Biocatalysis to Integrate Organic Chemistry into a Molecular Biology Laboratory Course

    Science.gov (United States)

    Beers, Mande; Archer, Crystal; Feske, Brent D.; Mateer, Scott C.

    2012-01-01

    Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We…

  18. Integration of Bioinformatics into an Undergraduate Biology Curriculum and the Impact on Development of Mathematical Skills

    Science.gov (United States)

    Wightman, Bruce; Hark, Amy T.

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this…

  19. Biodiesel and Integrated STEM: Vertical Alignment of High School Biology/Biochemistry and Chemistry

    Science.gov (United States)

    Burrows, Andrea C.; Breiner, Jonathan M.; Keiner, Jennifer; Behm, Chris

    2014-01-01

    This article explores the vertical alignment of two high school classes, biology and chemistry, around the core concept of biodiesel fuel production. High school teachers and university faculty members investigated biodiesel as it relates to societal impact through a National Science Foundation Research Experience for Teachers. Using an action…

  20. Using biocatalysis to integrate organic chemistry into a molecular biology laboratory course.

    Science.gov (United States)

    Beers, Mande; Archer, Crystal; Feske, Brent D; Mateer, Scott C

    2012-01-01

    Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We have developed an inquiry-based module that uses the mutagenesis of the yeast reductase, YDL124w, to study the bioorganic synthesis of the taxol side-chain, a pharmacologically important molecule. Using related structures, students identify regions they think will affect enzyme stereoselective, design and generate site-specific mutants, and then characterize the effect of these changes on enzyme activity. This laboratory activity gives our students experience, working in a scientific discipline outside of biology and exposes them to techniques and equipment they do not normally work with in a molecular biology course. These inter-disciplinary experiences not only show the relevance of other sciences to biology, but also give our students the ability to communicate more effectively with scientists outside their discipline.

  1. An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes with Molecular Mechanisms

    Science.gov (United States)

    Kudish, Philip; Schlag, Erin; Kaplinsky, Nicholas J.

    2015-01-01

    We developed a multi-week laboratory in which college-level introductory biology students investigate Mendel's stem length phenotype in peas. Students collect, analyze and interpret convergent evidence from molecular and physiological techniques. In weeks 1 and 2, students treat control and experimental plants with Gibberellic Acid (GA) to…

  2. Integration of biological control and transgenic insect protection for mitigation of mycotoxins in corn

    Science.gov (United States)

    Biological control is known to be effective in reducing aflatoxin contamination of corn and some transgenic corn hybrids incur greatly reduced damage from corn earworm (Helicoverpa zea). We conducted seven field trials over two years to test the hypothesis that transgenic insect protection and biol...

  3. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

    NARCIS (Netherlands)

    Canelas, A.B.; Harrison, N.; Fazio, A.; Zhang, J.; Pitkänen, J.P.; Brink, J. van den; Bakker, B.M.; Bogner, L.; Bouwman, J.; Castrillo, J.I.; Cankorur, A.; Chumnanpuen, P.; Daran-Lapujade, P.; Dikicioglu, D.; Eunen, K. van; Ewald, J.C.; Heijnen, J.J.; Kirdar, B.; Mattila, I.; Mensonides, F.I.; Niebel, A.; Penttilä, M.; Pronk, J.T.; Reuss, M.; Salusjärvi, L.; Sauer, U.; Sherman, D.; Siemann-Herzberg, M; Westerhoff, H.; Winde, J.de; Petranovic, D.; Oliver, S.G.; Workman, C.T.; Zamboni, N.; Nielsen, J.

    2010-01-01

    The field of systems biology is often held back by difficulties in obtaining comprehensive, high-quality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae, a

  4. Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

    Directory of Open Access Journals (Sweden)

    Resendis-Antonio Osbaldo

    2011-07-01

    Full Text Available Abstract Background Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to understanding the metabolic activity during bacterial nitrogen fixation. This undertaking is not trivial, and the development of computational methods useful in accomplishing an integrative, descriptive and predictive framework is a crucial issue to decoding the principles that regulated the metabolic activity of this biological process. Results In this work we present a systems biology description of the metabolic activity in bacterial nitrogen fixation. This was accomplished by an integrative analysis involving high-throughput data and constraint-based modeling to characterize the metabolic activity in Rhizobium etli bacteroids located at the root nodules of Phaseolus vulgaris (bean plant. Proteome and transcriptome technologies led us to identify 415 proteins and 689 up-regulated genes that orchestrate this biological process. Taking into account these data, we: 1 extended the metabolic reconstruction reported for R. etli; 2 simulated the metabolic activity during symbiotic nitrogen fixation; and 3 evaluated the in silico results in terms of bacteria phenotype. Notably, constraint-based modeling simulated nitrogen fixation activity in such a way that 76.83% of the enzymes and 69.48% of the genes were experimentally justified. Finally, to further assess the predictive scope of the computational model, gene deletion analysis was carried out on nine metabolic enzymes. Our model concluded that an altered metabolic activity on these enzymes induced

  5. Integrated, multi-scale, spatial-temporal cell biology--A next step in the post genomic era.

    Science.gov (United States)

    Horwitz, Rick

    2016-03-01

    New microscopic approaches, high-throughput imaging, and gene editing promise major new insights into cellular behaviors. When coupled with genomic and other 'omic information and "mined" for correlations and associations, a new breed of powerful and useful cellular models should emerge. These top down, coarse-grained, and statistical models, in turn, can be used to form hypotheses merging with fine-grained, bottom up mechanistic studies and models that are the back bone of cell biology. The goal of the Allen Institute for Cell Science is to develop the top down approach by developing a high throughput microscopy pipeline that is integrated with modeling, using gene edited hiPS cell lines in various physiological and pathological contexts. The output of these experiments and models will be an "animated" cell, capable of integrating and analyzing image data generated from experiments and models.

  6. Uncovering the Molecular Machinery of the Human Spindle-An Integration of Wet and Dry Systems Biology

    DEFF Research Database (Denmark)

    Rojas, Ana M.; Santamaria, Anna; Malik, Rainer

    2012-01-01

    The mitotic spindle is an essential molecular machine involved in cell division, whose composition has been studied extensively by detailed cellular biology, high-throughput proteomics, and RNA interference experiments. However, because of its dynamic organization and complex regulation it is dif....... Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system....... it is difficult to obtain a complete description of its molecular composition. We have implemented an integrated computational approach to characterize novel human spindle components and have analysed in detail the individual candidates predicted to be spindle proteins, as well as the network of predicted...... of interactions is still poorly characterised by experimental means and which are thought to influence the functionality of the mitotic spindle on a large scale. Our analyses suggest that we are still far from knowing the complete repertoire of functionally important components of the human spindle network...

  7. Integrating phenotypic data from electronic patient records with molecular level systems biology

    DEFF Research Database (Denmark)

    Brunak, Søren

    2011-01-01

    Electronic patient records remain a rather unexplored, but potentially rich data source for discovering correlations between diseases. We describe a general approach for gathering phenotypic descriptions of patients from medical records in a systematic and non-cohort dependent manner. By extracti...... Classification of Disease ontology and is therefore in principle language independent. As a use case we show how records from a Danish psychiatric hospital lead to the identification of disease correlations, which subsequently are mapped to systems biology frameworks....

  8. Integrated Pest Management of Aphis spiraecola (Hemiptera: Aphididae) in clementines: enhancing its biological control

    OpenAIRE

    GOMEZ MARCO, FRANCESC

    2016-01-01

    [EN] Aphis spiraecola Patch. (Hemiptera: Aphididae) is a key pest of clementines. Biological control of A. spiraecola is still poorly known and efforts were based on the use and conservation of parasitoids but it did not success. With all this said, the aims of this thesis were: i) to disentangle the reasons behind the low parasitism of A. spiraecola; ii) to determine when and how predators can control A. spiraecola populations; and, finally, iii) to evaluate whether a ground cover of Poaceae...

  9. BIOLOGY STUDENTS’ TEACHER OPINIONS ABOUT THE INTEGRATION OF ICT INTO THE LEARNING AND TEACHING PROCESS

    Directory of Open Access Journals (Sweden)

    Andreja Špernjak

    2014-05-01

    Full Text Available Biology laboratory work can be performed in various ways, even using information and communication technologies (ICT. Whether a teacher incorporates it into laboratory work is related to different factors, but educators can influence students’ beliefs about the value of ICT through their pedagogical practice. In our study, student teachers of biology gave opinions on how successfully university professors use ICT in the classroom, where they acquired most knowledge about ICT and their attitude towards using of ICT in laboratory work. Student teachers were critical about the knowledge and usage of ICT of university professors in class. During their student teachers mostly failed to acquire knowledge about ICT and practice in incorporating it into daily routines. These results will be presented to our university professors, at which time we will suggest how they could use ICT more effectively in daily practice because, on the one hand, they are responsible for students teacher attitudes and for the level of student teacher knowledge, while, on the others, they precipitate indirectly in forming the pupils’ attitudes and determining the level of the pupils’ knowledge of ICT. The study was done on 85 student teachers of biology. Attitudes toward ICT are statistically significant by gender.

  10. Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology.

    Science.gov (United States)

    Margaritelis, Nikos V; Cobley, James N; Paschalis, Vassilis; Veskoukis, Aristidis S; Theodorou, Anastasios A; Kyparos, Antonios; Nikolaidis, Michalis G

    2016-04-01

    The equivocal role of reactive species and redox signaling in exercise responses and adaptations is an example clearly showing the inadequacy of current redox biology research to shed light on fundamental biological processes in vivo. Part of the answer probably relies on the extreme complexity of the in vivo redox biology and the limitations of the currently applied methodological and experimental tools. We propose six fundamental principles that should be considered in future studies to mechanistically link reactive species production to exercise responses or adaptations: 1) identify and quantify the reactive species, 2) determine the potential signaling properties of the reactive species, 3) detect the sources of reactive species, 4) locate the domain modified and verify the (ir)reversibility of post-translational modifications, 5) establish causality between redox and physiological measurements, 6) use selective and targeted antioxidants. Fulfilling these principles requires an idealized human experimental setting, which is certainly a utopia. Thus, researchers should choose to satisfy those principles, which, based on scientific evidence, are most critical for their specific research question.

  11. Integration of physics and biology: synergistic undergraduate education for the 21st century.

    Science.gov (United States)

    Woodin, Terry; Vasaly, Helen; McBride, Duncan; White, Gary

    2013-06-01

    This is an exciting time to be a biologist. The advances in our field and the many opportunities to expand our horizons through interaction with other disciplines are intellectually stimulating. This is as true for people tasked with helping the field move forward through support of research and education projects that serve the nation's needs as for those carrying out that research and educating the next generation of biologists. So, it is a pleasure to contribute to this edition of CBE-Life Sciences Education. This column will cover three aspects of the interactions of physics and biology as seen from the viewpoint of four members of the Division of Undergraduate Education of the National Science Foundation. The first section places the material to follow in context. The second reviews some of the many interdisciplinary physics-biology projects we support. The third highlights mechanisms available for supporting new physics-biology undergraduate education projects based on ideas that arise, focusing on those needing and warranting outside support to come to fruition.

  12. Integrated Biological Warfare Technology Platform (IBWTP). Intelligent Software Supporting Situation Awareness, Response, and Operations

    Science.gov (United States)

    2007-01-01

    21 4.3.1. Existing Biosurveillance Systems .............................................................. 22 4.3.2. Automatic Integration...Expert Team Risk Assessment Emergency Plans Command Centers IPE – Intelligent Portal - IPE Interactive Knowledge Wall Presentation Collaboration...such as existing biosurveillance systems, information produced via technological approaches can be incorporated into IBWTP in a fairly transparent

  13. A Holistic Approach Including Biological and Geological Criteria for Integrative Management in Protected Areas

    Science.gov (United States)

    Peña, Lorena; Monge-Ganuzas, Manu; Onaindia, Miren; De Manuel, Beatriz Fernández; Mendia, Miren

    2017-02-01

    Biodiversity hotspots and geosites are indivisible parts of natural heritage. Therefore, an adequate spatial delimitation and understanding of both and their linkages are necessary in order to be able to establish conservation policies. Normally, biodiversity hotspots are a typical target for those policies but, generally, geosites are not taken into account. Thus, this paper aims to fill this gap by providing an easily replicable method for the identification and integration of the geosites and the biodiversity hotspots in a Network for Integrative Nature Conservation that highlights their linkages. The method here presented has been applied to Urdaibai Biosphere Reserve situated in southeastern of the Bay of Biscay. The obtained results indicate that some geosites that are not directly related with biodiversity hotspots remain unprotected. Thus, from the study carried out, it can be stated that we conserving just the biodiversity hotspots is not enough to conserve the whole natural heritage of a protected area, as some plots interesting due to their relevant geoheritage remain unprotected. Therefore, it is necessary to fully integrate geosites into the planning documents of protected areas as a part of an ecosystem approach. The ecosystem approach recognizes the integrity of abiotic and biotic elements in nature conservation policies. Moreover, the proposed framework and the innovative methodology can be used as an easy input to identify priority areas for conservation, to improve the protected areas conservation planning, and to demonstrate the linkages between biodiversity hotspots and geosites.

  14. Gene Detection in Complex Biological Media Using Semiconductor Nanorods within an Integrated Microfluidic Device.

    Science.gov (United States)

    Bi, Xinyan; Adriani, Giulia; Xu, Yang; Chakrabortty, Sabyasachi; Pastorin, Giorgia; Ho, Han Kiat; Ang, Wee Han; Chan, Yinthai

    2015-10-20

    The salient optical properties of highly luminescent semiconductor nanocrystals render them ideal fluorophores for clinical diagnostics, therapeutics, and highly sensitive biochip applications. Microfluidic systems allow miniaturization and integration of multiple biochemical processes in a single device and do not require sophisticated diagnostic tools. Herein, we describe a microfluidic system that integrates RNA extraction, reverse transcription to cDNA, amplification and detection within one integrated device to detect histidine decarboxylase (HDC) gene directly from human white blood cells samples. When anisotropic semiconductor nanorods (NRs) were used as the fluorescent probes, the detection limit was found to be 0.4 ng of total RNA, which was much lower than that obtained using spherical quantum dots (QDs) or organic dyes. This was attributed to the large action cross-section of NRs and their high probability of target capture in a pull-down detection scheme. The combination of large scale integrated microfluidics with highly fluorescent semiconductor NRs may find widespread utility in point-of-care devices and multitarget diagnostics.

  15. Impacts of agricultural land use on biological integrity: A causal analysis

    Science.gov (United States)

    Riseng, C.M.; Wiley, M.J.; Black, R.W.; Munn, M.D.

    2011-01-01

    Agricultural land use has often been linked to nutrient enrichment, habitat degradation, hydrologic alteration, and loss of biotic integrity in streams. The U.S. Geological Survey's National Water Quality Assessment Program sampled 226 stream sites located in eight agriculture-dominated study units across the United States to investigate the geographic variability and causes of agricultural impacts on stream biotic integrity. In this analysis we used structural equation modeling (SEM) to develop a national and set of regional causal models linking agricultural land use to measured instream conditions. We then examined the direct, indirect, and total effects of agriculture on biotic integrity as it acted through multiple water quality and habitat pathways. In our nation-wide model, cropland affected benthic communities by both altering structural habitats and by imposing water quality-related stresses. Regionspecific modeling demonstrated that geographic context altered the relative importance of causal pathways through which agricultural activities affected stream biotic integrity. Cropland had strong negative total effects on the invertebrate community in the national, Midwest, and Western models, but a very weak effect in the Eastern Coastal Plain model. In theWestern Arid and Eastern Coastal Plain study regions, cropland impacts were transmitted primarily through dissolved water quality contaminants, but in the Midwestern region, they were transmitted primarily through particulate components of water quality. Habitat effects were important in the Western Arid model, but negligible in the Midwest and Eastern Coastal Plain models. The relative effects of riparian forested wetlands also varied regionally, having positive effects on biotic integrity in the Eastern Coastal Plain andWestern Arid region models, but no statistically significant effect in the Midwest. These differences in response to cropland and riparian cover suggest that best management practices and

  16. Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

    Science.gov (United States)

    Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

    2007-12-11

    Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

  17. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

    Directory of Open Access Journals (Sweden)

    de los Reyes Benildo G

    2008-04-01

    Full Text Available Abstract Background Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths and depths, while databases contain biological information based on established facts or published data. Integrating these complementary datasets helps infer a mutually consistent transcriptional regulatory network (TRN with strong similarity to the structure of the underlying genetic regulatory modules. Decomposing the TRN into a small set of recurring regulatory patterns, called network motifs (NM, facilitates the inference. Identifying NMs defined by specific transcription factors (TF establishes the framework structure of a TRN and allows the inference of TF-target gene relationship. This paper introduces a computational framework for utilizing data from multiple sources to infer TF-target gene relationships on the basis of NMs. The data include time course gene expression profiles, genome-wide location analysis data, binding sequence data, and gene ontology (GO information. Results The proposed computational framework was tested using gene expression data associated with cell cycle progression in yeast. Among 800 cell cycle related genes, 85 were identified as candidate TFs and classified into four previously defined NMs. The NMs for a subset of TFs are obtained from literature. Support vector machine (SVM classifiers were used to estimate NMs for the remaining TFs. The potential downstream target genes for the TFs were clustered into 34 biologically significant groups. The relationships between TFs and potential target gene clusters were examined by training recurrent neural networks whose topologies mimic the NMs to which the TFs are classified. The identified relationships between TFs and gene clusters were evaluated using the following biological validation and statistical analyses: (1 Gene set enrichment

  18. Gene Selection Integrated with Biological Knowledge for Plant Stress Response Using Neighborhood System and Rough Set Theory.

    Science.gov (United States)

    Meng, Jun; Zhang, Jing; Luan, Yushi

    2015-01-01

    Mining knowledge from gene expression data is a hot research topic and direction of bioinformatics. Gene selection and sample classification are significant research trends, due to the large amount of genes and small size of samples in gene expression data. Rough set theory has been successfully applied to gene selection, as it can select attributes without redundancy. To improve the interpretability of the selected genes, some researchers introduced biological knowledge. In this paper, we first employ neighborhood system to deal directly with the new information table formed by integrating gene expression data with biological knowledge, which can simultaneously present the information in multiple perspectives and do not weaken the information of individual gene for selection and classification. Then, we give a novel framework for gene selection and propose a significant gene selection method based on this framework by employing reduction algorithm in rough set theory. The proposed method is applied to the analysis of plant stress response. Experimental results on three data sets show that the proposed method is effective, as it can select significant gene subsets without redundancy and achieve high classification accuracy. Biological analysis for the results shows that the interpretability is well.

  19. An Integrated Review of Psychological Stress in Parkinson’s Disease: Biological Mechanisms and Symptom and Health Outcomes

    Directory of Open Access Journals (Sweden)

    Kim Wieczorek Austin

    2016-01-01

    Full Text Available Parkinson’s disease (PD is characterized by complex symptoms and medication-induced motor complications that fluctuate in onset, severity, responsiveness to treatment, and disability. The unpredictable and debilitating nature of PD and the inability to halt or slow disease progression may result in psychological stress. Psychological stress may exacerbate biological mechanisms believed to contribute to neuronal loss in PD and lead to poorer symptom and health outcomes. The purpose of this integrated review is to summarize and appraise animal and human research studies focused on biological mechanisms, symptom, and health outcomes of psychological stress in PD. A search of the electronic databases PubMed/Medline and CINAHL from 1980 to the present using the key words Parkinson’s disease and stress, psychological stress, mental stress, and chronic stress resulted in 11 articles that met inclusion criteria. The results revealed significant associations between psychological stress and increased motor symptom severity and loss of dopamine-producing neurons in animal models of PD and between psychological stress and increased symptom severity and poorer health outcomes in human subjects with PD. Further research is needed to fully elucidate the underlying biological mechanisms responsible for these relationships, for the ultimate purpose of designing targeted interventions that may modify the disease trajectory.

  20. ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

    Science.gov (United States)

    Fucile, Geoffrey; Di Biase, David; Nahal, Hardeep; La, Garon; Khodabandeh, Shokoufeh; Chen, Yani; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence; Provart, Nicholas J

    2011-01-10

    Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).

  1. ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

    Directory of Open Access Journals (Sweden)

    Geoffrey Fucile

    Full Text Available Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org.

  2. The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.

    Science.gov (United States)

    Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J; Inzé, Dirk; Van de Peer, Yves

    2013-03-01

    Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.

  3. An integrated assessment of pollution and biological effects in flounder, mussels and sediment in the southern Baltic Sea coastal area.

    Science.gov (United States)

    Dabrowska, Henryka; Kopko, Orest; Lehtonen, Kari K; Lang, Thomas; Waszak, Ilona; Balode, Maija; Strode, Evita

    2017-02-01

    Organic and metal contaminants and biological effects were investigated in flounder, mussels, and sediments in the southern Baltic Sea coastal area in order to assess environmental quality status in that area. Four sites were selected, including two within the Gulf of Gdańsk (GoG). In biota and sediment at each site, DDTs dominated over PCBs and PBDEs were the least abundant among organic contaminants. Their concentrations decreased progressively outward from GoG. Among metal contaminants, the levels of Hg, Pb, and Cd were elevated in GoG. Biomarkers in flounder, EROD activity and DNA SB, showed moderate positive correlations with organic and metal contaminants. In flounder, the integrated biomarker index (IBR/n) presented a spatial trend coherent with chemical pollution index (CPI), but there was no clear spatial correspondence between IBR/n and CPI in mussels nor between sediment toxicity index (STI) and sediment CPI. The integrated assessment of contaminant and biological effect data against available assessment criteria indicated that in biota, the contaminant assessment thresholds were most often exceeded by CB-118, heptachlor, PBDE, and Hg (in the GoG sediments by p,p'-DDT, Hg and Cd), while of the biological determinants, the threshold was breeched by AChE activity in mussels in GoG. Applying the ICES/OSPAR traffic-light approach showed that of the 50 parameters assessed at each site, there were 18% of determinants in the red color category in the two GoG sites and 8% of determinants in the two sites outside GoG, which indicated that none of the four investigated sites attained good environmental status (GES).

  4. Metals and the integrity of a biological coating: the cuticle of mussel byssus.

    Science.gov (United States)

    Holten-Andersen, Niels; Mates, Thomas E; Toprak, Muhammet S; Stucky, Galen D; Zok, Frank W; Waite, J Herbert

    2009-04-09

    The cuticle of mussel byssal threads is a robust natural coating that combines high extensibility with high stiffness and hardness. In this study, fluorescence microscopy and elemental analysis were exploited to show that the 3,4-dihydroxyphenyl-L-alanine (dopa) residues of mussel foot protein-1 colocalize with Fe and Ca distributions in the cuticle of Mytilus galloprovincialis mussel byssal threads. Chelated removal of Fe and Ca from the cuticle of intact threads resulted in a 50% reduction in cuticle hardness, and thin sections subjected to the same treatment showed a disruption of cuticle integrity. Dopa-metal complexes may provide significant interactions for the integrity of composite cuticles deformed under tension.

  5. [Clinical features, biology and neuropsychology of the autistic disorder: towards an integrative perspective].

    Science.gov (United States)

    Cukier, Sebastián H

    2005-01-01

    Autism constitutes one of the most investigated disorders in child psychiatry. The heterogeneous clinical phenomena that characterize it have been exhaustibly described along the last 62 years. Multiple aetiological hypothesis, neuropsychological theories and physiopathological mechanisms, sometimes complementary and other times mutually exclusive, and different descriptions of neurobiological alterations that resulted, in general, of low replicability, have attempted to account for the marked variability of its manifestations. An integration of these different levels of analysis results even harder than the comprehension of each of them separately. In this article the author revises the three aspects considered the most characteristic of the syndrome (social interaction, communication and flexibility) and tries to integrate its clinical manifestations with some neuropsychological variables and the neurobiological substrates.

  6. Pyrolyzed Photoresist Electrodes for Integration in Microfluidic Chips for Transmitter Detection from Biological Cells

    DEFF Research Database (Denmark)

    Larsen, Simon Tylsgaard; Argyraki, Aikaterini; Amato, Letizia;

    2013-01-01

    In this study, we show how pyrolyzed photoresist carbon electrodes can be used for amperometric detection of potassium-induced transmitter release from large groups of neuronal PC 12 cells. This opens the way for the use of carbon film electrodes in microfabricated devices for neurochemical drug...... by the difference in photoresist viscosity. By adding a soft bake step to the fabrication procedure, the flatness of pyrolyzed AZ 5214 electrodes could be improved which would facilitate their integration in microfluidic chip devices....

  7. Integration of Biological Specificity with Solid-State Devices for Selective Chemical Sensing

    Science.gov (United States)

    2016-01-29

    transferred from air into a liquid or hydrogel layer that passes over a bank of aptamer functionalized sensor arrays. Figure 5. A multi-tip nanoscale...see any limitations for the integration of solid-state aptamer sensors with liquid flow cells. We have also investigated the scaling of chemiresistors...complex 3D structure. However, we did not test the aptamer against the ATP target, because the latter requires a liquid solution environment and our

  8. Characterization of an Optically Integrated Mach-Zehnder Interferometer for the Detection of Biological Agents

    Science.gov (United States)

    1997-04-01

    nanotechnology for chemical and biochemical analysis. The integration of planar waveguides with these technologies can provide new methods of detection...Project Group 33 on automated biosensors. The work described herein is relevant to NATO Panel 7 in that it presents a novel method of chemical-optical...the analytes possess flu- P502399.PDF [Page: 12 of 62] UNCLASSIFIED 2 orescence labels) or by refractometry . Surface plasmon resonance (Refs. 1 and 2

  9. Integration of biological method and membrane technology in treating palm oil mill effluent.

    Science.gov (United States)

    Zhang, Yejian; Yan, Li; Qiao, Xiangli; Chi, Lina; Niu, Xiangjun; Mei, Zhijian; Zhang, Zhenjia

    2008-01-01

    Palm oil industry is the most important agro-industry in Malaysia, but its by-product-palm oil mill effluent (POME), posed a great threat to water environment. In the past decades, several treatment and disposal methods have been proposed and investigated to solve this problem. A two-stage pilot-scale plant was designed and constructed for POME treatment. Anaerobic digestion and aerobic biodegradation constituted the first biological stage, while ultrafiltration (UF) and reverse osmosis (RO) membrane units were combined as the second membrane separation stage. In the anaerobic expanded granular sludge bed (EGSB) reactor, about 43% organic matter in POME was converted into biogas, and COD reduction efficiency reached 93% and 22% in EGSB and the following aerobic reactor, respectively. With the treatment in the first biological stage, suspended solids and oil also decreased to a low degree. All these alleviated the membrane fouling and prolonged the membrane life. In the membrane process unit, almost all the suspended solids were captured by UF membranes, while RO membrane excluded most of the dissolved solids or inorganic salts from RO permeate. After the whole treatment processes, organic matter in POME expressed by BOD and COD was removed almost thoroughly. Suspended solids and color were not detectable in RO permeate any more, and mineral elements only existed in trace amount (except for K and Na). The high-quality effluent was crystal clear and could be used as the boiler feed water.

  10. Predicting the effect of climate change on African trypanosomiasis: integrating epidemiology with parasite and vector biology.

    Science.gov (United States)

    Moore, Sean; Shrestha, Sourya; Tomlinson, Kyle W; Vuong, Holly

    2012-05-07

    Climate warming over the next century is expected to have a large impact on the interactions between pathogens and their animal and human hosts. Vector-borne diseases are particularly sensitive to warming because temperature changes can alter vector development rates, shift their geographical distribution and alter transmission dynamics. For this reason, African trypanosomiasis (sleeping sickness), a vector-borne disease of humans and animals, was recently identified as one of the 12 infectious diseases likely to spread owing to climate change. We combine a variety of direct effects of temperature on vector ecology, vector biology and vector-parasite interactions via a disease transmission model and extrapolate the potential compounding effects of projected warming on the epidemiology of African trypanosomiasis. The model predicts that epidemics can occur when mean temperatures are between 20.7°C and 26.1°C. Our model does not predict a large-range expansion, but rather a large shift of up to 60 per cent in the geographical extent of the range. The model also predicts that 46-77 million additional people may be at risk of exposure by 2090. Future research could expand our analysis to include other environmental factors that influence tsetse populations and disease transmission such as humidity, as well as changes to human, livestock and wildlife distributions. The modelling approach presented here provides a framework for using the climate-sensitive aspects of vector and pathogen biology to predict changes in disease prevalence and risk owing to climate change.

  11. Integration of biological method and membrane technology in treating palm oil mill effluent

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yejian; YAN Li; QIAO Xiangli; CHI Lina; NIU Xiangjun; MEI Zhijian; ZHANG Zhenjia

    2008-01-01

    Palm oil industry is the most important agro-industry in Malaysia, but its by-product-palm oil mill effluent (POME), posed a great threat to water environment. In the past decades, several treatment and disposal methods have been proposed and investigated to solve this problem. A two-stage pilot-scale plant was designed and constructed for POME treatment. Anaerobic digestion and aerobic biodegradation constituted the first biological stage, while ultrafiltration (UF) and reverse osmosis (RO) membrane units were combined as the second membrane separation stage. In the anaerobic expanded granular sludge bed (EGSB) reactor, about 43% organic matter in POME was converted into biogas, and COD reduction efficiency reached 93% and 22% in EGSB and the following aerobic reactor, respectively. With the treatment in the first biological stage, suspended solids and oil also decreased to a low degree. All these alleviated the membrane fouling and prolonged the membrane life. In the membrane process unit, almost all the suspended solids were captured by UF membranes, while RO membrane excluded most of the dissolved solids or inorganic salts from RO permeate. After the whole treatment processes, organic matter in POME expressed by BOD and COD was removed almost thoroughly. Suspended solids and color were not detectable in RO permeate any more, and mineral elements only existed in trace amount (except for K and Na). The high-quality effluent was crystal clear and could be used as the boiler feed water.

  12. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2).

    Science.gov (United States)

    Murphy, Shawn N; Weber, Griffin; Mendis, Michael; Gainer, Vivian; Chueh, Henry C; Churchill, Susanne; Kohane, Isaac

    2010-01-01

    Informatics for Integrating Biology and the Bedside (i2b2) is one of seven projects sponsored by the NIH Roadmap National Centers for Biomedical Computing (http://www.ncbcs.org). Its mission is to provide clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart. i2b2 software may be used by an enterprise's research community to find sets of interesting patients from electronic patient medical record data, while preserving patient privacy through a query tool interface. Project-specific mini-databases ("data marts") can be created from these sets to make highly detailed data available on these specific patients to the investigators on the i2b2 platform, as reviewed and restricted by the Institutional Review Board. The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software.

  13. Introduction to the Special Issue: Beyond traits: integrating behaviour into plant ecology and biology.

    Science.gov (United States)

    Cahill, James F

    2015-10-26

    The way that plants are conceptualized in the context of ecological understanding is changing. In one direction, a reductionist school is pulling plants apart into a list of measured 'traits', from which ecological function and outcomes of species interactions may be inferred. This special issue offers an alternative, and more holistic, view: that the ecological functions performed by a plant will be a consequence not only of their complement of traits but also of the ways in which their component parts are used in response to environmental and social conditions. This is the realm of behavioural ecology, a field that has greatly advanced our understanding of animal biology, ecology and evolution. Included in this special issue are 10 articles focussing not on the tried and true metaphor that plant growth is similar to animal movement, but instead on how application of principles from animal behaviour can improve our ability to understand plant biology and ecology. The goals are not to draw false parallels, nor to anthropomorphize plant biology, but instead to demonstrate how existing and robust theory based on fundamental principles can provide novel understanding for plants. Key to this approach is the recognition that behaviour and intelligence are not the same. Many organisms display complex behaviours despite a lack of cognition (as it is traditionally understood) or any hint of a nervous system. The applicability of behavioural concepts to plants is further enhanced with the realization that all organisms face the same harsh forces of natural selection in the context of finding resources, mates and coping with neighbours. As these ecological realities are often highly variable in space and time, it is not surprising that all organisms-even plants-exhibit complex behaviours to handle this variability. The articles included here address diverse topics in behavioural ecology, as applied to plants: general conceptual understanding, plant nutrient foraging, root

  14. toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research.

    Science.gov (United States)

    Rhee, David B; Croken, Matthew McKnight; Shieh, Kevin R; Sullivan, Julie; Micklem, Gos; Kim, Kami; Golden, Aaron

    2015-01-01

    Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it is still not fully known which genetic or epigenetic factors are involved in regulating virulence traits of T. gondii. There are on-going efforts to elucidate the mechanisms regulating the stage transition process via the application of high-throughput epigenomics, genomics and proteomics techniques. Given the range of experimental conditions and the typical yield from such high-throughput techniques, a new challenge arises: how to effectively collect, organize and disseminate the generated data for subsequent data analysis. Here, we describe toxoMine, which provides a powerful interface to support sophisticated integrative exploration of high-throughput experimental data and metadata, providing researchers with a more tractable means toward understanding how genetic and/or epigenetic factors play a coordinated role in determining pathogenicity of T. gondii. As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward user interaction. Furthermore, toxoMine allows users to define their own parameters during the search process that gives users near-limitless search and query capabilities. The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine complements the major community database ToxoDB by providing a data warehouse that enables more extensive integrative studies for T. gondii. Given all these factors, we believe it will become an indispensable resource to the greater infectious disease research community.

  15. Mechanical integrity and adhesion of thin films for applications in electronics packaging and cell biology

    Energy Technology Data Exchange (ETDEWEB)

    Duan Jin; Wan Kaitak; Chian Kermsin

    2003-01-22

    A new theoretical model was developed for a pull-off adhesion test using an axisymmetric flat punch and a rectangular flat punch adhered to a thin polymer film interface. An elastic solution was derived to portray the mechanical integrity of the thin film. A mechanical energy release rate was calculated numerically. As the punch was pulled away from the adhered film, the film deformed under mixed bending and stretching. Both stiffness and thickness of the film were allowed to vary. The derived solid-film 'pull-off' events sharply contrast with the abrupt pull-off in solid-solid adhesion as predicted by the classical JKR theory.

  16. Towards integrated operation of membrane bioreactors: effects of aeration on biological and filtration performance.

    Science.gov (United States)

    Dalmau, M; Monclús, H; Gabarrón, S; Rodriguez-Roda, I; Comas, J

    2014-11-01

    Two experimental studies evaluated the effect of aerobic and membrane aeration changes on sludge properties, biological nutrient removal and filtration processes in a pilot plant membrane bioreactor. The optimal operating conditions were found at an aerobic dissolved oxygen set-point (DO) of 0.5 mg O2 L(-1) and a membrane specific aeration demand (SADm) of 1 m h(-1), where membrane aeration can be used for nitrification. Under these conditions, a total flow reduction of 42% was achieved (75% energy reduction) without compromising nutrient removal efficiencies, maintaining sludge characteristics and controlled filtration. Below these optimal operating conditions, the nutrient removal efficiency was reduced, increasing 20% for soluble microbial products, 14% for capillarity suction time and reducing a 15% for filterability. Below this DO set-point, fouling increased with a transmembrane pressure 75% higher. SADm below 1 m h(-1) doubled the values of transmembrane pressure, without recovery after achieving the initial conditions.

  17. Integration of an Online Discussion Forum in a Campus-based Undergraduate Biology Class

    Directory of Open Access Journals (Sweden)

    Sandrine Turcotte

    2004-06-01

    Full Text Available This research paper describes the use of computer mediated conferencing (CMC to support the teaching of biology to undergraduates. The use of this pedagogical innovation was a first-time experience for both the instructor and his students. The objectives of this project were to increase students' active participation, to facilitate collaborative knowledge building, and to enhance the use of the scientific approach in problemsolving activities. The data indicate that some positive results were achieved for each objective. The use of online computer conferences shows a lot of promise when it is based on reflection, problem-solving, collaborative learning and knowledge building. Internet conferencing tools support students as they reflect and work together and open doors to numerous new educational experiences for both the students and the professors.

  18. Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications.

    Science.gov (United States)

    D'Souza, Malcolm J; Kashmar, Richard J; Hurst, Kent; Fiedler, Frank; Gross, Catherine E; Deol, Jasbir K; Wilson, Alora

    Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004-2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average.

  19. Integrating Distributed Physical and Biological Marine data using OGC Web Services

    Science.gov (United States)

    Gemmell, A. L.; Blower, J. D.; Haines, K.; Price, M.; Millard, K.; Harpham, Q.

    2008-12-01

    Earth scientists use highly diverse sources of data, including in-situ measurements, remotely-sensed information and the results of numerical simulations. The ability to access, visualize, combine and compare these datasets is at the core of scientific investigation, but such tasks have hitherto been very difficult or impossible due to a fundamental lack of harmonization of data products. As a result, much valuable data remains underused. We present a web portal that visualizes and compares physical and biological marine data from both numerical models and in-situ observations. The model data are obtained via an Open Geospatial Consortium (OGC)-compatible Web Map Service (WMS), and the observed data are obtained via an OGC Web Feature Service (WFS). The physical model WMS, the biological model WMS and the WFS are located at three different institutes. This ability to display in-situ point observations alongside model data facilitates much valuable work on model validation. As models become increasingly complex, and sources of observed data become more numerous, it is important to be able to access and compare this growing amount of data efficiently, to ensure cross-checking and consistency between models and observations. The web portal is being applied in a large European operational oceanography project (ECOOP), where it is used to provide support to ecosystem modellers, and specifically to aid detection of potentially harmful algal blooms in coastal areas. The development of this system has been enabled by the conceptual framework of the Climate Science Modelling Language (CSML), which provides a common view onto all these datasets, independent of their storage format or physical location. CSML is based upon emerging international standards, enabling interoperability with other standards-based infrastructures. By creating a reusable Java library that embodies the CSML concepts we are able to apply these techniques to a number of other projects.

  20. DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.

    Science.gov (United States)

    Nguyen, Lan K; Degasperi, Andrea; Cotter, Philip; Kholodenko, Boris N

    2015-07-29

    Biochemical networks are dynamic and multi-dimensional systems, consisting of tens or hundreds of molecular components. Diseases such as cancer commonly arise due to changes in the dynamics of signalling and gene regulatory networks caused by genetic alternations. Elucidating the network dynamics in health and disease is crucial to better understand the disease mechanisms and derive effective therapeutic strategies. However, current approaches to analyse and visualise systems dynamics can often provide only low-dimensional projections of the network dynamics, which often does not present the multi-dimensional picture of the system behaviour. More efficient and reliable methods for multi-dimensional systems analysis and visualisation are thus required. To address this issue, we here present an integrated analysis and visualisation framework for high-dimensional network behaviour which exploits the advantages provided by parallel coordinates graphs. We demonstrate the applicability of the framework, named "Dynamics Visualisation based on Parallel Coordinates" (DYVIPAC), to a variety of signalling networks ranging in topological wirings and dynamic properties. The framework was proved useful in acquiring an integrated understanding of systems behaviour.

  1. Hand synergies: Integration of robotics and neuroscience for understanding the control of biological and artificial hands

    Science.gov (United States)

    Santello, Marco; Bianchi, Matteo; Gabiccini, Marco; Ricciardi, Emiliano; Salvietti, Gionata; Prattichizzo, Domenico; Ernst, Marc; Moscatelli, Alessandro; Jörntell, Henrik; Kappers, Astrid M. L.; Kyriakopoulos, Kostas; Albu-Schäffer, Alin; Castellini, Claudio; Bicchi, Antonio

    2016-07-01

    The term 'synergy' - from the Greek synergia - means 'working together'. The concept of multiple elements working together towards a common goal has been extensively used in neuroscience to develop theoretical frameworks, experimental approaches, and analytical techniques to understand neural control of movement, and for applications for neuro-rehabilitation. In the past decade, roboticists have successfully applied the framework of synergies to create novel design and control concepts for artificial hands, i.e., robotic hands and prostheses. At the same time, robotic research on the sensorimotor integration underlying the control and sensing of artificial hands has inspired new research approaches in neuroscience, and has provided useful instruments for novel experiments. The ambitious goal of integrating expertise and research approaches in robotics and neuroscience to study the properties and applications of the concept of synergies is generating a number of multidisciplinary cooperative projects, among which the recently finished 4-year European project "The Hand Embodied" (THE). This paper reviews the main insights provided by this framework. Specifically, we provide an overview of neuroscientific bases of hand synergies and introduce how robotics has leveraged the insights from neuroscience for innovative design in hardware and controllers for biomedical engineering applications, including myoelectric hand prostheses, devices for haptics research, and wearable sensing of human hand kinematics. The review also emphasizes how this multidisciplinary collaboration has generated new ways to conceptualize a synergy-based approach for robotics, and provides guidelines and principles for analyzing human behavior and synthesizing artificial robotic systems based on a theory of synergies.

  2. Hand synergies: Integration of robotics and neuroscience for understanding the control of biological and artificial hands.

    Science.gov (United States)

    Santello, Marco; Bianchi, Matteo; Gabiccini, Marco; Ricciardi, Emiliano; Salvietti, Gionata; Prattichizzo, Domenico; Ernst, Marc; Moscatelli, Alessandro; Jörntell, Henrik; Kappers, Astrid M L; Kyriakopoulos, Kostas; Albu-Schäffer, Alin; Castellini, Claudio; Bicchi, Antonio

    2016-07-01

    The term 'synergy' - from the Greek synergia - means 'working together'. The concept of multiple elements working together towards a common goal has been extensively used in neuroscience to develop theoretical frameworks, experimental approaches, and analytical techniques to understand neural control of movement, and for applications for neuro-rehabilitation. In the past decade, roboticists have successfully applied the framework of synergies to create novel design and control concepts for artificial hands, i.e., robotic hands and prostheses. At the same time, robotic research on the sensorimotor integration underlying the control and sensing of artificial hands has inspired new research approaches in neuroscience, and has provided useful instruments for novel experiments. The ambitious goal of integrating expertise and research approaches in robotics and neuroscience to study the properties and applications of the concept of synergies is generating a number of multidisciplinary cooperative projects, among which the recently finished 4-year European project "The Hand Embodied" (THE). This paper reviews the main insights provided by this framework. Specifically, we provide an overview of neuroscientific bases of hand synergies and introduce how robotics has leveraged the insights from neuroscience for innovative design in hardware and controllers for biomedical engineering applications, including myoelectric hand prostheses, devices for haptics research, and wearable sensing of human hand kinematics. The review also emphasizes how this multidisciplinary collaboration has generated new ways to conceptualize a synergy-based approach for robotics, and provides guidelines and principles for analyzing human behavior and synthesizing artificial robotic systems based on a theory of synergies.

  3. Visualising biological data: a semantic approach to tool and database integration

    Directory of Open Access Journals (Sweden)

    Marsh James

    2009-06-01

    Full Text Available Abstract Motivation In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research. Methods To confront these issues, harnessing expertise in human-computer interaction (HCI, high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their

  4. Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium.

    Science.gov (United States)

    Salomonis, Nathan; Dexheimer, Phillip J; Omberg, Larsson; Schroll, Robin; Bush, Stacy; Huo, Jeffrey; Schriml, Lynn; Ho Sui, Shannan; Keddache, Mehdi; Mayhew, Christopher; Shanmukhappa, Shiva Kumar; Wells, James; Daily, Kenneth; Hubler, Shane; Wang, Yuliang; Zambidis, Elias; Margolin, Adam; Hide, Winston; Hatzopoulos, Antonis K; Malik, Punam; Cancelas, Jose A; Aronow, Bruce J; Lutzko, Carolyn

    2016-07-12

    The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability and downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental and genomic analyses of 58 iPSC from ten laboratories generated using a variety of reprogramming genes, vectors, and cells. Associated global molecular characterization studies identified functionally informative correlations in gene expression, DNA methylation, and/or copy-number variation among key developmental and oncogenic regulators as a result of donor, sex, line stability, reprogramming technology, and cell of origin. Furthermore, X-chromosome inactivation in PSC produced highly correlated differences in teratoma-lineage staining and regulator expression upon differentiation. All experimental results, and raw, processed, and metadata from these analyses, including powerful tools, are interactively accessible from a new online portal at https://www.synapse.org to serve as a reusable resource for the stem cell community.

  5. Integrating biological treatment of crop residue into a hydroponic sweetpotato culture.

    Science.gov (United States)

    Trotman, A A; David, P P; Bonsi, C K; Hill, W A; Mortley, D G; Loretan, P A

    1997-01-01

    Residual biomass from hydroponic culture of sweetpotato [Ipomoea batatas (L.) Lam.] was degraded using natural bacterial soil isolates. Sweetpotato was grown for 120 days in hydroponic culture with a nutrient solution comprised of a ratio of 80% modified half Hoagland solution to 20% filtered effluent from an aerobic starch hydrolysis bioreactor. The phytotoxicity of the effluent was assayed with Waldmann's Green' lettuce (Lactuca sativa L.) and the ratio selected after a 60-day bioassay using sweetpotato plants propagated vegetatively from cuttings. Controlled environment chamber experiments were conducted to investigate the impact of filtrate from biological treatment of crop residue on growth and storage root production with plants grown in a modified half Hoagland solution. Incorporation of bioreactor effluent, reduced storage root yield of 'Georgia Jet' sweetpotato but the decrease was not statistically significant when compared with yield for plants cultured in a modified half Hoagland solution without filtrate. However, yield of 'TU-82-155' sweetpotato was significantly reduced when grown in a modified half Hoagland solution into which filtered effluent had been incorporated. Total biomass was significantly reduced for both sweetpotato cultivars when grown in bioreactor effluent. The leaf area and dry matter accumulation were significantly (P < 0.05) reduced for both cultivars when grown in solution culture containing 20% filtered effluent.

  6. Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

    Directory of Open Access Journals (Sweden)

    Nathan Salomonis

    2016-07-01

    Full Text Available The rigorous characterization of distinct induced pluripotent stem cells (iPSC derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability and downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental and genomic analyses of 58 iPSC from ten laboratories generated using a variety of reprogramming genes, vectors, and cells. Associated global molecular characterization studies identified functionally informative correlations in gene expression, DNA methylation, and/or copy-number variation among key developmental and oncogenic regulators as a result of donor, sex, line stability, reprogramming technology, and cell of origin. Furthermore, X-chromosome inactivation in PSC produced highly correlated differences in teratoma-lineage staining and regulator expression upon differentiation. All experimental results, and raw, processed, and metadata from these analyses, including powerful tools, are interactively accessible from a new online portal at https://www.synapse.org to serve as a reusable resource for the stem cell community.

  7. Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

    Science.gov (United States)

    MacLeod, Miles; Nersessian, Nancy J

    2015-02-01

    In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding."

  8. Integrating biological treatment of crop residue into a hydroponic sweetpotato culture

    Science.gov (United States)

    Trotman, A. A.; David, P. P.; Bonsi, C. K.; Hill, W. A.; Mortley, D. G.; Loretan, P. A.

    1997-01-01

    Residual biomass from hydroponic culture of sweetpotato [Ipomoea batatas (L.) Lam.] was degraded using natural bacterial soil isolates. Sweetpotato was grown for 120 days in hydroponic culture with a nutrient solution comprised of a ratio of 80% modified half Hoagland solution to 20% filtered effluent from an aerobic starch hydrolysis bioreactor. The phytotoxicity of the effluent was assayed with `Waldmann's Green' lettuce (Lactuca sativa L.) and the ratio selected after a 60-day bioassay using sweetpotato plants propagated vegetatively from cuttings. Controlled environment chamber experiments were conducted to investigate the impact of filtrate from biological treatment of crop residue on growth and storage root production with plants grown in a modified half Hoagland solution. Incorporation of bioreactor effluent, reduced storage root yield of `Georgia Jet' sweetpotato but the decrease was not statistically significant when compared with yield for plants cultured in a modified half Hoagland solution without filtrate. However, yield of `TU-82-155' sweetpotato was significantly reduced when grown in a modified half Hoagland solution into which filtered effluent had been incorporated. Total biomass was significantly reduced for both sweetpotato cultivars when grown in bioreactor effluent. The leaf area and dry matter accumulation were significantly (P < 0.05) reduced for both cultivars when grown in solution culture containing 20% filtered effluent.

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

    Science.gov (United States)

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

    2016-05-01

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

  10. Integrating silicon nanowire field effect transistor, microfluidics and air sampling techniques for real-time monitoring biological aerosols.

    Science.gov (United States)

    Shen, Fangxia; Tan, Miaomiao; Wang, Zhenxing; Yao, Maosheng; Xu, Zhenqiang; Wu, Yan; Wang, Jindong; Guo, Xuefeng; Zhu, Tong

    2011-09-01

    Numerous threats from biological aerosol exposures, such as those from H1N1 influenza, SARS, bird flu, and bioterrorism activities necessitate the development of a real-time bioaerosol sensing system, which however is a long-standing challenge in the field. Here, we developed a real-time monitoring system for airborne influenza H3N2 viruses by integrating electronically addressable silicon nanowire (SiNW) sensor devices, microfluidics and bioaerosol-to-hydrosol air sampling techniques. When airborne influenza H3N2 virus samples were collected and delivered to antibody-modified SiNW devices, discrete nanowire conductance changes were observed within seconds. In contrast, the conductance levels remained relatively unchanged when indoor air or clean air samples were delivered. A 10-fold increase in virus concentration was found to give rise to about 20-30% increase in the sensor response. The selectivity of the sensing device was successfully demonstrated using H1N1 viruses and house dust allergens. From the simulated aerosol release to the detection, we observed a time scale of 1-2 min. Quantitative polymerase chain reaction (qPCR) tests revealed that higher virus concentrations in the air samples generally corresponded to higher conductance levels in the SiNW devices. In addition, the display of detection data on remote platforms such as cell phone and computer was also successfully demonstrated with a wireless module. The work here is expected to lead to innovative methods for biological aerosol monitoring, and further improvements in each of the integrated elements could extend the system to real world applications.

  11. Integration of a zebrafish research project into a molecular biology course to support critical thinking and course content goals.

    Science.gov (United States)

    Felzien, Lisa K

    2016-11-12

    Engaging undergraduates in research is essential for teaching them to think like scientists, and it has become a desired component of classroom and laboratory instruction. Research projects that span an entire semester expose students to a variety of concepts and techniques and allow students to use experiments to learn scientific principles, understand why specific techniques are applicable, critically analyze varied data, and examine how experimentation leads to acquiring knowledge. To provide an experience with these features, a semester long research project was integrated into a combined lecture and laboratory course, Molecular Biology. The project utilized the zebrafish model to examine gene expression during embryonic development and required students to develop and test hypotheses about the timing of expression of previously uncharacterized genes. The main goals for the project were to provide opportunities for students to develop critical thinking skills required for conducting research and to support the content goals of the course. To determine whether these goals were met, student performance on the steps of the project and related pre-test and post-test questions was examined. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):565-573, 2016.

  12. EVALUATING THE ECOLOGICAL RESILIENT DRIVEN PERFORMANCE OF A TROPICAL WASTE STABILIZATION POND SYSTEM USING ECOLOGICAL SIGNATURE OF BIOLOGICAL INTEGRITY

    Directory of Open Access Journals (Sweden)

    Susmita Lahiri Ganguly

    2015-06-01

    Full Text Available Using ecological signature of biological integrity as a measure of performance, the reclamation efficiency of waste stabilization ponds was evaluated over a period of four years in a tropical sewage treatment plant – cum fish culture consisting of two anaerobic, two facultative and four maturation ponds located serially across the sewage effluent gradient. The four maturation ponds were used for batch culture of fish. Samples of surface and bottom water as well as surface sediment were collected twice a month from different ponds of the system and examined for some nutrient cycling bacteria, primary production, chlorophyll content of micro-algae, phytoplankton, zooplankton abundance, fish growth and water quality parameters. Computation of ecological signature using aerobic mineralization index for heterotrophic and ammonifying bacteria revealed steady increase across the sewage effluent gradient. The heterotrophic and ammonifying bacterial populations appeared to have a direct function with the concentrations of chemical oxygen demand of water. The sum of total scores for different optimal conditions for fish growth increased as a function of the distance from the source of effluent implying that ecological resilience of the waste stabilization ponds has been accomplished by the sedimentation, chelation, and biological functional attributes mediated through redundancy of different subsystems, self- purification capacity of the system as a whole.

  13. Linking biological integrity and watershed models to assess the impacts of historical land use and climate changes on stream health.

    Science.gov (United States)

    Einheuser, Matthew D; Nejadhashemi, A Pouyan; Wang, Lizhu; Sowa, Scott P; Woznicki, Sean A

    2013-06-01

    Land use change and other human disturbances have significant impacts on physicochemical and biological conditions of stream systems. Meanwhile, linking these disturbances with hydrology and water quality conditions is challenged due to the lack of high-resolution datasets and the selection of modeling techniques that can adequately deal with the complex and nonlinear relationships of natural systems. This study addresses the above concerns by employing a watershed model to obtain stream flow and water quality data and fill a critical gap in data collection. The data were then used to estimate fish index of biological integrity (IBI) within the Saginaw Bay basin in Michigan. Three methods were used in connecting hydrology and water quality variables to fish measures including stepwise linear regression, partial least squares regression, and fuzzy logic. The IBI predictive model developed using fuzzy logic showed the best performance with the R (2) = 0.48. The variables that identified as most correlated to IBI were average annual flow, average annual organic phosphorus, average seasonal nitrite, average seasonal nitrate, and stream gradient. Next, the predictions were extended to pre-settlement (mid-1800s) land use and climate conditions. Results showed overall significantly higher IBI scores under the pre-settlement land use scenario for the entire watershed. However, at the fish sampling locations, there was no significant difference in IBI. Results also showed that including historical climate data have strong influences on stream flow and water quality measures that interactively affect stream health; therefore, should be considered in developing baseline ecological conditions.

  14. Integrating Facebook in Upper Secondary Biology Instruction: A Case Study of Students' Situational Interest and Participation in Learning Communication

    Science.gov (United States)

    Dohn, Niels Bonderup; Dohn, Nina Bonderup

    2017-01-01

    The sciences are often perceived by students as irrelevant as they do not see the content of science as related to their daily lives. Web 2.0-mediated activities are characterized by user-driven content production, collaboration, and multi-way communication. It has been proposed that employing Web 2.0 in educational activities will promote richer opportunities for making learning personally meaningful, collaborative, and socially relevant. Since Facebook is already in use among youths, it potentially provides a communicative link between educational content and students' lives. The present study was conducted as a case study to provide an inductive, explorative investigation of whether and how the integration of Facebook into upper secondary biology can affect interest in biology and participation in learning communication. The results indicate that the coupling of formal and informal communication practices on Facebook serves to maintain interest and open up new learning possibilities while at the same time creating barriers to communication. These barriers are due to distractions, ethical issues, and a certain depreciation of the activities ensuing from the everydayness of Facebook as a communication platform. In conclusion, use of Facebook as an educational platform is not clearly good or bad.

  15. Engineering challenges of BioNEMS: the integration of microfluidics, micro- and nanodevices, models and external control for systems biology.

    Science.gov (United States)

    Wikswo, J P; Prokop, A; Baudenbacher, F; Cliffel, D; Csukas, B; Velkovsky, M

    2006-08-01

    Systems biology, i.e. quantitative, postgenomic, postproteomic, dynamic, multiscale physiology, addresses in an integrative, quantitative manner the shockwave of genetic and proteomic information using computer models that may eventually have 10(6) dynamic variables with non-linear interactions. Historically, single biological measurements are made over minutes, suggesting the challenge of specifying 10(6) model parameters. Except for fluorescence and micro-electrode recordings, most cellular measurements have inadequate bandwidth to discern the time course of critical intracellular biochemical events. Micro-array expression profiles of thousands of genes cannot determine quantitative dynamic cellular signalling and metabolic variables. Major gaps must be bridged between the computational vision and experimental reality. The analysis of cellular signalling dynamics and control requires, first, micro- and nano-instruments that measure simultaneously multiple extracellular and intracellular variables with sufficient bandwidth; secondly, the ability to open existing internal control and signalling loops; thirdly, external BioMEMS micro-actuators that provide high bandwidth feedback and externally addressable intracellular nano-actuators; and, fourthly, real-time, closed-loop, single-cell control algorithms. The unravelling of the nested and coupled nature of cellular control loops requires simultaneous recording of multiple single-cell signatures. Externally controlled nano-actuators, needed to effect changes in the biochemical, mechanical and electrical environment both outside and inside the cell, will provide a major impetus for nanoscience.

  16. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps.

    Science.gov (United States)

    Kuperstein, I; Bonnet, E; Nguyen, H-A; Cohen, D; Viara, E; Grieco, L; Fourquet, S; Calzone, L; Russo, C; Kondratova, M; Dutreix, M; Barillot, E; Zinovyev, A

    2015-01-01

    Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network of molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application of bioinformatics and systems biology methods for analysis of high-throughput data in cancer research heavily depends on availability of global and detailed reconstructions of signalling networks amenable for computational analysis. We present here the Atlas of Cancer Signalling Network (ACSN), an interactive and comprehensive map of molecular mechanisms implicated in cancer. The resource includes tools for map navigation, visualization and analysis of molecular data in the context of signalling network maps. Constructing and updating ACSN involves careful manual curation of molecular biology literature and participation of experts in the corresponding fields. The cancer-oriented content of ACSN is completely original and covers major mechanisms involved in cancer progression, including DNA repair, cell survival, apoptosis, cell cycle, EMT and cell motility. Cell signalling mechanisms are depicted in detail, together creating a seamless 'geographic-like' map of molecular interactions frequently deregulated in cancer. The map is browsable using NaviCell web interface using the Google Maps engine and semantic zooming principle. The associated web-blog provides a forum for commenting and curating the ACSN content. ACSN allows uploading heterogeneous omics data from users on top of the maps for visualization and performing functional analyses. We suggest several scenarios for ACSN application in cancer research, particularly for visualizing high-throughput data, starting from small interfering RNA-based screening results or mutation frequencies to innovative ways of exploring transcriptomes and phosphoproteomes. Integration and analysis of these data in the context of ACSN may help interpret their biological significance and formulate mechanistic hypotheses

  17. Integrating biologically inspired nanomaterials and table-top stereolithography for 3D printed biomimetic osteochondral scaffolds.

    Science.gov (United States)

    Castro, Nathan J; O'Brien, Joseph; Zhang, Lijie Grace

    2015-09-01

    The osteochondral interface of an arthritic joint is notoriously difficult to regenerate due to its extremely poor regenerative capacity and complex stratified architecture. Native osteochondral tissue extracellular matrix is composed of numerous nanoscale organic and inorganic constituents. Although various tissue engineering strategies exist in addressing osteochondral defects, limitations persist with regards to tissue scaffolding which exhibit biomimetic cues at the nano to micro scale. In an effort to address this, the current work focused on 3D printing biomimetic nanocomposite scaffolds for improved osteochondral tissue regeneration. For this purpose, two biologically-inspired nanomaterials have been synthesized consisting of (1) osteoconductive nanocrystalline hydroxyapatite (nHA) (primary inorganic component of bone) and (2) core-shell poly(lactic-co-glycolic) acid (PLGA) nanospheres encapsulated with chondrogenic transforming growth-factor β1 (TGF-β1) for sustained delivery. Then, a novel table-top stereolithography 3D printer and the nano-ink (i.e., nHA + nanosphere + hydrogel) were employed to fabricate a porous and highly interconnected osteochondral scaffold with hierarchical nano-to-micro structure and spatiotemporal bioactive factor gradients. Our results showed that human bone marrow-derived mesenchymal stem cell adhesion, proliferation, and osteochondral differentiation were greatly improved in the biomimetic graded 3D printed osteochondral construct in vitro. The current work served to illustrate the efficacy of the nano-ink and current 3D printing technology for efficient fabrication of a novel nanocomposite hydrogel scaffold. In addition, tissue-specific growth factors illustrated a synergistic effect leading to increased cell adhesion and directed stem cell differentiation.

  18. Integrating biologically inspired nanomaterials and table-top stereolithography for 3D printed biomimetic osteochondral scaffolds

    Science.gov (United States)

    Castro, Nathan J.; O'Brien, Joseph; Zhang, Lijie Grace

    2015-08-01

    The osteochondral interface of an arthritic joint is notoriously difficult to regenerate due to its extremely poor regenerative capacity and complex stratified architecture. Native osteochondral tissue extracellular matrix is composed of numerous nanoscale organic and inorganic constituents. Although various tissue engineering strategies exist in addressing osteochondral defects, limitations persist with regards to tissue scaffolding which exhibit biomimetic cues at the nano to micro scale. In an effort to address this, the current work focused on 3D printing biomimetic nanocomposite scaffolds for improved osteochondral tissue regeneration. For this purpose, two biologically-inspired nanomaterials have been synthesized consisting of (1) osteoconductive nanocrystalline hydroxyapatite (nHA) (primary inorganic component of bone) and (2) core-shell poly(lactic-co-glycolic) acid (PLGA) nanospheres encapsulated with chondrogenic transforming growth-factor β1 (TGF-β1) for sustained delivery. Then, a novel table-top stereolithography 3D printer and the nano-ink (i.e., nHA + nanosphere + hydrogel) were employed to fabricate a porous and highly interconnected osteochondral scaffold with hierarchical nano-to-micro structure and spatiotemporal bioactive factor gradients. Our results showed that human bone marrow-derived mesenchymal stem cell adhesion, proliferation, and osteochondral differentiation were greatly improved in the biomimetic graded 3D printed osteochondral construct in vitro. The current work served to illustrate the efficacy of the nano-ink and current 3D printing technology for efficient fabrication of a novel nanocomposite hydrogel scaffold. In addition, tissue-specific growth factors illustrated a synergistic effect leading to increased cell adhesion and directed stem cell differentiation.

  19. A tiered, integrated biological and chemical monitoring framework for contaminants of emerging concern in aquatic ecosystems.

    Science.gov (United States)

    Maruya, Keith A; Dodder, Nathan G; Mehinto, Alvine C; Denslow, Nancy D; Schlenk, Daniel; Snyder, Shane A; Weisberg, Stephen B

    2016-07-01

    The chemical-specific risk-based paradigm that informs monitoring and assessment of environmental contaminants does not apply well to the many thousands of new chemicals that are being introduced into ambient receiving waters. We propose a tiered framework that incorporates bioanalytical screening tools and diagnostic nontargeted chemical analysis to more effectively monitor for contaminants of emerging concern (CECs). The framework is based on a comprehensive battery of in vitro bioassays to first screen for a broad spectrum of CECs and nontargeted analytical methods to identify bioactive contaminants missed by the currently favored targeted analyses. Water quality managers in California have embraced this strategy with plans to further develop and test this framework in regional and statewide pilot studies on waterbodies that receive discharge from municipal wastewater treatment plants and stormwater runoff. In addition to directly informing decisions, the data obtained using this framework can be used to construct and validate models that better predict CEC occurrence and toxicity. The adaptive interplay among screening results, diagnostic assessment and predictive modeling will allow managers to make decisions based on the most current and relevant information, instead of extrapolating from parameters with questionable linkage to CEC impacts. Integr Environ Assess Manag 2016;12:540-547. © 2015 SETAC.

  20. Tsetse flies: their biology and control using area-wide integrated pest management approaches.

    Science.gov (United States)

    Vreysen, Marc J B; Seck, Momar Talla; Sall, Baba; Bouyer, Jérémy

    2013-03-01

    Tsetse flies are the cyclical vectors of trypanosomes, the causative agents of 'sleeping sickness' or human African trypanosomosis (HAT) in humans and 'nagana' or African animal trypanosomosis (AAT) in livestock in Sub-saharan Africa. Many consider HAT as one of the major neglected tropical diseases and AAT as the single greatest health constraint to increased livestock production. This review provides some background information on the taxonomy of tsetse flies, their unique way of reproduction (adenotrophic viviparity) making the adult stage the only one easily accessible for control, and how their ecological affinities, their distribution and population dynamics influence and dictate control efforts. The paper likewise reviews four control tactics (sequential aerosol technique, stationary attractive devices, live bait technique and the sterile insect technique) that are currently accepted as friendly to the environment, and describes their limitations and advantages and how they can best be put to practise in an IPM context. The paper discusses the different strategies for tsetse control i.e. localised versus area-wide and focusses thereafter on the principles of area-wide integrated pest management (AW-IPM) and the phased-conditional approach with the tsetse project in Senegal as a recent example. We argue that sustainable tsetse-free zones can be created on Africa mainland provided certain managerial and technical prerequisites are in place.

  1. In Vivo Integrity and Biological Fate of Chelator-Free Zirconium-89-Labeled Mesoporous Silica Nanoparticles.

    Science.gov (United States)

    Chen, Feng; Goel, Shreya; Valdovinos, Hector F; Luo, Haiming; Hernandez, Reinier; Barnhart, Todd E; Cai, Weibo

    2015-08-25

    Traditional chelator-based radio-labeled nanoparticles and positron emission tomography (PET) imaging are playing vital roles in the field of nano-oncology. However, their long-term in vivo integrity and potential mismatch of the biodistribution patterns between nanoparticles and radio-isotopes are two major concerns for this approach. Here, we present a chelator-free zirconium-89 ((89)Zr, t1/2 = 78.4 h) labeling of mesoporous silica nanoparticle (MSN) with significantly enhanced in vivo long-term (>20 days) stability. Successful radio-labeling and in vivo stability are demonstrated to be highly dependent on both the concentration and location of deprotonated silanol groups (-Si-O(-)) from two types of silica nanoparticles investigated. This work reports (89)Zr-labeled MSN with a detailed labeling mechanism investigation and long-term stability study. With its attractive radio-stability and the simplicity of chelator-free radio-labeling, (89)Zr-MSN offers a novel, simple, and accurate way for studying the in vivo long-term fate and PET image-guided drug delivery of MSN in the near future.

  2. Meta-analysis method for discovering reliable biomarkers by integrating statistical and biological approaches: An application to liver toxicity.

    Science.gov (United States)

    Cho, Hyeyoung; Kim, Hyosil; Na, Dokyun; Kim, So Youn; Jo, Deokyeon; Lee, Doheon

    2016-03-04

    Biomarkers that are identified from a single study often appear to be biologically irrelevant or false positives. Meta-analysis techniques allow integrating data from multiple studies that are related but independent in order to identify biomarkers across multiple conditions. However, existing biomarker meta-analysis methods tend to be sensitive to the dataset being analyzed. Here, we propose a meta-analysis method, iMeta, which integrates t-statistic and fold change ratio for improved robustness. For evaluation of predictive performance of the biomarkers identified by iMeta, we compare our method with other meta-analysis methods. As a result, iMeta outperforms the other methods in terms of sensitivity and specificity, and especially shows robustness to study variance increase; it consistently shows higher classification accuracy on diverse datasets, while the performance of the others is highly affected by the dataset being analyzed. Application of iMeta to 59 drug-induced liver injury studies identified three key biomarker genes: Zwint, Abcc3, and Ppp1r3b. Experimental evaluation using RT-PCR and qRT-PCR shows that their expressional changes in response to drug toxicity are concordant with the result of our method. iMeta is available at http://imeta.kaist.ac.kr/index.html.

  3. Integrated perspectives on geological and biological dynamics in ancient Lake Ohrid

    Science.gov (United States)

    Wagner, Bernd; Wilke, Thomas; Krastel, Sebastian; Zanchetta, Giovanni; Leng, Melanie; Wonik, Thomas; Francke, Alexander; Leicher, Niklas; Just, Janna; Lacey, Jack; Baumgarten, Henrike; Levkov, Zlatko; Reed, Jane; Cvetkoska, Aleksandra; Vogel, Hendrik; Sadori, Laura

    2016-04-01

    Lake Ohrid on the Balkan Peninsula is one of the very few lakes in the world that provides a continuous and high-resolution record of environmental change of >1.2 Ma. The outstanding number of endemic taxa (>300 endemic taxa) in Lake Ohrid in combination with its long existence makes Lake Ohrid a unique target to study the drivers of speciation and endemism. For this purpose, a 569 m long sediment sequence was recovered from the central part of the lake in spring 2013 within the scope of the International Continental Scientific Drilling Program (ICDP) and the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) project. In January 2016, the lowermost core sections of the 569 m long sediment sequence were opened. Ongoing work comprises core correlation to a composite sequence and various geological and biological analyses on the sediment material. Here, we present the results of analyses of the upper 248 m of this sequence, which covers the last ca. 640 ka according to an age model based on tephrostratigraphy as well as tuning of in situ physical and biogeochemical proxy data to orbital parameters and supported by paleomagnetic studies. The sedimentological, physical, and geochemical data from the sediment sequence indicate changes in primary productivity, water column stratification, and water depth of the lake, and in weathering and erosion processes in the catchment. These changes can be clearly correlated with orbitally driven environmental change, such as the intensity of glacial and interglacial periods as well as stadials and interstadials. These long-term changes are interspersed by short-term events, such as the deposition of tephra horizons. More than 30 tephra layers were found in the upper 248 m. The comparison of long-term and short-term environmental changes with paleontological and molecular clock analyses indicates that catastrophic extinction events in the endemic species community did not occur over the last 640 ka in Lake

  4. Integration of an innovative biological treatment with physical or chemical disinfection for wastewater reuse.

    Science.gov (United States)

    De Sanctis, Marco; Del Moro, Guido; Levantesi, Caterina; Luprano, Maria Laura; Di Iaconi, Claudio

    2016-02-01

    In the present paper, the effectiveness of a Sequencing Batch Biofilter Granular Reactor (SBBGR) and its integration with different disinfection strategies (UV irradiation, peracetic acid) for producing an effluent suitable for agricultural use was evaluated. The plant treated raw domestic sewage, and its performances were evaluated in terms of the removal efficiency of a wide group of physical, chemical and microbiological parameters. The SBBGR resulted really efficient in removing suspended solids, COD and nitrogen with an average effluent concentration of 5, 32 and 10 mg/L, respectively. Lower removal efficiency was observed for phosphorus with an average concentration in the effluent of 3 mg/L. Plant effluent was also characterized by an average electrical conductivity and sodium adsorption ratio of 680 μS/cm and 2.9, respectively. Therefore, according to these gross parameters, the SBBGR effluent was conformed to the national standards required in Italy for agricultural reuse. Moreover, disinfection performances of the SBBGR was higher than that of conventional municipal wastewater treatment plants and met the quality criteria suggested by WHO (Escherichia colitreatment by SBBGR removed 3.8±0.4 log units of Giardia lamblia, 2.8±0.8 log units of E. coli, 2.5±0.7 log units of total coliforms, 2.0±0.3 log units of Clostridium perfringens, 2.0±0.4 log units of Cryptosporidium parvum and 1.7±0.7 log units of Somatic coliphages. The investigated disinfection processes (UV and peracetic acid) resulted very effective for total coliforms, E. coli and somatic coliphages. In particular, a UV radiation and peracetic acid doses of 40 mJ/cm(2) and 1 mg/L respectively reduced E. coli content in the effluent below the limit for agricultural reuse in Italy (10 CFU/100 mL). Conversely, they were both ineffective on C.perfringens spores.

  5. Eco-friendly and facile integrated biological-cum-photo assisted electrooxidation process for degradation of textile wastewater.

    Science.gov (United States)

    Aravind, Priyadharshini; Subramanyan, Vasudevan; Ferro, Sergio; Gopalakrishnan, Rajagopal

    2016-04-15

    The present article reports an integrated treatment method viz biodegradation followed by photo-assisted electrooxidation, as a new approach, for the abatement of textile wastewater. In the first stage of the integrated treatment scheme, the chemical oxygen demand (COD) of the real textile effluent was reduced by a biodegradation process using hydrogels of cellulose-degrading Bacillus cereus. The bio-treated effluent was then subjected to the second stage of the integrated scheme viz indirect electrooxidation (InDEO) as well as photo-assisted indirect electro oxidation (P-InDEO) process using Ti/IrO2-RuO2-TiO2 and Ti as electrodes and applying a current density of 20 mA cm(-2). The influence of cellulose in InDEO has been reported here, for the first time. UV-Visible light of 280-800 nm has been irradiated toward the anode/electrolyte interface in P-InDEO. The effectiveness of this combined treatment process in textile effluent degradation has been probed by chemical oxygen demand (COD) measurements and (1)H - nuclear magnetic resonance spectroscopy (NMR). The obtained results indicate that the biological treatment allows obtaining a 93% of cellulose degradation and 47% of COD removal, increasing the efficiency of the subsequent InDEO by a 33%. In silico molecular docking analysis ascertained that cellulose fibers affect the InDEO process by interacting with the dyes that are responsible of the COD. On the other hand, P-InDEO resulted in both 95% of decolorization and 68% of COD removal, as a result of radical mediators. Free radicals generated during P-InDEO were characterized as oxychloride (OCl) by electron paramagnetic resonance spectroscopy (EPR). This form of coupled approach is especially suggested for the treatment of textile wastewater containing cellulose.

  6. 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.

  7. Integration

    DEFF Research Database (Denmark)

    Emerek, Ruth

    2004-01-01

    Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration......Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration...

  8. Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology.

    Directory of Open Access Journals (Sweden)

    Ana M Rojas

    Full Text Available The mitotic spindle is an essential molecular machine involved in cell division, whose composition has been studied extensively by detailed cellular biology, high-throughput proteomics, and RNA interference experiments. However, because of its dynamic organization and complex regulation it is difficult to obtain a complete description of its molecular composition. We have implemented an integrated computational approach to characterize novel human spindle components and have analysed in detail the individual candidates predicted to be spindle proteins, as well as the network of predicted relations connecting known and putative spindle proteins. The subsequent experimental validation of a number of predicted novel proteins confirmed not only their association with the spindle apparatus but also their role in mitosis. We found that 75% of our tested proteins are localizing to the spindle apparatus compared to a success rate of 35% when expert knowledge alone was used. We compare our results to the previously published MitoCheck study and see that our approach does validate some findings by this consortium. Further, we predict so-called "hidden spindle hub", proteins whose network of interactions is still poorly characterised by experimental means and which are thought to influence the functionality of the mitotic spindle on a large scale. Our analyses suggest that we are still far from knowing the complete repertoire of functionally important components of the human spindle network. Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system.

  9. Actin Immobilization on Chitin for Purifying Myosin II: A Laboratory Exercise That Integrates Concepts of Molecular Cell Biology and Protein Chemistry

    Science.gov (United States)

    de Souza, Marcelle Gomes; Grossi, Andre Luiz; Pereira, Elisangela Lima Bastos; da Cruz, Carolina Oliveira; Mendes, Fernanda Machado; Cameron, Luiz Claudio; Paiva, Carmen Lucia Antao

    2008-01-01

    This article presents our experience on teaching biochemical sciences through an innovative approach that integrates concepts of molecular cell biology and protein chemistry. This original laboratory exercise is based on the preparation of an affinity chromatography column containing F-actin molecules immobilized on chitin particles for purifying…

  10. Workshop on Biological Integrity of Coral Reefs August 21-22, 2012, Caribbean Coral Reef Institute, Isla Magueyes, La Parguera, Puerto Rico.

    Science.gov (United States)

    This report summarizes an EPA-sponsored workshop on coral reef biological integrity held at the Caribbean Coral Reef Institute in La Parguera, Puerto Rico on August 21-22, 2012. The goals of this workshop were to:• Identify key qualitative and quantitative ecological characterist...

  11. Integration of principles of systems biology and radiation biology: toward development of in silico models to optimize IUdR-mediated radiosensitization of DNA mismatch repair-deficient (damage tolerant human cancers

    Directory of Open Access Journals (Sweden)

    Timothy James Kinsella

    2011-08-01

    Full Text Available Over the last 7 years, we have focused our experimental and computational research efforts on improving our understanding of the biochemical, molecular, and cellular processing of iododeoxyuridine (IUdR and ionizing radiation (IR induced DNA base damage by DNA mismatch repair (MMR. These coordinated research efforts, sponsored by the National Cancer Institute Integrative Cancer Biology Program (ICBP, brought together system scientists with expertise in engineering, mathematics, and complex systems theory and translational cancer researchers with expertise in radiation biology. Our overall goal was to begin to develop computational models of IUdR- and/or IR- induced base damage processing by MMR that may provide new clinical strategies to optimize IUdR-mediated radiosensitiztion in MMR deficient (MMR- damage tolerant human cancers. Using multiple scales of experimental testing, ranging from purified protein systems to in vitro (cellular and to in vivo (human tumor xenografts in athymic mice models, we have begun to integrate and interpolate these experimental data with hybrid stochastic biochemical models of MMR damage processing and probabilistic cell cycle regulation models through a systems biology approach. In this article, we highlight the results and current status of our integration of radiation biology approaches and computational modeling to enhance IUdR-mediated radiosensitization in MMR- damage tolerant cancers.

  12. MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.

    Science.gov (United States)

    Hwang, Sohyun; Kim, Eiru; Yang, Sunmo; Marcotte, Edward M; Lee, Insuk

    2014-07-01

    Despite recent advances in human genetics, model organisms are indispensable for human disease research. Most human disease pathways are evolutionally conserved among other species, where they may phenocopy the human condition or be associated with seemingly unrelated phenotypes. Much of the known gene-to-phenotype association information is distributed across diverse databases, growing rapidly due to new experimental techniques. Accessible bioinformatics tools will therefore facilitate translation of discoveries from model organisms into human disease biology. Here, we present a web-based discovery tool for human disease studies, MORPHIN (model organisms projected on a human integrated gene network), which prioritizes the most relevant human diseases for a given set of model organism genes, potentially highlighting new model systems for human diseases and providing context to model organism studies. Conceptually, MORPHIN investigates human diseases by an orthology-based projection of a set of model organism genes onto a genome-scale human gene network. MORPHIN then prioritizes human diseases by relevance to the projected model organism genes using two distinct methods: a conventional overlap-based gene set enrichment analysis and a network-based measure of closeness between the query and disease gene sets capable of detecting associations undetectable by the conventional overlap-based methods. MORPHIN is freely accessible at http://www.inetbio.org/morphin.

  13. [Community structure and biological integrity of periphyton in Hunhe River water system of Liaoning Province, Northeast China].

    Science.gov (United States)

    Yin, Xu-wang; Zhang, Yuan; Qu, Xiao-dong; Liu, Ying; Li, Qing-nan; Meng, Wei

    2011-10-01

    Taking the Hunhe River water system in Liaoning Province of Northeast China as a case, this paper investigated the community structure of periphyton and the physical and chemical characteristics of water environment at 62 sampling sites, and, by using the biological integrity index of periphyton (P-IBI) and the habitat environment quality index (QHEI), a health assessment on the aquatic ecosystem of the water system was conducted. There was a great spatial heterogeneity in the periphyton community structure, and the sampling sites could be divided into 4 groups, with significant differences in the community structure, species richness, density, and Shannon diversity index among the groups. Canonical correspondence analysis (CCA) showed that ammonia nitrogen (NH4(+)-N) and dissolved phosphorus (PO4(3-)-P) were the main water environment factors driving the formation of the periphyton community structure in the water system. The health assessment of the water system based on P-IBI and QHEI was basically in consistency, though the assessment of several reaches had large discrepancy. Overall, the Suzi River at the upper reaches of the water system had a better health status, while the upper reaches of Hunhe River and the main stream of Hunhe River at its middle and lower reaches were worse in health.

  14. Biological analysis of chronic lymphocytic leukemia: integration of mRNA and microRNA expression profiles.

    Science.gov (United States)

    Dong, L; Bi, K H; Huang, N; Chen, C Y

    2016-01-08

    Chronic lymphocytic leukemia (CLL) is a disease that involves progressive accumulation of nonfunctioning lymphocytes and has a low cure rate. There is an urgent requirement to determine the molecular mechanism underlying this disease in order to improve the early diagnosis and treatment of CLL. In this study, genes differentially expressed between CLL samples and age-matched controls were identified using microRNA (miRNA) and mRNA expression profiles. Differentially expressed (DE) miRNA targets were predicted by combining five algorithms. Common genes were obtained on overlapping the DE mRNA and DE miRNA targets. Then, network and module analyses were performed. A total of 239 miRNA targets were predicted and 357 DE mRNAs were obtained. On intersecting miRNA targets and DE mRNAs, 33 common genes were obtained. The protein-protein interaction network and module analysis identified several crucial genes and modules that might be associated with the development of CLL. These DE mRNAs were significantly enriched in the hematopoietic cell lineage (P = 2.58E-4), mitogen-activated protein kinase signaling pathway (P = 0.0025), and leukocyte transendothelial migration pathway (P = 0.0026). Thus, we conducted biological analysis on integration of DE mRNAs and DE miRNAs in CLL, determined gene expression patterns, and screened out several important genes that might be related to CLL.

  15. Plants in silico: why, why now and what?--an integrative platform for plant systems biology research.

    Science.gov (United States)

    Zhu, Xin-Guang; Lynch, Jonathan P; LeBauer, David S; Millar, Andrew J; Stitt, Mark; Long, Stephen P

    2016-05-01

    A paradigm shift is needed and timely in moving plant modelling from largely isolated efforts to a connected community endeavour that can take full advantage of advances in computer science and in mechanistic understanding of plant processes. Plants in silico (Psi) envisions a digital representation of layered dynamic modules, linking from gene networks and metabolic pathways through to cellular organization, tissue, organ and whole plant development, together with resource capture and use efficiency in dynamic competitive environments, ultimately allowing a mechanistically rich simulation of the plant or of a community of plants in silico. The concept is to integrate models or modules from different layers of organization spanning from genome to phenome to ecosystem in a modular framework allowing the use of modules of varying mechanistic detail representing the same biological process. Developments in high-performance computing, functional knowledge of plants, the internet and open-source version controlled software make achieving the concept realistic. Open source will enhance collaboration and move towards testing and consensus on quantitative theoretical frameworks. Importantly, Psi provides a quantitative knowledge framework where the implications of a discovery at one level, for example, single gene function or developmental response, can be examined at the whole plant or even crop and natural ecosystem levels.

  16. Ozone-biological activated carbon integrated treatment for removal of precursors of halogenated nitrogenous disinfection by-products.

    Science.gov (United States)

    Chu, Wenhai; Gao, Naiyun; Yin, Daqiang; Deng, Yang; Templeton, Michael R

    2012-03-01

    Pilot-scale tests were performed to reduce the formation of several nitrogenous and carbonaceous disinfection by-products (DBPs) with an integrated ozone and biological activated carbon (O(3)-BAC) treatment process following conventional water treatment processes (coagulation-sedimentation-filtration). Relative to the conventional processes alone, O(3)-BAC significantly improved the removal of turbidity, dissolved organic carbon, UV(254), NH(4)(+) and dissolved organic nitrogen from 98-99%, 58-72%, 31-53%, 16-93% and 35-74%, respectively, and enhanced the removal efficiency of the precursors for the measured DBPs. The conventional process was almost ineffective in removing the precursors of trichloronitromethane (TCNM) and dichloroacetamide (DCAcAm). Ozonation could not substantially reduce the formation of DCAcAm, and actually increased the formation potential of TCNM; it chemically altered the molecular structures of the precursors and increased the biodegradability of N-containing organic compounds. Consequently, the subsequent BAC filtration substantially reduced the formation of the both TCNM and DCAcAm, thus highlighting a synergistic effect of O(3) and BAC. Additionally, O(3)-BAC was effective at controlling the formation of the total organic halogen, which can be considered as an indicator of the formation of unidentified DBPs.

  17. Development of an Integrated Microfluidic Perfusion Cell Culture System for Real-Time Microscopic Observation of Biological Cells

    Directory of Open Access Journals (Sweden)

    Chih-Chin Oh-Yang

    2011-08-01

    Full Text Available This study reports an integrated microfluidic perfusion cell culture system consisting of a microfluidic cell culture chip, and an indium tin oxide (ITO glass-based microheater chip for micro-scale perfusion cell culture, and its real-time microscopic observation. The system features in maintaining both uniform, and stable chemical or thermal environments, and providing a backflow-free medium pumping, and a precise thermal control functions. In this work, the performance of the medium pumping scheme, and the ITO glass microheater were experimentally evaluated. Results show that the medium delivery mechanism was able to provide pumping rates ranging from 15.4 to 120.0 μL·min−1. In addition, numerical simulation and experimental evaluation were conducted to verify that the ITO glass microheater was capable of providing a spatially uniform thermal environment, and precise temperature control with a mild variation of ±0.3 °C. Furthermore, a perfusion cell culture was successfully demonstrated, showing the cultured cells were kept at high cell viability of 95 ± 2%. In the process, the cultured chondrocytes can be clearly visualized microscopically. As a whole, the proposed cell culture system has paved an alternative route to carry out real-time microscopic observation of biological cells in a simple, user-friendly, and low cost manner.

  18. SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance.

    Science.gov (United States)

    Chowbina, Sudhir; Hammamieh, Rasha; Kumar, Raina; Chakraborty, Nabarun; Yang, Ruoting; Mudunuri, Uma; Jett, Marti; Palma, Joseph M; Stephens, Robert

    2013-01-01

    SysBioCube is an integrated data warehouse and analysis platform for experimental data relating to diseases of military relevance developed for the US Army Medical Research and Materiel Command Systems Biology Enterprise (SBE). It brings together, under a single database environment, pathophysio-, psychological, molecular and biochemical data from mouse models of post-traumatic stress disorder and (pre-) clinical data from human PTSD patients.. SysBioCube will organize, centralize and normalize this data and provide an access portal for subsequent analysis to the SBE. It provides new or expanded browsing, querying and visualization to provide better understanding of the systems biology of PTSD, all brought about through the integrated environment. We employ Oracle database technology to store the data using an integrated hierarchical database schema design. The web interface provides researchers with systematic information and option to interrogate the profiles of pan-omics component across different data types, experimental designs and other covariates.

  19. Extensive gaps and biases in our knowledge of a well-known fauna: Implications for integrating biological traits into macroecology

    KAUST Repository

    Tyler, Elizabeth

    2011-12-09

    Aim Ecologists seeking to describe patterns at ever larger scales require compilations of data on the global abundance and distribution of species. Comparable compilations of biological data are needed to elucidate the mechanisms behind these patterns, but have received far less attention. We assess the availability of biological data across an entire assemblage: the well-documented demersal marine fauna of the United Kingdom. We also test whether data availability for a species depends on its taxonomic group, maximum body size, the number of times it has been recorded in a global biogeographic database, or its commercial and conservation importance. Location Seas of the United Kingdom. Methods We defined a demersal marine fauna of 973 species from 15 phyla and 40 classes using five extensive surveys around the British Isles. We then quantified the availability of data on eight key biological traits (termed biological knowledge) for each species from online databases. Relationships between biological knowledge and our predictors were tested with generalized linear models. Results Full data on eight fundamental biological traits exist for only 9% (n= 88) of the UK demersal marine fauna, and 20% of species completely lack data. Clear trends in our knowledge exist: fish (median biological knowledge score = six traits) are much better known than invertebrates (one trait). Biological knowledge increases with biogeographic knowledge and (to a lesser extent) with body size, and is greater in species that are commercially exploited or of conservation concern. Main conclusions Our analysis reveals deep ignorance of the basic biology of a well-studied fauna, highlighting the need for far greater efforts to compile biological trait data. Clear biases in our knowledge, relating to how well sampled or \\'important\\' species are suggests that caution is required in extrapolating small subsets of biologically well-known species to ecosystem-level studies. © 2011 Blackwell

  20. IsoBED: a tool for automatic calculation of biologically equivalent fractionation schedules in radiotherapy using IMRT with a simultaneous integrated boost (SIB) technique

    OpenAIRE

    2011-01-01

    Abstract Background An advantage of the Intensity Modulated Radiotherapy (IMRT) technique is the feasibility to deliver different therapeutic dose levels to PTVs in a single treatment session using the Simultaneous Integrated Boost (SIB) technique. The paper aims to describe an automated tool to calculate the dose to be delivered with the SIB-IMRT technique in different anatomical regions that have the same Biological Equivalent Dose (BED), i.e. IsoBED, compared to the standard fractionation....

  1. Fluorescent biological aerosol particles measured with the Waveband Integrated Bioaerosol Sensor WIBS-4: laboratory tests combined with a one year field study

    Directory of Open Access Journals (Sweden)

    E. Toprak

    2013-01-01

    Full Text Available In this paper bioaerosol measurements conducted with the Waveband Integrated Bioaerosol Sensor mark 4 (WIBS-4 are presented. The measurements comprise aerosol chamber characterization experiments and a one-year ambient measurement period at a semi-rural site in South Western Germany. This study aims to investigate the sensitivity of WIBS-4 to biological and non-biological aerosols and detection of biological particles in the ambient aerosol. Several types of biological and non-biological aerosol samples, including fungal spores, bacteria, mineral dust, ammonium sulphate, combustion soot, and fluorescent polystyrene spheres, were analyzed by WIBS-4 in the laboratory. The results confirm the sensitivity of the ultraviolet light-induced fluorescence (UV-LIF method to biological fluorophores and show the good discrimination capabilities of the two excitation wavelengths/detection wavebands method applied in WIBS-4. However, a weak cross-sensitivity to non-biological fluorescent interferers remains and is discussed in this paper.

    All the laboratory studies have been undertaken in order to prepare WIBS-4 for ambient aerosol measurements. According to the one-year ambient aerosol study, number concentration of fluorescent biological aerosol particles (FBAP show strong seasonal and diurnal variability. The highest number concentration of FBAP was measured during the summer term and decreased towards the winter period when colder and drier conditions prevail. Diurnal FBAP concentrations start to increase after sunset and reach maximum values during the late night and early morning hours. On the other hand, the total aerosol number concentration was almost always higher during daytime than during nighttime and a sharp decrease after sunset was observed. There was no correlation observed between the FBAP concentration and the meteorological parameters temperature, precipitation, wind direction and wind speed. However, a clear correlation was

  2. Fluorescent biological aerosol particles measured with the Waveband Integrated Bioaerosol Sensor WIBS-4: laboratory tests combined with a one year field study

    Science.gov (United States)

    Toprak, E.; Schnaiter, M.

    2013-01-01

    In this paper bioaerosol measurements conducted with the Waveband Integrated Bioaerosol Sensor mark 4 (WIBS-4) are presented. The measurements comprise aerosol chamber characterization experiments and a one-year ambient measurement period at a semi-rural site in South Western Germany. This study aims to investigate the sensitivity of WIBS-4 to biological and non-biological aerosols and detection of biological particles in the ambient aerosol. Several types of biological and non-biological aerosol samples, including fungal spores, bacteria, mineral dust, ammonium sulphate, combustion soot, and fluorescent polystyrene spheres, were analyzed by WIBS-4 in the laboratory. The results confirm the sensitivity of the ultraviolet light-induced fluorescence (UV-LIF) method to biological fluorophores and show the good discrimination capabilities of the two excitation wavelengths/detection wavebands method applied in WIBS-4. However, a weak cross-sensitivity to non-biological fluorescent interferers remains and is discussed in this paper. All the laboratory studies have been undertaken in order to prepare WIBS-4 for ambient aerosol measurements. According to the one-year ambient aerosol study, number concentration of fluorescent biological aerosol particles (FBAP) show strong seasonal and diurnal variability. The highest number concentration of FBAP was measured during the summer term and decreased towards the winter period when colder and drier conditions prevail. Diurnal FBAP concentrations start to increase after sunset and reach maximum values during the late night and early morning hours. On the other hand, the total aerosol number concentration was almost always higher during daytime than during nighttime and a sharp decrease after sunset was observed. There was no correlation observed between the FBAP concentration and the meteorological parameters temperature, precipitation, wind direction and wind speed. However, a clear correlation was identified between the FBAP

  3. Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of three-dimensional catalytic electro-Fenton and membrane bioreactor.

    Science.gov (United States)

    Jia, Shengyong; Han, Hongjun; Hou, Baolin; Zhuang, Haifeng

    2015-12-01

    Laboratorial scale experiments were conducted to investigate a novel system three-dimensional catalytic electro-Fenton (3DCEF, catalyst of sewage sludge based activated carbon which loaded Fe3O4) integrating with membrane bioreactor (3DCEF-MBR) on advanced treatment of biologically pretreated coal gasification wastewater. The results indicated that 3DCEF-MBR represented high efficiencies in eliminating COD and total organic carbon, giving the maximum removal efficiencies of 80% and 75%, respectively. The integrated 3DCEF-MBR system significantly reduced the transmembrane pressure, giving 35% lower than conventional MBR after 30 days operation. The enhanced hydroxyl radical oxidation and bacteria self repair function were the mechanisms for 3DCEF-MBR performance. Therefore, the integrated 3DCEF-MBR was expected to be the promising technology for advanced treatment in engineering applications.

  4. 'More than two': integrating biological control and sterile insects, from factory to field, and the possibility of its implementation in Argentina

    Energy Technology Data Exchange (ETDEWEB)

    Cladera, Jorge L.; Viscarret, Mariana M.; Carabajal Paladino, Leonela Z.; Pietrek, Alejandro [Instituto de Tecnologia Agropecuaria (INTA), Castelar (Argentina). Inst. de Genetica; Soria, M. Alejandra; Ovruski, Sergio M. [Consejo Nacional de Investigaciones Cientificas y Tecnicas (PROIMI/CONICET), Tucuman (Argentina). Planta Piloto de Procesos Industrials Microbiolo

    2006-07-01

    No single control measure is able to provide full control of a pest. Integration of techniques like the sterile insect (SIT) with biological control practices (BC) should be intensively sough for. This possibility is revised here in connection with the fruit fly pest problems in Argentina. Theoretical reasons as well as practical conveniences for this integration are reviewed in this paper, the intention of which is to promote a discussion on how to approach the experimental study of the SIT+CB integration problem, i.e. how to measure the effects of each separate control measure as well as that of both acting together, in a repeatable manner. Arguments are advanced in favor of the joint production and releases of sterile fruit flies and parasitoids. (author)

  5. Biological stress response terminology: Integrating the concepts of adaptive response and preconditioning stress within a hormetic dose-response framework.

    Science.gov (United States)

    Calabrese, Edward J; Bachmann, Kenneth A; Bailer, A John; Bolger, P Michael; Borak, Jonathan; Cai, Lu; Cedergreen, Nina; Cherian, M George; Chiueh, Chuang C; Clarkson, Thomas W; Cook, Ralph R; Diamond, David M; Doolittle, David J; Dorato, Michael A; Duke, Stephen O; Feinendegen, Ludwig; Gardner, Donald E; Hart, Ronald W; Hastings, Kenneth L; Hayes, A Wallace; Hoffmann, George R; Ives, John A; Jaworowski, Zbigniew; Johnson, Thomas E; Jonas, Wayne B; Kaminski, Norbert E; Keller, John G; Klaunig, James E; Knudsen, Thomas B; Kozumbo, Walter J; Lettieri, Teresa; Liu, Shu-Zheng; Maisseu, Andre; Maynard, Kenneth I; Masoro, Edward J; McClellan, Roger O; Mehendale, Harihara M; Mothersill, Carmel; Newlin, David B; Nigg, Herbert N; Oehme, Frederick W; Phalen, Robert F; Philbert, Martin A; Rattan, Suresh I S; Riviere, Jim E; Rodricks, Joseph; Sapolsky, Robert M; Scott, Bobby R; Seymour, Colin; Sinclair, David A; Smith-Sonneborn, Joan; Snow, Elizabeth T; Spear, Linda; Stevenson, Donald E; Thomas, Yolene; Tubiana, Maurice; Williams, Gary M; Mattson, Mark P

    2007-07-01

    Many biological subdisciplines that regularly assess dose-response relationships have identified an evolutionarily conserved process in which a low dose of a stressful stimulus activates an adaptive response that increases the resistance of the cell or organism to a moderate to severe level of stress. Due to a lack of frequent interaction among scientists in these many areas, there has emerged a broad range of terms that describe such dose-response relationships. This situation has become problematic because the different terms describe a family of similar biological responses (e.g., adaptive response, preconditioning, hormesis), adversely affecting interdisciplinary communication, and possibly even obscuring generalizable features and central biological concepts. With support from scientists in a broad range of disciplines, this article offers a set of recommendations we believe can achieve greater conceptual harmony in dose-response terminology, as well as better understanding and communication across the broad spectrum of biological disciplines.

  6. Toward an Integration of Psychologic, Social, and Biologic Factors in Depression: Effects on Outcome and Course of Cognitive Therapy.

    Science.gov (United States)

    Simons, Anne D.; And Others

    1995-01-01

    Integrates key variables from three major domains (cognition, stress, and psychobiology) that are typically studied separately. Dysfunctional attitudes, negative life events, or sleep electroencephalogram were assessed in 53 outpatients before treatment with cognitive therapy. Results are discussed in terms of the promise of integrative research.…

  7. 'Integration'

    DEFF Research Database (Denmark)

    Olwig, Karen Fog

    2011-01-01

    After a long history dominated by out-migration, Denmark, Norway and Sweden have, in the past 50 years, become immigration societies. This article compares how these Scandinavian welfare societies have sought to incorporate immigrants and refugees into their national communities. It suggests that......, while the countries have adopted disparate policies and ideologies, differences in the actual treatment and attitudes towards immigrants and refugees in everyday life are less clear, due to parallel integration programmes based on strong similarities in the welfare systems and in cultural notions...... of equality in the three societies. Finally, it shows that family relations play a central role in immigrants’ and refugees’ establishment of a new life in the receiving societies, even though the welfare society takes on many of the social and economic functions of the family....

  8. Combined Pre-Precipitation, Biological Sludge Hydrolysis and Nitrogen Reduction - A Pilot Demonstration of Integrated Nutrient Removal

    DEFF Research Database (Denmark)

    Kristensen, G. H.; Jørgensen, P. E.; Strube, R.

    1992-01-01

    A pilot study was performed to investigate advanced wastewater treatment by pre-precipitation in combination with biological nitrogen removal supported by biological sludge hydrolysis. The influent wastewater was pretreated by addition of a pre-polymerized aluminum salt, followed by flocculation...... solubilization was 10-13% of the suspended COD. The liquid phase of the hydrolyzed sludge, the hydrolysate, was separated from the suspended fraction by centrifugation and added to the biological nitrogen removal stage to support denitrification. The hydrolysate COD consisted mainly of volatile fatty acids......, resulting in high denitrification rates. Nitrogen reduction was performed based on the Bio-Denitro principle in an activated sludge system. Nitrogen was reduced from 45 mg/l to 9 mg/l and phosphorus was reduced from 11 mg/l to 0.5 mg/l. The sludge yield was low, approx. 0.3-0.4 gCOD/gCOD removed...

  9. From systems biology to photosynthesis and whole-plant modeling: a conceptual model for integrating multi-scale networks

    Energy Technology Data Exchange (ETDEWEB)

    Weston, David [ORNL; Hanson, Paul J [ORNL; Norby, Richard J [ORNL; Tuskan, Gerald A [ORNL; Wullschleger, Stan D [ORNL

    2012-01-01

    Network analysis is now a common statistical tool for molecular biologists. Network algorithms are readily used to model gene, protein and metabolic correlations providing insight into pathways driving biological phenomenon. One output from such an analysis is a candidate gene list that can be responsible, in part, for the biological process of interest. The question remains, however, as to whether molecular network analysis can be used to inform process models at higher levels of biological organization. In our previous work, transcriptional networks derived from three plant species were constructed, interrogated for orthology and then correlated to photosynthetic inhibition at elevated temperature. One unique aspect of that study was the link from co-expression networks to net photosynthesis. In this addendum, we propose a conceptual model where traditional network analysis can be linked to whole-plant models thereby informing predictions on key processes such as photosynthesis, nutrient uptake and assimilation, and C partitioning.

  10. [Effect of cytokines and stromal cells of adipose tissue on integration of a two-component composite net imlant into biological tissues].

    Science.gov (United States)

    Dubinina, V G; Chetverikov, S G; Luk'ianchuk, O V; Rosha, L G; Sazhienko, V V; Lysenko, M A; Mikhaĭlov, A S; Chetverikov, M S

    2014-02-01

    Morphological changes in biological tissues, surrounding the composite net-like implant, owing large pores "Ultrapro", and also its combination with adipose transplant, fibrin, enriched with thrombocytes, were studied in experiment on 36 adult male rats of a Wistar line. While application of such construction the processes of creation and organization of connective tissue, neoangiogenesis as well as development of a new adipose tissue are improved. As a consequence of increase of concentration of highly active biological substances and regenerative cytokines in combination of the net implant with adipose transplant, containing multipotent stem cells, proliferative activity of all cellular elements, surrounding the net implant, is raising, what predispose its optimal integration into surrounding tissues.

  11. Comparison of single-photon counting and charge-integrating detectors for X-ray high-resolution imaging of small biological objects

    Science.gov (United States)

    Frallicciardi, Paola Maria; Jakubek, Jan; Vavrik, Daniel; Dammer, Jiri

    2009-08-01

    This work presents a direct comparison of two pixel detectors: a charge-integrating flat panel imager coupled to a CsI:Tl scintillator and a hybrid silicon detector of Medipix2 type, working in a single-photon counting mode. The comparison concerns image quality in terms of system-spatial resolution, signal-to-noise ratio and contrast in imaging of small biological objects. It will be shown that, at photon energies below 40 keV and for low attenuating biological objects, single-photon counting detectors are more appropriate for small-animal imaging than flat panel devices right due to better spatial resolution, signal-to-noise ratio and contrast.

  12. Bio-sequestration of CO2 Using Carbonic Anhydrase in situ Encapsulated Inside Electrospun Hollow Fibers%静电纺丝制备中空纤维原位固定化碳酸酐酶用于二氧化碳的吸收

    Institute of Scientific and Technical Information of China (English)

    崔建东; 李莹; 姬晓元; 边红杰; 张羽飞; 苏志国; 马光辉; 张松平

    2014-01-01

    Carbonic anhydrase catalyzed bio-sequestration of CO2 to form HCO-3 , followed by trapping as solid CaCO3 is one of the most promising technologies for CO2 capturing. The effects of reaction condition on the CO2 hydration using free carbonic anhydrase were systematically investigated. In order to improve the stability of the enzyme and facility its recycling, the carbonic anhydrase was in situ encapsulated inside hollow fibers via a novel co-axial electrospinning technology. Compared with the free enzyme, the immobilized carbonic an-hydrase showed much improved thermal stability and suffered much reduced inhibitory effects from cation ions, such as Cu2+ and Fe3+. After 11 reuses, the immobilized enzyme retained about 81. 9% of its original activity by comparing the amount of formed CaCO3 precipitation. In the presence of immobilized carbonic anhydrase, both calcite and vaterite CaCO3 solid were formed;while in the absence of enzyme or with free carbonic anhy-drase, only calcite CaCO3 was observed.%考察了游离碳酸酐酶吸收CO2水合体系反应条件,并通过同轴共纺静电纺丝技术制备出中空结构纤维,实现了碳酸酐酶在中空纤维中的原位包埋,提高了酶的稳定性并便于回收和重复利用.实验结果表明,固定化碳酸酐酶的热稳定性显著增强,受Cu2+和Fe3+等金属离子的抑制作用大幅度降低.连续使用11次后所生成的CaCO3沉淀量仍能达到首次使用的81.9%.固定化酶体系生成的CaCO3沉淀包括方解石型和球文石型2种晶形,而无酶和加入游离碳酸酐酶的反应体系则主要生成方解石型CaCO3沉淀.

  13. Integrated analysis of microRNA and mRNA expression: Adding biological significance to microRNA target predictions

    NARCIS (Netherlands)

    M. van Iterson (Mat); S. Bervoets (Sander); E.J. de Meijer (Emile); H.P. Buermans (Henk); P.A.C. 't Hoen (Peter); R.X. Menezes (Renée); J.M. Boer (Judith)

    2013-01-01

    textabstractCurrent microRNA target predictions are based on sequence information and empirically derived rules but do not make use of the expression of microRNAs and their targets. This study aimed to improve microRNA target predictions in a given biological context, using in silico predictions, mi

  14. The Effects of Meiosis/Genetics Integration and Instructional Sequence on College Biology Student Achievement in Genetics.

    Science.gov (United States)

    Browning, Mark

    The purpose of the research was to manipulate two aspects of genetics instruction in order to measure their effects on college, introductory biology students' achievement in genetics. One instructional sequence that was used dealt first with monohybrid autosomal inheritance patterns, then sex-linkage. The alternate sequence was the reverse.…

  15. Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications

    Science.gov (United States)

    The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-based clones to expres...

  16. Integrated catalytic wet air oxidation and aerobic biological treatment in a municipal WWTP of a high-strength o-cresol wastewater.

    Science.gov (United States)

    Suarez-Ojeda, María Eugenia; Guisasola, Albert; Baeza, Juan A; Fabregat, Azael; Stüber, Frank; Fortuny, Agustí; Font, Josep; Carrera, Julián

    2007-02-01

    This study examines the feasibility of coupling a Catalytic Wet Air Oxidation (CWAO), with activated carbon (AC) as catalyst, and an aerobic biological treatment to treat a high-strength o-cresol wastewater. Two goals are pursued: (a) To determine the effect of the main AC/CWAO intermediates on the activated sludge of a municipal WasteWater Treatment Plant (WWTP) and (b) To demonstrate the feasibility of coupling the AC/CWAO effluent as a part of the influent of a municipal WWTP. In a previous study, a high-strength o-cresol wastewater was treated by AC/CWAO aiming to establish the distribution of intermediates and the biodegradability enhancement. In this work, the biodegradability, toxicity and inhibition of the most relevant intermediates detected in the AC/CWAO effluent were determined by respirometry. Also, the results of a pilot scale municipal WWTP study for an integrated AC/CWAO-aerobic biological treatment of this effluent are presented. The biodegradation parameters (i.e. maximum oxygen uptake rate and oxygen consumption) of main AC/CWAO intermediates allowed the classification of the intermediates into readily biodegradable, inert or toxic/inhibitory compounds. This detailed study, allowed to understand the biodegradability enhancement exhibited by an AC/CWAO effluent and to achieve a successful strategy for coupling the AC/CWAO step with an aerobic biological treatment for a high-strength o-cresol wastewater. Using 30%, as COD, of AC/CWAO effluent in the inlet to the pilot scale WWTP, the integrated AC/CWAO-biological treatment achieved a 98% of total COD removal and, particularly, a 91% of AC/CWAO effluent COD removal without any undesirable effect on the biomass.

  17. Fluorescent biological aerosol particles (FBAPs measured with the Waveband Integrated Bioaerosol Sensor WIBS-4: laboratory tests combined with a one year field study

    Directory of Open Access Journals (Sweden)

    E. Toprak

    2012-07-01

    Full Text Available In this paper bioaerosol measurements conducted with the Waveband Integrated Bioaerosol Sensor mark 4 (WIBS-4 are presented. The measurements comprise aerosol chamber characterization experiments and a one-year ambient measurement period at a semi-rural site in South Western Germany. This study aims to investigate the sensitivity of WIBS-4 to biological and non-biological aerosols, performance of WIBS-4 for discrimination of several types of aerosols, and the detection and identification of biological particles in the ambient aerosol. Several types of biological and non-biological aerosol samples including spores, bacteria, pollen, mineral dust, ammonium sulphate, combustion soot, and fluorescent polystyrene spheres were analysed by WIBS-4 in the laboratory. The results confirm the sensitivity of the Ultra Violet Light Induced Fluorescence (UV-LIF method to biological fluorophores and show the good discrimination capabilities of the two wavelengths excitation/two wavebands detection method applied in WIBS-4. However, a weak cross-sensitivity to non-biological fluorescent interferers remains and is discussed in this paper.

    All the laboratory studies have been undertaken in order to prepare WIBS-4 for ambient aerosol measurements. According to the one year ambient aerosol study, number concentration of fluorescent biological aerosol particles (FBAP show strong seasonal and diurnal variability. The highest number concentration of FBAP was measured during the summer term and it decreases towards the winter period when colder and drier conditions are prevailing. Diurnal FBAP concentrations start to increase after sunset and reach maximum values during the late night and early morning hours. On the other hand the total aerosol number concentration was always higher during day time than during night time and a sharp decrease after sunset was observed. There was no correlation observed between the FBAP concentration and the meteorological

  18. Fluorescent biological aerosol particles (FBAPs) measured with the Waveband Integrated Bioaerosol Sensor WIBS-4: laboratory tests combined with a one year field study

    Science.gov (United States)

    Toprak, E.; Schnaiter, M.

    2012-07-01

    In this paper bioaerosol measurements conducted with the Waveband Integrated Bioaerosol Sensor mark 4 (WIBS-4) are presented. The measurements comprise aerosol chamber characterization experiments and a one-year ambient measurement period at a semi-rural site in South Western Germany. This study aims to investigate the sensitivity of WIBS-4 to biological and non-biological aerosols, performance of WIBS-4 for discrimination of several types of aerosols, and the detection and identification of biological particles in the ambient aerosol. Several types of biological and non-biological aerosol samples including spores, bacteria, pollen, mineral dust, ammonium sulphate, combustion soot, and fluorescent polystyrene spheres were analysed by WIBS-4 in the laboratory. The results confirm the sensitivity of the Ultra Violet Light Induced Fluorescence (UV-LIF) method to biological fluorophores and show the good discrimination capabilities of the two wavelengths excitation/two wavebands detection method applied in WIBS-4. However, a weak cross-sensitivity to non-biological fluorescent interferers remains and is discussed in this paper. All the laboratory studies have been undertaken in order to prepare WIBS-4 for ambient aerosol measurements. According to the one year ambient aerosol study, number concentration of fluorescent biological aerosol particles (FBAP) show strong seasonal and diurnal variability. The highest number concentration of FBAP was measured during the summer term and it decreases towards the winter period when colder and drier conditions are prevailing. Diurnal FBAP concentrations start to increase after sunset and reach maximum values during the late night and early morning hours. On the other hand the total aerosol number concentration was always higher during day time than during night time and a sharp decrease after sunset was observed. There was no correlation observed between the FBAP concentration and the meteorological parameters temperature

  19. Integration of basic biological sciences and clinical dentistry in the dental curriculum. A clinically orientated approach to teaching oral and dental anatomy.

    Science.gov (United States)

    Gotjamanos, T

    1990-06-01

    Although dental curricula have undergone significant revision during the past three decades, the problem of linking basic science with clinical dentistry often remains an unmet challenge in dental education. This paper describes the content and method of presentation of a course in oral and dental anatomy which aims to integrate closely basic biological science and clinical dental practice. The course holds considerable promise for overcoming one of the major deficiencies of the horizontally structured curriculum by presenting basic science information and detailing its clinical relevance simultaneously. The academic background, clinical experience, and educational philosophy of the course co-ordinator and assisting teaching staff are undoubtedly important factors in determining the extent to which integration between basic and clinical science can be achieved.

  20. Application of hierarchical dissociated neural network in closed-loop hybrid system integrating biological and mechanical intelligence.

    Directory of Open Access Journals (Sweden)

    Yongcheng Li

    Full Text Available Neural networks are considered the origin of intelligence in organisms. In this paper, a new design of an intelligent system merging biological intelligence with artificial intelligence was created. It was based on a neural controller bidirectionally connected to an actual mobile robot to implement a novel vehicle. Two types of experimental preparations were utilized as the neural controller including 'random' and '4Q' (cultured neurons artificially divided into four interconnected parts neural network. Compared to the random cultures, the '4Q' cultures presented absolutely different activities, and the robot controlled by the '4Q' network presented better capabilities in search tasks. Our results showed that neural cultures could be successfully employed to control an artificial agent; the robot performed better and better with the stimulus because of the short-term plasticity. A new framework is provided to investigate the bidirectional biological-artificial interface and develop new strategies for a future intelligent system using these simplified model systems.

  1. Application of hierarchical dissociated neural network in closed-loop hybrid system integrating biological and mechanical intelligence.

    Science.gov (United States)

    Li, Yongcheng; Sun, Rong; Zhang, Bin; Wang, Yuechao; Li, Hongyi

    2015-01-01

    Neural networks are considered the origin of intelligence in organisms. In this paper, a new design of an intelligent system merging biological intelligence with artificial intelligence was created. It was based on a neural controller bidirectionally connected to an actual mobile robot to implement a novel vehicle. Two types of experimental preparations were utilized as the neural controller including 'random' and '4Q' (cultured neurons artificially divided into four interconnected parts) neural network. Compared to the random cultures, the '4Q' cultures presented absolutely different activities, and the robot controlled by the '4Q' network presented better capabilities in search tasks. Our results showed that neural cultures could be successfully employed to control an artificial agent; the robot performed better and better with the stimulus because of the short-term plasticity. A new framework is provided to investigate the bidirectional biological-artificial interface and develop new strategies for a future intelligent system using these simplified model systems.

  2. Integration of complex data sources to provide biologic insight into pulmonary vascular disease (2015 Grover Conference Series)

    Science.gov (United States)

    Chan, Stephen Y.

    2016-01-01

    Abstract The application of complex data sources to pulmonary vascular diseases is an emerging and promising area of investigation. The use of -omics platforms, in silico modeling of gene networks, and linkage of large human cohorts with DNA biobanks are beginning to bear biologic insight into pulmonary hypertension. These approaches to high-throughput molecular phenotyping offer the possibility of discovering new therapeutic targets and identifying variability in response to therapy that can be leveraged to improve clinical care. Optimizing the methods for analyzing complex data sources and accruing large, well-phenotyped human cohorts linked to biologic data remain significant challenges. Here, we discuss two specific types of complex data sources—gene regulatory networks and DNA-linked electronic medical record cohorts—that illustrate the promise, challenges, and current limitations of these approaches to understanding and managing pulmonary vascular disease. PMID:27683602

  3. Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

    Energy Technology Data Exchange (ETDEWEB)

    Vavpetič, P., E-mail: primoz.vavpetic@ijs.si [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Vogel-Mikuš, K. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Jeromel, L. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Ogrinc Potočnik, N. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); FOM-Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); Pongrac, P. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Department of Plant Physiology, University of Bayreuth, Universitätstr. 30, 95447 Bayreuth (Germany); Drobne, D.; Pipan Tkalec, Ž.; Novak, S.; Kos, M.; Koren, Š.; Regvar, M. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Pelicon, P. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia)

    2015-04-01

    The analysis of biological samples in frozen-hydrated state with micro-PIXE technique at Jožef Stefan Institute (JSI) nuclear microprobe has matured to a point that enables us to measure and examine frozen tissue samples routinely as a standard research method. Cryotome-cut slice of frozen-hydrated biological sample is mounted between two thin foils and positioned on the sample holder. The temperature of the cold stage in the measuring chamber is kept below 130 K throughout the insertion of the samples and the proton beam exposure. Matrix composition of frozen-hydrated tissue is consisted mostly of ice. Sample deterioration during proton beam exposure is monitored during the experiment, as both Elastic Backscattering Spectrometry (EBS) and Scanning Transmission Ion Microscopy (STIM) in on–off axis geometry are recorded together with the events in two PIXE detectors and backscattered ions from the chopper in a single list-mode file. The aim of this experiment was to determine differences and similarities between two kinds of biological sample preparation techniques for micro-PIXE analysis, namely freeze-drying and frozen-hydrated sample preparation in order to evaluate the improvements in the elemental localisation of the latter technique if any. In the presented work, a standard micro-PIXE configuration for tissue mapping at JSI was used with five detection systems operating in parallel, with proton beam cross section of 1.0 × 1.0 μm{sup 2} and a beam current of 100 pA. The comparison of the resulting elemental distributions measured at the biological tissue prepared in the frozen-hydrated and in the freeze-dried state revealed differences in elemental distribution of particular elements at the cellular level due to the morphology alteration in particular tissue compartments induced either by water removal in the lyophilisation process or by unsatisfactory preparation of samples for cutting and mounting during the shock-freezing phase of sample preparation.

  4. Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

    Science.gov (United States)

    Vavpetič, P.; Vogel-Mikuš, K.; Jeromel, L.; Ogrinc Potočnik, N.; Pongrac, P.; Drobne, D.; Pipan Tkalec, Ž.; Novak, S.; Kos, M.; Koren, Š.; Regvar, M.; Pelicon, P.

    2015-04-01

    The analysis of biological samples in frozen-hydrated state with micro-PIXE technique at Jožef Stefan Institute (JSI) nuclear microprobe has matured to a point that enables us to measure and examine frozen tissue samples routinely as a standard research method. Cryotome-cut slice of frozen-hydrated biological sample is mounted between two thin foils and positioned on the sample holder. The temperature of the cold stage in the measuring chamber is kept below 130 K throughout the insertion of the samples and the proton beam exposure. Matrix composition of frozen-hydrated tissue is consisted mostly of ice. Sample deterioration during proton beam exposure is monitored during the experiment, as both Elastic Backscattering Spectrometry (EBS) and Scanning Transmission Ion Microscopy (STIM) in on-off axis geometry are recorded together with the events in two PIXE detectors and backscattered ions from the chopper in a single list-mode file. The aim of this experiment was to determine differences and similarities between two kinds of biological sample preparation techniques for micro-PIXE analysis, namely freeze-drying and frozen-hydrated sample preparation in order to evaluate the improvements in the elemental localisation of the latter technique if any. In the presented work, a standard micro-PIXE configuration for tissue mapping at JSI was used with five detection systems operating in parallel, with proton beam cross section of 1.0 × 1.0 μm2 and a beam current of 100 pA. The comparison of the resulting elemental distributions measured at the biological tissue prepared in the frozen-hydrated and in the freeze-dried state revealed differences in elemental distribution of particular elements at the cellular level due to the morphology alteration in particular tissue compartments induced either by water removal in the lyophilisation process or by unsatisfactory preparation of samples for cutting and mounting during the shock-freezing phase of sample preparation.

  5. Determining sexual dimorphism in frog measurement data: integration of statistical significance, measurement error, effect size and biological significance

    Directory of Open Access Journals (Sweden)

    Hayek Lee-Ann C.

    2005-01-01

    Full Text Available Several analytic techniques have been used to determine sexual dimorphism in vertebrate morphological measurement data with no emergent consensus on which technique is superior. A further confounding problem for frog data is the existence of considerable measurement error. To determine dimorphism, we examine a single hypothesis (Ho = equal means for two groups (females and males. We demonstrate that frog measurement data meet assumptions for clearly defined statistical hypothesis testing with statistical linear models rather than those of exploratory multivariate techniques such as principal components, correlation or correspondence analysis. In order to distinguish biological from statistical significance of hypotheses, we propose a new protocol that incorporates measurement error and effect size. Measurement error is evaluated with a novel measurement error index. Effect size, widely used in the behavioral sciences and in meta-analysis studies in biology, proves to be the most useful single metric to evaluate whether statistically significant results are biologically meaningful. Definitions for a range of small, medium, and large effect sizes specifically for frog measurement data are provided. Examples with measurement data for species of the frog genus Leptodactylus are presented. The new protocol is recommended not only to evaluate sexual dimorphism for frog data but for any animal measurement data for which the measurement error index and observed or a priori effect sizes can be calculated.

  6. The use of innate immune responses as biomarkers in a programme of integrated biological effects monitoring on flounder (Platichthys flesus) from the southern North Sea

    Science.gov (United States)

    Skouras, Andreas; Broeg, Katja; Dizer, Halim; von Westernhagen, Hein; Hansen, Peter-Diedrich; Steinhagen, Dieter

    2003-10-01

    Immunological biomarkers that reflect the effects of exposure to environmental contaminants in coastal marine habitats were sought in European flounder (Platichthys flesus) from five locations in the German Bight with different anthropogenic impacts. During a 2-year period of sampling, innate immune responses were monitored from a total of 331 individual flounder of a body length of 18 to 25 cm. From the fish, plasma lysozyme, phagocytosis and respiratory burst activity of head kidney leucocytes were analysed and implemented as part of an integrated biological effects monitoring programme. As the measurements of the parameters applied here varied within wide ranges at some locations, spatial differences could not always be established, but some general trends could be drawn: plasma lysozyme activity was decreased in flounder contaminated with DDT adducts and some PCBs, while cellular functions such as phagocytosis and respiratory burst were stimulated by some chlorinated hydrocarbons. Correlation analysis also revealed connections not only between the parameters applied here and some contaminants but also with some biochemical parameters used as biomarkers in pollution monitoring: in flounder with decreased integrity of hepatocyte lysosomal membranes, immune functions also were impaired, and plasma lysozyme as well as phagocytosis activity of head kidney cells were impaired when the activity of cytochrome P450 1A was induced. The data presented here indicate that innate immune responses may be useful parameters to monitor cellular functions in a battery of biomarkers of different levels of biological organisation.

  7. Integrative analyses of miRNA and proteomics identify potential biological pathways associated with onset of pulmonary fibrosis in the bleomycin rat model

    Energy Technology Data Exchange (ETDEWEB)

    Fukunaga, Satoki [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-Naka, Konohana-ku, Osaka 554-8558 (Japan); Kakehashi, Anna [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Sumida, Kayo; Kushida, Masahiko; Asano, Hiroyuki [Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-Naka, Konohana-ku, Osaka 554-8558 (Japan); Gi, Min [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Wanibuchi, Hideki, E-mail: wani@med.osaka-cu.ac.jp [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan)

    2015-08-01

    To determine miRNAs and their predicted target proteins regulatory networks which are potentially involved in onset of pulmonary fibrosis in the bleomycin rat model, we conducted integrative miRNA microarray and iTRAQ-coupled LC-MS/MS proteomic analyses, and evaluated the significance of altered biological functions and pathways. We observed that alterations of miRNAs and proteins are associated with the early phase of bleomycin-induced pulmonary fibrosis, and identified potential target pairs by using ingenuity pathway analysis. Using the data set of these alterations, it was demonstrated that those miRNAs, in association with their predicted target proteins, are potentially involved in canonical pathways reflective of initial epithelial injury and fibrogenic processes, and biofunctions related to induction of cellular development, movement, growth, and proliferation. Prediction of activated functions suggested that lung cells acquire proliferative, migratory, and invasive capabilities, and resistance to cell death especially in the very early phase of bleomycin-induced pulmonary fibrosis. The present study will provide new insights for understanding the molecular pathogenesis of idiopathic pulmonary fibrosis. - Highlights: • We analyzed bleomycin-induced pulmonary fibrosis in the rat. • Integrative analyses of miRNA microarray and proteomics were conducted. • We determined the alterations of miRNAs and their potential target proteins. • The alterations may control biological functions and pathways in pulmonary fibrosis. • Our result may provide new insights of pulmonary fibrosis.

  8. Integrated risk assessment for WFD ecological status classification applied to Llobregat river basin (Spain). Part I-Fuzzy approach to aggregate biological indicators.

    Science.gov (United States)

    Gottardo, S; Semenzin, E; Giove, S; Zabeo, A; Critto, A; de Zwart, D; Ginebreda, A; Marcomini, A

    2011-10-15

    Water Framework Directive (WFD) requirements and recommendations for Ecological Status (ES) classification of surface water bodies do not address all issues that Member States have to face in the implementation process, such as selection of appropriate stressor-specific environmental indicators, definition of class boundaries, aggregation of heterogeneous data and information and uncertainty evaluation. In this context the "One-Out, All-Out" (OOAO) principle is the suggested approach to lead the entire classification procedure and ensure conservative results. In order to support water managers in achieving a more comprehensive and realistic evaluation of ES, an Integrated Risk Assessment (IRA) methodology was developed. It is based on the Weight of Evidence approach and implements a Fuzzy Inference System in order to hierarchically aggregate a set of environmental indicators, which are grouped into five Lines of Evidence (i.e. Biology, Chemistry, Ecotoxicology, Physico-chemistry and Hydromorphology). The whole IRA methodology has been implemented as an individual module into a freeware GIS (Geographic Information System)-based Decision Support System (DSS), named MODELKEY DSS. The paper focuses on the conceptual and mathematical procedure underlying the evaluation of the most complex Line of Evidence, i.e. Biology, which identifies the biological communities that are potentially at risk and the stressors that are most likely responsible for the observed alterations. The results obtained from testing the procedure through application of the MODELKEY DSS to the Llobregat case study are reported and discussed.

  9. Sleep as spatiotemporal integration of biological processes that evolved to periodically reinforce neurodynamic and metabolic homeostasis: The 2m3d paradigm of sleep.

    Science.gov (United States)

    Mader, Edward Claro; Mader, Annie Cielo Llave

    2016-08-15

    Sleep continues to perplex scientists and researchers. Despite decades of sleep research, we still lack a clear understanding of the biological functions and evolution of sleep. In this review, we will examine sleep from a functional and phylogenetic perspective and describe some important conceptual gaps in understanding sleep. Classical theories of the biology and evolution of sleep emphasize sensory activation, energy balance, and metabolic homeostasis. Advances in electrophysiology, functional neuroimaging, and neuroplasticity allow us to view sleep within the framework of neural dynamics. With this paradigm shift, we have come to realize the importance of neurodynamic homeostasis in shaping the biology of sleep. Evidently, animals sleep to achieve neurodynamic and metabolic homeostasis. We are not aware of any framework for understanding sleep where neurodynamic, metabolic, homeostatic, chronophasic, and afferent variables are all taken into account. This motivated us to propose the two-mode three-drive (2m3d) paradigm of sleep. In the 2m3d paradigm, local neurodynamic/metabolic (N/M) processes switch between two modes-m0 and m1-in response to three drives-afferent, chronophasic, and homeostatic. The spatiotemporal integration of local m0/m1 operations gives rise to the global states of sleep and wakefulness. As a framework of evolution, the 2m3d paradigm allows us to view sleep as a robust adaptive strategy that evolved so animals can periodically reinforce neurodynamic and metabolic homeostasis while remaining sensitive to their internal and external environment.

  10. Two-stage coal liquefaction process materials from the Wilsonville Facility operated in the nonintegrated and integrated modes: chemical analyses and biological testing

    Energy Technology Data Exchange (ETDEWEB)

    Later, D.W.

    1985-01-01

    This document reports the results from chemical analyses and biological testing of process materials sampled during operation of the Wilsonville Advanced Coal Liquefaction Research and Development Facility (Wilsonville, Alabama) in both the noncoupled or nonintegrated (NTSL Run 241) and coupled or integrated (ITSL Run 242) two-stage liquefaction operating modes. Mutagenicity and carcinogenicity assays were conducted in conjunction with chromatographic and mass spectrometric analyses to provide detailed, comparative chemical and biological assessments of several NTSL and ITSL process materials. In general, the NTSL process materials were biologically more active and chemically more refractory than analogous ITSL process materials. To provide perspective, the NTSL and ITSL results are compared with those from similar testing and analyses of other direct coal liquefaction materials from the solvent refined coal (SRC) I, SRC II and EDS processes. Comparisons are also made between two-stage coal liquefaction materials from the Wilsonville pilot plant and the C.E. Lummus PDU-ITSL Facility in an effort to assess scale-up effects in these two similar processes. 36 references, 26 figures, 37 tables.

  11. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

    Directory of Open Access Journals (Sweden)

    Tilton Susan C

    2012-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single

  12. Dissecting functions of the retinoblastoma tumor suppressor and the related pocket proteins by integrating genetic, cell biology, and electrophoretic techniques

    DEFF Research Database (Denmark)

    Hansen, Klaus; Lukas, J; Holm, K;

    1999-01-01

    The members of the 'pocket protein' family, comprising the retinoblastoma tumor suppressor (pRB) and its relatives, p107 and p130, negatively regulate cell proliferation and modulate fundamental biological processes including embryonic development, differentiation, homeostatic tissue renewal...... phosphorylation events on multiple serine and threonine residues of pRB, p107, and p130, events which are carried out, at least in part, by the cyclin-dependent kinases that form the key elements of the cell cycle machinery. Here we discuss the recently obtained new insights into the diverse functions of the pRB...

  13. Assembling the elephant: Integrating perspectives in personality psychology. Comment on "Personality from a cognitive-biological perspective" by Y. Neuman

    Science.gov (United States)

    Haslam, Nick; Holland, Elise

    2014-12-01

    Neuman [1] has made an ambitious attempt to integrate perspectives on the psychology of personality that usually run in parallel. The field calls to mind the fable of the blind men and the elephant: each perspective makes different claims about the person based on the aspect it apprehends. Neuman links cognition, affective neuroscience and psychodynamics in a bold effort to sketch the entire beast. However, his hefty framework has some elephantine elements, and is at times conceptually loose and baggy.

  14. Integration of robotics and neuroscience beyond the hand: What kind of synergies?. Comment on "Hand synergies: Integration of robotics and neuroscience for understanding the control of biological and artificial hands" by Marco Santello et al.

    Science.gov (United States)

    d'Avella, Andrea

    2016-07-01

    Santello et al. [1] review an impressive amount of work on the control of biological and artificial hands that demonstrates how the concept of synergies can lead to a successful integration of robotics and neuroscience. Is it possible to generalize the same approach to the control of biological and artificial limbs and bodies beyond the hand? The human hand synergies that appear most relevant for robotic hands are those defined at the kinematic level, i.e. postural synergies [2]. Postural synergies capture the geometric relations among the many joints of the hand and allow for a low dimensional characterization and synthesis of the static hand postures involved in grasping and manipulating a large set of objects. However, many other complex motor skills such as walking, reaching, throwing, and catching require controlling multi-articular time-varying trajectories rather than static postures. Dynamic control of biological and artificial limbs and bodies, especially when geometric and inertial parameters are uncertain and the joints are compliant, poses great challenges. What kind of synergies might simplify the dynamic control of motor skills involving upper and lower limbs as well as the whole body?

  15. Before and after Silent Spring: from chemical pesticides to biological control and integrated pest management--Britain, 1945-1980.

    Science.gov (United States)

    Gay, Hannah

    2012-07-01

    The use of chemical pesticides increased considerably after World War II, and ecological damage was noticeable by the late 1940s. This paper outlines some ecological problems experienced during the post-war period in the UK, and in parts of what is now Malaysia. Also discussed is the government's response. Although Rachel Carson's book, Silent Spring (1962), was important in bringing the problems to a wider public, she was not alone in sounding the alarm. Pressure from the public and from British scientists led, among other things, to the founding of the Natural Environment Research Council in 1965. By the 1970s, environmentalism was an important movement, and funding for ecological and environmental research was forthcoming even during the economic recession. Some of the recipients were ecologists working at Imperial College London. Moved by the political climate, and by the evidence of ecological damage, they carried out research on the biological control of insect pests.

  16. A Novel Robot System Integrating Biological and Mechanical Intelligence Based on Dissociated Neural Network-Controlled Closed-Loop Environment

    Science.gov (United States)

    Wang, Yuechao; Li, Hongyi; Zheng, Xiongfei

    2016-01-01

    We propose the architecture of a novel robot system merging biological and artificial intelligence based on a neural controller connected to an external agent. We initially built a framework that connected the dissociated neural network to a mobile robot system to implement a realistic vehicle. The mobile robot system characterized by a camera and two-wheeled robot was designed to execute the target-searching task. We modified a software architecture and developed a home-made stimulation generator to build a bi-directional connection between the biological and the artificial components via simple binomial coding/decoding schemes. In this paper, we utilized a specific hierarchical dissociated neural network for the first time as the neural controller. Based on our work, neural cultures were successfully employed to control an artificial agent resulting in high performance. Surprisingly, under the tetanus stimulus training, the robot performed better and better with the increasement of training cycle because of the short-term plasticity of neural network (a kind of reinforced learning). Comparing to the work previously reported, we adopted an effective experimental proposal (i.e. increasing the training cycle) to make sure of the occurrence of the short-term plasticity, and preliminarily demonstrated that the improvement of the robot’s performance could be caused independently by the plasticity development of dissociated neural network. This new framework may provide some possible solutions for the learning abilities of intelligent robots by the engineering application of the plasticity processing of neural networks, also for the development of theoretical inspiration for the next generation neuro-prostheses on the basis of the bi-directional exchange of information within the hierarchical neural networks. PMID:27806074

  17. Integrated study of geophysical and biological anomalies before earthquakes (seismic and non-seismic), in Austria and Indonesia

    Science.gov (United States)

    Straka, Wolfgang; Assef, Rizkita; Faber, Robert; Ferasyi, Reza

    2015-04-01

    Earthquakes are commonly seen as unpredictable. Even when scientists believe an earthquake is likely, it is still hard to understand the indications observed, as well as their theoretical and practical implications. There is some controversy surrounding the concept of using animals as a precursor of earthquakes. Nonetheless, several institutes at University of Natural Resources and Life Sciences, and Vienna University of Technology, both Vienna, Austria, and Syiah Kuala University, Banda Aceh, as well as Terramath Indonesia, Buleleng, both Indonesia, cooperate in a long-term project, funded by Red Bull Media House, Salzburg, Austria, which aims at getting some decisive step forward from anecdotal to scientific evidence of those interdependencies, and show their possible use in forecasting seismic hazard on a short-term basis. Though no conclusive research has yet been published, an idea in this study is that even if animals do not respond to specific geophysical precursors and with enough notice to enable earthquake forecasting on that basis, they may at least enhance, in conjunction with other indications, the degree of certainty we can get of a prediction of an impending earthquake. In Indonesia, indeed, before the great earthquakes of 2004 and 2005, ominous geophysical as well as biological phenomena occurred (but were realized as precursors only in retrospect). Numerous comparable stories can be told from other times and regions. Nearly 2000 perceptible earthquakes (> M3.5) occur each year in Indonesia. Also, in 2007, the government has launched a program, focused on West Sumatra, for investigating earthquake precursors. Therefore, Indonesia is an excellent target area for a study concerning possible interconnections between geophysical and biological earthquake precursors. Geophysical and atmospheric measurements and behavioral observation of several animal species (elephant, domestic cattle, water buffalo, chicken, rat, catfish) are conducted in three areas

  18. Feedback control system simulator for the control of biological cells in microfluidic cross slots and integrated microfluidic systems.

    Science.gov (United States)

    Curtis, Michael D; Sheard, Gregory J; Fouras, Andreas

    2011-07-21

    Control systems for lab on chip devices require careful characterisation and design for optimal performance. Traditionally, this involves either extremely computationally expensive simulations or lengthy iteration of laboratory experiments, prototype design, and manufacture. In this paper, an efficient control simulation technique, valid for typical microchannels, Computed Interpolated Flow Hydrodynamics (CIFH), is described that is over 500 times faster than conventional time integration techniques. CIFH is a hybrid approach, utilising a combination of pre-computed flows and hydrodynamic equations and allows the efficient simulation of dynamic control systems for the transport of cells through micro-fluidic devices. The speed-ups achieved by using pre-computed CFD solutions mapped to an n-dimensional control parameter space, significantly accelerate the evaluation and improvement of control strategies and chip design. Here, control strategies for a naturally unstable device geometry, the microfluidic cross-slot, have been simulated and optimal parameters have been found for proposed devices capable of trapping and sorting cells.

  19. Bioregulatory Systems Medicine: An Innovative Approach to Integrating the Science of Molecular Networks, Inflammation and Systems Biology with the Patient’s Autoregulatory Capacity?

    Directory of Open Access Journals (Sweden)

    Alyssa W Goldman

    2015-08-01

    Full Text Available Bioregulatory systems medicine is a paradigm that aims to advance current medical practices. The basic scientific and clinical tenets of this approach embrace an interconnected picture of human health, supported largely by recent advances in systems biology and genomics, and focuses on the implications of multi-scale interconnectivity for improving therapeutic approaches to disease. This article introduces the formal incorporation of these scientific and clinical elements into a cohesive theoretical model of the bioregulatory systems medicine approach. The authors review this integrated body of knowledge and discuss how the emergent conceptual model offers the medical field a new avenue for extending the armamentarium of current treatment and healthcare, with the ultimate goal of improving population health.

  20. Integrating cell biology, image analysis, and computational mechanical modeling to analyze the contributions of cellulose and xyloglucan to stomatal function.

    Science.gov (United States)

    Rui, Yue; Yi, Hojae; Kandemir, Baris; Wang, James Z; Puri, Virendra M; Anderson, Charles T

    2016-06-01

    Cell walls are likely to be essential determinants of the amazing strength and flexibility of the guard cells that surround each stomatal pore in plants, but surprisingly little is known about cell wall composition, organization, and dynamics in guard cells. Recent analyses of cell wall organization and stomatal function in the guard cells of Arabidopsis thaliana mutants with defects in cellulose and xyloglucan have allowed for the development of new hypotheses about the relative contributions of these components to guard cell function. Advanced image analysis methods can allow for the automated detection of key structures, such as microtubules (MTs) and Cellulose Synthesis Complexes (CSCs), in guard cells, to help determine their contributions to stomatal function. A major challenge in the mechanical modeling of dynamic biological structures, such as guard cell walls, is to connect nanoscale features (e.g., wall polymers and their molecular interactions) with cell-scale mechanics; this challenge can be addressed by applying multiscale computational modeling that spans multiple spatial scales and physical attributes for cell walls.

  1. Integration of biological ion channels onto optically addressable micro-fluidic electrode arrays for single molecule characterization.

    Energy Technology Data Exchange (ETDEWEB)

    Brozik, Susan Marie; Frink, Laura J. Douglas; Bachand, George David; Keller, David J. (University of New Mexico, Albuquerque, NM); Patrick, Elizabeth L.; Marshall, Jason A. (University of New Mexico, Albuquerque, NM); Ortiz, Theodore P. (University of New Mexico, Albuquerque, NM); Meyer, Lauren A. (University of New Mexico, Albuquerque, NM); Davis, Ryan W. (University of New Mexico, Albuquerque, NM); Brozik, James A. (University of New Mexico, Albuquerque, NM); Flemming, Jeb Hunter

    2004-12-01

    The challenge of modeling the organization and function of biological membranes on a solid support has received considerable attention in recent years, primarily driven by potential applications in biosensor design. Affinity-based biosensors show great promise for extremely sensitive detection of BW agents and toxins. Receptor molecules have been successfully incorporated into phospholipid bilayers supported on sensing platforms. However, a collective body of data detailing a mechanistic understanding of membrane processes involved in receptor-substrate interactions and the competition between localized perturbations and delocalized responses resulting in reorganization of transmembrane protein structure, has yet to be produced. This report describes a systematic procedure to develop detailed correlation between (recognition-induced) protein restructuring and function of a ligand gated ion channel by combining single molecule fluorescence spectroscopy and single channel current recordings. This document is divided into three sections: (1) reported are the thermodynamics and diffusion properties of gramicidin using single molecule fluorescence imaging and (2) preliminary work on the 5HT{sub 3} serotonin receptor. Thirdly, we describe the design and fabrication of a miniaturized platform using the concepts of these two technologies (spectroscopic and single channel electrochemical techniques) for single molecule analysis, with a longer term goal of using the physical and electronic changes caused by a specific molecular recognition event as a transduction pathway in affinity based biosensors for biotoxin detection.

  2. The Principle of Integration in International Sustainable Development Law (ISDL with Reference to the Biological Weapons Convention (BWC

    Directory of Open Access Journals (Sweden)

    Marina Abdul Majid

    2016-02-01

    Full Text Available The Biological Weapons Convention (BWC does not explicitly refer to sustainable development despite the fact that other United Nations (UN disarmament documents prescribe that international environmental law principles and sustainable development be considered among arms control agreements. This study’s objective is to utilize the principle of integration’s three components of environmental, economic, and social development, as found in the International Sustainable Development Law (ISDL from the New Delhi Declaration (Delhi Declaration of Principles of International Law Relating to Sustainable Development, in order to evaluate whether the BWC contains such components; thereby, making it possible for the BWC to contribute to sustainable development. The methodology of this study is necessarily qualitative, given that it is a socio-legal research that relies on international agreements such as the BWC, declarations, resolutions, plans of implementation, other non-binding documents of the UN, and secondary resources—all of which are analyzed through a document analysis. The results show that the BWC addresses the environment (Article II, prohibits transfers relating to export controls, international trade, and economic development (Article III, while at the same time, covering social development concerns, health, and diseases that make up the international social law (Article X. Since the BWC is found to be capable of contributing to sustainable development, it is concluded that ISDL cannot be restricted to international environmental, economic, and social law, but should be expanded to include international arms control law.

  3. Promise and peril in nanomedicine: the challenges and needs for integrated systems biology approaches to define health risk.

    Science.gov (United States)

    Halappanavar, Sabina; Vogel, Ulla; Wallin, Hakan; Yauk, Carole L

    2017-03-15

    In the 1966s visionary film 'Fantastic Voyage' a submarine crew was shrunk to 100 nm in size and injected into the body of an injured scientist to repair his damaged brain. The movie (written by Harry Kleiner; directed by Richard Fleischer; novel by Isaac Asimov) drew attention to the potential power of engineered nanoscale structures and devices to construct, monitor, control, treat, and repair individual cells. Even more interesting was the fact that the film elegantly noted that the structure had to be miniaturized to a size that is not detected by the body's immune surveillance system, and highlighted the many physiological barriers that are encountered on the submarine's long journey to the target. Although the concept of miniaturizing humans remains an element of science fiction, targeted drug delivery through nanobots to treat diseases such as cancer is now a reality. The ability of nanobots to evade immune surveillance is one of the most attractive features of nanoscale materials that are exploited in the field of medicine for molecular diagnostics, targeted drug delivery, and therapy of diseases. This article will provide a concise opinion on the state-of-the-art, the challenges, and the use of systems biology-another equally revolutionary field of science-to assess the unique health hazards of nanomaterial exposures. For further resources related to this article, please visit the WIREs website.

  4. Inorganic nitrogen transformations in the bed of the Shingobee River, Minnesota: Integrating hydrologic and biological processes using sediment perfusion cores

    Science.gov (United States)

    Sheibley, R.W.; Duff, J.H.; Jackman, A.P.; Triska, F.J.

    2003-01-01

    Inorganic N transformations were examined in streambed sediments from the Shingobee River using sediment perfusion cores. The experimental design simulated groundwater-stream water mixing within sediment cores, which provided a well-defined one-dimensional representation of in situ hydrologic conditions. Two distinct hydrologic and chemical settings were preserved in the sediment cores: the lowermost sediments, perfused with groundwater, remained anaerobic during the incubations, whereas the uppermost sediments, perfused with oxic water pumped from the overlying water column, simulated stream water penetration into the bed. The maintenance of oxic and anoxic zones formed a biologically active aerobic-anaerobic interface. Ammonium (NH4+) dissolved in groundwater was transported conservatively through the lower core zone but was removed as it mixed with aerated recycle water. Concurrently, a small quantity of nitrate (NO3-) equaling ???25% of the NH4+ loss was produced in the upper sediments. The NH4+ and NO3- profiles in the uppermost sediments resulted from coupled nitrification-denitrification, because assimilation and sorption were negligible. We hypothesize that anaerobic microsites within the aerated upper sediments supported denitrification. Rates of nitrification and denitrification in the perfusion cores ranged 42-209 and 53-160 mg N m-2 day-1, respectively. The use of modified perfusion cores permitted the identification and quantification of N transformations and verified process control by surface water exchange into the shallow hyporheic zone of the Shingobee River.

  5. AN INTEGRATIVE WAY OF TEACHING MOLECULAR CELL BIOLOGY AND PROTEIN CHEMISTRY USING ACTIN IMMOBILIZATION ON CHITIN FOR PURIFYING MYOSIN II.

    Directory of Open Access Journals (Sweden)

    M.G. Souza

    2007-05-01

    Full Text Available Our intent is to present our experience on teaching Molecular Cell Biology andProtein Chemistry at UNIRIO through an innovative approach that includes myosin IIextraction and purification. We took advantage of the properties of muscle contractionand propose a simple method for purifying myosin II by affinity chromatography. Thisoriginal method is based on the preparation of an affinity column containing actinmolecules covalently bound to chitin particles. We propose a three-week syllabus thatincludes lectures and bench experimental work. The syllabus favors the activelearning of protein extraction and purification, as well as, of scientific concepts suchas muscle contraction, cytoskeleton structure and its importance for the living cell. Italso promotes the learning of the biotechnological applications of chitin and theapplications of protein immobilization in different industrial fields. Furthermore, theactivities also target the development of laboratorial technical abilities, thedevelopment of problem solving skills and the ability to write up a scientific reportfollowing the model of a scientific article. It is very important to mention that thissyllabus can be used even in places where a facility such as ultra-centrifugation islacking.

  6. Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

    Directory of Open Access Journals (Sweden)

    Tung Shu-Yun

    2011-04-01

    Full Text Available Abstract Background Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as Arabidopsis thaliana do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied. Results Several molecular biology tools were used to isolate flower-specific gene promoters from Oncidium 'Gower Ramsey' (Onc. GR. A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in Onc. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (TI genes (OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable A. thaliana transformation analyses. Conclusions By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.

  7. Integration of pharmacokinetic and NRF2 system biology models to describe reactive oxygen species production and subsequent glutathione depletion in liver microfluidic biochips after flutamide exposure.

    Science.gov (United States)

    Leclerc, Eric; Hamon, Jeremy; Legendre, Audrey; Bois, Frederic Y

    2014-10-01

    We present a systems biology analysis of rat primary hepatocytes response after exposure to 10 μM and 100 μM flutamide in liver microfluidic biochips. We coupled an in vitro pharmacokinetic (PK) model of flutamide to a system biology model of its reactive oxygen species (ROS) production and scavenging by the Nrf2 regulated glutathione production. The PK model was calibrated using data on flutamide kinetics, hydroxyflutamide and glutathione conjugates formation in microfluidic conditions. The parameters of Nrf2-related gene activities and the subsequent glutathione depletion were calibrated using microarray data from our microfluidic experiments and literature information. Following a 10 μM flutamide exposure, the model predicted a recovery time to baseline levels of glutathione (GSH) and ROS in agreement with our experimental observations. At 100 μM, the model predicted that metabolism saturation led to an important accumulation of flutamide in cells, a high ROS production and complete GSH depletion. The high levels of ROS predicted were consistent with the necrotic switch observed by transcriptomics, and the high cell mortality we had experimentally observed. The model predicted a transition between recoverable GSH depletion and deep GSH depletion at about 12.5 μM of flutamide (single perfusion exposure). Our work shows that in vitro biochip experiments can provide supporting information for complex in silico modeling including data from extra cellular and intra cellular levels. We believe that this approach can be an efficient strategy for a global integrated methodology in predictive toxicology.

  8. Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses.

    Science.gov (United States)

    de Oliveira Dal'Molin, Cristiana G; Orellana, Camila; Gebbie, Leigh; Steen, Jennifer; Hodson, Mark P; Chrysanthopoulos, Panagiotis; Plan, Manuel R; McQualter, Richard; Palfreyman, Robin W; Nielsen, Lars K

    2016-01-01

    The urgent need for major gains in industrial crops productivity and in biofuel production from bioenergy grasses have reinforced attention on understanding C4 photosynthesis. Systems biology studies of C4 model plants may reveal important features of C4 metabolism. Here we chose foxtail millet (Setaria italica), as a C4 model plant and developed protocols to perform systems biology studies. As part of the systems approach, we have developed and used a genome-scale metabolic reconstruction in combination with the use of multi-omics technologies to gain more insights into the metabolism of S. italica. mRNA, protein, and metabolite abundances, were measured in mature and immature stem/leaf phytomers, and the multi-omics data were integrated into the metabolic reconstruction framework to capture key metabolic features in different developmental stages of the plant. RNA-Seq reads were mapped to the S. italica resulting for 83% coverage of the protein coding genes of S. italica. Besides revealing similarities and differences in central metabolism of mature and immature tissues, transcriptome analysis indicates significant gene expression of two malic enzyme isoforms (NADP- ME and NAD-ME). Although much greater expression levels of NADP-ME genes are observed and confirmed by the correspondent protein abundances in the samples, the expression of multiple genes combined to the significant abundance of metabolites that participates in C4 metabolism of NAD-ME and NADP-ME subtypes suggest that S. italica may use mixed decarboxylation modes of C4 photosynthetic pathways under different plant developmental stages. The overall analysis also indicates different levels of regulation in mature and immature tissues in carbon fixation, glycolysis, TCA cycle, amino acids, fatty acids, lignin, and cellulose syntheses. Altogether, the multi-omics analysis reveals different biological entities and their interrelation and regulation over plant development. With this study, we demonstrated

  9. Integrated design of teaching system of macro-biology experiment%宏观生物学实验教学体系综合设计

    Institute of Scientific and Technical Information of China (English)

    陈杰; 王魏根

    2012-01-01

    目前宏观生物学实验教学不能适应高等教育的发展,难以实现培养高素质、创新型人才的目的。结合实验教学中存在的问题,对宏观生物学实验教学体系进行了综合设计。从教学内容的模块化与分类组织,根据实验性质采取有区别的教学方法,优化整合传统的与新增的教学资源,实施过程与效果评价完善考核方式,以及设置宏观生物学实验室理顺管理机制等方面,初步构建了宏观生物学实验教学体系,以期能够促进实验教学,满足人才培养与学科发展的需要。%Current macro-biology experiment teaching can not meet the development of modern higher education,and it is difficult to achieve the purpose of cultivating high-quality,innovative talents.The teaching system of macro-biology experiment is comprehensively designed on the basis of problems in the experiment teaching.This teaching system includes five aspects as follows: modular and classified organization of the teaching contents,using different teaching methods according to the type of experiment,integration of the traditional and new teaching resources,implementing the process and effect evaluation to improve the examination,and setting the macro-biology laboratory to rationalize management mechanism,which will be helpful to promote experiment teaching and meet the needs of personal training and disciplinary development.

  10. Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses

    Science.gov (United States)

    de Oliveira Dal'Molin, Cristiana G.; Orellana, Camila; Gebbie, Leigh; Steen, Jennifer; Hodson, Mark P.; Chrysanthopoulos, Panagiotis; Plan, Manuel R.; McQualter, Richard; Palfreyman, Robin W.; Nielsen, Lars K.

    2016-01-01

    The urgent need for major gains in industrial crops productivity and in biofuel production from bioenergy grasses have reinforced attention on understanding C4 photosynthesis. Systems biology studies of C4 model plants may reveal important features of C4 metabolism. Here we chose foxtail millet (Setaria italica), as a C4 model plant and developed protocols to perform systems biology studies. As part of the systems approach, we have developed and used a genome-scale metabolic reconstruction in combination with the use of multi-omics technologies to gain more insights into the metabolism of S. italica. mRNA, protein, and metabolite abundances, were measured in mature and immature stem/leaf phytomers, and the multi-omics data were integrated into the metabolic reconstruction framework to capture key metabolic features in different developmental stages of the plant. RNA-Seq reads were mapped to the S. italica resulting for 83% coverage of the protein coding genes of S. italica. Besides revealing similarities and differences in central metabolism of mature and immature tissues, transcriptome analysis indicates significant gene expression of two malic enzyme isoforms (NADP- ME and NAD-ME). Although much greater expression levels of NADP-ME genes are observed and confirmed by the correspondent protein abundances in the samples, the expression of multiple genes combined to the significant abundance of metabolites that participates in C4 metabolism of NAD-ME and NADP-ME subtypes suggest that S. italica may use mixed decarboxylation modes of C4 photosynthetic pathways under different plant developmental stages. The overall analysis also indicates different levels of regulation in mature and immature tissues in carbon fixation, glycolysis, TCA cycle, amino acids, fatty acids, lignin, and cellulose syntheses. Altogether, the multi-omics analysis reveals different biological entities and their interrelation and regulation over plant development. With this study, we demonstrated

  11. Integrated chemical and biological analysis to explain estrogenic potency in bile extracts of red mullet (Mullus barbatus).

    Science.gov (United States)

    Martínez-Gómez, Concepción; Lamoree, M; Hamers, T; van Velzen, M; Kamstra, J H; Fernández, B; Benedicto, J; León, V M; Vethaak, A D

    2013-06-15

    A biological screening was performed to establish the total exposure to estrogenic compounds of red mullet (Mullus barbatus) collected at several sites along the Spanish Mediterranean coast by testing male fish bile extracts using the in vitro ER-LUC reporter gene assay. In addition, major metabolites were identified and measurements of OH-PAHs (1-naphthol, 9-phenantrol, 9-fluorenol, 1-pyrenol, 1OH-BaP and 3OH-BaP) and alkylphenols (4-n-nonylphenol (4-n-NP) and 4-tertoctylphenol (4-tert-OP)) in the same fish bile extracts were taken by gas chromatography-mass spectrometry in electron ionization mode (GC-EI-MS). Relative in vitro estrogenic potencies of the chemically quantified compounds were also tested. The highest biliary concentrations of 1-pyrenol, 9-fluorenol and 4-n-NP were found in fish from Barcelona and from the Mar Menor coastal lagoon. However, these concentrations can be considered relatively low compared to values reported in red mullet from other polluted waters in the Mediterranean Sea. The contribution of 1-pyrenol, 4-n-NP and 4-tert-OP to the total estrogenic potency measured in male fish bile was found to be negligible, indicating the presence of other estrogenic compounds in red mullet bile. Estrogenic potency in bile from male fish was markedly elevated in Mar Menor lagoon (234.8±5.7 pg E2EQ/μl), and further research will be necessary to explain whether the presence of natural and synthetic-hormones in the lagoon contributed to this finding. Values of approximately 15-16E2EQ pg/mg bile can be regarded as preliminary baseline levels of bile estrogenicity in male red mullet from the western Mediterranean Sea.

  12. Biological testing and chemical analysis of process materials from an integrated two stage coal liquefaction: a status report

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, B.W.; Buhl, P.; Moroni, E.C.

    1983-07-01

    Samples for chemical characterization and biological testing were obtained from ITSL runs 3LCF7, 3LCF8 and 3LCF9. Chemical analysis of these materials showed that SCT products were composed of fewer compounds than analogous materials from Solvent Refined Coal (SRC) processes. Major components in the SCT materials were three-, four-, five- and six-ring neutral polycyclic aromatic hydrocarbons (PAH). Methyl(C/sub 1/) and C/sub 2/ homologs of these compounds were present in relatively low concentrations, compared to their non-alkylated homologs. Organic nitrogen was primarily in the form of tertiary polycyclic aromatic nitrogen heterocycles and carbazoles. Little or no amino PAH (APAH) or cyano PAH were detected in samples taken during normal PDU operations, however, mutagenic APAH were produced during off-normal operation. Microbial mutagenicity appeared to be due mainly to the presence of APAH which were probably formed in the LC finer due to failure of the catalyst to promote deamination following carbon-nitrogen bond scission of nitrogen-containing hydroaromatics. This failure was observed for the off-normal runs where it was likely that the catalyst had been deactivated. Carcinogenic activity of ITSL materials as assessed by (tumors per animal) in the initiation/promotion mouse skin painting assay was slightly reduced for materials produced with good catalyst under normal operation compared to those collected during recycle of the LC Finer feed. Initiation activity of the latter samples did not appear to be significantly different from that of other coal derived materials with comparable boiling ranges. The observed initiation activity was not unexpected, considering analytical data which showed the presence of four-, five- and six-ring PAH in ITSL materials.

  13. Enhanced biological nutrients removal using an integrated oxidation ditch with vertical circle from wastewater by adding an anaerobic column

    Institute of Scientific and Technical Information of China (English)

    WANG Shu-mei; LIU Jun-xin

    2005-01-01

    Compared to conventional oxidation ditches, an integrated oxidation ditch with vertical circle(IODVC) has the characters of concise configuration, simple operation and maintenance, land saving and automatical sludge returning. By the utilization of vertical circulation, an aerobic zone and an anoxic zone can be unaffectedly formed in the IODVC. Therefore, COD and nitrogen can be efficiently removed. However, the removal efficiency of phosphorus was Iow in the IODVC. In the experiment described, a laboratory scale system to add an anaerobic column to the IODVC has been tested to investigate the removal of phosphorus from wastewater. The experimental results showed that the removal efficiency of TP with the anaerobic column was increased to 54.0 % from 22.3 % without the anaerobic column. After the acetic sodium was added into the influent as carbon sources, the mean TP removal efficency of 77.5 % was obtained. At the same time, the mean removal efficiencies of COD, TN and NH3-N were 92.2%, 81.6% and 98.1%, respectively, at 12 h of HRT and 21-25 d of SRT. The optimal operational conditions in this study were as follows: recycle rate = 1.5-2.0, COD/TN > 6, COD/TP > 40,COD loading rate = 0.26-0.32 kgCOD/(kgSS·d), TN loading rate =0.028-0.034 kgTN/(kgSS·d) and TP loading rate = 0.003-0.005kgTP/(kgSS·d), respectively.

  14. Biological preconcentrator

    Science.gov (United States)

    Manginell, Ronald P.; Bunker, Bruce C.; Huber, Dale L.

    2008-09-09

    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  15. Integration of an optical CMOS sensor with a microfluidic channel allows a sensitive readout for biological assays in point-of-care tests.

    Science.gov (United States)

    Van Dorst, Bieke; Brivio, Monica; Van Der Sar, Elfried; Blom, Marko; Reuvekamp, Simon; Tanzi, Simone; Groenhuis, Roelf; Adojutelegan, Adewole; Lous, Erik-Jan; Frederix, Filip; Stuyver, Lieven J

    2016-04-15

    In this manuscript, a microfluidic detection module, which allows a sensitive readout of biological assays in point-of-care (POC) tests, is presented. The proposed detection module consists of a microfluidic flow cell with an integrated Complementary Metal-Oxide-Semiconductor (CMOS)-based single photon counting optical sensor. Due to the integrated sensor-based readout, the detection module could be implemented as the core technology in stand-alone POC tests, for use in mobile or rural settings. The performance of the detection module was demonstrated in three assays: a peptide, a protein and an antibody detection assay. The antibody detection assay with readout in the detection module proved to be 7-fold more sensitive that the traditional colorimetric plate-based ELISA. The protein and peptide assay showed a lower limit of detection (LLOD) of 200 fM and 460 fM respectively. Results demonstrate that the sensitivity of the immunoassays is comparable with lab-based immunoassays and at least equal or better than current mainstream POC devices. This sensitive readout holds the potential to develop POC tests, which are able to detect low concentrations of biomarkers. This will broaden the diagnostic capabilities at the clinician's office and at patient's home, where currently only the less sensitive lateral flow and dipstick POC tests are implemented.

  16. Bases biológicas de la dependencia de las drogas: hacia un enfoque integral del proglema Biologic bases of drug dependence: toward an integral approach of the problem

    Directory of Open Access Journals (Sweden)

    Jorge Mario Tamayo

    1998-04-01

    Full Text Available El abuso y la dependencia de las drogas son problemas complejos y costosos que requieren una intervención terapéutica polimodal e integral. En los últimos años se han dado varios descubrimientos científicos relacionados con las bases biológicas de estos trastornos. Ello ha permitido desarrollar programas que incluyen el uso de diferentes psicofármacos y técnicas psicoterapéuticas que posibilitan una modulación de las vías neuronales disfuncionales. La investigación del sistema mesolímbico dopaminérgico y de los receptores opioides del tallo cerebral y del núcleo accumbens sumada al develamiento de los diferentes mecanismos intraneuronales, han permitido comprender me. jorlos cambios cerebrales ycomportamentales debidos al consumo agudo y crónico de drogas. Tales hallazgos biológicos son el propósito de esta revisión basada en una búsqueda de artículos a través de MEDLINE.. Drugs abuse and dependence are complex and expensive disorders that require a polymodal and integral therapeutic intervention. Several scientific discoveries related to the biological bases of these disorders have recently arisen. These discoveries guide the design of programs that include different psychotropic drugs and psychotherapeutic technics that allow a modulation of the neuronal dysfunction process. Research on the mesolimbic dopaminergic system and the opioid receptors in the brain stem and the nucleus accumbens added to new knowledge of different intraneuronal mechanisms, allow a better understanding of cerebral and behavioral changes due to acute and chronic consumption of drugs. Such biological findings are the purpose of this review based on a MEDLINE search of articles.

  17. Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes

    Directory of Open Access Journals (Sweden)

    Price Jennifer

    2011-01-01

    Full Text Available Abstract Background The molecular pathways involved in the interstitial lung diseases (ILDs are poorly understood. Systems biology approaches, with global expression data sets, were used to identify perturbed gene networks, to gain some understanding of the underlying mechanisms, and to develop specific hypotheses relevant to these chronic lung diseases. Methods Lung tissue samples from patients with different types of ILD were obtained from the Lung Tissue Research Consortium and total cell RNA was isolated. Global mRNA and microRNA were profiled by hybridization and amplification-based methods. Differentially expressed genes were compiled and used to identify critical signaling pathways and potential biomarkers. Modules of genes were identified that formed a regulatory network, and studies were performed on cultured cells in vitro for comparison with the in vivo results. Results By profiling mRNA and microRNA (miRNA expression levels, we found subsets of differentially expressed genes that distinguished patients with ILDs from controls and that correlated with different disease stages and subtypes of ILDs. Network analysis, based on pathway databases, revealed several disease-associated gene modules, involving genes from the TGF-β, Wnt, focal adhesion, and smooth muscle actin pathways that are implicated in advancing fibrosis, a critical pathological process in ILDs. A more comprehensive approach was also adapted to construct a putative global gene regulatory network based on the perturbation of key regulatory elements, transcription factors and microRNAs. Our data underscores the importance of TGF-β signaling and the persistence of smooth muscle actin-containing fibroblasts in these diseases. We present evidence that, downstream of TGF-β signaling, microRNAs of the miR-23a cluster and the transcription factor Zeb1 could have roles in mediating an epithelial to mesenchymal transition (EMT and the resultant persistence of mesenchymal cells

  18. Integrated Surface and Mechanical Characterization of Freestanding Biological and Other Nano-Structures Using Atomic Force Microscopy

    Science.gov (United States)

    Wang, Xin

    This dissertation is focused on surface and mechanical characterization of freestanding biological and other nano-structures using atomic force microscopy including two parts: cell mechanics and nano-structure mechanics. The main purpose of this work is to investigate how the nano- / micro-scale mechanical properties affect macro-scale function. In cancer cells, efficacy of drug delivery is oftentimes declined due to the thick dendritic network of oligosaccharide mucin chains on the cell surface. AFM is used to measure the force needed to pierce the mucin layer to reach the cell surface. A pool of ovarian, pancreatic, lung, colorectal and breast cancer cells are characterized. The studies offer additional support for the development of clinical and pharmaceutical approaches to combat mucin over-expression in tumors during cancer chemotherapy. Macroscopic adhesion-aggregation and subsequent transportation of microorganisms in porous medium are closely related to the microscopic deformation and adhesion mechanical properties. The classical Tabor's parameter is modified. Multiple bacterial strains are characterized in terms of aggregates size, aggregation index and transportation kinetics. AFM is employed to obtain the microscopic coupled adhesion-deformation properties. The strong correlation between Tabor's parameter and aggregation-deposition-transportation suggests the AFM characterization is capable of making reliable predication of macroscopic behavior. A novel "nano-cheese-cutter" is fabricated on tipless AFM cantilever to measure elastic modulus and interfacial adhesion of a 1-D freestanding nano-structure. A single electrospun fiber is attached to the free end of AFM cantilever, while another fiber is similarly prepared on a mica substrate in an orthogonal direction. An external load is applied to deform the two fibers into complementary V-shapes. This work is extended to investigate the interfacial adhesion energy between dissimilar materials. SWCNT thin

  19. Integrated chemical and biological analysis to explain estrogenic potency in bile extracts of red mullet (Mullus barbatus)

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Gómez, Concepción, E-mail: concepcion.martinez@mu.ieo.es [Instituto Español de Oceanografía, Oceanografic Centre of Murcia, Varadero 1, San Pedro del Pinatar, 30740 Murcia (Spain); Lamoree, M.; Hamers, T.; Velzen, M. van; Kamstra, J.H. [VU University Amsterdam, Amsterdam Global Change Institute, Institute for Environmental Studies, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands); Fernández, B.; Benedicto, J.; León, V.M. [Instituto Español de Oceanografía, Oceanografic Centre of Murcia, Varadero 1, San Pedro del Pinatar, 30740 Murcia (Spain); Vethaak, A.D. [VU University Amsterdam, Amsterdam Global Change Institute, Institute for Environmental Studies, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands); Deltares, Marine and Coastal Systems, P.O. Box 177, 2600 MH Delft (Netherlands)

    2013-06-15

    Highlights: •In vitro estrogenic activity was quantified in male bile extracts of feral red mullet. •Major PAH metabolites and alkylphenols were quantified in the same fish bile extracts. •Contribution of these compounds to the estrogenicity measured was found negligible. •PAH and alkylphenol fish exposure was low in most of the studied Mediterranean sites. •High estrogenicity in male fish from Mar Menor lagoon warrants further studies. -- Abstract: A biological screening was performed to establish the total exposure to estrogenic compounds of red mullet (Mullus barbatus) collected at several sites along the Spanish Mediterranean coast by testing male fish bile extracts using the in vitro ER-LUC reporter gene assay. In addition, major metabolites were identified and measurements of OH-PAHs (1-naphthol, 9-phenantrol, 9-fluorenol, 1-pyrenol, 1OH-BaP and 3OH-BaP) and alkylphenols (4-n-nonylphenol (4-n-NP) and 4-tertoctylphenol (4-tert-OP)) in the same fish bile extracts were taken by gas chromatography–mass spectrometry in electron ionization mode (GC–EI-MS). Relative in vitro estrogenic potencies of the chemically quantified compounds were also tested. The highest biliary concentrations of 1-pyrenol, 9-fluorenol and 4-n-NP were found in fish from Barcelona and from the Mar Menor coastal lagoon. However, these concentrations can be considered relatively low compared to values reported in red mullet from other polluted waters in the Mediterranean Sea. The contribution of 1-pyrenol, 4-n-NP and 4-tert-OP to the total estrogenic potency measured in male fish bile was found to be negligible, indicating the presence of other estrogenic compounds in red mullet bile. Estrogenic potency in bile from male fish was markedly elevated in Mar Menor lagoon (234.8 ± 5.7 pg E2EQ/μl), and further research will be necessary to explain whether the presence of natural and synthetic-hormones in the lagoon contributed to this finding. Values of approximately 15–16 E2EQ pg

  20. Integrated real-time control strategy in multi-tank A2O process for biological nutrient removal treating real domestic wastewater

    Directory of Open Access Journals (Sweden)

    Saad Abualhail

    2017-02-01

    Full Text Available An integrated real-time anaerobic–anoxic/oxic (A2O operated with multi-tank called IMT–A2O process was designed and operated with fluctuating influent loads for biological nutrient removal for treating real domestic wastewater. IMT–A2O process, a “phased isolation tank” technology, varies both aeration pattern and flow path in a continuous flow multi-tank system to force fluctuation of organic and nutrient concentrations in process reactors. Using an eight-phase cycle, desired biochemical transformations, are accomplished at different times in the same tank. On-line sensors (pH, ORP, and DO were used as real-time control parameters to adjust the duration of each operational phase in the IMT–A2O process. The control system is an algorithm that automatically adjusts the cycle length to the influent wastewater characteristics according to the end points. It was found that on-line sensor values of pH, ORP, and DO were somehow related with the dynamic behaviors of nutrient concentrations in IMT–A2O. The algorithm acts in the reaction phases of the IMT–A2O cycle using ORP and pH break points of tank one to distinguish the end of denitrification and the beginning of phosphorus release, pH break point of tank two to control the end of denitrification and beginning of phosphorus release and a sudden increase in DO pattern, pH break point and ORP to control phosphorus uptake and the end of the nitrification process. Although the fluctuations in raw wastewater concentration are extreme; an influent with a low C/N ratio is deficient in organic carbon, and a low carbon source level can limit the overall biological denitrification process, the average removal efficiencies achieved for COD, ammonia–nitrogen, total nitrogen and total phosphorus were not less than 76.11%, 87.78%, 76.45% and 83.75%, respectively, using the integrated real-time control strategy. The integrated IMT–A2O exhibited a better performance in nutrient removal than the

  1. 应用生物完整性指数评价水生态系统健康的研究进展%Research progress on using index of biological integrity to assess aquatic ecosystem health

    Institute of Scientific and Technical Information of China (English)

    廖静秋; 黄艺

    2013-01-01

    Index of biological integrity (IBI) is one of the most important and popular tools in as-sessing aquatic ecosystem health. This paper reviewed the selection of indicator species for IBI, its construction process, and its applications in assessing aquatic ecosystem health, summarized the commonly used candidate biological parameter indices of fish-index of biological integrity (F-IBI), benthos-index of biological integrity (B-IBI) , and periphyton-index of biological integrity (P-IBI) , and pointed out the feasibility and necessity of using microbe-index of biological integrity (M-IBI) to assess the health of aquatic ecosystem.%生物完整性指数(IBI)法是评价水生态系统健康的一种重要且被广泛应用的方法.本文综述了生物完整性指数的指示物种选择原因、构建方法以及在水生态系统健康评价中的应用,并总结了现阶段生态系统评估常用的鱼类完整性指数(F-IBI)、底栖无脊椎动物完整性指数(B-IBI)和着生藻类完整性指数(P-IBI)中候选生物状况参数指标,提出了使用微生物完整性指数(M-IBI)评价水生态系统健康的可行性和必要性.

  2. IsoBED: a tool for automatic calculation of biologically equivalent fractionation schedules in radiotherapy using IMRT with a simultaneous integrated boost (SIB technique

    Directory of Open Access Journals (Sweden)

    Benassi Marcello

    2011-05-01

    Full Text Available Abstract Background An advantage of the Intensity Modulated Radiotherapy (IMRT technique is the feasibility to deliver different therapeutic dose levels to PTVs in a single treatment session using the Simultaneous Integrated Boost (SIB technique. The paper aims to describe an automated tool to calculate the dose to be delivered with the SIB-IMRT technique in different anatomical regions that have the same Biological Equivalent Dose (BED, i.e. IsoBED, compared to the standard fractionation. Methods Based on the Linear Quadratic Model (LQM, we developed software that allows treatment schedules, biologically equivalent to standard fractionations, to be calculated. The main radiobiological parameters from literature are included in a database inside the software, which can be updated according to the clinical experience of each Institute. In particular, the BED to each target volume will be computed based on the alpha/beta ratio, total dose and the dose per fraction (generally 2 Gy for a standard fractionation. Then, after selecting the reference target, i.e. the PTV that controls the fractionation, a new total dose and dose per fraction providing the same isoBED will be calculated for each target volume. Results The IsoBED Software developed allows: 1 the calculation of new IsoBED treatment schedules derived from standard prescriptions and based on LQM, 2 the conversion of the dose-volume histograms (DVHs for each Target and OAR to a nominal standard dose at 2Gy per fraction in order to be shown together with the DV-constraints from literature, based on the LQM and radiobiological parameters, and 3 the calculation of Tumor Control Probability (TCP and Normal Tissue Complication Probability (NTCP curve versus the prescribed dose to the reference target.

  3. Analysis of the biological response of mouse liver (Mus musculus) exposed to As2O3 based on integrated -omics approaches.

    Science.gov (United States)

    García-Sevillano, M A; García-Barrera, T; Navarro, F; Gómez-Ariza, J L

    2013-12-01

    Organic and inorganic mass spectrometries were used to investigate the biochemical response of mice (Mus musculus) to inorganic arsenic exposure using liver as the target organ. The toxicological effects of trivalent inorganic arsenic after oral administration (3 mg kg(-1) body weight and per day) were investigated over a period of 7 days using metallomics, metabonomics and redox proteomics approaches. Size-exclusion chromatography (SEC) with ICP-MS detection was combined with anion exchange chromatography (AEC) to characterize the biological response of the exposed mice. On the other hand, direct infusion mass spectrometry (DI-ESI-QTOF-MS) of polar and lipophilic extracts using positive and negative modes of acquisition (ESI+/ESI-) provided information about time-dependent changes in endogenous metabolites identified by Partial Least Square-Discriminant Analysis (PLS-DA). Finally, the study has been complemented with the evaluation of up/down-regulation of enzymes related to oxidative stress such as superoxide dismutase (SOD), glutathione reductase (GR), catalase (CAT) and peroxidases in connection with metal toxicity issues. The results show that the inorganic arsenic methylation in the liver may reach the saturation point upon chronic exposure to the element. On the other hand, SEC-ICP-MS coupling provided information about metal containing-proteins and metabolites related to arsenic exposure (metallomics) which has been correlated with the changes in the global metabolism (metabonomics), also considering their consequences on the redox status of protein and protein expression (redox proteomics). Our study shows that arsenic causes biochemical pathway alterations, such as energy metabolism (e.g. glycolysis, Krebs cycle), amino acid metabolism, choline metabolism and degradation of membrane phospholipids (apoptosis). This work illustrates the high reliability of the integrated use of organic mass spectrometry for the metabonomic study of biochemical effects

  4. The response of Isidorella newcombi to copper exposure: Using an integrated biological framework to interpret transcriptomic responses from RNA-seq analysis.

    Science.gov (United States)

    Ubrihien, Rodney P; Ezaz, Tariq; Taylor, Anne M; Stevens, Mark M; Krikowa, Frank; Foster, Simon; Maher, William A

    2017-04-01

    This study describes the transcriptomic response of the Australian endemic freshwater gastropod Isidorella newcombi exposed to 80±1μg/L of copper for 3days. Analysis of copper tissue concentration, lysosomal membrane destabilisation and RNA-seq were conducted. Copper tissue concentrations confirmed that copper was bioaccumulated by the snails. Increased lysosomal membrane destabilisation in the copper-exposed snails indicated that the snails were stressed as a result of the exposure. Both copper tissue concentrations and lysosomal destabilisation were significantly greater in snails exposed to copper. In order to interpret the RNA-seq data from an ecotoxicological perspective an integrated biological response model was developed that grouped transcriptomic responses into those associated with copper transport and storage, survival mechanisms and cell death. A conceptual model of expected transcriptomic changes resulting from the copper exposure was developed as a basis to assess transcriptomic responses. Transcriptomic changes were evident at all the three levels of the integrated biological response model. Despite lacking statistical significance, increased expression of the gene encoding copper transporting ATPase provided an indication of increased internal transport of copper. Increased expression of genes associated with endocytosis are associated with increased transport of copper to the lysosome for storage in a detoxified form. Survival mechanisms included metabolic depression and processes associated with cellular repair and recycling. There was transcriptomic evidence of increased cell death by apoptosis in the copper-exposed organisms. Increased apoptosis is supported by the increase in lysosomal membrane destabilisation in the copper-exposed snails. Transcriptomic changes relating to apoptosis, phagocytosis, protein degradation and the lysosome were evident and these processes can be linked to the degradation of post-apoptotic debris. The study

  5. Integrative miRNA-Gene Expression Analysis Enables Refinement of Associated Biology and Prediction of Response to Cetuximab in Head and Neck Squamous Cell Cancer

    Directory of Open Access Journals (Sweden)

    Loris De Cecco

    2017-01-01

    Full Text Available This paper documents the process by which we, through gene and miRNA expression profiling of the same samples of head and neck squamous cell carcinomas (HNSCC and an integrative miRNA-mRNA expression analysis, were able to identify candidate biomarkers of progression-free survival (PFS in patients treated with cetuximab-based approaches. Through sparse partial least square–discriminant analysis (sPLS-DA and supervised analysis, 36 miRNAs were identified in two components that clearly separated long- and short-PFS patients. Gene set enrichment analysis identified a significant correlation between the miRNA first-component and EGFR signaling, keratinocyte differentiation, and p53. Another significant correlation was identified between the second component and RAS, NOTCH, immune/inflammatory response, epithelial–mesenchymal transition (EMT, and angiogenesis pathways. Regularized canonical correlation analysis of sPLS-DA miRNA and gene data combined with the MAGIA2 web-tool highlighted 16 miRNAs and 84 genes that were interconnected in a total of 245 interactions. After feature selection by a smoothed t-statistic support vector machine, we identified three miRNAs and five genes in the miRNA-gene network whose expression result was the most relevant in predicting PFS (Area Under the Curve, AUC = 0.992. Overall, using a well-defined clinical setting and up-to-date bioinformatics tools, we are able to give the proof of principle that an integrative miRNA-mRNA expression could greatly contribute to the refinement of the biology behind a predictive model.

  6. Integrated systems biology analysis of transcriptomes reveals candidate genes for acidity control in developing fruits of sweet orange (Citrus sinensis L. Osbeck

    Directory of Open Access Journals (Sweden)

    Dingquan eHuang

    2016-04-01

    Full Text Available Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck with varying fruit acidity, Succari (acidless, Bingtang (low acid, and Newhall and Xinhui (normal acid. Fruits of these varieties at 45 days post anthesis (DPA, which corresponds to Stage I (cell division, had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion. Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis. Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AH10, degradation (such as APD2 and transcription (such as AIL6 and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control.

  7. A Systems Biology Approach to Reveal Putative Host-Derived Biomarkers of Periodontitis by Network Topology Characterization of MMP-REDOX/NO and Apoptosis Integrated Pathways.

    Science.gov (United States)

    Zeidán-Chuliá, Fares; Gürsoy, Mervi; Neves de Oliveira, Ben-Hur; Özdemir, Vural; Könönen, Eija; Gürsoy, Ulvi K

    2015-01-01

    Periodontitis, a formidable global health burden, is a common chronic disease that destroys tooth-supporting tissues. Biomarkers of the early phase of this progressive disease are of utmost importance for global health. In this context, saliva represents a non-invasive biosample. By using systems biology tools, we aimed to (1) identify an integrated interactome between matrix metalloproteinase (MMP)-REDOX/nitric oxide (NO) and apoptosis upstream pathways of periodontal inflammation, and (2) characterize the attendant topological network properties to uncover putative biomarkers to be tested in saliva from patients with periodontitis. Hence, we first generated a protein-protein network model of interactions ("BIOMARK" interactome) by using the STRING 10 database, a search tool for the retrieval of interacting genes/proteins, with "Experiments" and "Databases" as input options and a confidence score of 0.400. Second, we determined the centrality values (closeness, stress, degree or connectivity, and betweenness) for the "BIOMARK" members by using the Cytoscape software. We found Ubiquitin C (UBC), Jun proto-oncogene (JUN), and matrix metalloproteinase-14 (MMP14) as the most central hub- and non-hub-bottlenecks among the 211 genes/proteins of the whole interactome. We conclude that UBC, JUN, and MMP14 are likely an optimal candidate group of host-derived biomarkers, in combination with oral pathogenic bacteria-derived proteins, for detecting periodontitis at its early phase by using salivary samples from patients. These findings therefore have broader relevance for systems medicine in global health as well.

  8. The `What is a system' reflection interview as a knowledge integration activity for high school students' understanding of complex systems in human biology

    Science.gov (United States)

    Tripto, Jaklin; Ben-Zvi Assaraf, Orit; Snapir, Zohar; Amit, Miriam

    2016-03-01

    This study examined the reflection interview as a tool for assessing and facilitating the use of 'systems language' amongst 11th grade students who have recently completed their first year of high school biology. Eighty-three students composed two concept maps in the 10th grade-one at the beginning of the school year and one at its end. The first part of the interview is dedicated to guiding the students through comparing their two concept maps and by means of both explicit and non-explicit teaching. Our study showed that the explicit guidance in comparing the two concept maps was more effective than the non-explicit, eliciting a variety of different, more specific, types of interactions and patterns (e.g. 'hierarchy', 'dynamism', 'homeostasis') in the students' descriptions of the human body system. The reflection interview as a knowledge integration activity was found to be an effective tool for assessing the subjects' conceptual models of 'system complexity', and for identifying those aspects of a system that are most commonly misunderstood.

  9. Pathway of FeEDTA transformation and its impact on performance of NOx removal in a chemical absorption-biological reduction integrated process.

    Science.gov (United States)

    Li, Wei; Zhao, Jingkai; Zhang, Lei; Xia, Yinfeng; Liu, Nan; Li, Sujing; Zhang, Shihan

    2016-01-01

    A novel chemical absorption-biological reduction (CABR) integrated process, employing ferrous ethylenediaminetetraacetate (Fe(II)EDTA) as a solvent, is deemed as a potential option for NOx removal from the flue gas. Previous work showed that the Fe(II)EDTA concentration was critical for the NOx removal in the CABR process. In this work, the pathway of FeEDTA (Fe(III)/Fe(II)-EDTA) transformation was investigated to assess its impact on the NOx removal in a biofilter. Experimental results revealed that the FeEDTA transformation involved iron precipitation and EDTA degradation. X-ray photoelectron spectroscopy analysis confirmed the iron was precipitated in the form of Fe(OH)3. The iron mass balance analysis showed 44.2% of the added iron was precipitated. The EDTA degradation facilitated the iron precipitation. Besides chemical oxidation, EDTA biodegradation occurred in the biofilter. The addition of extra EDTA helped recover the iron from the precipitation. The transformation of FeEDTA did not retard the NO removal. In addition, EDTA rather than the iron concentration determined the NO removal efficiency.

  10. Ecological health assessments based on whole effluent toxicity tests and the index of biological integrity in temperate streams influenced by wastewater treatment plant effluents.

    Science.gov (United States)

    Ra, Jin Sung; Kim, Sang Don; Chang, Nam Ik; An, Kwang-Guk

    2007-09-01

    Whole effluent toxicity (WET) tests and ecosystem health assessments, based on test guidelines of U.S. Environmental Protection Agency (U.S. EPA) and index of biological integrity (IBI), were conducted on various streams located in Youngsan River watershed, Korea. The WET tests showed that about 33 and 82% of wastewater treatment plants (WWTPs) exhibited significant toxicity to Daphnia magna and Selenastrum capricornutum, respectively. Small WWTPs with low discharge volumes contributed less than 1% to the total stream toxicity. Fish community compositions and trophic guild analysis showed that the diversity index was greater in the control than in impacted streams, and the proportion of omnivore species was less in the control. Also, ecosystem health assessments, based on the IBI, showed distinct differences between the control and impacted sites of WWTPs. Model values of the IBI, based on 12 stream data sets, averaged 28, which is judged as a fair to poor condition according to the U.S. EPA criteria. The mean IBI in the control sites was 42, indicating good stream condition, whereas the impacted sites was scored 21, indicating poor condition. Overall, WET tests and ecosystem health assessments suggested the WWTP effluents had evident toxic effects on the biota, and impacted the species compositions and trophic guilds, resulting in degradation of the stream ecosystem health.

  11. Incorporating Informatics for Integrating Biology and the Bedside (i2b2) into Predoctoral Trainee Curriculum to Evaluate Student-Generated Hypotheses.

    Science.gov (United States)

    Schieffer, Kathleen M; Peters, Douglas G; Richter, Chesney K; Loc, Welley S; Pawelczyk, James A

    2015-12-01

    As part of the Clinical and Translational Science Institute predoctoral TL1 training program at the Pennsylvania State University, a multidisciplinary team of predoctoral trainees representing the Chemistry, Neurosurgery, Nutritional Sciences, and Public Health Sciences departments were introduced to the NIH-sponsored Informatics for Integrating Biology and the Bedside (i2b2) database to test the following student-generated hypothesis: children with iron deficiency anemia (IDA) are at increased risk of attention deficit-hyperactivity disorder (ADHD). Children aged 4-12 and 4-17 years were categorized into IDA and control groups. De-identified medical records from the Penn State Milton S. Hershey Medical Center (HMC) and the Virginia Commonwealth University Medical Center (VCUMC) were used for the analysis. Overall, ADHD prevalence at each institution was lower than 2011 state estimates. There was a significant association between IDA and ADHD in the 4-17-year-old age group for all children (OR: 1.902 [95% CI: 1.363-2.656]), Caucasian children (OR: 1.802 [95% CI: 1.133-2.864]), and African American children (OR: 1.865 [95% CI: 1.152-3.021]). Clinical and Translational Science Award (CTSA) infrastructure is particularly useful for trainees to answer de novo scientific questions with minimal additional training and technical expertise. Moreover, projects can be expanded by collaborating within the CTSA network.

  12. Integrated biological and advanced oxidation based treatment of hexamine bearing wastewater: Effect of cow-dung as a co-substrate.

    Science.gov (United States)

    Gupta, Mandeep Kumar; Mittal, Atul K

    2016-05-05

    This work examines the treatment of hexamethylenetetramine (HMT) bearing effluent from N, N-dinitroso pentamethylene tetra-mine producing industrial plants in India. Chemical treatment using Fenton's reagent and aerobic treatment using batch reactors with co-substrate were investigated. Aerobic batch reactors integrated with advanced oxidation process of Fenton's reagent provides effective treatment of HMT effluents. Influence of Fenton's reagent dose reaction/contact and effect of varying co-substrate with effluent initial concentration was observed. Higher dose 100 mL of Fenton's reagent with higher reaction time 20 h resulted better degradation (34.88%) of wastewater. HMT hydrolyzes in acidic environment to ammonia and formaldehyde. Formaldehyde under normal conditions is toxic for biological treatment processes. When hydrolysis and acidification in the reactors are accompanied by low pH, aerobic batch reactors with use of co-substrates glucose, sucrose, and cow-dung extract separately in different proportion to wastewater ranging from 0.67 to 4.00, degraded wastewater effectively. Higher proportion of co-substrate to wastewater resulted better degradation. The relationships between nitrate, pH, turbidity and COD are discussed.

  13. Fostering synergy between cell biology and systems biology

    OpenAIRE

    2015-01-01

    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...

  14. 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.

  15. Investigation of ifosfamide and chloroacetaldehyde renal toxicity through integration of in vitro liver-kidney microfluidic data and pharmacokinetic-system biology models.

    Science.gov (United States)

    Leclerc, Eric; Hamon, Jeremy; Bois, Frederic Yves

    2016-02-01

    We have integrated in vitro and in silico data to describe the toxicity of chloroacetaldehyde (CAA) on renal cells via its production from the metabolism of ifosfamide (IFO) by hepatic cells. A pharmacokinetic (PK) model described the production of CAA by the hepatocytes and its transport to the renal cells. A system biology model was coupled to the PK model to describe the production of reactive oxygen species (ROS) induced by CAA in the renal cells. In response to the ROS production, the metabolism of glutathione (GSH) and its depletion were modeled by the action of an NFE2L2 gene-dependent pathway. The model parameters were estimated in a Bayesian context via Markov Chain Monte Carlo (MCMC) simulations based on microfluidic experiments and literature in vitro data. Hepatic IFO and CAA in vitro intrinsic clearances were estimated to be 1.85 x 10(-9) μL s(-1) cell(-1) and 0.185 x 10(-9) μL s(-1) cell(-1) ,respectively (corresponding to an in vivo intrinsic IFO clearance estimate of 1.23 l h(-1) , to be compared to IFO published values ranging from 3 to 10 l h(-1) ). After model calibration, simulations made at therapeutic doses of IFO showed CAA renal intracellular concentrations ranging from 11 to 131 μM. Intracellular CAA concentrations above 70 μM induced intense ROS production and GSH depletion. Those responses were time and dose dependent, showing transient and non-linear kinetics. Those results are in agreement with literature data reporting that intracellular CAA toxic concentrations range from 35 to 320 μM, after therapeutic ifosfamide dosing. The results were also consistent with in vitro CAA renal cytotoxicity data.

  16. Magellan: A Web Based System for the Integrated Analysis of Heterogeneous Biological Data and Annotations; Application to DNA Copy Number and Expression Data in Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Chris B. Kingsley

    2006-01-01

    Full Text Available Recent advances in high throughput biological methods allow researchers to generate enormous amounts of data from a single experiment. In order to extract meaningful conclusions from this tidal wave of data, it will be necessary to develop analytical methods of sufficient power and utility. It is particularly important that biologists themselves be able to perform many of these analyses, such that their background knowledge of the experimental system under study can be used to interpret results and direct further inquiries. We have developed a web-based system, Magellan, which allows the upload, storage, and analysis of multivariate data and textual or numerical annotations. Data and annotations are treated as abstract entities, to maximize the different types of information the system can store and analyze. Annotations can be used in analyses/visualizations, as a means of subsetting data to reduce dimensionality, or as a means of projecting variables from one data type or data set to another. Analytical methods are deployed within Magellan such that new functionalities can be added in a straightforward fashion. Using Magellan, we performed an integrated analysis of genome-wide comparative genomic hybridization (CGH, mRNA expression, and clinical data from ovarian tumors. Analyses included the use of permutation-based methods to identify genes whose mRNA expression levels correlated with patient survival, a nearest neighbor classifier to predict patient survival from CGH data, and curated annotations such as genomic position and derived annotations such as statistical computations to explore the quantitative relationship between CGH and mRNA expression data.

  17. Magellan: a web based system for the integrated analysis of heterogeneous biological data and annotations; application to DNA copy number and expression data in ovarian cancer.

    Science.gov (United States)

    Kingsley, Chris B; Kuo, Wen-Lin; Polikoff, Daniel; Berchuck, Andy; Gray, Joe W; Jain, Ajay N

    2007-02-05

    Recent advances in high throughput biological methods allow researchers to generate enormous amounts of data from a single experiment. In order to extract meaningful conclusions from this tidal wave of data, it will be necessary to develop analytical methods of sufficient power and utility. It is particularly important that biologists themselves be able to perform many of these analyses, such that their background knowledge of the experimental system under study can be used to interpret results and direct further inquiries. We have developed a web-based system, Magellan, which allows the upload, storage, and analysis of multivariate data and textual or numerical annotations. Data and annotations are treated as abstract entities, to maximize the different types of information the system can store and analyze. Annotations can be used in analyses/visualizations, as a means of subsetting data to reduce dimensionality, or as a means of projecting variables from one data type or data set to another. Analytical methods are deployed within Magellan such that new functionalities can be added in a straightforward fashion. Using Magellan, we performed an integrated analysis of genome-wide comparative genomic hybridization (CGH), mRNA expression, and clinical data from ovarian tumors. Analyses included the use of permutation-based methods to identify genes whose mRNA expression levels correlated with patient survival, a nearest neighbor classifier to predict patient survival from CGH data, and curated annotations such as genomic position and derived annotations such as statistical computations to explore the quantitative relationship between CGH and mRNA expression data.

  18. 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/.

  19. Integration of Biological, Physical/Chemical and Energy Efficient Systems in the CELSS Antarctic Analog: Performance of Prototype Systems and Issues for Life Support

    Science.gov (United States)

    Bubenheim, David L.; Flynn, Michael T.; Lamparter, Richard; Bates, Maynard; Kliss, Mark (Technical Monitor)

    1998-01-01

    The Controlled Ecological Life Support System (CELSS) Antarctic Analog Project (CAAP) is a joint endeavor between the National Science Foundation, Office of Polar Programs (NSF-OPP), and the National Aeronautics and Space Administration (NASA). The fundamental objective is to develop, deploy, and operate a testbed of advanced life support technologies at the Amundsen-Scott South Pole Station that enable the objectives of both the NSF and NASA. The functions of food production, water purification, and waste treatment, recycle, and reduction provided by CAAP will improve the quality of life for the South Pole inhabitants, reduce logistics dependence, enhance safety, and minimize environmental impacts associated with human presence on the polar plateau. Because of the analogous technical, scientific, and mission features with Planetary missions, such as a mission to Mars, CAAP provides NASA with a method for validating technologies and overall approaches to supporting humans. Prototype systems for waste treatment, water recycle, resource recovery and crop production are being evaluated in a testbed at Ames Research Center. The combined performance of these biological and physical/chemical systems as an integrated function in support of the human habitat will be discussed. Overall system performance will be emphasized. The effectiveness and efficiency of component technologies will be discussed in the context of energy and mass flow within the system and contribution to achieving a mass and energy conservative system. Critical to the discussion are interfaces with habitat functions outside of the closed-loop life support: the ability of the system to satisfy the life support requirements of the habitat and the ability to define input requirements. The significance of analog functions in relation to future Mars habitats will be discussed.

  20. Introduction to systems biology

    NARCIS (Netherlands)

    Bruggeman, F.J.; Hornberg, J.J.; Boogerd, F.C.; Westerhoff, H.V.; Boogerd, F.C.; Bruggeman, F.J.; Hofmeyr, J.H.S.; Westerhoff, H.V.

    2007-01-01

    The developments in the molecular biosciences have made possible a shift to combined molecular and system-level approaches to biological research under the name of Systems Biology. It integrates many types of molecular knowledge, which can best be achieved by the synergistic use of models and experi

  1. 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...

  2. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  3. Immobilization and characterization of a crude preparation of Escherichia coli trehalase: A laboratory exercise that integrates concepts of enzymology and molecular biology

    Directory of Open Access Journals (Sweden)

    A. S. Martins

    2009-05-01

    Full Text Available This paper  presents  a laboratory exercise for teaching  enzyme technology through  an  approach that integrates concepts of enzymology and molecular biology.  This  Laboratory Exercise  is based on the  extraction  of trehalase (EC 3.21.28 from a Escherichia coli  strain Mph2 (carrying the plasmid pTRE11 that harbors the gene TreA+ and immobilization of the enzyme on chitin. Therefore, the students  participate in bacterium cultivation, protein extraction from  E.coli  periplasmic space, preparation of chitin particles and enzyme immobilization.  Trehalase  was chosen because it  can be easily released by osmotic shock and it is not necessary to purify  it  from the osmotic shock fluid (OSF because  it is free of any other glycosidase. This lab exercise also teaches how to determine the kinetic parameters (Michaelis constant- Km and maximum velocity- Vm for free and immobilized enzymes.  It is obvious that the determination of kinetic parameters using the Michaelis-Menten model is not a novelty.  Nevertheless, an experimental class that includes the comparison of these parameters for free and immobilized enzymes, using the students´ own experimental data, would be extremely useful for teaching the subject. The students can identify and compare these parameters, as well  as discuss the differences and similarities among them. This discussion points towards issues such as  enzyme  conformation and structural rigidity related to changes in kinetic parameters mainly Km.  This Laboratory Exercise  was designed for graduate students that have a good background in Biochemistry and have joined courses involving either Enzymology or Enzyme Technology.

  4. Synthetic biology: insights into biological computation.

    Science.gov (United States)

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  5. 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...

  6. All biology is computational biology

    Science.gov (United States)

    2017-01-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science. PMID:28278152

  7. 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."

  8. Weeds of Hawaii’s lands devoted to watershed protection and biodiversity conservation: Role of biological control as the missing piece in an integrated pest management strategy

    Science.gov (United States)

    Medeiros, Arthur C.; Loope, L.L.

    2011-01-01

    Despite Hawaii’s reputation as an extinction icon, significant biological resources remain, especially in watersheds, natural areas, and specialized edaphic sites (e.g., lava dry forest, coastal). While direct habitat destruction by humans continues, human-facilitated biological invaders are currently the primary agents of continuing degradation. The ability of invasive plants to have prolific seed production, efficient dispersal systems, and to become established in dense vegetation, complicated by Hawaii’s rugged topography, appears to render mechanical and chemical control as mere holding actions. Costly, ‘environmentally unfriendly’, and often ineffective, strategies using chemical and mechanical control on a large scale, despite the most valiant of efforts, can be viewed simply as attempts to buy time. Without increased levels of safely tested biological control, the seemingly inevitable result is the landscape level transformation of native forests, with potentially catastrophic consequences to cultural, biological, water, and economic resources. Increased levels of effective biological control for certain intractable invasive species appear to comprise a conspicuous ‘missing piece’ in our efforts to protect Hawaiian watersheds and other conservation lands.

  9. An integrated chemical-biological study using caged mussels (Mytilus trossulus) along a pollution gradient in the Archipelago Sea (SW Finland, Baltic Sea).

    Science.gov (United States)

    Lehtonen, Kari K; Turja, Raisa; Budzinski, Hélène; Devier, Marie-Hélène

    2016-08-01

    Mussels (Mytilus trossulus) were caged along a known pollution gradient in the inner Archipelago Sea (northern Baltic Sea) and retrieved after 71 and 121 d for the measurement of selected chemical contaminants in tissues and biological endpoints including biochemical biomarkers and growth. Additional samples were collected during the growth season from a native mussel population at an alleged reference site. Elevated concentrations of numerous contaminants (e.g., PAH) were observed in spring, apparently due to the loss of tissue mass during the winter, while also the levels of many biomarkers (e.g., glutathione S-transferase activity) were elevated. Spatial and temporal changes in the accumulation of contaminants and biological parameters were observed with some of them (e.g., growth) linked to seasonal changes in environmental factors. The results underline the importance of understanding the effects of seasonal natural factors on the growth dynamics and general condition of mussels when assessing tissue concentrations of contaminants and biological effects.

  10. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research.

    Science.gov (United States)

    Yang, Jack Y; Niemierko, Andrzej; Bajcsy, Ruzena; Xu, Dong; Athey, Brian D; Zhang, Aidong; Ersoy, Okan K; Li, Guo-Zheng; Borodovsky, Mark; Zhang, Joe C; Arabnia, Hamid R; Deng, Youping; Dunker, A Keith; Liu, Yunlong; Ghafoor, Arif

    2010-12-01

    Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (ISIBM IJCBS 2009) attracted more than 300 papers and 400 researchers and medical doctors world-wide. It was the only inter/multidisciplinary conference aimed to promote synergistic research and education in bioinformatics, systems biology and intelligent computing. The conference committee was very grateful for the valuable advice and suggestions from honorary chairs, steering committee members and scientific leaders including Dr. Michael S. Waterman (USC, Member of United States National Academy of Sciences), Dr. Chih-Ming Ho (UCLA, Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Wing H. Wong (Stanford, Member of United States National Academy of Sciences), Dr. Ruzena Bajcsy (UC Berkeley, Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Qu Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Andrzej Niemierko (Harvard), Dr. A. Keith Dunker (Indiana), Dr. Brian D. Athey (Michigan), Dr. Weida Tong (FDA, United States Department of Health and Human Services), Dr. Cathy H. Wu (Georgetown), Dr. Dong Xu (Missouri), Drs. Arif Ghafoor and Okan K Ersoy (Purdue), Dr. Mark Borodovsky (Georgia Tech, President of ISIBM), Dr. Hamid R. Arabnia (UGA, Vice-President of ISIBM), and other scientific leaders. The committee presented the 2009 ISIBM Outstanding Achievement Awards to Dr. Joydeep Ghosh (UT

  11. Integrated Model of Chemical Perturbations of a Biological PathwayUsing 18 In Vitro High Throughput Screening Assays for the Estrogen Receptor

    Science.gov (United States)

    We demonstrate a computational network model that integrates 18 in vitro, high-throughput screening assays measuring estrogen receptor (ER) binding, dimerization, chromatin binding, transcriptional activation and ER-dependent cell proliferation. The network model uses activity pa...

  12. The "What Is a System" Reflection Interview as a Knowledge Integration Activity for High School Students' Understanding of Complex Systems in Human Biology

    Science.gov (United States)

    Tripto, Jaklin; Ben-Zvi Assaraf, Orit; Snapir, Zohar; Amit, Miriam

    2016-01-01

    This study examined the reflection interview as a tool for assessing and facilitating the use of "systems language" amongst 11th grade students who have recently completed their first year of high school biology. Eighty-three students composed two concept maps in the 10th grade--one at the beginning of the school year and one at its end.…

  13. Design and construction of a first-generation high-throughput integrated molecular biology platform for production of optimized synthetic genes and improved industrial strains

    Science.gov (United States)

    The molecular biological techniques for plasmid-based assembly and cloning of synthetic assembled gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-bas...

  14. Towards a synergy framework across neuroscience and robotics: Lessons learned and open questions. Reply to comments on: "Hand synergies: Integration of robotics and neuroscience for understanding the control of biological and artificial hands"

    Science.gov (United States)

    Santello, Marco; Bianchi, Matteo; Gabiccini, Marco; Ricciardi, Emiliano; Salvietti, Gionata; Prattichizzo, Domenico; Ernst, Marc; Moscatelli, Alessandro; Jorntell, Henrik; Kappers, Astrid M. L.; Kyriakopoulos, Kostas; Schaeffer, Alin Abu; Castellini, Claudio; Bicchi, Antonio

    2016-07-01

    We would like to thank all commentators for their insightful commentaries. Thanks to their diverse and complementary expertise in neuroscience and robotics, the commentators have provided us with the opportunity to further discuss state-of-the-art and gaps in the integration of neuroscience and robotics reviewed in our article. We organized our reply in two sections that capture the main points of all commentaries [1-9]: (1) Advantages and limitations of the synergy approach in neuroscience and robotics, and (2) Learning and role of sensory feedback in biological and robotics synergies.

  15. Working hard to make a simple definition of synergies. Comment on: "Hand synergies: Integration of robotics and neuroscience for understanding the control of biological and artificial hands" by Marco Santello et al.

    Science.gov (United States)

    Alessandro, Cristiano; Oliveira Barroso, Filipe; Tresch, Matthew

    2016-07-01

    The paper "Hand synergies: Integration of robotics and neuroscience for understanding the control of biological and artificial hands" [1] presents a comprehensive review of the work carried out as part of the EU funded project "The Hand Embodied". The work uses the concept of "synergy" to study the neuromuscular control of the human hand and to design novel robotics systems. The project has been very productive and has made important contributions. We are therefore confident that it will lead to further advancements and experiments in the future.

  16. Multiple sclerosis: integration of modeling with biology, clinical and imaging measures to provide better monitoring of disease progression and prediction of outcome.

    Science.gov (United States)

    Goodwin, Shikha Jain

    2016-12-01

    Multiple Sclerosis (MS) is a major cause of neurological disability in adults and has an annual cost of approximately $28 billion in the United States. MS is a very complex disorder as demyelination can happen in a variety of locations throughout the brain; therefore, this disease is never the same in two patients making it very hard to predict disease progression. A modeling approach which combines clinical, biological and imaging measures to help treat and fight this disorder is needed. In this paper, I will outline MS as a very heterogeneous disorder, review some potential solutions from the literature, demonstrate the need for a biomarker and will discuss how computational modeling combined with biological, clinical and imaging data can help link disparate observations and decipher complex mechanisms whose solutions are not amenable to simple reductionism.

  17. Integration of Genomic, Biologic, and Chemical Approaches to Target p53 Loss and Gain-of-Function in Triple Negative Breast Cancer

    Science.gov (United States)

    2014-09-01

    Approaches to Target p53 Loss and Gain-of-Function in Triple Negative Breast Cancer PRINCIPAL INVESTIGATOR: Jennifer A. Pietenpol, Ph.D...Biologic, and Chemical Approaches to Target p53 Loss and Gain-of-Function in Triple Negative Breast Cancer 5a. CONTRACT NUMBER...states resulting from alterations in the p53 signaling pathway in triple negative breast cancer (TNBC). Development of therapies for TNBC is a

  18. Integration of biological monitoring, environmental monitoring and computational modelling into the interpretation of pesticide exposure data: introduction to a proposed approach.

    Science.gov (United States)

    Colosio, Claudio; Rubino, Federico M; Alegakis, Athanasios; Ariano, Eugenio; Brambilla, Gabri; Mandic-Rajcevic, Stefan; Metruccio, Francesca; Minoia, Claudio; Moretto, Angelo; Somaruga, Chiara; Tsatsakis, Aristidis; Turci, Roberta; Vellere, Francesca

    2012-08-13

    Open field, variability of climatic and working conditions, and the use of complex mixtures of pesticides makes biological and environmental monitoring in agriculture, and therefore risk assessment and management, very complicated. A need of pointing out alternative risk assessment approaches, not necessarily based on measures, but simple, user-friendly and reliable, feasible also in the less advanced situations and in particular in small size enterprises, arises. This aim can be reached through a combination of environmental monitoring, biological monitoring and computational modelling. We have used this combination of methods for the creation of "exposure and risk profiles" to be applied in specific exposure scenarios, and we have tested this approach on a sample of Italian rice and maize herbicide applicators. We have given specific "toxicity scores" to the different products used and we have identified, for each of the major working phases, that is mixing and loading, spraying, maintenance and cleaning of equipment, the main variables affecting exposure and inserted them into a simple algorithm, able to produce "exposure indices". Based on the combination of toxicity indices and exposure indices it is possible to obtain semiquantitative estimates of the risk levels experienced by the workers in the exposure scenarios considered. Results of operator exposure data collected under real-life conditions can be used to validate and refine the algorithms; moreover, the AOEL derived from pre-marketing studies can be combined to estimate tentative biological exposure limits for pesticides, useful to perform individual risk assessment based on technical surveys and on simple biological monitoring. A proof of principle example of this approach is the subject of this article.

  19. Ecological and Socio-Economic Modeling of Consequences of Biological Management Scenarios Implementation in Integrated Watershed Management (Case Study: Simindasht Catchment

    Directory of Open Access Journals (Sweden)

    A. R. Keshtkar

    2016-09-01

    Full Text Available Integrated watershed management is considered as a new principle for development planning and management of water and soil resources emphasizing on socio-economic characteristics of the region to sustainable livelihoods without vulnerability for plants and the residents of an area. This research, in line with the objectives of integrated management, has been carried out for modelling and evaluating the effects of ecological, socio-economic consequences resulting from the implementation of the proposed management plans on the vegetation changes with a focus on the problems in Simindasht catchment, located in Semnan and Tehran Provinces. After standardization of indices by distance method and weighing them, the scenarios were prioritized using multi-criteria decision-making technique. Trade-off analysis of the results indicates that in the integrated management of Simindasht catchment more than one single management solution, covering all aspects of the system can be recommended in different weighting approaches. The approach used herein, considering the results of different models and comparing the results, is an efficient tool to represent the watershed system as a whole and to facilitate decision making for integrated watershed management.

  20. In Search of a Unified Theory of Biological Organization: What Does the Motor System of a Sea Slug Tell Us About Human Motor Integration?

    Science.gov (United States)

    1992-04-07

    integrated activity of large numbers of neurons might arise from interactions occurring localy between indi- vidual neurons. Thanks to the work of Rene ... Descartes and Euclid wouid like us to believe. the possibility of high-dimensiona space. of noniinearities. and of the dialectic be- tween structure

  1. Biological computation

    CERN Document Server

    Lamm, Ehud

    2011-01-01

    Introduction and Biological BackgroundBiological ComputationThe Influence of Biology on Mathematics-Historical ExamplesBiological IntroductionModels and Simulations Cellular Automata Biological BackgroundThe Game of Life General Definition of Cellular Automata One-Dimensional AutomataExamples of Cellular AutomataComparison with a Continuous Mathematical Model Computational UniversalitySelf-Replication Pseudo Code Evolutionary ComputationEvolutionary Biology and Evolutionary ComputationGenetic AlgorithmsExample ApplicationsAnalysis of the Behavior of Genetic AlgorithmsLamarckian Evolution Genet

  2. Preliminary Discussion on the Integrative Experiment Teaching Innovation of Biological Control of Plant Disease%《植物病害生物防治学》综合性实验的教学改革初探

    Institute of Scientific and Technical Information of China (English)

    丁婷; 齐永霞; 孙微微; 江海洋

    2013-01-01

    The design principle, teaching model, teaching effect of the integrative experiment of biological control of plant disease which was the undergraduate course in plant protection professional were discussed and analyzed in this paper.It suggested that teaching model of integrative experiment course expanded the knowledge of students , enabled the students to have a visual perceptual knowledge of biological control of plant disease , improved the comprehensive experimental skills and abilities and laid the foundation for the corresponding professional research of students in the future.%对植物保护专业本科生课程---《植物病害生物防治学》综合性实验的设计基本思路、教学方式、教学实施效果等进行了综合讨论与分析。综合性实验课教学模式扩大了学生的知识面,使学生对植物病害生物防治知识有了直观的感性认识,提高了综合实验技能和动手能力,为学生今后从事相应的专业研究奠定了基础。

  3. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

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

  4. The on-line detection of biological particle emissions from selected agricultural materials using the WIBS-4 (Waveband Integrated Bioaerosol Sensor) technique

    Science.gov (United States)

    O'Connor, David J.; Healy, David A.; Sodeau, John R.

    2013-12-01

    Agricultural activities have, for some time, been linked to adverse health effects such as Farmers' lung, hypersensitivity pneumonitis, aspergillosis and chronic obstructive pulmonary disease (COPD) This connection is known to be, at least in part, due to the numerous microbiological organisms that live and grow on materials found in occupational settings such as barns, animal shelters, stables and composting sites. Traditional techniques for determining biological release of fungal spores and bacteria require intensive, experienced human resources and considerable time to determine ambient concentrations. However more recently the fluorescence and light scattering signals obtained from primary biological aerosol particles (PBAP) have been utilised for their near real-time counting and characterisation abilities. In the current study, data collected for the bioaerosol types released from hay and silage were counted and identified using a combination of the WIBS-4 bioaerosol sensor approach and impaction/optical microscopy. Particle emissions were characterised according to particle numbers, their size distributions, particle asymmetry values and fluorescence characteristics. The variables obtained were shown to provide potential “fingerprint” signatures for PBAP emissions emanating from two important compost components, namely, silage and hay. Comparisons between the data acquired by the WIBS-4 bioaerosol sensor, optical microscopy findings and also previous literature suggest that the likely identification of Aspergillus/Penicillium type spores and bacterial species released from hay and silage was achieved on a relatively rapid time-scale.

  5. [Biological weapons].

    Science.gov (United States)

    Kerwat, K; Becker, S; Wulf, H; Densow, D

    2010-08-01

    Biological weapons are weapons of mass destruction that use pathogens (bacteria, viruses) or the toxins produced by them to target living organisms or to contaminate non-living substances. In the past, biological warfare has been repeatedly used. Anthrax, plague and smallpox are regarded as the most dangerous biological weapons by various institutions. Nowadays it seems quite unlikely that biological warfare will be employed in any military campaigns. However, the possibility remains that biological weapons may be used in acts of bioterrorism. In addition all diseases caused by biological weapons may also occur naturally or as a result of a laboratory accident. Risk assessment with regard to biological danger often proves to be difficult. In this context, an early identification of a potentially dangerous situation through experts is essential to limit the degree of damage.

  6. Integrated pathway-based and network-based analysis of GC-MS rice metabolomics data under diazinon stress to infer affected biological pathways.

    Science.gov (United States)

    Mahdavi, Vahideh; Ghanati, Faezeh; Ghassempour, Alireza

    2016-02-01

    Diazinon insecticide is widely applied in rice (Oryza sativa L.) fields in Iran. However, concerns are now being raised about its potential adverse impacts on rice. In this study, a time-course metabolic change in rice plants was investigated after diazinon treatment using gas chromatography-mass spectrometry (GC-MS) and subsequently three different methods, MetaboAnalyst, MetaboNetwork, and analysis of reporter reactions, as a potential multivariate method were used to find the underlying changes in metabolism with stronger evidence in order to link differentially expressed metabolites to biological pathways. Results clearly showed the similarity of acetylcholinesterase (AChE) of rice plants to that of animals in terms of its inhibitability by diazinon and emphasized that subsequent accumulation of AChE mainly affects the metabolism of osmolites and tricarboxylic acid intermediates subsequent accumulation of ACh mainly affects the metabolism of osmolites and TCA intermediates.

  7. BIological Psychology, Exercise, and Stress.

    Science.gov (United States)

    Dishman, Rod K.

    1994-01-01

    Reviews theory and methods used by the field of biological psychology to study stress that have potential for understanding how behavioral and biological adaptations to the stress of exercise are integrated. The overview focuses on anxiety, depression, and physiological responsiveness to nonexercise stressors from the perspective of biological…

  8. An Exercise in Biological Control.

    Science.gov (United States)

    Lennox, John; Duke, Michael

    1997-01-01

    Discusses the history of the use of pesticides and biological control. Introduces the concept of biological control as illustrated in the use of the entomopathogenic bacterium Bacillus thuringiensis and highlights laboratory demonstrations of Koch's postulates. Includes an exercise that offers the student and teacher several integrated learning…

  9. 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.

  10. The removal of formaldehyde from concentrated synthetic wastewater using O3/MgO/H2O2 process integrated with the biological treatment.

    Science.gov (United States)

    Moussavi, Gholamreza; Yazdanbakhsh, Ahmadreza; Heidarizad, Mahdi

    2009-11-15

    The catalytic advanced oxidation process (CAOP) of O(3)/MgO/H(2)O(2) was integrated with a sequencing batch reactor (SBR) system to completely treat concentrated formaldehyde wastewater, demonstrating that this combination is an effective method for treating such wastewaters. The influence of several operational variables--including pH, MgO powder dosage, and the concentrations of H(2)O(2) and O(3)--was investigated for the O(3)/MgO/H(2)O(2) degradation of a 7000 mg/L formaldehyde wastewater. The optimum conditions were found to be a pH of 8, 5 g/L dose of MgO powder, 0.09 mole/L concentration of H(2)O(2), and 0.153 g/L min dose of O(3). The formaldehyde and COD concentrations were reduced 79% and 65.6%, respectively, in the CAOP for 120 min of reaction time under the optimum condition stated above. The remaining concentrations of formaldehyde and COD were 1500 mg/L and 3200 mg/L, respectively, in the effluent. The degradation of formaldehyde in CAOP was determined to be a first-order reaction with a constant of 0.015/min, and radical oxidation was the predominant degradation mechanism. This effluent was post-treated in SBR system for a total cycle time of 24h. The SBR completely removed the formaldehyde and removed 98% of the COD, reducing the COD concentration to lower than 60 mg/L. Therefore, the integrated O(3)/MgO/H(2)O(2) and SBR process is demonstrated as a promising technology for the complete treatment of wastewater with high concentrations of toxic and inhibitory compounds such as formaldehyde.

  11. Development and integration of block operations for data invariant automation of digital preprocessing and analysis of biological and biomedical Raman spectra.

    Science.gov (United States)

    Schulze, H Georg; Turner, Robin F B

    2015-06-01

    High-throughput information extraction from large numbers of Raman spectra is becoming an increasingly taxing problem due to the proliferation of new applications enabled using advances in instrumentation. Fortunately, in many of these applications, the entire process can be automated, yielding reproducibly good results with significant time and cost savings. Information extraction consists of two stages, preprocessing and analysis. We focus here on the preprocessing stage, which typically involves several steps, such as calibration, background subtraction, baseline flattening, artifact removal, smoothing, and so on, before the resulting spectra can be further analyzed. Because the results of some of these steps can affect the performance of subsequent ones, attention must be given to the sequencing of steps, the compatibility of these sequences, and the propensity of each step to generate spectral distortions. We outline here important considerations to effect full automation of Raman spectral preprocessing: what is considered full automation; putative general principles to effect full automation; the proper sequencing of processing and analysis steps; conflicts and circularities arising from sequencing; and the need for, and approaches to, preprocessing quality control. These considerations are discussed and illustrated with biological and biomedical examples reflecting both successful and faulty preprocessing.

  12. UV-H2O2 based AOP and its integration with biological activated carbon treatment for DBP reduction in drinking water.

    Science.gov (United States)

    Toor, Ramn; Mohseni, Madjid

    2007-02-01

    The presence of disinfection byproducts (DBPs) such as trihalomethanes (THMs) and haloacetic acids (HAAs) in drinking water is of great concern due to their adverse effects on human health. Emerging regulation limiting the concentration of DBPs in drinking water has increased demands for technologies and processes which reduce the formation of DBPs in drinking water. In this study, UV-H2O2 based advance oxidation process (AOP) was used to treat raw surface water. Experiments were conducted using low pressure mercury vapor UV lamps in collimated beam and flow-through annular photoreactors. The effect of UV fluence (0-3500 mJ cm(-2)) and hydrogen peroxide concentration (0-23 mg l(-1)) in reducing the concentration of THMs and HAAs was examined. The UV-H2O2 AOP was then coupled with a downstream biological activated carbon (BAC) treatment to assess the synergetic benefits of combining the two treatments. It was observed that UV-H2O2 AOP was only effective at reducing DBPs at UV fluences of more than 1000 mJ cm(-2) and initial H2O2 concentrations of about or greater than 23 mg l(-1). However, the combined AOP-BAC treatment showed significant reductions of 43%, 52%, and 59% relative to untreated raw water for DBPs, TOC, and UV254, respectively.

  13. Application of Moving Bed Biofilm Reactor (MBBR) and Integrated Fixed Activated Sludge (IFAS) for Biological River Water Purification System: A Short Review

    Science.gov (United States)

    Lariyah, M. S.; Mohiyaden, H. A.; Hayder, G.; Hayder, G.; Hussein, A.; Basri, H.; Sabri, A. F.; Noh, MN

    2016-03-01

    This review paper present the MBBR and IFAS technology for urban river water purification including both conventional methods and new emerging technologies. The aim of this paper is to present the MBBR and IFAS technology as an alternative and successful method for treating different kinds of effluents under different condition. There are still current treatment technologies being researched and the outcomes maybe available in a while. The review also includes many relevant researches carried out at the laboratory and pilot scales. This review covers the important processes on MBBR and IFAS basic treatment process, affecting of carrier type and influent types. However, the research concluded so far are compiled herein and reported for the first time to acquire a better perspective and insight on the subject with a view of meeting the news approach. The research concluded so far are compiled herein and reported for the first time to acquire a better perspective and insight on the subject with a view of meeting the news approach. To this end, the most feasible technology could be the combination of advanced biological process (bioreactor systems) including MBBR and IFAS system.

  14. Treatment of an actual slaughterhouse wastewater by integration of biological and advanced oxidation processes: Modeling, optimization, and cost-effectiveness analysis.

    Science.gov (United States)

    Bustillo-Lecompte, Ciro Fernando; Mehrvar, Mehrab

    2016-11-01

    Biological and advanced oxidation processes are combined to treat an actual slaughterhouse wastewater (SWW) by a sequence of an anaerobic baffled reactor, an aerobic activated sludge reactor, and a UV/H2O2 photoreactor with recycle in continuous mode at laboratory scale. In the first part of this study, quadratic modeling along with response surface methodology are used for the statistical analysis and optimization of the combined process. The effects of the influent total organic carbon (TOC) concentration, the flow rate, the pH, the inlet H2O2 concentration, and their interaction on the overall treatment efficiency, CH4 yield, and H2O2 residual in the effluent of the photoreactor are investigated. The models are validated at different operating conditions using experimental data. Maximum TOC and total nitrogen (TN) removals of 91.29 and 86.05%, respectively, maximum CH4 yield of 55.72%, and minimum H2O2 residual of 1.45% in the photoreactor effluent were found at optimal operating conditions. In the second part of this study, continuous distribution kinetics is applied to establish a mathematical model for the degradation of SWW as a function of time. The agreement between model predictions and experimental values indicates that the proposed model could describe the performance of the combined anaerobic-aerobic-UV/H2O2 processes for the treatment of SWW. In the final part of the study, the optimized combined anaerobic-aerobic-UV/H2O2 processes with recycle were evaluated using a cost-effectiveness analysis to minimize the retention time, the electrical energy consumption, and the overall incurred treatment costs required for the efficient treatment of slaughterhouse wastewater effluents.

  15. Building multivariate systems biology models

    NARCIS (Netherlands)

    Kirwan, G.M.; Johansson, E.; Kleemann, R.; Verheij, E.R.; Wheelock, A.M.; Goto, S.; Trygg, J.; Wheelock, C.E.

    2012-01-01

    Systems biology methods using large-scale "omics" data sets face unique challenges: integrating and analyzing near limitless data space, while recognizing and removing systematic variation or noise. Herein we propose a complementary multivariate analysis workflow to both integrate "omics" data from

  16. Fully Integrated On-Chip Coil in 0.13 μm CMOS for Wireless Power Transfer Through Biological Media.

    Science.gov (United States)

    Zargham, Meysam; Gulak, P Glenn

    2015-04-01

    Delivering milliwatts of wireless power at centimeter distances is advantageous to many existing and emerging biomedical applications. It is highly desirable to fully integrate the receiver on a single chip in standard CMOS with no additional post-processing steps or external components. This paper presents a 2 × 2.18 mm(2) on-chip wireless power transfer (WPT) receiver (Rx) coil fabricated in 0.13 μm CMOS. The WPT system utilizes a 14.5 × 14.5 mm(2) transmitter (Tx) coil that is fabricated on a standard FR4 substrate. The on-chip power harvester demonstrates a peak WPT efficiency of -18.47 dB , -20.96 dB and -20.15 dB at 10 mm of separation through air, bovine muscle and 0.2 molar NaCl, respectively. The achieved efficiency enables the delivery of milliwatts of power to application circuits while staying below safe power density and electromagnetic (EM) exposure limits.

  17. A Systems Biology-Based Investigation into the Pharmacological Mechanisms of Sheng-ma-bie-jia-tang Acting on Systemic Lupus Erythematosus by Multi-Level Data Integration.

    Science.gov (United States)

    Huang, Lin; Lv, Qi; Liu, Fenfen; Shi, Tieliu; Wen, Chengping

    2015-11-12

    Sheng-ma-bie-jia-tang (SMBJT) is a Traditional Chinese Medicine (TCM) formula that is widely used for the treatment of Systemic Lupus Erythematosus (SLE) in China. However, molecular mechanism behind this formula remains unknown. Here, we systematically analyzed targets of the ingredients in SMBJT to evaluate its potential molecular mechanism. First, we collected 1,267 targets from our previously published database, the Traditional Chinese Medicine Integrated Database (TCMID). Next, we conducted gene ontology and pathway enrichment analyses for these targets and determined that they were enriched in metabolism (amino acids, fatty acids, etc.) and signaling pathways (chemokines, Toll-like receptors, adipocytokines, etc.). 96 targets, which are known SLE disease proteins, were identified as essential targets and the rest 1,171 targets were defined as common targets of this formula. The essential targets directly interacted with SLE disease proteins. Besides, some common targets also had essential connections to both key targets and SLE disease proteins in enriched signaling pathway, e.g. toll-like receptor signaling pathway. We also found distinct function of essential and common targets in immune system processes. This multi-level approach to deciphering the underlying mechanism of SMBJT treatment of SLE details a new perspective that will further our understanding of TCM formulas.

  18. 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%).

  19. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  20. Computational biology

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

  1. A geospatial data integration framework for mapping and monitoring tropical landscape diversity in Costa Rica's San Juan-La Selva Biological Corridor

    Science.gov (United States)

    Sesnie, Steven E.

    Landcover change has substantially reduced the amount of tropical rain forest since the 1950s. Little is known about the extent of remaining forest types. A multivariate analysis of 144 forest plots across Costa Rica's San Juan - La Selva Biological Corridor resulted in eight floristically defined old-growth forest categories. Spectral separability was tested between categories using Landsat TM bands and vegetation indices for old-growth types, palm swamps, tree plantations and regrowth. Image filtering and NDVI increased spectral separability among categories by 30%. Separability tests resulted in seven well-discriminated forest categories. Factors driving forest beta-diversity are not well quantified for wet tropical environments. We examined the relationship between rain forest composition and environmental variation for a 3000 km2 area in northeastern Costa Rica. Mid- to upper-canopy tree species abundance and soil characteristics were measured from 127, 0.25-ha plots across Caribbean lowlands and foothills. Partial Mantel tests produced significant correlations between floristic distance and soil, terrain, and climate variables controlling the effects of geographical distance. Niche-factors showed a significant trend with forest composition more than dispersal limitation or disturbance related factors. Variables such as terrain features, climatic variation and Landsat TM bands associated with forest composition were assessed with two decision tree models. Thirty-two landcover types were compared for a 15-year time interval. Ten were floristic alliances from a cluster analysis of forest plots and wetland categories. A subset of 12 spectral and spatial predictor variables produced accuracies of 93%+/-7% and 83%+/-15% for QUEST and CRUISE classifiers, respectively. The QUEST classifier was accurate for habitat mapping and change detection important to biodiversity monitoring objectives. A 1996 Forestry Law initiated environmental service payments and prohibited

  2. Diferenças de gênero no desenvolvimento sexual: integração dos paradigmas biológico, psicanalítico e evolucionista Gender differences in sexual development: biologic, psychoanalytic and evolutionary paradigms integration

    Directory of Open Access Journals (Sweden)

    Luciana Parisotto

    2003-04-01

    Full Text Available O desenvolvimento sexual masculino e feminino tem sido fonte de incontáveis questionamentos em várias áreas do conhecimento humano ao longo da história da humanidade. Diversas especialidades têm estudado o tópico da sexualidade de forma dissociada, dificultando a sua compreensão global e a abordagem terapêutica de seus transtornos. A busca de integração de diferentes teorias oriundas, tanto dos processos fisiológicos básicos que originam a vida, quanto dos campos mais complexos da psicanálise, tem sido um dos grandes desafios da prática clínica. Propõe-se, então, um artigo com o objetivo de descrever as diferenças de gênero no desenvolvimento sexual humano, à luz dos vértices biológico, psicanalítico e evolucionista, buscando-se pontes de conexão entre estes paradigmas, para uma visão mais integrada do processo de ser masculino ou feminino.Male and female sexual development has been source of many controversies through the human history. Many specialties have studied the sexuality from a disconnected point of view, raising difficulties to its integral understanding and therapeutic approach. The search for integration between physiology and psychoanalysis has been one of the major challenges in clinical practice. In this article we describe gender differences in sexual human development under the biological, psychoanalytical and evolutionary perspectives, searching connections between these paradigms in order to find a more integrated vision of male and female development.

  3. [Research progress of cardiac systems biology].

    Science.gov (United States)

    Wang, Juan; Shang, Tong

    2009-04-01

    Systems Biology is one of the most widely discussed fields among emerging post-genomic disciplines. Medical systems biology is an important component of systems biology. The goals of medical systems biology are gaining a complete understanding of human body in normal and disease states. Driven by the great importance of cardiovascular diseases, cardiac systems biology is improving rapidly. This review provides an overview of major themes in the developing field of cardiac systems biology, including some of the high-throughput experiments and strategies used to integrate the datasets, various types of computational approaches used for developing useful quantitative models, and successful examples, future directions of cardiac systems biology.

  4. Biological Oceanography

    Science.gov (United States)

    Dyhrman, Sonya

    2004-10-01

    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  5. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  6. Foldit Biology

    Science.gov (United States)

    2015-07-31

    Report 8/1/2013-7/31/2015 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Foldit Biology NOOO 14-13-C-0221 Sb. GRANT NUMBER N/A Sc. PROGRAM ELEMENT...Include area code) Unclassified Unclassified Unclassified (206) 616-2660 Zoran Popović Foldit Biology (Task 1, 2, 3, 4) Final Report...Period Covered by the Report August 1, 2013 – July 31, 2015 Date of Report: July 31, 2015 Project Title: Foldit Biology Contract Number: N00014-13

  7. Scientific integrity

    DEFF Research Database (Denmark)

    Merlo, Domenico Franco; Vahakangas, Kirsi; Knudsen, Lisbeth E.

    2008-01-01

    Environmental health research is a relatively new scientific area with much interdisciplinary collaboration. Regardless of which human population is included in field studies (e.g., general population, working population, children, elderly, vulnerable sub-groups, etc.) their conduct must guarantee...... well acknowledged ethical principles. These principles, along with codes of conduct, are aimed at protecting study participants from research-related undesired effects and guarantee research integrity. A central role is attributed to the need for informing potential participants (i.e., recruited...... to know or not know. This is specifically relevant for studies including biological markers and/or storing biological samples that might be analysed years later to tackle research objectives that were specified and communicated to participants at the time of recruitment or that may be formulated after...

  8. Biological Soft Robotics.

    Science.gov (United States)

    Feinberg, Adam W

    2015-01-01

    In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

  9. Integrated Technology of Ozone Catalysis Oxidation -Modified Biological Aeration Filter -Ultrafiltration and Reverse Osmosis for Deep Treatment of Coking-Plant Wastewater%臭氧催化氧化-MBAF-UF-RO处理焦化废水

    Institute of Scientific and Technical Information of China (English)

    文志军; 赵爱国; 郎晓政

    2014-01-01

    China Energy Conservation and Reduction Co., LTD Construct the wastewatert reatment plant for a coking –plant by BT mode. Through analysis and argumentation, the main treatment process is a integrated technology of ozone catalysis oxidation – modified biological aeration filter – ultrafiltration and reverse os⁃mosis. The result shows that the treated water of water treatment system can meet the requirement of make-up water requirement, and the ozone catalytic oxidation reactor makes effective degradation of small molecule organic matter, at the same time, it can effectively improve the biodegradability of wastewater, which is subse⁃quent for the aeration biological filter (MBAF) and the deep desalting system (UF + RO).%中国节能减排有限公司以BT模式承建焦化废水深度处理工程。经过分析和论证,确定以臭氧催化氧化反应器+MBAF反应器+UF+RO作为水处理主体工艺。项目建成后,系统出水水质优于循环冷却补给水要求,特别是臭氧催化氧化反应器在降解小分子有机物的同时,有效改善废水可生化性,为后续改良曝气生物滤池(MBAF)进一步生物降解有机物提供了有利条件,从而确保深度脱盐系统(UF+RO)的高效、稳定运行。

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

    Science.gov (United States)

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

    2010-03-01

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

  11. Bridging the gap between systems biology and synthetic biology.

    Science.gov (United States)

    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, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology.

  12. Towards Systems Biology of Mycotoxin Regulation

    OpenAIRE

    Christof Rampitsch; Rajagopal Subramaniam

    2013-01-01

    Systems biology is a scientific approach that integrates many scientific disciplines to develop a comprehensive understanding of biological phenomena, thus allowing the prediction and accurate simulation of complex biological behaviors. It may be presumptuous to write about toxin regulation at the level of systems biology, but the last decade of research is leading us closer than ever to this approach. Past research has delineated multiple levels of regulation in the pathways leading to the b...

  13. Use of global sensitivity analysis in quantitative microbial risk assessment: application to the evaluation of a biological time temperature integrator as a quality and safety indicator for cold smoked salmon.

    Science.gov (United States)

    Ellouze, M; Gauchi, J-P; Augustin, J-C

    2011-06-01

    The aim of this study was to apply a global sensitivity analysis (SA) method in model simplification and to evaluate (eO)®, a biological Time Temperature Integrator (TTI) as a quality and safety indicator for cold smoked salmon (CSS). Models were thus developed to predict the evolutions of Listeria monocytogenes and the indigenous food flora in CSS and to predict TTIs endpoint. A global SA was then applied on the three models to identify the less important factors and simplify the models accordingly. Results showed that the subset of the most important factors of the three models was mainly composed of the durations and temperatures of two chill chain links, out of the control of the manufacturers: the domestic refrigerator and the retail/cabinet links. Then, the simplified versions of the three models were run with 10(4) time temperature profiles representing the variability associated to the microbial behavior, to the TTIs evolution and to the French chill chain characteristics. The results were used to assess the distributions of the microbial contaminations obtained at the TTI endpoint and at the end of the simulated profiles and proved that, in the case of poor storage conditions, the TTI use could reduce the number of unacceptable foods by 50%.

  14. Integrated monitoring of chemicals and their effects on four sentinel species, Limanda limanda, Platichthys flesus, Nucella lapillus and Mytilus sp., in Seine Bay: A key step towards applying biological effects to monitoring.

    Science.gov (United States)

    Burgeot, Thierry; Akcha, Farida; Ménard, Dominique; Robinson, Craig; Loizeau, Véronique; Brach-Papa, Christophe; Martínez-Gòmez, Concepción; Le Goff, Jérémie; Budzinski, Hélène; Le Menach, Karine; Cachot, Jérome; Minier, Christophe; Broeg, Katja; Hylland, Ketil

    2017-03-01

    The International workshop on Integrated Assessment of CONtaminants impacts on the North sea (ICON) provided a framework to validate the application of chemical and biological assessment thresholds (BACs and EACs) in the Seine Bay in France. Bioassays (oyster larval anomalies, Corophium arenarium toxicity assay and DR Calux) for sediment and biomarkers: ethoxyresorufin-O-deethylase (EROD) activity, acetylcholinesterase (AChE) activity, lysosomal membrane stability (LMS), DNA strand breaks using the Comet assay, DNA adducts, micronucleus (MN), PAH metabolites, imposex, intersex and fish external pathologies were analysed in four marine sentinel species (Platichthys flesus, Limanda limanda, Mytilus sp. and Nucella lapilus). Polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and heavy metals were analysed in biota and sediment. Results for sediment and four species in 2008-2009 made it possible to quantify the impact of contaminants using thresholds (Environmental Assessment Criteria/EAC2008: 70% and EAC2009: 60%) and effects (EAC2008: 50% and EAC2009: 40%) in the Seine estuary. The Seine estuary is ranked among Europe's most highly polluted sites.

  15. Systems biology of human atherosclerosis.

    Science.gov (United States)

    Shalhoub, Joseph; Sikkel, Markus B; Davies, Kerry J; Vorkas, Panagiotis A; Want, Elizabeth J; Davies, Alun H

    2014-01-01

    Systems biology describes a holistic and integrative approach to understand physiology and pathology. The "omic" disciplines include genomics, transcriptomics, proteomics, and metabolic profiling (metabonomics and metabolomics). By adopting a stance, which is opposing (yet complimentary) to conventional research techniques, systems biology offers an overview by assessing the "net" biological effect imposed by a disease or nondisease state. There are a number of different organizational levels to be understood, from DNA to protein, metabolites, cells, organs and organisms, even beyond this to an organism's context. Systems biology relies on the existence of "nodes" and "edges." Nodes are the constituent part of the system being studied (eg, proteins in the proteome), while the edges are the way these constituents interact. In future, it will be increasingly important to collaborate, collating data from multiple studies to improve data sets, making them freely available and undertaking integrative analyses.

  16. Advanced treatment of port cabin washing wastewater by integrated process ozonization-biological aerated filter-biological aerated filter%一体化O3-BAF—BAF组合工艺深度处理港口洗舱废水

    Institute of Scientific and Technical Information of China (English)

    葛启龙; 汪晓军

    2013-01-01

    采用一体化臭氧曝气生物滤池(O3-BAF)—曝气生物滤池(BAF)组合工艺对二级生化处理后的港口码头洗舱化学品废水进行深度处理,进水COD约为200~240 mg/L,色度为16~32倍时,经该工艺处理后出水COD<30mg/L,去除率>91%,色度降到4倍以下,出水水质达到《生活杂用水水质标准》(CJ/T48-1999)要求.工程运行实践表明,该深度处理系统运行稳定,处理效率高,具有良好的经济效益与环境效益.%The integrated ozonization-biological aerated filter-biological aerated filter combined process has been applied to the advanced treatment of port cabin washing wastewater after secondary biochemical treatment.When the COD of the influent is 200-240 mg/L,and chroma is 16-32 times,COD of effluent is reduced to less than 30 mg/L after treatment,the removing rate is more than 91%,and chroma is reduced to less than 4 times,reaching the specified Miscellaneous Domestic Water Quality Standard(CJ/T 48-1999).The result shows that the advanced treatment system runs stably,and has high treatment efficiency.It has great economic and environmental benefits.

  17. Integrative biology of tail autotomy in lizards.

    Science.gov (United States)

    Higham, Timothy E; Russell, Anthony P; Zani, Peter A

    2013-01-01

    Self-amputation (autotomy) of the tail is essential for the survival of many lizards. Accordingly, it has garnered the attention of scientists for more than 200 years. Several factors can influence the release of the tail, such as the size, sex, and age of the lizard; type of predator; ecology; and evolutionary history of the lineage. Once lost, the tail will writhe for seconds to minutes, and these movements likely depend on the size and physiology of the tail, habitat of the lizard, and predation pressure. Loss of the tail will, in turn, have impacts on the lizard, such as modified locomotor performance and mechanics, as well as escape behavior. However, the tail is almost always regenerated, and this involves wound healing, altered investment of resources, and tissue differentiation. The regenerated tail generally differs from the original in several ways, including size, shape, and function. Here we summarize recent findings of research pertaining to tail autotomy, and we propose a framework for future investigations.

  18. Integration of Chemical and Biological Catalysis

    DEFF Research Database (Denmark)

    Schwartz, Thomas J.; Goodman, Samuel M.; Osmundsen, Christian Mårup;

    2013-01-01

    Furylglycolic acid (FA), a pseudoaromatic hydroxy-acid suitable for copolymerization with lactic acid, can be produced from glucose via enzymatically derived cortalcerone using a combination of Bronsted and Lewis acid catalysts. Cortalcerone is first converted to furylglyoxal hydrate (FH) over a ...

  19. Integrated physiology and systems biology of PPARa

    NARCIS (Netherlands)

    Kersten, A.H.

    2014-01-01

    The Peroxisome Proliferator Activated Receptor alpha (PPARa) is a transcription factor that plays a major role in metabolic regulation. This review addresses the functional role of PPARa in intermediary metabolism and provides a detailed overview of metabolic genes targeted by PPARa, with a focus on

  20. Biology Notes.

    Science.gov (United States)

    School Science Review, 1981

    1981-01-01

    Outlines a variety of laboratory procedures, techniques, and materials including construction of a survey frame for field biology, a simple tidal system, isolation and applications of plant protoplasts, tropisms, teaching lung structure, and a key to statistical methods for biologists. (DS)

  1. (Biological dosimetry)

    Energy Technology Data Exchange (ETDEWEB)

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  2. Marine Biology

    Science.gov (United States)

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  3. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  4. Biology Notes.

    Science.gov (United States)

    School Science Review, 1984

    1984-01-01

    Presents information on the teaching of nutrition (including new information relating to many current O-level syllabi) and part 16 of a reading list for A- and S-level biology. Also includes a note on using earthworms as a source of material for teaching meiosis. (JN)

  5. Applicability of Computational Systems Biology in Toxicology

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...... 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...

  6. Grand challenges for biological engineering.

    Science.gov (United States)

    Yoon, Jeong-Yeol; Riley, Mark R

    2009-09-22

    Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE) released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE) conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented by the NAE. This letter presents a brief outline of how biological engineers are working to solve these large scale and integrated problems of our society.

  7. Grand challenges for biological engineering

    Directory of Open Access Journals (Sweden)

    Riley Mark R

    2009-09-01

    Full Text Available Abstract Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented by the NAE. This letter presents a brief outline of how biological engineers are working to solve these large scale and integrated problems of our society.

  8. Mesoscopic biology

    Indian Academy of Sciences (India)

    G V Shivashankar

    2002-02-01

    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological systems. In recent years advances in technology have led to the study of some of the design principles of these machines; in particular at the level of an individual molecule. For example, the forces that operate in molecular interactions, the stochasticity involved in these interactions and their spatio-temporal dynamics are beginning to be explored. Understanding such design principles is opening new possibilities in mesoscopic physics with potential applications.

  9. Marine biology

    Energy Technology Data Exchange (ETDEWEB)

    Thurman, H.V.; Webber, H.H.

    1984-01-01

    This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the nature of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index.

  10. Implementing Recommendations for Introductory Biology by Writing a New Textbook

    Science.gov (United States)

    Barsoum, Mark J.; Sellers, Patrick J.; Campbell, A. Malcolm; Heyer, Laurie J.; Paradise, Christopher J.

    2013-01-01

    We redesigned the undergraduate introductory biology course by writing a new textbook ("Integrating Concepts in Biology" ["ICB"]) that follows first principles of learning. Our approach emphasizes primary data interpretation and the utility of mathematics in biology, while de-emphasizing memorization. This redesign divides biology into five big…

  11. 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....

  12. The Physics of Marine Biology.

    Science.gov (United States)

    Conn, Kathleen

    1992-01-01

    Discusses ways in which marine biology can be integrated into the physics classroom. Topics suggested for incorporation include the harmonic motion of ocean waves, ocean currents, the interaction of visible light with ocean water, pressure, light absorption, and sound transfer in water. (MDH)

  13. Biological Databases

    Directory of Open Access Journals (Sweden)

    Kaviena Baskaran

    2013-12-01

    Full Text Available Biology has entered a new era in distributing information based on database and this collection of database become primary in publishing information. This data publishing is done through Internet Gopher where information resources easy and affordable offered by powerful research tools. The more important thing now is the development of high quality and professionally operated electronic data publishing sites. To enhance the service and appropriate editorial and policies for electronic data publishing has been established and editors of article shoulder the responsibility.

  14. 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.

  15. 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.

  16. Biological biomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Jorge-Herrero, E. [Servicio de Cirugia Experimental. Clinica Puerta de Hierro, Madrid (Spain)

    1997-05-01

    There are a number of situations in which substances of biological origin are employed as biomaterials. Most of them are macromolecules derived from isolated connective tissue or the connective tissue itself in membrane form, in both cases, the tissue can be used in its natural form or be chemically treated. In other cases, certain blood vessels can be chemically pretreated and used as vascular prostheses. Proteins such as albumin, collagen and fibrinogen are employed to coat vascular prostheses. Certain polysaccharides have also been tested for use in controlled drug release systems. Likewise, a number of tissues, such as dura mater, bovine pericardium, procine valves and human valves, are used in the preparation of cardiac prostheses. We also use veins from animals or humans in arterial replacement. In none of these cases are the tissues employed dissimilar to the native tissues as they have been chemically modified, becoming a new bio material with different physical and biochemical properties. In short, we find that natural products are being utilized as biomaterials and must be considered as such; thus, it is necessary to study both their chemicobiological and physicomechanical properties. In the present report, we review the current applications, problems and future prospects of some of these biological biomaterials. (Author) 84 refs.

  17. Synthesizing Novel Anthraquinone Natural Product-Like Compounds to Investigate Protein-Ligand Interactions in Both an in Vitro and in Vivo Assay: An Integrated Research-Based Third-Year Chemical Biology Laboratory Course

    Science.gov (United States)

    McKenzie, Nancy; McNulty, James; McLeod, David; McFadden, Meghan; Balachandran, Naresh

    2012-01-01

    A new undergraduate program in chemical biology was launched in 2008 to provide a unique learning experience for those students interested in this interdisciplinary science. An innovative undergraduate chemical biology laboratory course at the third-year level was developed as a key component of the curriculum. The laboratory course introduces…

  18. The relativity of biological function.

    Science.gov (United States)

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

    2015-12-01

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

  19. Crossing Boundaries in Undergraduate Biology Education

    Science.gov (United States)

    Vanderklein, Dirk; Munakata, Mika; McManus, Jason

    2016-01-01

    In an effort to make mathematics relevant to biology students, the authors developed two modules that sought to integrate mathematics and ecology instruction to differing degrees. The modules were developed by a team of biology and mathematics educators and were implemented in an ecology course using three different instructional methods for three…

  20. Structural Biology Fact Sheet

    Science.gov (United States)

    ... Home > Science Education > Structural Biology Fact Sheet Structural Biology Fact Sheet Tagline (Optional) Middle/Main Content Area What is structural biology? Structural biology is a field of science focused ...

  1. Emphasis on the integration of advanced biological technology in retinal degenerative diseases%重视前沿生物技术在视网膜退行性疾病中的整合应用

    Institute of Scientific and Technical Information of China (English)

    张敬学; 卢清君

    2015-01-01

    Retinal degenerative diseases , such as retinitis pigmentosa ( RP ) , age-related macular degeneration ( AMD ) , as well as glaucoma and other diseases the main pathological basis of abnormal structure and function of retinal neurons at all levels ,resulting in irreversible damage to the visual acuity ,is the leading cause of irreversible blindness , and lack of effective treatment methods .With the rapid development of science and technology in recent years , gene therapy , stem cell therapy , adaptive optics technology and artificial vision to the treatment of these diseases may be provided .The completion of the human genome project and the wide application of the related sequencing technology have brought a new revolution to the nature of the disease ,and also brought new impetus to the disease molecular classification , biological diagnosis and gene therapy .People′s understanding of the eye disease is also more comprehensive , the treatment plan on the basis of gene replacement therapy ,and further integrated cell factor therapy ,and the treatment of light genetics , etc..The gene therapy technology has made great progress in Department of Ophthalmology ,but it can not stop some of the functions of cell apoptosis , which requires us to combine a class of genes that can save the cell apoptosis ,or need to use alternative treatment ,the functional cells instead of the injured cells , thereby restoring its function .Because of the unlimited proliferation and multi differentiation potential of stem cells ,it has become a new hope for cell replacement therapy .The retinal stem cell transplantation ,which is integrated into the retina ,and differentiated into the target cells ,to reconstruct the retinal function , has brought the light to the irreversible blindness .The self-renewal and multiple differentiation potential of neural stem cells ,which are suitable for the cell transplantation ,and the expansion of the widely used neural stem cells in vitro and in

  2. Simulating Biological and Non-Biological Motion

    Science.gov (United States)

    Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas

    2008-01-01

    It is widely accepted that the brain processes biological and non-biological movements in distinct neural circuits. Biological motion, in contrast to non-biological motion, refers to active movements of living beings. Aim of our experiment was to investigate the mechanisms underlying mental simulation of these two movement types. Subjects had to…

  3. A Brief Introduction to Chinese Biological Biological

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Chinese Biological Abstracts sponsored by the Library, the Shanghai Institutes for Biological Sciences, the Biological Documentation and Information Network, all of the Chinese Academy of Sciences, commenced publication in 1987 and was initiated to provide access to the Chinese information in the field of biology.

  4. 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’.

  5. Artful interfaces within biological materials

    Directory of Open Access Journals (Sweden)

    John W.C. Dunlop

    2011-03-01

    Full Text Available Biological materials have a wide range of mechanical properties matching their biological function. This is achieved via complex structural hierarchies, spanning many length scales, arising from the assembly of different sized building blocks during growth. The interfaces between these building blocks can increase resistance to fracture, join materials of different character, make them deform more easily and provide motility. While they represent only a tiny fraction of the overall volume, interfaces are essential for the integrity and function of the overall tissue. Understanding their construction principles, often based on specialized molecular assemblies, may change our current thinking about composite materials.

  6. Nanoplasmonic and Microfluidic Devices for Biological Sensing

    KAUST Repository

    Perozziello, G.

    2017-02-16

    In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

  7. Cell biology perspectives in phage biology.

    Science.gov (United States)

    Ansaldi, Mireille

    2012-01-01

    Cellular biology has long been restricted to large cellular organisms. However, as the resolution of microscopic methods increased, it became possible to study smaller cells, in particular bacterial cells. Bacteriophage biology is one aspect of bacterial cell biology that has recently gained insight from cell biology. Despite their small size, bacteriophages could be successfully labeled and their cycle studied in the host cells. This review aims to put together, although non-extensively, several cell biology studies that recently pushed the elucidation of key mechanisms in phage biology, such as the lysis-lysogeny decision in temperate phages or genome replication and transcription, one step further.

  8. Plant Vascular Biology 2010

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Biao

    2014-11-17

    This grant supported the Second International Conference on Plant Vascular Biology (PVB 2010) held July 24-28, 2010 on the campus of Ohio State University, Columbus, Ohio. Biao Ding (Ohio State University; OSU) and David Hannapel (Iowa State University; ISU) served as co-chairs of this conference. Biao Ding served as the local organizer. PVB is defined broadly here to include studies on the biogenesis, structure and function of transport systems in plants, under conditions of normal plant growth and development as well as of plant interactions with pathogens. The transport systems cover broadly the xylem, phloem, plasmodesmata and vascular cell membranes. The PVB concept has emerged in recent years to emphasize the integrative nature of the transport systems and approaches to investigate them.

  9. Biology of Sexual Dysfunction

    Directory of Open Access Journals (Sweden)

    Anil Kumar Mysore Nagaraj

    2009-05-01

    Full Text Available Sexual activity is a multifaceted activity, involving complex interactions between the nervous system, the endocrine system, the vascular system and a variety of structures that are instrumental in sexual excitement, intercourse and satisfaction. Sexual function has three components i.e., desire, arousal and orgasm. Many sexual dysfunctions can be categorized according to the phase of sexual response that is affected. In actual clinical practice however, sexual desire, arousal and orgasmic difficulties more often than not coexist, suggesting an integration of phases. Sexual dysfunction can result from a wide variety of psychological and physiological causes including derangements in the levels of sex hormones and neurotrensmitters. This review deals with the biology of different phases of sexual function as well as implications of hormones and neurotransmitters in sexual dysfunction

  10. Biology of Schwann cells.

    Science.gov (United States)

    Kidd, Grahame J; Ohno, Nobuhiko; Trapp, Bruce D

    2013-01-01

    The fundamental roles of Schwann cells during peripheral nerve formation and regeneration have been recognized for more than 100 years, but the cellular and molecular mechanisms that integrate Schwann cell and axonal functions continue to be elucidated. Derived from the embryonic neural crest, Schwann cells differentiate into myelinating cells or bundle multiple unmyelinated axons into Remak fibers. Axons dictate which differentiation path Schwann cells follow, and recent studies have established that axonal neuregulin1 signaling via ErbB2/B3 receptors on Schwann cells is essential for Schwann cell myelination. Extracellular matrix production and interactions mediated by specific integrin and dystroglycan complexes are also critical requisites for Schwann cell-axon interactions. Myelination entails expansion and specialization of the Schwann cell plasma membrane over millimeter distances. Many of the myelin-specific proteins have been identified, and transgenic manipulation of myelin genes have provided novel insights into myelin protein function, including maintenance of axonal integrity and survival. Cellular events that facilitate myelination, including microtubule-based protein and mRNA targeting, and actin based locomotion, have also begun to be understood. Arguably, the most remarkable facet of Schwann cell biology, however, is their vigorous response to axonal damage. Degradation of myelin, dedifferentiation, division, production of axonotrophic factors, and remyelination all underpin the substantial regenerative capacity of the Schwann cells and peripheral nerves. Many of these properties are not shared by CNS fibers, which are myelinated by oligodendrocytes. Dissecting the molecular mechanisms responsible for the complex biology of Schwann cells continues to have practical benefits in identifying novel therapeutic targets not only for Schwann cell-specific diseases but other disorders in which axons degenerate.

  11. NASA Biological Specimen Repository

    Science.gov (United States)

    McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.

    2010-01-01

    The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

  12. Teaching biology with engineering practices

    Science.gov (United States)

    Potter, Stephen

    The Next Generation Science Standards (NGSS) expresses a vision of science education that requires students to not only have an understanding of science concepts but be able to investigate the natural world through process of science inquiry or to solve meaningful problems though the practices of engineering design. While incorporating engineering practices into our science curriculum will soon be requirement of the new state standards, there is little research published as to how this should be implemented in a biology classroom. The goal of this study was to measure the effectiveness of incorporating engineering design into a biology curriculum on student understanding of engineering practices and science content knowledge. The results of this study indicate that the integration of engineering design in a biology curriculum has a positive effect on student's science content knowledge as well as their understanding of engineering design principles.

  13. Bringing RNA into View: RNA and Its Roles in Biology.

    Science.gov (United States)

    Atkins, John F.; Ellington, Andrew; Friedman, B. Ellen; Gesteland, Raymond F.; Noller, Harry F.; Pasquale, Stephen M.; Storey, Richard D.; Uhlenbeck, Olke C.; Weiner, Alan M.

    This guide presents a module for college students on ribonucleic acid (RNA) and its role in biology. The module aims to integrate the latest research and its findings into college-level biology and provide an opportunity for students to understand biological processes. Four activities are presented: (1) "RNA Structure: Tapes to Shapes"; (2) "RNA…

  14. Mesangial cell biology

    Energy Technology Data Exchange (ETDEWEB)

    Abboud, Hanna E., E-mail: Abboud@uthscsa.edu

    2012-05-15

    Mesangial cells originate from the metanephric mesenchyme and maintain structural integrity of the glomerular microvascular bed and mesangial matrix homeostasis. In response to metabolic, immunologic or hemodynamic injury, these cells undergo apoptosis or acquire an activated phenotype and undergo hypertrophy, proliferation with excessive production of matrix proteins, growth factors, chemokines and cytokines. These soluble factors exert autocrine and paracrine effects on the cells or on other glomerular cells, respectively. MCs are primary targets of immune-mediated glomerular diseases such as IGA nephropathy or metabolic diseases such as diabetes. MCs may also respond to injury that primarily involves podocytes and endothelial cells or to structural and genetic abnormalities of the glomerular basement membrane. Signal transduction and oxidant stress pathways are activated in MCs and likely represent integrated input from multiple mediators. Such responses are convenient targets for therapeutic intervention. Studies in cultured MCs should be supplemented with in vivo studies as well as examination of freshly isolated cells from normal and diseases glomeruli. In addition to ex vivo morphologic studies in kidney cortex, cells should be studied in their natural environment, isolated glomeruli or even tissue slices. Identification of a specific marker of MCs should help genetic manipulation as well as selective therapeutic targeting of these cells. Identification of biological responses of MCs that are not mediated by the renin–angiotensin system should help development of novel and effective therapeutic strategies to treat diseases characterized by MC pathology.

  15. On Biology as an Emergent Science

    CERN Document Server

    Noyes, H Pierre

    2007-01-01

    Biology is considered here as an "emergent science" in the sense of Anderson and of Laughlin and Pines. It is demonstrated that a straightforward mathematical definition of "biological system" is useful in showing how biology differs in structure from the lower levels in Anderson's "More is Different" hierarchy. Using cells in a chemostat as a paradigmatic exemplar of a biological system, it is found that a coherent collection of metabolic pathways through a single cell in the chemostat also satisfies the proposed definition of a biological system. This provides a theoretical and mathematical underpinning for Young's fundamental model of biological organization and integration. Evidence for the therapeutic efficacy of Young's method of analysis is provided by preliminary results of clinical trials of a specific application of Young's model to the treatment of cancer cachexia.

  16. Understanding biological complexity: lessons from the past.

    Science.gov (United States)

    Weiss, James N; Qu, Zhilin; Garfinkel, Alan

    2003-01-01

    Advances in molecular biology now permit complex biological systems to be tracked at an exquisite level of detail. The information flow is so great, however, that using intuition alone to draw connections is unrealistic. Thus, the need to integrate mathematical biology with experimental biology is greater than ever. To achieve this integration, obstacles that have traditionally prevented effective communication between theoreticians and experimentalists must be overcome, so that experimentalists learn the language of mathematics and dynamical modeling and theorists learn the language of biology. Fifty years ago Alan Hodgkin and Andrew Huxley published their quantitative model of the nerve action potential; in the same year, Alan Turing published his work on pattern formation in activator-inhibitor systems. These classic studies illustrate two ends of the spectrum in mathematical biology: the detailed model approach and the minimal model approach. When combined, they are highly synergistic in analyzing the mechanisms underlying the behavior of complex biological systems. Their effective integration will be essential for unraveling the physical basis of the mysteries of life.

  17. 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.

  18. Biological warfare agents.

    Science.gov (United States)

    Pohanka, Miroslav; Kuca, Kamil

    2010-01-01

    Biological warfare agents are a group of pathogens and toxins of biological origin that can be potentially misused for military or criminal purposes. The present review attempts to summarize necessary knowledge about biological warfare agents. The historical aspects, examples of applications of these agents such as anthrax letters, biological weapons impact, a summary of biological warfare agents and epidemiology of infections are described. The last section tries to estimate future trends in research on biological warfare agents.

  19. Frameworks for programming biological function through RNA parts and devices.

    Science.gov (United States)

    Win, Maung Nyan; Liang, Joe C; Smolke, Christina D

    2009-03-27

    One of the long-term goals of synthetic biology is to reliably engineer biological systems that perform human-defined functions. Currently, researchers face several scientific and technical challenges in designing and building biological systems, one of which is associated with our limited ability to access, transmit, and control molecular information through the design of functional biomolecules exhibiting novel properties. The fields of RNA biology and nucleic acid engineering, along with the tremendous interdisciplinary growth of synthetic biology, are fueling advances in the emerging field of RNA programming in living systems. Researchers are designing functional RNA molecules that exhibit increasingly complex functions and integrating these molecules into cellular circuits to program higher-level biological functions. The continued integration and growth of RNA design and synthetic biology presents exciting potential to transform how we interact with and program biology.

  20. Biological pest control in Mexico.

    Science.gov (United States)

    Williams, Trevor; Arredondo-Bernal, Hugo C; Rodríguez-del-Bosque, Luis A

    2013-01-01

    Mexico is a megadiverse country that forms part of the Mesoamerican biological corridor that connects North and South America. Mexico's biogeographical situation places it at risk from inv