WorldWideScience

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. Integrative radiation systems biology.

    Science.gov (United States)

    Unger, Kristian

    2014-01-01

    Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer" of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology. PMID:24411063

  3. Integrative radiation systems biology

    International Nuclear Information System (INIS)

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

  4. Integrated Biological Control

    International Nuclear Information System (INIS)

    Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response

  5. Synthetic Biology: Integrated Gene Circuits

    OpenAIRE

    Nandagopal, Nagarajan; Michael B Elowitz

    2011-01-01

    A major goal of synthetic biology is to develop a deeper understanding of biological design principles from the bottom up, by building circuits and studying their behavior in cells. Investigators initially sought to design circuits “from scratch” that functioned as independently as possible from the underlying cellular system. More recently, researchers have begun to develop a new generation of synthetic circuits that integrate more closely with endogenous cellular processes. These approaches...

  6. Integrating phosphoproteomics in systems biology

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-07-01

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

  7. The Virtual Institute for Integrative Biology (VIIB)

    OpenAIRE

    Rivera, Gustavo; González-Nilo, Fernando; Perez-Acle, Tomás; Isea, Raul; Holmes, David S.

    2010-01-01

    The Virtual Institute for Integrative Biology (VIIB) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, metagenomics, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomics, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and med...

  8. Semantic Web meets Integrative Biology: a survey.

    Science.gov (United States)

    Chen, Huajun; Yu, Tong; Chen, Jake Y

    2013-01-01

    Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB. PMID:22492191

  9. Limits to the potential of bio-fuels and bio-sequestration of carbon

    International Nuclear Information System (INIS)

    This document examines bio-physical limits of bio-fuels and bio-sequestration of carbon by examining available solar radiation and observed efficiencies with which natural ecosystems and agricultural systems convert that energy to biomass. It compares these energy/carbon exchanges with national levels of energy use and carbon emissions for Australia, Brazil, China, Japan, Republic of Korea, New Zealand, Papua New Guinea, Singapore, Sweden, United Kingdom and United States. Globally primary energy consumption (related carbon emissions) is currently equivalent to ∼0.06% of the incident solar energy, and 43% of the energy (carbon) captured by photosynthesis. The nations fall into three categories. Those with primary energy consumption that is: 1–10% (Japan, Korea and Singapore); ∼0.1% (China, UK and the US) and; 0.1–0.01% (Australia, Brazil, Papua New Guinea, New Zealand and Sweden) of incident solar radiation. The percentage of energy captured in biomass follows this pattern, but generally lower by ∼3 orders of magnitude. The energy content of traded wheat, corn and rice represents conversion efficiencies of solar radiation of 0.08–0.17% and for sugar close to 1%, ignoring energy use in production and conversion of biomass to fuels. The study implies that bio-fuels or bio-sequestration can only be a small part of an inclusive portfolio of actions towards a low carbon future and minimised net emissions of carbon to the atmosphere. - Highlights: • Global energy consumption is ∼0.06% of solar; 43% of net primary production. • 11 nations studied fall into 3 groups: consumption/solar=1–10%; ∼0.1%; 0.1–0.01%. • % of energy captured in biomass is lower by ∼3 orders of magnitude. • Crops and natural ecosystems capture 0.1–0.3% and sugar 1% of solar energy. • Significant bio-energy/carbon sequestration via biomass is unrealistic

  10. Network biology methods integrating biological data for translational science

    OpenAIRE

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

    2012-01-01

    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 betw...

  11. 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 sev...

  12. Integrative Systems Biology: Elucidating Complex Traits

    DEFF Research Database (Denmark)

    Pers, Tune Hannes

    human 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 for...... body-mass index associated gene products coalesce onto distinct protein complexes, and show that these putative risk modules incriminate novel candidate obesitysusceptibility genes. e last overall line of research presented here, provides examples on how networks of human metabolism may serve as a...

  13. 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. PMID:27284024

  14. 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. ...

  15. The Virtual Institute for Integrative Biology (VIIB)

    International Nuclear Information System (INIS)

    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)

  16. 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)

  17. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

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

  18. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-02-11

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

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

    OpenAIRE

    Smolke, Christina D.; Silver, Pamela A.

    2011-01-01

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

  20. 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

  1. 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…

  2. 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…

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

    OpenAIRE

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

    2014-01-01

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

  4. Toward Integration: From Quantitative Biology to Mathbio-Biomath?

    OpenAIRE

    Marsteller, Pat; de Pillis, Lisette; Findley, Ann; Joplin, Karl; Pelesko, John; Nelson, Karen; Thompson, Katerina; Usher, David; Watkins, Joseph

    2010-01-01

    In response to the call of BIO2010 for integrating quantitative skills into undergraduate biology education, 30 Howard Hughes Medical Institute (HHMI) Program Directors at the 2006 HHMI Program Directors Meeting established a consortium to investigate, implement, develop, and disseminate best practices resulting from the integration of math and biology. With the assistance of an HHMI-funded mini-grant, led by Karl Joplin of East Tennessee State University, and support in institutional HHMI gr...

  5. 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.

  6. ECOLOGICAL IMPACT OF INTEGRATED CHEMICAL AND BIOLOGICAL AQUATIC WEED CONTROL

    Science.gov (United States)

    This final report presents results of a four-year study of the ecological impacts of chemical, biological, and integrated methods of aquatic weed control. Biological and water quality changes occurred as abundance of macrophytic vegetation was altered by natural factors or manage...

  7. Integration of proteomics into systems biology of cancer

    OpenAIRE

    Hanash, S; Schliekelman, M.; Q. Zhang; 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.

  8. Data mining and data integration in biology

    DEFF Research Database (Denmark)

    Ólason, Páll Ísólfur

    2008-01-01

    Last decade saw an explosion in DNA sequencing and the draft version of the human genome. Now, proteomics is experiencing the same growth. With proteins being the functional elements of living cells, high-throughput proteomics promises more understanding of cellular functions and the interactions...... 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...

  9. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    that were in concordance with their effects in experimental animals. In project II, I profiled the effects on rat liver gene expression levels following exposure to a 14-chemical mixture ± the presence of an endocrine disrupting chemical. This project helped us shed light on the mechanism of action of......Humans are exposed to various chemical agents through food, cosmetics, pharmaceuticals and other sources. Exposure to chemicals is suspected of playing a main role in the development of some adverse health effects in humans. Additionally, European regulatory authorities have recognized the risk...... 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...

  10. 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. PMID:24169619

  11. Exploiting and integrating rich features for biological literature classification

    OpenAIRE

    Zhu Xiaoyan; Ding Shilin; Huang Minlie; Wang Hongning

    2008-01-01

    Abstract Background Efficient features play an important role in automated text classification, which definitely facilitates the access of large-scale data. In the bioscience field, biological structures and terminologies are described by a large number of features; domain dependent features would significantly improve the classification performance. How to effectively select and integrate different types of features to improve the biological literature classification performance is the major...

  12. Bayesian variable selection and data integration for biological regulatory networks

    OpenAIRE

    Jensen, Shane T; Chen, Guang; Stoeckert, Jr, Christian J.

    2007-01-01

    A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in living cells. Previous statistical approaches for identifying gene regulatory networks have used gene expression data, ChIP binding data or promoter sequence data, but each of these resources provides only partial information. We present a Bayesian hierarchical model that integrates all three dat...

  13. Determination of Death: A Scientific Perspective on Biological Integration.

    Science.gov (United States)

    Condic, Maureen L

    2016-06-01

    Human life is operationally defined by the onset and cessation of organismal function. At postnatal stages of life, organismal integration critically and uniquely requires a functioning brain. In this article, a distinction is drawn between integrated and coordinated biologic activities. While communication between cells can provide a coordinated biologic response to specific signals, it does not support the integrated function that is characteristic of a living human being. Determining the loss of integrated function can be complicated by medical interventions (i.e., "life support") that uncouple elements of the natural biologic hierarchy underlying our intuitive understanding of death. Such medical interventions can allow living human beings who are no longer able to function in an integrated manner to be maintained in a living state. In contrast, medical intervention can also allow the cells and tissues of an individual who has died to be maintained in a living state. To distinguish between a living human being and living human cells, two criteria are proposed: either the persistence of any form of brain function or the persistence of autonomous integration of vital functions. Either of these criteria is sufficient to determine a human being is alive. PMID:27075193

  14. Report from the First Snake Genomics and Integrative Biology Meeting

    OpenAIRE

    Castoe, Todd A.; Braun, Edward L.; Bronikowski, Anne M.; Cox, Christian L.; Rabosky, Alison R. Davis; de Koning, A. P. Jason; Dobry, Jason; Fujita, Matthew; Giorgianni, Matt W.; Hargreaves, Adam; Henkel, Christiaan V.; Mackessy, Stephen P.; O’Meally, Denis; Rokyta, Darin R.; Secor, Stephen M

    2012-01-01

    This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems.

  15. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach

    OpenAIRE

    Bourdon, Jérémie; Eveillard, Damien; Gabillard, Samuel; Merle, Theo

    2007-01-01

    Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on qualitative behaviors of macromolecular networks, others approaches show partial quantitative informations like protein concentration variations over times. We consider that both informations, qualitative and quantitative, have to be combined into a modeling...

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

    Directory of Open Access Journals (Sweden)

    Taishin eNomura

    2010-12-01

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

  17. 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.

  18. Assessment of Constructed Wetland Biological Integrity Using Aquatic Macroinvertebrates

    OpenAIRE

    C. Galbrand; I. G. Lemieux; Abdel E. Ghaly; Côté, R.; Verma, M.

    2007-01-01

    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) ...

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

    Science.gov (United States)

    Faini, Marco; Stengel, Florian; Aebersold, Ruedi

    2016-04-01

    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.

  20. 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.

  1. 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.

  2. Modeling Cancer Metastasis using Global, Quantitative and Integrative Network Biology

    DEFF Research Database (Denmark)

    Schoof, Erwin; Erler, Janine

    understanding of molecular processes which are fundamental to tumorigenesis. In Article 1, we propose a novel framework for how cancer mutations can be studied by taking into account their effect at the protein network level. In Article 2, we demonstrate how global, quantitative data on phosphorylation dynamics...... can be generated using MS, and how this can be modeled using a computational framework for deciphering kinase-substrate dynamics. This framework is described in depth in Article 3, and covers the design of KinomeXplorer, which allows the prediction of kinases responsible for modulating observed...... phosphorylation dynamics in a given biological sample. In Chapter III, we move into Integrative Network Biology, where, by combining two fundamental technologies (MS & NGS), we can obtain more in-depth insights into the links between cellular phenotype and genotype. Article 4 describes the proof...

  3. 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.

  4. 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.

  5. 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.

  6. Using biological networks to integrate, visualize and analyze genomics data.

    Science.gov (United States)

    Charitou, Theodosia; Bryan, Kenneth; Lynn, David J

    2016-01-01

    Network biology is a rapidly developing area of biomedical research and reflects the current view that complex phenotypes, such as disease susceptibility, are not the result of single gene mutations that act in isolation but are rather due to the perturbation of a gene's network context. Understanding the topology of these molecular interaction networks and identifying the molecules that play central roles in their structure and regulation is a key to understanding complex systems. The falling cost of next-generation sequencing is now enabling researchers to routinely catalogue the molecular components of these networks at a genome-wide scale and over a large number of different conditions. In this review, we describe how to use publicly available bioinformatics tools to integrate genome-wide 'omics' data into a network of experimentally-supported molecular interactions. In addition, we describe how to visualize and analyze these networks to identify topological features of likely functional relevance, including network hubs, bottlenecks and modules. We show that network biology provides a powerful conceptual approach to integrate and find patterns in genome-wide genomic data but we also discuss the limitations and caveats of these methods, of which researchers adopting these methods must remain aware. PMID:27036106

  7. Towards Improving the Integration of Undergraduate Biology and Mathematics Education

    Directory of Open Access Journals (Sweden)

    Christopher Bergevin

    2010-04-01

    Full Text Available 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.

  8. 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..

  9. Australian pyrolysis technology leads the world in demonstrating renewable energy production and biosequestration

    International Nuclear Information System (INIS)

    Full text: Australian-developed slow pyrolysis technology is leading the world in carbon negative (removing C02 from the atmosphere) renewable energy production. The collaborative research, development and commercialisation program between BEST Energies and the NSW Department of Primary Industries (DPI) was awarded the United Nations Association of Australia 2007 World Environment Day Awards top honour for 'Meeting the Greenhouse Challenge'. 'BEST Energies' Australian developed pyrolysis technology is a genuinely innovative project with huge potential to reduce greenhouse gas emissions' according to the UN World Environment Day Awards Judging Panel. The technology has been recognised as a vital tool for climate change mitigation because it not only produces a renewable energy to displace the use of fossil fuel, but it also produces a very stable form of solid carbon which can be beneficially sequestered over the long term in soils. The technology involves heating low grade biomass without oxygen to generate a gaseous biofuel and a very stable, carbon-rich, char product. BEST Energies has a fully integrated pilot plant which has demonstrated the viability of the technology and assisted the design of commercial scale units. It is accepted that immediate action is required to reverse the adverse impacts on atmospheric C02 levels resulting from industrial processes. The logical next step for this technology is immediate industry adoption and large-scale roll out. Preliminary life cycle assessments have demonstrated that pyrolysis technology will deliver significant reductions in atmospheric C02 at a global scale in a relatively short time frame. Prof. Johannes Lehmann from Cornell University estimates that by the end of this century, char schemes and pyrolysis programs could store up to 9.5 billion tons of carbon a year. Once the high carbon char product is added as an amendment to agricultural soils some of the most remarkable and promising benefits of this technology

  10. A framework for integrating thermal biology into fragmentation research.

    Science.gov (United States)

    Tuff, K T; Tuff, T; Davies, K F

    2016-04-01

    Habitat fragmentation changes thermal conditions in remnant patches, and thermal conditions strongly influence organism morphology, distribution, and activity patterns. However, few studies explore temperature as a mechanism driving ecological responses to fragmentation. Here we offer a conceptual framework that integrates thermal biology into fragmentation research to better understand individual, species, community, and ecosystem-level responses to fragmentation. Specifically, the framework addresses how fragmentation changes temperature and how the effects of those temperature changes spread through the ecosystem, from organism response via thermal sensitivity, to changes in species distribution and activity patterns, to shifts in community structure following species' responses, and ultimately to changes in ecosystem functions. We place a strong emphasis on future research directions by outlining "Critical gaps" for each step of the framework. Empirical efforts to apply and test this framework promise new understanding of fragmentation's ecological consequences and new strategies for conservation in an increasingly fragmented and warmer world. PMID:26892491

  11. Integrated Lipidomics in the Secreted Phospholipase A2 Biology

    Directory of Open Access Journals (Sweden)

    Kei Yamamoto

    2011-02-01

    Full Text Available Mammalian genomes encode genes for more than 30 phospholipase A2s (PLA2s or related enzymes, which are subdivided into several subgroups based on their structures, catalytic mechanisms, localizations and evolutionary relationships. More than one third of the PLA2 enzymes belong to the secreted PLA2 (sPLA2 family, which consists of low-molecular-weight, Ca2+-requiring extracellular enzymes, with a His-Asp catalytic dyad. Individual sPLA2 isoforms exhibit unique tissue and cellular localizations and enzymatic properties, suggesting their distinct pathophysiological roles. Recent studies using transgenic and knockout mice for several sPLA2 isoforms, in combination with lipidomics approaches, have revealed their distinct contributions to various biological events. Herein, we will describe several examples of sPLA2-mediated phospholipid metabolism in vivo, as revealed by integrated analysis of sPLA2 transgenic/knockout mice and lipid mass spectrometry. Knowledge obtained from this approach greatly contributes to expanding our understanding of the sPLA2 biology and pathophysiology.

  12. 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. PMID:23737624

  13. Integrated anaerobic/aerobic biological treatment for intensive swine production.

    Science.gov (United States)

    Bortone, Giuseppe

    2009-11-01

    Manure processing could help farmers to effectively manage nitrogen (N) surplus load. Many pig farms have to treat wastewater. Piggery wastewater treatment is a complex challenge, due to the high COD and N concentrations and low C/N ratio. Anaerobic digestion (AD) could be a convenient pre-treatment, particularly from the energetic view point and farm income, but this causes further reduction of C/N ratio and makes denitrification difficult. N removal can only be obtained integrating anaerobic/aerobic treatment by taking into account the best use of electron donors. Experiences gained in Italy during development of integrated biological treatment approaches for swine manure, from bench to full scale, are reported in this paper. Solid/liquid separation as pre-treatment of raw manure is an efficient strategy to facilitate liquid fraction treatment without significantly lowering C/N ratio. In Italy, two full scale SBRs showed excellent efficiency and reliability. Current renewable energy policy and incentives makes economically attractive the application of AD to the separated solid fraction using high solid anaerobic digester (HSAD) technology. Economic evaluation showed that energy production can reduce costs up to 60%, making sustainable the overall treatment. PMID:19135363

  14. 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

  15. 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/.

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

    OpenAIRE

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

    2013-01-01

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

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

    OpenAIRE

    Bor-Sen Chen; Chia-Chou Wu

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of...

  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. SEMEDA (Semantic Meta-Database) : ontology based semantic integration of biological databases

    OpenAIRE

    Köhler, Jacob

    2003-01-01

    The work presented in this thesis is outlined in the following. The state of the art in the relevant disciplines is introduced and reviewed in chapter 2. This includes on the one hand the current state of molecular biological databases, their heterogeneity and the integration of molecular biological databases. On the other hand the current usage of ontologies in general and with special regard to database integration is described. The principles of semantic database integration as introdu...

  20. A Conceptual Framework for the Integration of 21st Century Skills in Biology Education

    OpenAIRE

    Lee Chuo Hiong; Kamisah Osman

    2013-01-01

    The main objective of this study is to propose the conceptual framework for the integration of 21st century skills in biology education in Malaysia. An interdisciplinary approach for Biology, Technology, Engineering and Mathematics (BTEM) is suggested to imbibe 21st century skills into the existing Biology curriculum. Solving complex and interdisciplinary worldwide biology problems will require students to understand what connections exist across disciplines and how to make those connections....

  1. 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

  2. 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.

  3. CO2 bio-sequestration by Chlorella vulgaris and Spirulina platensis in response to different levels of salinity and CO2

    Directory of Open Access Journals (Sweden)

    M. Shabani

    2016-06-01

    Full Text Available The limitation of fresh water and the exorbitant cost of land to grow such plants, algae are the most optimum organisms for CO2 bio-sequestration and also microalgae cultures avail many characteristics that make them an arguable option for higher productivities as compared to higher plants. The aim of this study was the sequestrate CO2 by Spirulina platensis and Chlorella vulgaris under the different levels of salinity and CO2. The highest growth rate obtained during the first 4 days and higher biomass concentration at CO2 concentration from 0.03% to 10% respectively. The significant (p<0.05 biomass productivity, growth rate and CO2 sequestration rate under different level of CO2 and EC between Spirulina platensis and Chlorella vulgaris were detected. The ultimate CO2 sequestration rate of Spirulina platensis and Chlorella vulgaris were 0.49 and 0.152 g/L/d in natural water respectively, although in artificial sea water 0.419 and 0.097 g/L/d were recorded at 10% CO2 concentrations respectively.

  4. IntegromeDB: an integrated system and biological search engine

    Directory of Open Access Journals (Sweden)

    Baitaluk Michael

    2012-01-01

    Full Text Available Abstract Background With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Description Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. Conclusions The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

  5. KinomeXplorer: an integrated platform for kinome biology studies

    DEFF Research Database (Denmark)

    Horn, Heiko; Schoof, Erwin; Kim, Jinho; Robin, Xavier; Miller, Martin Lee; Diella, Francesca; Palma, Anita; Cesareni, Gianni; Jensen, Lars Juhl; Linding, Rune

    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....

  6. Building Better Biology Undergraduates through Information Literacy Integration

    Science.gov (United States)

    Winterman, Brian

    2009-01-01

    Biology undergraduates at Indiana University have often been expected to find information for course exercises or written reports, but the skills necessary to do so are not taught consistently in the curriculum. Other efforts described in the literature have been successful in teaching information literacy skills, but not always in a way that is…

  7. 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...

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

    OpenAIRE

    Adam P. Henne; Drew, Joshua A.

    2006-01-01

    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 disciplin...

  9. 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...

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

    OpenAIRE

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

    2016-01-01

    Recent reports have called for integrating quantitative reasoning into biology courses to prepare students for careers in research and medicine. This article describes the development, implementation, and assessment of modules designed to incorporate quantitative reasoning and skill development into introductory biology courses.

  11. Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology

    OpenAIRE

    Hill Steven M; Neve Richard M; Bayani Nora; Kuo Wen-Lin; Ziyad Safiyyah; Spellman Paul T; Gray Joe W; Mukherjee Sach

    2012-01-01

    Abstract Background An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biological information concerning the variables of interest. Pathway and network maps are one example of a source of such information. However, although ancillary informatio...

  12. Towards Improving the Integration of Undergraduate Biology and Mathematics Education

    OpenAIRE

    Christopher Bergevin

    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 spi...

  13. Integrity and Biological Activity of DNA after UV Exposure

    Science.gov (United States)

    Lyon, Delina Y.; Monier, Jean-Michel; Dupraz, Sébastien; Freissinet, Caroline; Simonet, Pascal; Vogel, Timothy M.

    2010-04-01

    The field of astrobiology lacks a universal marker with which to indicate the presence of life. This study supports the proposal to use nucleic acids, specifically DNA, as a signature of life (biosignature). In addition to its specificity to living organisms, DNA is a functional molecule that can confer new activities and characteristics to other organisms, following the molecular biology dogma, that is, DNA is transcribed to RNA, which is translated into proteins. Previous criticisms of the use of DNA as a biosignature have asserted that DNA molecules would be destroyed by UV radiation in space. To address this concern, DNA in plasmid form was deposited onto different surfaces and exposed to UVC radiation. The surviving DNA was quantified via the quantitative polymerase chain reaction (qPCR). Results demonstrate increased survivability of DNA attached to surfaces versus non-adsorbed DNA. The DNA was also tested for biological activity via transformation into the bacterium Acinetobacter sp. and assaying for antibiotic resistance conferred by genes encoded by the plasmid. The success of these methods to detect DNA and its gene products after UV exposure (254 nm, 3.5 J/m2s) not only supports the use of the DNA molecule as a biosignature on mineral surfaces but also demonstrates that the DNA retained biological activity.

  14. Integrated graphene/nanoparticle hybrids for biological and electronic applications

    Science.gov (United States)

    Nguyen, Kim Truc; Zhao, Yanli

    2014-05-01

    The development of novel graphene/nanoparticle hybrid materials is currently the subject of tremendous research interest. The intrinsic exceptional assets of both graphene (including graphene oxide and reduced graphene oxide) and nanoparticles render their hybrid materials synergic properties that can be useful in various applications. In this feature review, we highlight recent developments in graphene/nanoparticle hybrids and their promising potential in electronic and biological applications. First, the latest advances in synthetic methods for the preparation of the graphene/nanoparticle hybrids are introduced, with the emphasis on approaches to (1) decorate nanoparticles onto two-dimensional graphene and (2) wrap nanoparticles with graphene sheets. The pros and cons of large-scale synthesis are also discussed. Then, the state-of-the-art of graphene/nanoparticle hybrids in electronic and biological applications is reviewed. For electronic applications, we focus on the advantages of using these hybrids in transparent conducting films, as well as energy harvesting and storage. Biological applications, electrochemical biosensing, bioimaging, and drug delivery using the hybrids are showcased. Finally, the future research prospects and challenges in this rapidly developing area are discussed.

  15. Integration of biological networks and gene expression data using Cytoscape

    DEFF Research Database (Denmark)

    Cline, M.S.; Smoot, M.; Cerami, E.;

    2007-01-01

    interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules...

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

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

    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...

  17. Integrative biological studies of anti-tumour agents

    OpenAIRE

    Johnson, L. A.

    2009-01-01

    3, 11-difluoro-6, 8, 13-trimethyl-8H- quino [4, 3, 2-kl] acridinium methosulfate (RHPS4) is a member of a series of pentacyclic acridines developed at the University of Nottingham, which bind to, and stabilise the structure of G-quadruplex DNA and inhibit the action of telomerase at sub-micromolar concentrations in the cell free TRAP assay and limit cancer cell growth therefore leading to the conclusion that RHPS4 has potential anti-tumour activity. Previous biological studies, however, have...

  18. Information Integration from Semantically Heterogeneous Biological Data Sources

    OpenAIRE

    Caragea, Doina; Bao, Jie; Pathak, Jyotishman; Silvescu, Adrian; Andorf, Carson; Dobbs, Drena; HONAVAR, VASANT

    2005-01-01

    We present the first prototype of INDUS (Intelligent Data Understanding System), a federated, query-centric system for information integration and knowledge acquisition from distributed, semantically heterogeneous data sources that can be viewed (conceptually) as tables. INDUS employs ontologies and inter-ontology mappings, to enable a user to view a collection of such data sources (regardless of location, internal structure and query interfaces) as though they were a collection of tables str...

  19. History matters: ecometrics and integrative climate change biology

    OpenAIRE

    Polly, P. David; Eronen, Jussi; Fred, Marianne; Dietl, Gregory P.; Mosbrugger, Volker; Scheidegger, Christoph; Frank, David C.; Damuth, John; Stenseth, Nils C.; Fortelius, Mikael

    2011-01-01

    Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which ...

  20. 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...

  1. 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.

  2. 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. PMID:26561020

  3. Total Integrated Sample Preparation for Microfluidic Immunoassays in Complex Biological Matrices

    OpenAIRE

    Apori, Akwasi Asare

    2011-01-01

    A high-throughput protein analysis platform with integrated sample preparation is developed to address the identified technology gaps in biomarker validation, clinical and point-of-care diagnostics. The goals of the technology are to automate and integrate protein sample preparation with electrokinetic separations, implement immunoassays capable of processing raw biological fluids, and perform high-throughput protein assays targeted for disease diagnosis.Integration of multiple functions is ...

  4. Increasing algal photosynthetic productivity by integrating ecophysiology with systems biology.

    Science.gov (United States)

    Peers, Graham

    2014-11-01

    Oxygenic photosynthesis is the process by which plants, algae, and cyanobacteria convert sunlight and CO2 into chemical energy and biomass. Previously published estimates suggest that algal photosynthesis is, at best, able to convert approximately 5-7% of incident light energy to biomass and there is opportunity for improvement. Recent analyses of in situ photophysiology in mass cultures of algae and cyanobacteria show that cultivation methods can have detrimental effects on a cell's photophysiology - reinforcing the need to understand the complex responses of cell biology to a highly variable environment. A systems-based approach to understanding the stresses and efficiencies associated with light-energy harvesting, CO2 fixation, and carbon partitioning will be necessary to make major headway toward improving photosynthetic yields. PMID:25306192

  5. Information Integration from Semantically Heterogeneous Biological Data Sources.

    Science.gov (United States)

    Caragea, Doina; Bao, Jie; Pathak, Jyotishman; Silvescu, Adrian; Andorf, Carson; Dobbs, Drena; Honavar, Vasant

    2005-08-26

    We present the first prototype of INDUS (Intelligent Data Understanding System), a federated, query-centric system for information integration and knowledge acquisition from distributed, semantically heterogeneous data sources that can be viewed (conceptually) as tables. INDUS employs ontologies and inter-ontology mappings, to enable a user to view a collection of such data sources (regardless of location, internal structure and query interfaces) as though they were a collection of tables structured according to an ontology supplied by the user. This allows INDUS to answer user queries against distributed, semantically heterogeneous data sources without the need for a centralized data warehouse or a common global ontology. PMID:20802821

  6. 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.

  7. A strategy for xenobiotic removal using photocatalytic treatment, microbial degradation or integrated photocatalytic-biological process

    OpenAIRE

    Lapertot, Miléna

    2006-01-01

    According to the limited natural resources and due to the risks of anthropogenic pollution, it appears necessary to react efficiently in order to remove existing contaminations and avoid the creation of new ones. Therefore, the purpose of this thesis is to propose a sustainable strategy for treating problematic pollutants with the most adequate process. First, an overview of the different treatment processes has been given. In particular, biological, photocatalytic and integrated biological-p...

  8. A strategy for xenobiotic removal using photocatalytic treatment, microbial degradation or integrated photocatalytic-biological process

    OpenAIRE

    Lapertot, Miléna; Pulgarin, César

    2007-01-01

    According to the limited natural resources and due to the risks of anthropogenic pollution, it appears necessary to react efficiently in order to remove existing contaminations and avoid the creation of new ones. Therefore, the purpose of this thesis is to propose a sustainable strategy for treating problematic pollutants with the most adequate process. First, an overview of the different treatment processes has been given. In particular, biological, photocatalytic and integrated biological-p...

  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)

    Carbonell, Pablo; Currin, Andrew; Jervis, Adrian J; Rattray, Nicholas J W; Swainston, Neil; Yan, Cunyu; Takano, Eriko; Breitling, Rainer

    2016-08-27

    Covering: 2000 to 2016Progress 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. A cooperative framework for molecular biology database integration using image object selection.

    OpenAIRE

    Khan, Nawaz

    2004-01-01

    The theme and the concept of 'Molecular Biology Database Integration’ and the problems associated with this concept initiated the idea for this Ph.D research. The available technologies facilitate to analyse the data independently and discretely but it fails to integrate the data resources for more meaningful information. This along with the integration issues created the scope for this Ph.D research. The research has reviewed the 'database interoperability' problems and it has suggested a...

  13. Simple model of self-organized biological evolution as completely integrable dissipative system

    OpenAIRE

    Pis'mak, Yu. M.

    1998-01-01

    The Bak-Sneppen model of self-organized biological evolution of an infinite ecosystem of randomly interacting species is represented in terms of an infinite set of variables which can be considered as an analog to the set of integrals of motion of completely integrable system. Each of this variables remains to be constant but its influence on the evolution process is restricted in time and after definite moment its value is excluded from description of the system dynamics.

  14. A framework for molecular biology databases integration using context graph keying.

    OpenAIRE

    Khan, Nawaz; Stockman, A. G.; Rahman, Shahedur

    2004-01-01

    This paper proposed a novel framework for integrating public domain molecular biology databases with the aid of a context graph. A context graph is used to map data in order to establish an integration domain for the participating multi-resource database federation. Data are presented in a consolidated form upon retrieval from the multiple databases. The approach presented in this paper is novel in the sense that, it can be implemented within a component database and can initiate data consoli...

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

    OpenAIRE

    J. J. Diao; Qing Cao

    2011-01-01

    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.

  16. 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.

  17. Integrating Literacy and Science in Biology: Teaching and Learning Impacts of Reading Apprenticeship Professional Development

    Science.gov (United States)

    Greenleaf, Cynthia L.; Litman, Cindy; Hanson, Thomas L.; Rosen, Rachel; Boscardin, Christy K.; Herman, Joan; Schneider, Steven A.

    2011-01-01

    This study examined the effects of professional development integrating academic literacy and biology instruction on science teachers' instructional practices and students' achievement in science and literacy. The intervention consisted of 10 days of professional development in Reading Apprenticeship, an instructional framework integrating…

  18. 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. 

  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. A Conceptual Framework for the Integration of 21st Century Skills in Biology Education

    Directory of Open Access Journals (Sweden)

    Lee Chuo Hiong

    2013-09-01

    Full Text Available The main objective of this study is to propose the conceptual framework for the integration of 21st century skills in biology education in Malaysia. An interdisciplinary approach for Biology, Technology, Engineering and Mathematics (BTEM is suggested to imbibe 21st century skills into the existing Biology curriculum. Solving complex and interdisciplinary worldwide biology problems will require students to understand what connections exist across disciplines and how to make those connections. BTEM allows students to master biological knowledge and at the same time to be adroit in other sub disciplinary skills. The main teaching and learning strategies that apply in the BTEM subjects are problem-based learning and inquiry-based learning which require the coordination of both knowledge and skills simultaneously. This is intended to enhance the students’ abilities to construct their own knowledge through the relevant hands-on and minds-on activities. The essence of engineering is production of design for the inventive problem solving. Integrating advanced information communication technologies such as e-tools and World Wide Web resources are believed to be able to fulfil the learning style needs of the current ‘Net Generation’. Mathematics plays an important role providing computational tools for biology and engineering, especially in analysing data. The expected outcomes of BTEM implementation are the inculcation of 21st century skills digital literacy, inventive thinking, effective communication, high productivity, spiritual and noble values in Malaysian students.

  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. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  3. Kinetic analysis of enhanced biological phosphorus removal in a hybrid integrated fixed film activated sludge process

    International Nuclear Information System (INIS)

    Hybrid integrated fixed film activated sludge is a promising process for the enhancement of nitrification, denitrification and phosphorus removal in conventional activated sludge systems that can be used for upgrading biological nutrient removal, particularly when they have space limitations or need modifications that will require large monetary expenses. In this research, successful implementation of hybrid integrated fixed film activated sludge process at temperate zone wastewater treatment facilities has been studied by the placement of fixed film media into aerobic, anaerobic and anoxic zones. The primary objective of this study was to investigate the incorporation of enhanced biological phosphorus removal into hybrid integrated fixed film activated sludge systems and study the interactions between the fixed biomass and the mixed liquor suspended solids with respect to substrate competition and nutrient removal efficiencies. A pilot-scale anaerobic-anoxic-oxic configuration system was used. The system was operated at different mean cell residence times and influent chemical oxygen demand/total phosphorus ratios and with split influent flows. The experimental results confirmed that enhanced biological phosphorus removal could be incorporated successfully into hybrid integrated fixed film activated sludge system, but the redistribution of biomass resulting from the integration of fixed film media and the competition of organic substrate between enhanced biological phosphorus removal and denitrification would affect performances. Also, kinetic analysis of the reactor with regarding to phosphorus removal has been studied with different kinetic models and consequently the modified Stover-Kincannon kinetic model has been chosen for modeling studies and experimental data analysis of the hybrid integrated fixed film activated sludge reactor

  4. 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. PMID:15533022

  5. 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

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

    Science.gov (United States)

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

    2015-05-01

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

  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. Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside

    OpenAIRE

    Klann, Jeffrey Gordon; Murphy, Shawn Norman

    2013-01-01

    Background: The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databa...

  11. Classification of Time Series Gene Expression in Clinical Studies via Integration of Biological Network

    OpenAIRE

    Liwei Qian; Haoran Zheng; Hong Zhou; Ruibin Qin; Jinlong Li

    2013-01-01

    The increasing availability of time series expression datasets, although promising, raises a number of new computational challenges. Accordingly, the development of suitable classification methods to make reliable and sound predictions is becoming a pressing issue. We propose, here, a new method to classify time series gene expression via integration of biological networks. We evaluated our approach on 2 different datasets and showed that the use of a hidden Markov model/Gaussian mixture mode...

  12. Double integrating spheres: A method for assessment of optical properties of biological tissues

    OpenAIRE

    Poppendieck, Wigand

    2004-01-01

    The determination of the optical properties of biological tissue is an important issue in laser medicine. The optical properties define the tissue´s absorption and scattering behaviour, and can be expressed by quantities such as the albedo, the optical thickness and the anisotropy coefficient. During this project, a measurement system for the determination of the optical properties was built up. The system consists of a double integrating sphere set-up to perform the necessary reflection and ...

  13. Biological soil loosening by grasses from genus Brachiaria in crop-livestock integration

    OpenAIRE

    José Flávio Neto; Eduardo da Costa Severiano; Kátia Aparecida de Pinho Costa; Wellingthon Silva Guimarães Junnyor; Wainer Gomes Gonçalves; Renata Andrade

    2015-01-01

    Soil compaction associated with pastures degradation can decrease animal productivity, forage longevity and compromise environmental sustainability. To confront this serious issue, the loosening potential of forages should be recognized. We evaluated the least limiting water range as indicator of biological loosening potential in relation to cultivation of grasses the genus Brachiaria in crop-livestock integration. We also evaluated the water availability to soybean crop that succeeded these ...

  14. Large-scale executable biology using rapid integration of computational models

    OpenAIRE

    Vladimir Rogojin; Ion Petre

    2016-01-01

    We plan to develop a systematic framework for assembling large-scale computational biological models by reusing and combining already existing modelling efforts. Our goal is to build a software platform that will compile large-scale biomodels through successive integrations of smaller modules. The modules can be arbitrary executable programs accompanied by a set of (I/O) interface variables; they may also have an internal structure (such as a metabolic network, interaction network, etc.) that...

  15. Human Cancer Classification: A Systems Biology- Based Model Integrating Morphology, Cancer Stem Cells, Proteomics, and Genomics

    OpenAIRE

    Halliday A Idikio

    2011-01-01

    Human cancer classification is currently based on the idea of cell of origin, light and electron microscopic attributes of the cancer. What is not yet integrated into cancer classification are the functional attributes of these cancer cells. Recent innovative techniques in biology have provided a wealth of information on the genomic, transcriptomic and proteomic changes in cancer cells. The emergence of the concept of cancer stem cells needs to be included in a classification model to capture...

  16. 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. PMID:27146161

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Adam P. Henne

    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.

  19. 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.

  20. 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.

  1. 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. PMID:20419428

  2. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Kempa Stefan

    2009-05-01

    Full Text Available Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

  3. The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources.

    Science.gov (United States)

    Köhler, Jacob; Schulze-Kremer, Steffen

    2002-01-01

    A system for "intelligent" semantic integration and querying of federated databases is being implemented by using three main components: A component which enables SQL access to integrated databases by database federation (MARGBench), an ontology based semantic metadatabase (SEMEDA) and an ontology based query interface (SEMEDA-query). In this publication we explain and demonstrate the principles, architecture and the use of SEMEDA. Since SEMEDA is implemented as 3 tiered web application database providers can enter all relevant semantic and technical information about their databases by themselves via a web browser. SEMEDA' s collaborative ontology editing feature is not restricted to database integration, and might also be useful for ongoing ontology developments, such as the "Gene Ontology" [2]. SEMEDA can be found at http://www-bm.cs.uni-magdeburg.de/semeda/. We explain how this ontologically structured information can be used for semantic database integration. In addition, requirements to ontologies for molecular biological database integration are discussed and relevant existing ontologies are evaluated. We further discuss how ontologies and structured knowledge sources can be used in SEMEDA and whether they can be merged supplemented or updated to meet the requirements for semantic database integration. PMID:12542408

  4. 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

  5. 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 study, we deliberately integrated bioinformatics instruction at multiple course levels into an existing biology curriculum. Students in an introductory biology course, intermediate lab courses, and advanced project-oriented courses all participated in new course components designed to sequentially introduce bioinformatics skills and knowledge, as well as computational approaches that are common to many bioinformatics applications. In each course, bioinformatics learning was embedded in an existing disciplinary instructional sequence, as opposed to having a single course where all bioinformatics learning occurs. We designed direct and indirect assessment tools to follow student progress through the course sequence. Our data show significant gains in both student confidence and ability in bioinformatics during individual courses and as course level increases. Despite evidence of substantial student learning in both bioinformatics and mathematics, students were skeptical about the link between learning bioinformatics and learning mathematics. While our approach resulted in substantial learning gains, student "buy-in" and engagement might be better in longer project-based activities that demand application of skills to research problems. Nevertheless, in situations where a concentrated focus on project-oriented bioinformatics is not possible or desirable, our approach of integrating multiple smaller components into an existing curriculum provides an alternative. PMID:22987552

  6. 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.

  7. Polymer micro-grippers with an integrated force sensor for biological manipulation

    International Nuclear Information System (INIS)

    The development of a novel micro-system integrating SU-8 polymer micro-grippers with a tensile force sensor for handling and characterizing the mechanical properties of delicate biological materials, such as fibrils, is presented. The micro-grippers are actuated by the electro-thermal effect and have gripping forces comparable to the common ‘hot-and-cold-arm’ grippers. A robust finite element model was developed to investigate system performance and validated experimentally. A new micro-mechanical calibration method using a piezoelectric manipulator with a micro-force measurement system was successfully applied to test the structure. Both FEA simulation and micro-mechanical testing results indicated that the system could fulfil the requirements for micro-object manipulation within a biological environment. (paper)

  8. 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. PMID:27499843

  9. Biological Control of Water Hyacinth Under Conditions of Maintenance Management: Can Herbicides and Insects Be Integrated?

    Science.gov (United States)

    CENTER; DRAY JR; JUBINSKY; GRODOWITZ

    1999-02-01

    / We hypothesized that repeated herbicidal (maintenance) control of water hyacinth infestations in Florida suppressed biological control agent populations, especially the weevils Neochetina eichhorniae and N. bruchi. We therefore sampled water hyacinth and weevil populations at 54 sites distributed statewide. Half were under maintenance control, half were not treated with herbicides. General site conditions were assessed, demographic data were collected on weevil and plant populations, the reproductive condition of the weevils was determined, and plant nutrient and proximate composition of water hyacinth leaves were analyzed. Water hyacinth infestations under maintenance control were minimal when compared to unmanaged sites. Likewise, on a population basis, all weevil cohorts were much lower due to the paucity of plants. Plants at unmanaged sites, where weevil intensities were much higher, suffered high levels of stress and showed low growth potential. Lower percentages of the female weevils were reproductive at unmanaged sites when compared to managed sites, so densities of reproductives and immatures were similar at both site types. Reproductive status of the weevils improved with increased plant quality. Plant quality, in turn, declined as stresses arising from weevil feeding increased. Plant quality was positively correlated with plant growth potential and flower production. Thus, maintenance control improved plant nutritive quality thereby inducing reproductive vigor of the weevils, but ensuring plant regrowth and the need for future control. This suggests that biological and herbicidal controls should be integrated, using herbicides to maintain water hyacinth infestations below management thresholds but in a manner that conserves biological control agent populations. This approach would lead to improved plant nutritional quality that would, in turn, stimulate reproduction in biological control agent populations. KEY WORDS: Eichhornia crassipes; Neochetina

  10. 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

  11. 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.

  12. 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

  13. A Gauss-Kronrod-Trapezoidal integration scheme for modeling biological tissues with continuous fiber distributions.

    Science.gov (United States)

    Hou, Chieh; Ateshian, Gerard A

    2016-06-01

    Fibrous biological tissues may be modeled using a continuous fiber distribution (CFD) to capture tension-compression nonlinearity, anisotropic fiber distributions, and load-induced anisotropy. The CFD framework requires spherical integration of weighted individual fiber responses, with fibers contributing to the stress response only when they are in tension. The common method for performing this integration employs the discretization of the unit sphere into a polyhedron with nearly uniform triangular faces (finite element integration or FEI scheme). Although FEI has proven to be more accurate and efficient than integration using spherical coordinates, it presents three major drawbacks: First, the number of elements on the unit sphere needed to achieve satisfactory accuracy becomes a significant computational cost in a finite element (FE) analysis. Second, fibers may not be in tension in some regions on the unit sphere, where the integration becomes a waste. Third, if tensed fiber bundles span a small region compared to the area of the elements on the sphere, a significant discretization error arises. This study presents an integration scheme specialized to the CFD framework, which significantly mitigates the first drawback of the FEI scheme, while eliminating the second and third completely. Here, integration is performed only over the regions of the unit sphere where fibers are in tension. Gauss-Kronrod quadrature is used across latitudes and the trapezoidal scheme across longitudes. Over a wide range of strain states, fiber material properties, and fiber angular distributions, results demonstrate that this new scheme always outperforms FEI, sometimes by orders of magnitude in the number of computational steps and relative accuracy of the stress calculation. PMID:26291492

  14. GenFlow: generic flow for integration, management and analysis of molecular biology data

    Directory of Open Access Journals (Sweden)

    Marcio Katsumi Oikawa

    2004-01-01

    Full Text Available A large number of DNA sequencing projects all over the world have yielded a fantastic amount of data, whose analysis is, currently, a big challenge for computational biology. The limiting step in this task is the integration of large volumes of data stored in highly heterogeneous repositories of genomic and cDNA sequences, as well as gene expression results. Solving this problem requires automated analytical tools to optimize operations and efficiently generate knowledge. This paper presents an information flow model , called GenFlow, that can tackle this analytical task.

  15. CoreFlow: A computational platform for integration, analysis and modeling of complex biological data

    OpenAIRE

    Pasculescu, Adrian; Schoof, Erwin; Creixell, Pau; Zheng, Yong; Olhovsky, Marina; Tian, Ruijun; So, Jonathan; Vanderlaan, Rachel D.; Pawson, Tony; Linding, Rune; Colwill, Karen

    2014-01-01

    A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Pytho...

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

    OpenAIRE

    C. C. Galbrand; A. M. Snow; Abdel E. Ghaly; Côté, R.

    2007-01-01

    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 specie...

  17. 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…

  18. Hybrid integrated biological-solid-state system powered with adenosine triphosphate

    Science.gov (United States)

    Roseman, Jared M.; Lin, Jianxun; Ramakrishnan, Siddharth; Rosenstein, Jacob K.; Shepard, Kenneth L.

    2015-12-01

    There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na+/K+ adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 106 mm-2) are able to sustain a short-circuit current of 32.6 pA mm-2 and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm-2 from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%.

  19. 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...

  20. Drug side-effect prediction based on the integration of chemical and biological spaces.

    Science.gov (United States)

    Yamanishi, Yoshihiro; Pauwels, Edouard; Kotera, Masaaki

    2012-12-21

    Drug side-effects, or adverse drug reactions, have become a major public health concern and remain one of the main causes of drug failure and of drug withdrawal once they have reached the market. Therefore, the identification of potential severe side-effects is a challenging issue. In this paper, we develop a new method to predict potential side-effect profiles of drug candidate molecules based on their chemical structures and target protein information on a large scale. We propose several extensions of kernel regression model for multiple responses to deal with heterogeneous data sources. The originality lies in the integration of the chemical space of drug chemical structures and the biological space of drug target proteins in a unified framework. As a result, we demonstrate the usefulness of the proposed method on the simultaneous prediction of 969 side-effects for approved drugs from their chemical substructure and target protein profiles and show that the prediction accuracy consistently improves owing to the proposed regression model and integration of chemical and biological information. We also conduct a comprehensive side-effect prediction for uncharacterized drug molecules stored in DrugBank and confirm interesting predictions using independent information sources. The proposed method is expected to be useful at many stages of the drug development process. PMID:23157436

  1. Classification of time series gene expression in clinical studies via integration of biological network.

    Directory of Open Access Journals (Sweden)

    Liwei Qian

    Full Text Available The increasing availability of time series expression datasets, although promising, raises a number of new computational challenges. Accordingly, the development of suitable classification methods to make reliable and sound predictions is becoming a pressing issue. We propose, here, a new method to classify time series gene expression via integration of biological networks. We evaluated our approach on 2 different datasets and showed that the use of a hidden Markov model/Gaussian mixture models hybrid explores the time-dependence of the expression data, thereby leading to better prediction results. We demonstrated that the biclustering procedure identifies function-related genes as a whole, giving rise to high accordance in prognosis prediction across independent time series datasets. In addition, we showed that integration of biological networks into our method significantly improves prediction performance. Moreover, we compared our approach with several state-of-the-art algorithms and found that our method outperformed previous approaches with regard to various criteria. Finally, our approach achieved better prediction results on early-stage data, implying the potential of our method for practical prediction.

  2. Classification of time series gene expression in clinical studies via integration of biological network.

    Science.gov (United States)

    Qian, Liwei; Zheng, Haoran; Zhou, Hong; Qin, Ruibin; Li, Jinlong

    2013-01-01

    The increasing availability of time series expression datasets, although promising, raises a number of new computational challenges. Accordingly, the development of suitable classification methods to make reliable and sound predictions is becoming a pressing issue. We propose, here, a new method to classify time series gene expression via integration of biological networks. We evaluated our approach on 2 different datasets and showed that the use of a hidden Markov model/Gaussian mixture models hybrid explores the time-dependence of the expression data, thereby leading to better prediction results. We demonstrated that the biclustering procedure identifies function-related genes as a whole, giving rise to high accordance in prognosis prediction across independent time series datasets. In addition, we showed that integration of biological networks into our method significantly improves prediction performance. Moreover, we compared our approach with several state-of-the-art algorithms and found that our method outperformed previous approaches with regard to various criteria. Finally, our approach achieved better prediction results on early-stage data, implying the potential of our method for practical prediction. PMID:23516469

  3. Large-scale executable biology using rapid integration of computational models

    Directory of Open Access Journals (Sweden)

    Vladimir Rogojin

    2016-04-01

    Full Text Available We plan to develop a systematic framework for assembling large-scale computational biological models by reusing and combining already existing modelling efforts. Our goal is to build a software platform that will compile large-scale biomodels through successive integrations of smaller modules. The modules can be arbitrary executable programs accompanied by a set of (I/O interface variables; they may also have an internal structure (such as a metabolic network, interaction network, etc. that yields its executable part in a well defined way. Firstly, wherever possible, modules with the compatible internal structure will be joined by combining their structure and by producing new larger executable modules (like, combining two metabolic networks, etc.. Then, irrespective of the underlying internal structure and modelling formalisms, all the modules will be integrated through connecting their overlapping interface variables. The resulting composed model will be regarded as an executable program itself and it will be simulated by running its submodules in parallel and synchronizing them via their I/O variables. This composed model in its turn can also act as a sub-module for some other even large composite model. The major goal of this project is to deliver a powerful large-scale modeling methodology for the primary use in the fields of Computational Systems Biology and Bioinformatics.

  4. Biology of ICEBs1, an integrative and conjugative element in Bacillus subtilis.

    Science.gov (United States)

    Auchtung, Jennifer M; Aleksanyan, Naira; Bulku, Artemisa; Berkmen, Melanie B

    2016-07-01

    Horizontal gene transfer plays a profound role in bacterial evolution by propelling the rapid transfer of genes and gene cassettes. Integrative and conjugative elements (ICEs) are one important mechanism driving horizontal gene transfer. ICEs, also known as conjugative transposons, reside on the host chromosome but can excise to form a conjugative DNA circle that is capable of transfer to other cells. Analysis of the large number of completed bacterial genome sequences has revealed many previously unrecognized ICEs, including ICEBs1, found in the Gram-positive model bacterium Bacillus subtilis. The discovery of ICEBs1 in an organism with such an impressive array of molecular tools for genetics and molecular biology was fortuitous. Significant insights into ICE biology have resulted since its discovery reintegration, likely to be conserved across many ICEs. We will also highlight some of the more unexpected aspects of ICEBs1 biology, such as its ability to undergo plasmid-like replication after excision and its ability to mobilize plasmids lacking dedicated mobilization functions. A molecular understanding of ICEBs1 has led to additional insights into signals and mechanisms that promote horizontal gene transfer and shape bacterial evolution. PMID:27381852

  5. Biological invasions and the study of vertebrate dispersal of plants: Opportunities and integration

    Science.gov (United States)

    Westcott, David A.; Fletcher, Cameron S.

    2011-11-01

    Biological invasions are a key threat to natural ecosystems and consequently a major focus of ecological research. Even though it is dispersal processes that result in the movement of invasive populations through landscapes, dispersal ecology has played a relatively minor role in invasion ecology research. This is particularly true for vertebrate-dispersed plants. To encourage thinking around these issues and a greater involvement of dispersal ecologists in invasion research, we review contributions made to invasion ecology by dispersal ecology and highlight opportunities that the study of biological invasions offers for improving our understanding of dispersal processes. We suggest that by working in the context of invasions dispersal ecologists are not only able to contribute to the development of process-based management but also gain new opportunities for developing and testing predictions in their field. Because biological invasions are perturbations of natural systems they provide excellent opportunities for both natural and manipulative experimentation with potential for a range of forms of replication. Significantly, the need to develop a predictive understanding of population-level patterns of spread in order to manage invasives demands a shift away from studying individual vectors to developing predictions that integrate across all vectors and processes in the dispersal loop. This is a significant development for dispersal ecology and is a major opportunity for dispersal ecologists to contribute to a current environmental issue.

  6. 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

  7. Quality controls in integrative approaches to detect errors and inconsistencies in biological databases.

    Science.gov (United States)

    Ghisalberti, Giorgio; Masseroli, Marco; Tettamanti, Luca

    2010-01-01

    Numerous biomolecular data are available, but they are scattered in many databases and only some of them are curated by experts. Most available data are computationally derived and include errors and inconsistencies. Effective use of available data in order to derive new knowledge hence requires data integration and quality improvement. Many approaches for data integration have been proposed. Data warehousing seams to be the most adequate when comprehensive analysis of integrated data is required. This makes it the most suitable also to implement comprehensive quality controls on integrated data. We previously developed GFINDer (http://www.bioinformatics.polimi.it/GFINDer/), a web system that supports scientists in effectively using available information. It allows comprehensive statistical analysis and mining of functional and phenotypic annotations of gene lists, such as those identified by high-throughput biomolecular experiments. GFINDer backend is composed of a multi-organism genomic and proteomic data warehouse (GPDW). Within the GPDW, several controlled terminologies and ontologies, which describe gene and gene product related biomolecular processes, functions and phenotypes, are imported and integrated, together with their associations with genes and proteins of several organisms. In order to ease maintaining updated the GPDW and to ensure the best possible quality of data integrated in subsequent updating of the data warehouse, we developed several automatic procedures. Within them, we implemented numerous data quality control techniques to test the integrated data for a variety of possible errors and inconsistencies. Among other features, the implemented controls check data structure and completeness, ontological data consistency, ID format and evolution, unexpected data quantification values, and consistency of data from single and multiple sources. We use the implemented controls to analyze the quality of data available from several different biological

  8. 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

  9. 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.

  10. Integrative Approach for Producing Hydrogen and Polyhydroxyalkanoate from Mixed Wastes of Biological Origin.

    Science.gov (United States)

    Patel, Sanjay K S; Lee, Jung-Kul; Kalia, Vipin C

    2016-09-01

    In this study, an integrative approach to produce biohydrogen (H2) and polyhydroxyalkanoates (PHA) from the wastes of biological origin was investigated. A defined set of mixed cultures was used for hydrolysis and the hydrolysates were used to produce H2. The effluent from H2 production stage was used for PHA production. Under batch culture, a maximum of 62 l H2/kg of pure potato peels (Total solid, TS 2 %, w/v) and 54 l H2/kg of mixed biowastes (MBW1) was recorded. Using effluent from the H2 production stage of biowaste mixture (MBW1), Bacillus cereus EGU43 could produce 195 mg PHA/l and 15.6 % (w/w). Further, supplementation of GM-2 medium (0.1×) and glucose (0.5 %) in H2 production stage effluents, resulted in significant improvements of up to 11 and 41.7 % of PHA contents, respectively. An improvement of 3.9- and 17-fold in PHA yields as compared to with and without integrative H2 production from the MBW1 has been recorded. This integrative approach seems to be a suitable process to improve the yields of H2 and PHA by mixing biowastes. PMID:27407293

  11. 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

  12. Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information.

    Science.gov (United States)

    Masseroli, Marco; Mons, Barend; Bongcam-Rudloff, Erik; Ceri, Stefano; Kel, Alexander; Rechenmann, François; Lisacek, Frederique; Romano, Paolo

    2014-01-01

    Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information sources, but also the danger of producing too many solutions for the same problem. Methodological, technological, infrastructural and social aspects appear to be essential for the development of a new generation of best practices and tools. In this paper, we analyse and discuss these aspects from different perspectives, by extending some of the ideas that arose during the NETTAB 2012 Workshop, making reference especially to the European context. First, relevance of using data and software models for the management and analysis of biological data is stressed. Second, some of the most relevant community achievements of the recent years, which should be taken as a starting point for future efforts in this research domain, are presented. Third, some of the main outstanding issues, challenges and trends are analysed. The challenges related to the tendency to fund and create large scale international research infrastructures and public-private partnerships in order to address the complex challenges of data intensive science are especially discussed. The needs and opportunities of Genomic Computing (the integration, search and display of genomic information at a very specific level, e.g. at the level of a single DNA region) are then considered. In the current data and network-driven era, social aspects can become crucial bottlenecks. How these may best be tackled to unleash the technical abilities for effective data integration and validation efforts is then discussed. Especially the apparent lack of incentives for already overwhelmed researchers appears to be a limitation for sharing information and knowledge with other scientists. We point out as well how the bioinformatics market is growing at an unprecedented speed due to the impact that new powerful in silico

  13. Regression analysis of biologically effective integrated irradiances versus ozone, clouds and geometric factors

    Science.gov (United States)

    Díaz, S.; Deferrari, G.; Martinioni, D.; Oberto, A.

    2000-05-01

    Factors affecting UV radiation at the earth's surface include the solar zenith angle, earth-sun distance, clouds, aerosols, altitude, ozone and the ground's albedo. The variation of some factors, such as solar zenith angle and earth-sun distance, is well established. Total column ozone and UV radiation are inversely related, but the presence of clouds may affect the resulting UV in such a way that a depletion in the total column ozone may not always lead to an increase in the radiation at the earth's surface. The aim of this paper is to determine the contribution to the variation of the biologically effective irradiance by geometric factors, clouds and ozone, jointly and separately, in Ushuaia (54°49'S, 68°19'W, sea level), and the seasonal variation of this relationship, given the magnitude and seasonal distribution of the ozone depletion and the frequent presence of high cloud cover in this site. For this purpose, multivariate and simple regression analyses of daily and monthly integrated irradiances weighted by the DNA damage action spectrum as a function of total column ozone and the integrated irradiances in the band 337-342 nm (as a proxy for cloud cover and geometric factors) have been performed. For the analysed period (September 1989-December 1996) more than 97% of the variation of the DNA damage weighted daily integrated irradiances is described by changes in ozone, clouds and geometric factors. Simple regression analysis for daily integrated irradiances, grouped by month, shows that most of this variation is explained by clouds and geometric factors, except in spring, when strong ozone depletion occurs intermittently over this area. When monthly trends are removed, similar results are observed, except for late winter.

  14. Integration of Telomere Length Dynamics into Systems Biology Framework: A Review.

    Science.gov (United States)

    Nersisyan, Lilit

    2016-01-01

    Telomere length dynamics plays a crucial role in regulation of cellular processes and cell fate. In contrast to epidemiological studies revealing the association of telomere length with age, age-related diseases, and cancers, the role of telomeres in regulation of transcriptome and epigenome and the role of genomic variations in telomere lengthening are not extensively analyzed. This is explained by the fact that experimental assays for telomere length measurement are resource consuming, and there are very few studies where high-throughput genomics, transcriptomics, and/or epigenomics experiments have been coupled with telomere length measurements. Recent development of computational approaches for assessment of telomere length from whole genome sequencing data pave a new perspective on integration of telomeres into high-throughput systems biology analysis framework. Herein, we review existing methodologies for telomere length measurement and compare them to computational approaches, as well as discuss their applications in large-scale studies on telomere length dynamics. PMID:27346946

  15. Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells.

    Science.gov (United States)

    Angelici, Bartolomeo; Mailand, Erik; Haefliger, Benjamin; Benenson, Yaakov

    2016-08-30

    One of the goals of synthetic biology is to develop programmable artificial gene networks that can transduce multiple endogenous molecular cues to precisely control cell behavior. Realizing this vision requires interfacing natural molecular inputs with synthetic components that generate functional molecular outputs. Interfacing synthetic circuits with endogenous mammalian transcription factors has been particularly difficult. Here, we describe a systematic approach that enables integration and transduction of multiple mammalian transcription factor inputs by a synthetic network. The approach is facilitated by a proportional amplifier sensor based on synergistic positive autoregulation. The circuits efficiently transduce endogenous transcription factor levels into RNAi, transcriptional transactivation, and site-specific recombination. They also enable AND logic between pairs of arbitrary transcription factors. The results establish a framework for developing synthetic gene networks that interface with cellular processes through transcriptional regulators. PMID:27545896

  16. Sparse canonical methods for biological data integration: application to a cross-platform study

    Directory of Open Access Journals (Sweden)

    Robert-Granié Christèle

    2009-01-01

    Full Text Available Abstract Background In the context of systems biology, few sparse approaches have been proposed so far to integrate several data sets. It is however an important and fundamental issue that will be widely encountered in post genomic studies, when simultaneously analyzing transcriptomics, proteomics and metabolomics data using different platforms, so as to understand the mutual interactions between the different data sets. In this high dimensional setting, variable selection is crucial to give interpretable results. We focus on a sparse Partial Least Squares approach (sPLS to handle two-block data sets, where the relationship between the two types of variables is known to be symmetric. Sparse PLS has been developed either for a regression or a canonical correlation framework and includes a built-in procedure to select variables while integrating data. To illustrate the canonical mode approach, we analyzed the NCI60 data sets, where two different platforms (cDNA and Affymetrix chips were used to study the transcriptome of sixty cancer cell lines. Results We compare the results obtained with two other sparse or related canonical correlation approaches: CCA with Elastic Net penalization (CCA-EN and Co-Inertia Analysis (CIA. The latter does not include a built-in procedure for variable selection and requires a two-step analysis. We stress the lack of statistical criteria to evaluate canonical correlation methods, which makes biological interpretation absolutely necessary to compare the different gene selections. We also propose comprehensive graphical representations of both samples and variables to facilitate the interpretation of the results. Conclusion sPLS and CCA-EN selected highly relevant genes and complementary findings from the two data sets, which enabled a detailed understanding of the molecular characteristics of several groups of cell lines. These two approaches were found to bring similar results, although they highlighted the same

  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. 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. PMID:21877531

  19. Comparison of breast sequential and simultaneous integrated boost using the biologically effective dose volume histogram (BEDVH)

    International Nuclear Information System (INIS)

    A method is presented to radiobiologically compare sequential (SEQ) and simultaneously integrated boost (SIB) breast radiotherapy. The method is based on identically prescribed biologically effective dose (iso-BED) which was achieved by different prescribed doses due to different fractionation schemes. It is performed by converting the calculated three-dimensional dose distribution to the corresponding BED distribution taking into consideration the different number of fractions for generic α/β ratios. A cumulative BED volume histogram (BEDVH) is then derived from the BED distribution and is compared for the two delivery schemes. Ten breast cancer patients (4 right-sided and 6 left-sided) were investigated. Two tangential intensity modulated whole breast beams with two other oblique (with different gantry angles) beams for the boost volume were used. The boost and the breast target volumes with either α/β = 10 or 3 Gy, and ipsi-lateral and contra-lateral lungs, heart, and contra-lateral breast as organs at risk (OARs) with α/β = 3 Gy were compared. Based on the BEDVH comparisons, the use of SIB reduced the biological breast mean dose by about 3 %, the ipsi-lateral lung and heart by about 10 %, and contra-lateral breast and lung by about 7 %. BED based comparisons should always be used in comparing plans that have different fraction sizes. SIB schemes are dosimetrically more advantageous than SEQ in breast target volume and OARs for equal prescribed BEDs for breast and boost

  20. Biological and photocatalytic treatment integrated with separation and reuse of titanium dioxide on the removal of chlorophenols in tap water

    Energy Technology Data Exchange (ETDEWEB)

    Suryaman, Dhanus, E-mail: dhanussuryaman@yahoo.com [Agency for the Assessment and Application of Technology, M.H. Thamrin No. 8, Jakarta 10340 (Indonesia); Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan); Hasegawa, Kiyoshi [Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)

    2010-11-15

    We investigated biological, photocatalytic, and combination of biological and photocatalytic treatments in order to remove a mixture of 2-chlorophenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, and pentachlorophenol in tap water (total: 100 mg L{sup -1}, each: 25 mg L{sup -1}). The removal of chlorinated phenols was conducted with a flow biological treatment and a circulative flow photocatalytic treatment under black light and sunlight irradiations integrated with titanium dioxide separation and reuse. The combined biological-photocatalytic treatment significantly shortened the degradation and mineralization time of both the biological treatment and the photocatalytic treatment. The removed chlorophenols per hour by the combined biological-photocatalytic treatment was 25.8 mg h{sup -1}, whereas by the combined photocatalytic-biological treatment was 10.5 mg h{sup -1}. After a large portion of biodegradable 2-chlorophenol and 2,4-dichlorophenol, and around half amount of slightly biodegradable 2,4,5-trichlorophenol were removed by the biological treatment, the remained three chlorophenols, biorecalcitrant pentachlorophenol, and biodegradation products were completely removed by the subsequent photocatalytic treatment. Since titanium dioxide particles in tap water spontaneously sedimented on standing after the photocatalytic treatment, the combined treatment can be operated by integrating with the titanium dioxide separation and reuse. The TiO{sub 2} particles were recovered and reused at least three times without significantly decreasing the removal efficiency.

  1. Biological and photocatalytic treatment integrated with separation and reuse of titanium dioxide on the removal of chlorophenols in tap water

    International Nuclear Information System (INIS)

    We investigated biological, photocatalytic, and combination of biological and photocatalytic treatments in order to remove a mixture of 2-chlorophenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, and pentachlorophenol in tap water (total: 100 mg L-1, each: 25 mg L-1). The removal of chlorinated phenols was conducted with a flow biological treatment and a circulative flow photocatalytic treatment under black light and sunlight irradiations integrated with titanium dioxide separation and reuse. The combined biological-photocatalytic treatment significantly shortened the degradation and mineralization time of both the biological treatment and the photocatalytic treatment. The removed chlorophenols per hour by the combined biological-photocatalytic treatment was 25.8 mg h-1, whereas by the combined photocatalytic-biological treatment was 10.5 mg h-1. After a large portion of biodegradable 2-chlorophenol and 2,4-dichlorophenol, and around half amount of slightly biodegradable 2,4,5-trichlorophenol were removed by the biological treatment, the remained three chlorophenols, biorecalcitrant pentachlorophenol, and biodegradation products were completely removed by the subsequent photocatalytic treatment. Since titanium dioxide particles in tap water spontaneously sedimented on standing after the photocatalytic treatment, the combined treatment can be operated by integrating with the titanium dioxide separation and reuse. The TiO2 particles were recovered and reused at least three times without significantly decreasing the removal efficiency.

  2. Decision-Making Under Risk: Integrating Perspectives From Biology, Economics, and Psychology.

    Science.gov (United States)

    Mishra, Sandeep

    2014-04-25

    Decision-making under risk has been variably characterized and examined in many different disciplines. However, interdisciplinary integration has not been forthcoming. Classic theories of decision-making have not been amply revised in light of greater empirical data on actual patterns of decision-making behavior. Furthermore, the meta-theoretical framework of evolution by natural selection has been largely ignored in theories of decision-making under risk in the human behavioral sciences. In this review, I critically examine four of the most influential theories of decision-making from economics, psychology, and biology: expected utility theory, prospect theory, risk-sensitivity theory, and heuristic approaches. I focus especially on risk-sensitivity theory, which offers a framework for understanding decision-making under risk that explicitly involves evolutionary considerations. I also review robust empirical evidence for individual differences and environmental/situational factors that predict actual risky decision-making that any general theory must account for. Finally, I offer steps toward integrating various theoretical perspectives and empirical findings on risky decision-making. PMID:24769798

  3. Development of a flexible microfluidic system integrating magnetic micro-actuators for trapping biological species

    International Nuclear Information System (INIS)

    A flexible microfluidic system embedding microelectromagnets has been designed, modeled and fabricated by using a photosensitive resin as structural material. The fabrication process involves the integration of micro-coils in a multilayer SU-8 microfluidic system by combining standard electroplating and dry films lamination. This technique offers numerous advantages in terms of integration, biocompatibility and chemical resistance. Various designs of micro-coils, including spiral, square or serpentine wires, have been simulated and experimentally tested. It has been established that thermal dissipation in micro-coils depends strongly on the number of turns and current density but remains compatible with biological applications. Real-time experimentations show that these micro-actuators are efficient in trapping magnetic micro-beads without any external field source or a permanent magnet and highlight that the size of microfluidic channels has been adequately designed for optimal trapping. Moreover, we trap magnetic beads in less than 2 s and release them instantaneously into the micro-channel. The actuation solely relies on electric fields, which are easier to control than standard magneto-fluidic modules

  4. Integrated side-stream reactor for biological nutrient removal and minimization of sludge production.

    Science.gov (United States)

    Coma, M; Rovira, S; Canals, J; Colprim, J

    2015-01-01

    Integrated processes to reduce in situ the sludge production in wastewater treatment plants are gaining attention in order to facilitate excess sludge management. In contrast to post-treatments, such as anaerobic digestion which is placed between the activated sludge system and dewatering processes, integrated technologies are placed in the sludge return line. This study evaluates the application of an anoxic side-stream reactor (SSR) which creates a physiological shock and uncouples the biomass metabolism and diverts the activity from assimilation for biosynthesis to non-growth activities. The effect of this system in biological nutrient removal for both nitrogen and phosphorus was evaluated for the anaerobic, anoxic and aerobic reactors. The RedOx potential within the SSR was maintained at -150 mV while the sludge loading rate was modified by increasing the percentage of recycled activated sludge feed to the SSR (0 and 40% at laboratory scale and 0, 10, 50 and 100% at pilot scale). The use of the SSR presented a slight reduction of phosphorus removal but maintained the effluent quality to the required discharge values. Nitrogen removal efficiency increased from 75 to 86% while reducing the sludge production rate by 18.3%. PMID:25860709

  5. 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.

  6. Area-wide integration of lepidopteran F1 sterility and augmentative biological control

    International Nuclear Information System (INIS)

    Area-wide pest management (APM) and integrated pest management (IPM) originated from two different efforts to combine two or more control techniques into programmes in which each method could synergise the effectiveness of others and thus create a level of pest control that was greater than that of a single technique (Perkins 1982). Since then, the concept of APM has evolved to include many aspects of IPM and often is now referred to as area-wide IPM. Still, the element of total population management is central to this approach of insect pest management. In support of APM, Knipling (1998) stated that of the insect pests that were of major concern to agriculture before the newer classes of insecticides were available, most are still pests today, the major exceptions being the screw-worm fly and the boll weevil in the southeastern US cotton growing region. Knipling also noted that both of these pest species were subjected to area-wide suppression programmes. In response to the USDA IPM Initiative (USDA 1993, 1994) which seeks to achieve the national goal of having 75% of the crop acres under IPM by the year 2000, the Agricultural Research Service developed an Area-wide IPM Programme. This programme combines environmentally-sound pest control techniques with the advantages of APM and develops partnerships with other federal, state, local and private sector entities. Technologies such as the integration of lepidopteran F1 sterility and augmentative biological control may be considered for future programmes

  7. 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. PMID:21483730

  8. 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.

  9. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data

    OpenAIRE

    Smith, Richard N.; Aleksic, Jelena; Butano, Daniela; Carr, Adrian; Contrino, Sergio; Hu, Fengyuan; Lyne, Mike; Lyne, Rachel; Kalderimis, Alex; Rutherford, Kim; Stepan, Radek; Sullivan, Julie; Wakeling, Matthew; Watkins, Xavier; Micklem, Gos

    2012-01-01

    Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of ‘widgets’ performing various ...

  10. "Mangrove 'killifish': an exemplar of integrative biology": introduction to the symposium.

    Science.gov (United States)

    Orlando, Edward F

    2012-12-01

    The mangrove rivulus, Kryptolebias marmoratus, (hereafter, rivulus) is one of the only two vertebrates known to self-fertilize, with the other being a recently named close relative, Kryptolebias hermaphroditus (Tatarenkov et al. 2012). Rivulus is also the first fish species found to have environmental sex determination, whereby lower temperatures inhibit ovarian development, thus providing one potential route that avoids inbreeding depression (Harrington 1967; Conover 2004). Wild rivulus exist as androdioecious populations in which both hermaphrodites and, although relatively rare, males are found (Taylor 2000). In the laboratory, individual adult rivulus can produce isogenic embryos. Under as yet unknown environmental conditions, males develop and outcrossing between the hermaphrodites and males occurs (Taylor 2000; Mackiewicz et al. 2006a, 2006b). It is intriguing to consider the behavioral, neurological, and endocrinological control necessary to accommodate this reproductive strategy (Sakakura et al. 2006; Orlando et al. 2006; Earley et al. 2008). In addition to environmental sex determination and androdioecious reproduction, rivulus is also known to emerge from its aquatic surroundings and assume a transitory, terrestrial existence (Ong et al. 2007; Taylor et al. 2008; Cooper et al. 2012). Rivulus is an emerging and potentially powerful model for integrative and comparative biological research and, in part, this emergence has been catalyzed by this first symposium on its biology. The well-attended symposium comprised 11 speakers, which included four women and seven men, with academic ranks ranging from postdoctoral fellow to full professor, who came from four countries. This symposium will help drive future research within this taxon and will facilitate collaborations among researchers. It has already facilitated networking between heads of laboratories and current and potential future postdoctoral fellows and students. The organizing committee looks forward to

  11. 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.

  12. 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

  13. Uncharted waters: Bivalves of midway atoll and integrating mathematics into biology education

    Science.gov (United States)

    McCully, Kristin M.

    To protect and conserve the Earth's biodiversity and ecosystem services, it is important not only to understand and conserve species and ecosystems, but also to instill an understanding and appreciation for biodiversity and ecosystem services in the next generations of both scientists and citizens. Thus, this dissertation combines research into the ecology and identity of large bivalves at Midway Atoll in the Northwestern Hawaiian Islands (NWHI) with research on pedagogical strategies for integrating mathematics into undergraduate biology education. The NWHI is one of the few remaining large, mainly intact, predator-dominated coral reef ecosystems and one of the world's largest marine protected areas. Previous bivalve studies focused on the black-lipped pearl oyster, Pinctada margaritifera, which was heavily harvested in the late 1920s, has not recovered, and is now a candidate species for restoration. First, I combined remote sensing, geographic information systems, SCUBA, and mathematical modeling to quantify the abundance, spatial distributions, and filtration capacity of large epifaunal bivalves at Midway Atoll. These bivalves are most abundant on the forereef outside the atoll, but densities are much lower than reported on other reefs, and Midway's bivalves are unlikely to affect plankton abundance and productivity inside the lagoon. Second, I used molecular techniques and phylogenetic reconstructions to identify pearl oysters (Pinctada) from Midway Atoll as P. maculata , a species not previously reported in Hawaii. As a small morphologically cryptic species, P. maculata may be a native species that has not been collected previously, a native species that has been identified incorrectly as the morphologically similar P. radiata, or it may be a recent introduction or natural range extension from the western Pacific. Finally, I review science education literature integrating mathematics into undergraduate biology curricula, and then present and evaluate a

  14. 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…

  15. 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. PMID:26754812

  16. Developing terrestrial, multi-taxon indices of biological integrity: An example from coastal sage scrub

    Science.gov (United States)

    Diffendorfer, J.E.; Fleming, G.M.; Duggan, J.M.; Chapman, R.E.; Rahn, M.E.; Mitrovich, M.J.; Fisher, R.N.

    2007-01-01

    We screened 351 species or genera for their response to disturbance in coastal sage scrub (CSS) to develop a 15-metric, 5-taxon Index of Biological Integrity (IBI). We collected data on ants, birds, herpetofauna, small mammals, and plants for two years on 46 sites established across a gradient of disturbance in three reserves. The gradient spanned relatively intact CSS with thick stands of shrubs, to former CSS stands type-converted to exotic grasses. ANOVAs and clustering analyses indicated the IBI could distinguish four levels of disturbance in CSS. General measures of community structure, such as richness, did not show changes across the gradient for most taxa, and responses of taxa across the gradient were varied and rarely correlated. However, turnover in species or genera across the gradient was common across all taxa as shrub-obligate life forms were replaced by those favoring grassy or disturbed habitats. Our data indicate index-based approaches based on data collected across disturbance gradients may outperform more traditional community level metrics when responses to anthropogenic influences are complex and vary across species. ?? 2007 Elsevier Ltd. All rights reserved.

  17. Integrated physicochemical and biological treatment process for fluoride and phosphorus removal from fertilizer plant wastewater.

    Science.gov (United States)

    Gouider, Mbarka; Mlaik, Najwa; Feki, Mongi; Sayadi, Sami

    2011-08-01

    The phosphate fertilizer industry produces highly hazardous and acidic wastewaters. This study was undertaken to develop an integrated approach for the treatment of wastewaters from the phosphate industry. Effluent samples were collected from a local phosphate fertilizer producer and were characterized by their high fluoride and phosphate content. First, the samples were pretreated by precipitation of phosphate and fluoride ions using hydrated lime. The resulting low- fluoride and phosphorus effluent was then treated with the enhanced biological phosphorus removal (EBPR) process to monitor the simultaneous removal of carbon, nitrogen, and phosphorus. Phosphorus removal included a two-stage anaerobic/aerobic system operating under continuous flow. Pretreated wastewater was added to the activated sludge and operated for 160 days in the reactor. The operating strategy included increasing the organic loading rate (OLR) from 0.3 to 1.2 g chemical oxygen demand (COD)/L.d. The stable and high removal rates of COD, NH4(+)-N, and PO4(3-)-P were then recorded. The mean concentrations of the influent were approximately 3600 mg COD/L, 60 mg N/L, and 14 mg P/L, which corresponded to removal efficiencies of approximately 98%, 86%, and 92%, respectively. PMID:21905410

  18. From molecule to man: integrating molecular biology with whole organ physiology in studying respiratory disease.

    Science.gov (United States)

    Königshoff, Melanie; Uhl, Franziska; Gosens, Reinoud

    2011-10-01

    Chronic lung diseases such as asthma, chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF) are all characterized by structural changes of the airways and/or lungs that limit airflow and/or gas exchange. Currently, there is no therapy available that adequately targets the structural remodeling of the airways and lungs in these diseases. This underscores the great need for insight into the mechanisms that underpin the development of airway remodeling, fibrosis and emphysema in these diseases, in order to identify suitable drug targets. It is increasingly evident that structural cell-cell communication within the lung is central to the development of remodeling, indicating that a more integrative approach should be considered when studying molecular and cellular mechanisms of remodeling. Therefore, there is a great need to study molecular and cellular physiological and pathophysiological mechanisms in as much detail as possible, but with as little as possible loss of the physiological context. Here, we will review the use of models such as cellular co-culture, tissue culture, and lung slice culture, in which cell-cell communication and tissue architecture are better preserved or mimicked than in cell culture, and zoom in on the usefulness of molecular and cellular biological tools in these complex model systems to read out or control signaling and gene/protein regulation. PMID:21356323

  19. 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.

  20. The Index of Biological Integrity and the bootstrap revisited: an example from Minnesota streams

    Science.gov (United States)

    Dolph, Christine L.; Sheshukov, Aleksey Y.; Chizinski, Christopher J.; Vondracek, Bruce C.; Wilson, Bruce

    2010-01-01

    Multimetric indices, such as the Index of Biological Integrity (IBI), are increasingly used by management agencies to determine whether surface water quality is impaired. However, important questions about the variability of these indices have not been thoroughly addressed in the scientific literature. In this study, we used a bootstrap approach to quantify variability associated with fish IBIs developed for streams in two Minnesota river basins. We further placed this variability into a management context by comparing it to impairment thresholds currently used in water quality determinations for Minnesota streams. We found that 95% confidence intervals ranged as high as 40 points for IBIs scored on a 0–100 point scale. However, on average, 90% of IBI scores calculated from bootstrap replicate samples for a given stream site yielded the same impairment status as the original IBI score. We suggest that sampling variability in IBI scores is related to both the number of fish and the number of rare taxa in a field collection. A comparison of the effects of different scoring methods on IBI variability indicates that a continuous scoring method may reduce the amount of bias in IBI scores.

  1. 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.

  2. 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.

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    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 aer...

  5. 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

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

    OpenAIRE

    Briache, Abdelaali; Marrakchi, Kamar; 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 i...

  7. 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. PMID:26227570

  8. 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

  9. 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

  10. Rethinking the nature of fibrolamellar bone: an integrative biological revision of sauropod plexiform bone formation.

    Science.gov (United States)

    Stein, Koen; Prondvai, Edina

    2014-02-01

    palaeohistological studies, we introduce new osteohistological terms as well as revise widely used but incorrect terminology. To infer the role of woven bone in the bone formation of fast-growing tetrapods, we review some aspects of the interrelationships between the vascularity of bone tissues, basal metabolic rate, body size and growth rate. By putting our findings into the context of osteogenesis, we provide a new model for the diametrical limb bone growth of sauropods and present new implications for the evolution of fast growth in vertebrates. Since biomechanical studies of bone tissues suggest that predominant collagen fibre orientation (CFO) is controlled by endogenous, functional and perhaps phylogenetic factors, the relationship between CFO and bone growth rate as defined by Amprino's rule, which has been the basis for the biological interpretation of several osteohistological features, must be revised. Our findings draw attention to the urgent need for revising widely accepted basic concepts of palaeohistological studies, and for a more integrative approach to bone formation, biomechanics and bone microstructural features of extant and extinct vertebrates to infer life history traits of long extinct, iconic animals like dinosaurs. PMID:23647662

  11. 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.

  12. High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices.

    Science.gov (United States)

    Hopfgartner, Gérard; Tonoli, David; Varesio, Emmanuel

    2012-03-01

    Quantitative and qualitative high-resolution (HR) dependent and independent acquisition schemes on a QqTOF MS (with resolving power 20,000-40,000) were investigated for the analysis of pharmaceutical compounds in biological fluids. High-resolution selected reaction monitoring (HR-SRM) was found to be linear over three orders of magnitude for quantitative analysis of paracetamol in human plasma, offering a real alternative to triple quadrupole LC-SRM/MS. Metabolic stability of talinolol in microsomes was characterized by use of three different acquisition schemes: (i) information-dependent acquisition (IDA) with a TOF MS experiment as survey scan and product-ion scan as dependent scan; (ii) MS(ALL) by collecting TOF mass spectra with and without fragmentation by alternating the collision energy of the collision cell between a low (i.e., 10 eV) and high setting (i.e., 40 eV); and (iii) a novel independent acquisition mode referred to as "sequential window acquisition of all theoretical fragment-ion spectra" (SWATH) or "global precursor ions scan mode" (GPS) in which sequential precursor ions windows (typically 20 u) are used to collect the same spectrum precursor and fragment ions using a collision energy range. SWATH or GPS was found to be superior to IDA or MS(ALL) in combination with UHPLC for qualitative analysis but requires a rapidly acquiring mass spectrometer. Finally, the GPS concept was used for QUAL/QUAN analysis (i.e. integration of qualitative and quantitative analysis) of bosentan and its metabolites in urine over a concentration range from 5 to 2,500 ng mL(-1). PMID:22203371

  13. Preventive conservation of cultural heritage: an integrated system of biological and microclimate monitoring

    OpenAIRE

    Cesira Pasquarella; Carla Balocco; Giovanna Pasquariello; Roberto Albertini

    2013-01-01

    Cultural heritage preserved in indoor environments (museums, libraries, archives, etc.) is subject to biodeterioration caused by specific groups of biological agents called biodeteriogens. Several factors may affect the process of biodeterioration, depending on the chemical and physical characteristics of the materials, the state of conservation of the artefacts, the environmental conditions and the nutritional needs of biological agents. The biological components of air (bioaerosol) can ...

  14. 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. PMID:25936898

  15. Integration of biological and nursing sciences: a 10-year plan to enhance research and training.

    Science.gov (United States)

    Cowan, M J; Heinrich, J; Lucas, M; Sigmon, H; Hinshaw, A S

    1993-02-01

    A proposed multiyear plan of funding mechanisms by the National Center for Nursing Research (NCNR) to increase the use of biological theory and measurements in nursing research has been developed for both research training and research programs. The objectives of the research training programs are (a) to develop a cadre of nurse scientists with solid research training in the biological sciences, (b) to upgrade to state-of-the-art biological research for mid-career nurse scientists, and (c) to ensure adequate highly trained biological-nurse manpower will be available to accomplish the nation's nursing research agenda. The objectives of the research programs are (a) to stimulate nurse scientists to undertake novel, innovative research using state-of-the-art biological technology, (b) to link the behavioral and biological underpinnings of nursing science in specified areas of biomedical clinical research, and (c) to ensure that, in the coming decade, nursing science and behavioral research will be inextricably interwoven with biological research. The research training programs include: targeted predoctoral-postdoctoral transitional training, targeted predoctoral or postdoctoral fellowships, training awards for existing institutional training grants in other disciplines, mid-career awards, the Nurse Scientist award, and institutional training grants for biological nursing. The research programs include: small grants programs, augmentation of existing projects in other Institutes, Requests For Applications (RFA) in biobehavioral nursing, cluster studies, and clinical trials. PMID:8488310

  16. 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…

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

    OpenAIRE

    Susmita Lahiri Ganguly; Dipanwita Sarkar Paria; B. B. Jana

    2015-01-01

    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 collec...

  18. Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems

    OpenAIRE

    ClaudiaAngelini; ValerioCosta

    2014-01-01

    The availability of omic data produced from international consortia, as well as from worldwide laboratories, is offering the possibility both to answer long-standing questions in biomedicine/molecular biology and to formulate novel hypotheses to test. However, the impact of such data is not fully exploited due to a limited availability of multi-omic data integration tools and methods. In this paper, we discuss the interplay between gene expression and epigenetic markers/transcription factors....

  19. Mass-energy balance analysis for estimation of light energy conversion in an integrated system of biological H2 production

    OpenAIRE

    A.I. Gavrisheva; B.F. Belokopytov; V.I. Semina; E.S. Shastik; T.V. Laurinavichene; A.A. Tsygankov

    2015-01-01

    The present study investigated an integrated system of biological H2 production, which includes the accumulation of biomass of autotrophic microalgae, dark fermentation of biomass, and photofermentation of the dark fermentation effluent. Particular emphasis was placed on the estimation of the conversion efficiency of light into hydrogen energy at each stage of this system. For this purpose, the mass and energy balance regularities were applied. The efficiency of the energy transformation from...

  20. 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.

  1. In search of the Golden Fleece: Unraveling principles of morphogenesis by studying the integrative biology of skin appendages

    OpenAIRE

    Hughes, Michael W; Wu, Ping; Jiang, Ting-Xin; Lin, Sung-Jan; Dong, Chen-Yuan; Li, Ang; Hsieh, Fon-Jou; Widelitz, Randall B; Choung, Cheng Ming

    2011-01-01

    The mythological story of the Golden Fleece symbolizes the magical regenerative power of skin appendages. Similar to the adventurous pursuit of the Golden Fleece by the multi-talented Argonauts, today we also need an integrated multi-disciplined approach to understand the cellular and molecular processes during development, regeneration and evolution of skin appendages. To this end, we have explored several aspects of skin appendage biology that contribute to the Turing activator / inhibitor ...

  2. Harnessing the Power of Integrated Mitochondrial Biology and Physiology: A Special Report on the NHLBI Mitochondria in Heart Diseases Initiative

    OpenAIRE

    Ping, P.; Gustafsson, ÅB; Bers, DM; Blatter, LA; Cai, H; Jahangir, A; Kelly, D; Muoio, D; O'Rourke, B; Rabinovitch, P; Trayanova, N; van Eyk, J.; Weiss, JN; Wong, R; Longacre, LS

    2015-01-01

    © 2015 American Heart Association, Inc. Mitochondrial biology is the sum of diverse phenomena from molecular profiles to physiological functions. A mechanistic understanding of mitochondria in disease development, and hence the future prospect of clinical translations, relies on a systems-level integration of expertise from multiple fields of investigation. Upon the successful conclusion of a recent National Institutes of Health, National Heart, Lung, and Blood Institute initiative on integra...

  3. Studies of Complex Biological Systems with Applications to Molecular Medicine: The Need to Integrate Transcriptomic and Proteomic Approaches

    Directory of Open Access Journals (Sweden)

    Elena Silvestri

    2011-01-01

    Full Text Available Omics approaches to the study of complex biological systems with potential applications to molecular medicine are attracting great interest in clinical as well as in basic biological research. Genomics, transcriptomics and proteomics are characterized by the lack of an a priori definition of scope, and this gives sufficient leeway for investigators (a to discern all at once a globally altered pattern of gene/protein expression and (b to examine the complex interactions that regulate entire biological processes. Two popular platforms in “omics” are DNA microarrays, which measure messenger RNA transcript levels, and proteomic analyses, which identify and quantify proteins. Because of their intrinsic strengths and weaknesses, no single approach can fully unravel the complexities of fundamental biological events. However, an appropriate combination of different tools could lead to integrative analyses that would furnish new insights not accessible through one-dimensional datasets. In this review, we will outline some of the challenges associated with integrative analyses relating to the changes in metabolic pathways that occur in complex pathophysiological conditions (viz. ageing and altered thyroid state in relevant metabolically active tissues. In addition, we discuss several new applications of proteomic analysis to the investigation of mitochondrial activity.

  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. Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information

    OpenAIRE

    Masseroli, Marco; Mons, Barend; Bongcam-Rudloff, Erik; Ceri, Stefano; Kel, Alexander; Rechenmann, François; Lisacek, Frederique; Romano, Paolo

    2014-01-01

    Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information sources, but also the danger of producing too many solutions for the same problem. Methodological, technological, infrastructural and social aspects appear to be essential for the development of a new generation of best practices and tools. In this paper, we analyse and discuss these asp...

  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. An integrated strategy for biological effects monitoring in Scottish coastal waters

    International Nuclear Information System (INIS)

    The paper summarises SEPA's current programme of water quality and biological effects monitoring and, using recent examples, discusses the current environmental issues affecting the condition of our coastal waters. (author)

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

    OpenAIRE

    Andreja Špernjak

    2014-01-01

    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 attitu...

  9. Novel approaches to the integration and analysis of systems biology data

    OpenAIRE

    Ramírez, Fidel

    2011-01-01

    The opportunity to investigate whole cellular systems using experimental and computational high-throughput methods leads to the generation of unprecedented amounts of data. Processing of these data often results in large lists of genes or proteins that need to be analyzed and interpreted in the context of all other biological information that is already available. To support such analyses, repositories aggregating and merging the biological information contained in different databases are req...

  10. Combining physical, cultural and biological methods: prospects for integrated non-chemical weed management strategies

    OpenAIRE

    Hatcher, Lecturer Paul; Melander, Senior scientist Bo

    2003-01-01

    Physical, cultural and biological methods for weed control have developed largely independently and are often concerned with weed control in different systems: physical and cultural control in annual crops and biocontrol in extensive grasslands. We discuss the strengths and limitations of four physical and cultural methods for weed control: mechanical, thermal, cutting, and intercropping, and the advantages and disadvantages of combining biological control with them. These physical and cult...

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

    OpenAIRE

    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 biological knowledge can be functionally used in many work placement sites it is not evident that students recognize that this is the case. Workplace characteristics, participation in work actions and workp...

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

    OpenAIRE

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

    2013-01-01

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

  13. An integrated systems biology approach to the study of preterm birth using "-omic" technology - a guideline for research

    Directory of Open Access Journals (Sweden)

    Kelley Maureen

    2011-10-01

    Full Text Available Abstract Preterm birth is the leading cause of neonatal mortality and perinatal morbidity. The etiology of preterm is multi-factorial and still unclear. As evidence increases for a genetic contribution to PTB, so does the need to explore genomics, transcriptomics, proteomics and metabolomics in its study. This review suggests research guidelines for the conduct of high throughput systems biology investigations into preterm birth with the expectation that this will facilitate the sharing of samples and data internationally through consortia, generating the power needed to study preterm birth using integrated "-omics" technologies. The issues to be addressed include: (1 integrated "-omics" approaches, (2 phenotyping, (3 sample collection, (4 data management-integrative databases, (5 international consortia and (6 translational feasibility. This manuscript is the product of discussions initiated by the "-Omics" Working Group at the Preterm Birth International Collaborative Meeting held at the World Health Organization, Geneva, Switzerland in April 2009.

  14. The Potential for the Integration of Nuclear Techniques in Arthropod Biological Control

    International Nuclear Information System (INIS)

    Biological control is today being practised more widely than ever before and its popularity looks set to increase further in the future. While the discipline has historically been dominated by 'classical' biological control (the one-off introduction of natural enemies to control pests in their adventive range) augmentative biological control (the repeated introduction of biocontrol agents to a particular crop or forest) has increased substantially over the past 20 years and is likely to increase in importance further in the future. This view is supported by an assessment of some of the key issues facing the discipline of biological control today. There is no clear role for nuclear techniques in the future of classical biological control. However the use of irradiation as a means of creating increased rates of mutation in natural enemy populations being selected for enhanced beneficial traits (such as insecticide resistance), might be useful and could be investigated further. There is scope for the use of irradiation in killing or sterilising insect diets and hosts, a technique which has been used for over 25 years without gaining wide acceptance. Augmentative biological control as an adjunct to SIT may have a role in future pest control campaigns, although it is likely to prove difficult to provide a clear economic justification given the technical difficulties of measuring separately the effects of the two techniques. It is suggested that the technical advances in project development and implementation (e.g. insect rearing techniques and field application) which have been made by SIT practitioners have a potentially useful role in assisting the development of improved production and delivery of biological control agents for augmentative release (author)

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

    Directory of Open Access Journals (Sweden)

    JoyGuingab-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.

  16. Integration of proteomics, bioinformatics, and systems biology in traumatic brain injury biomarker discovery.

    Science.gov (United States)

    Guingab-Cagmat, J D; Cagmat, E B; Hayes, R L; Anagli, J

    2013-01-01

    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. PMID:23750150

  17. 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.

  18. 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

    2016-04-01

    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. PMID:26977068

  19. Mass-energy balance analysis for estimation of light energy conversion in an integrated system of biological H2 production

    Directory of Open Access Journals (Sweden)

    A.I. Gavrisheva

    2015-12-01

    Full Text Available The present study investigated an integrated system of biological H2 production, which includes the accumulation of biomass of autotrophic microalgae, dark fermentation of biomass, and photofermentation of the dark fermentation effluent. Particular emphasis was placed on the estimation of the conversion efficiency of light into hydrogen energy at each stage of this system. For this purpose, the mass and energy balance regularities were applied. The efficiency of the energy transformation from light into the microalgal biomass did not exceed 5%. The efficiency of the energy transformation from biomass to biological H2 during the dark fermentation stage stood at about 0.3%. The photofermentation stage using the model fermentation effluent could improve this estimation to 11%, resulting in an overall efficiency 0.55%. Evidently, this scheme is counterproductive for light energy bioconversion due to numerous intermediate steps even if the best published data would be taken into account.

  20. 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, II

    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.

  1. Improving the Quantitative Skills of Future Benthologists: Better Integration of Mathematics into Undergraduate Biology Curricula

    Science.gov (United States)

    Creed, R. P.; Marland, E. S.; Venable, M. E.; Arnholt, A. T.; Searcy, M. E.

    2005-05-01

    Some of the assumptions biology faculty make about the mathematical background of their students are unwarranted. Through assessment, we have found that students know far less about subjects such as graphing, logarithms etc. than we think. This obviously affects how we teach our classes, how much time we devote to covering topics such as statistical analysis and the degree of quantitative analysis we expect. At ASU we have taken several steps to improve the mathematical background of our students. The Math Department now offers statistics and calculus courses designed for biology majors. These courses are taught in computerized classrooms and are focused on biological data and modeling. By requiring these courses as prerequisites, we hope to reduce the review of basic mathematics in our classes and focus on the "important" topics. In Biology we have expanded on the level of quantitative rigor expected in our classes. In addition, we are increasing the use of modeling and computational exercises in these classes. We will present the results of our ongoing assessment approach and discuss how we are implementing some of our initiatives. This work is based on the recommendations outlined in the NRC's Bio2010 and the MAA's Math and Bio 2010.

  2. 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,...

  3. 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…

  4. Integrated quantification and identification of aldehydes and ketones in biological samples

    NARCIS (Netherlands)

    Siegel, David; Meinema, Anne C; Permentier, Hjalmar; Hopfgartner, Gérard; Bischoff, Rainer

    2014-01-01

    The identification of unknown compounds remains to be a bottleneck of mass spectrometry (MS)-based metabolomics screening experiments. Here, we present a novel approach which facilitates the identification and quantification of analytes containing aldehyde and ketone groups in biological samples by

  5. 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…

  6. Plant MetGenMAP: an integrative analysis system for plant systems biology

    Science.gov (United States)

    We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. P...

  7. 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…

  8. Disrupted seasonal biology impacts health, food security, and ecosystems: a call for integrated research

    NARCIS (Netherlands)

    Stevenson, T.J.; Visser, M.E.; Arnold, W.; Barrett, P.; Biello, S.; Dawson, A.; Denlinger, D.L.; Dominoni, D.; Ebling, F.J.; Elton, S.; Evans, N.; Ferguson, H.M.; Foster, R.G.; Hau, M.; Haydon, D.T.; Hazlerigg, D.G.; Heideman, P.; Hopcraft, J.G.C.; Jonsson, N.N.; Kronfeld-Schor, N.; Kumar, V.; Lincoln, G.A.; MacLeod, R.; Martin, S.A.M.; Martinez-Bakker, M.; Nelson, R.J.; Reed, T.; Robinso, J.E.; Rock, D.; Schwartz, W.J.; Steffan-Dewenter, I.; Tauber, E.; Thackeray, S.J.; Umstatter, C.; Yoshimura, T.; Helm, B.

    2015-01-01

    The rhythm of life on earth is shaped by seasonal changes in the environment. Plants and animals show profound annual cycles in physiology, health, morphology, behaviour and demography in response to environmental cues. Seasonal biology impacts ecosystems and agriculture, with consequences for human

  9. Participation in introductory biology laboratories: An integrated assessment based on surveys, behavioral observations, and qualitative interviews

    Science.gov (United States)

    Russell, Connie Adelle

    Scope and method of study. The purpose of this study was to evaluate the effect of gender, major, and prior knowledge of and attitude toward biology on participation in introductory biology laboratories. Subjects for this study were 3,527 students enrolled in college-level introductory biology courses. During the study, three introductory courses were replaced with one mixed-majors course. The new course adopted a different pedagological approach from the previous courses in that an inquiry-based approach was used in lectures and laboratories. All subjects completed a survey that measured content knowledge using the NABT/NSTA High School Biology Examination Version 1990 and attitude using Russell and Hollander's Biology Attitude Scale. I used and discuss the merits of using ethological methods and data collection software, EthoScribeTM (Tima Scientific) to collect behavioral data from 145 students. I also evaluated participation using qualitative interviews of 30 students. I analyzed content knowledge and attitude data using ANOVA and Pearson correlation, and behavioral data using Contingency Table Analysis. I analyzed interviews following methods outlined by Rubin and Rubin. Findings. Course style and gender were the most useful variables in distinguishing differences among groups of students with regard to attitude, content knowledge, and participation in laboratories. Attitude toward biology and achievement measured by the surveys were found to be positively correlated; however, gender, major, class standing, course style and interactions between these variables also had effects on these variables. I found a positive association among attitude, achievement and participation in hands-on activities in laboratories. Differences in participation also were associated group type. In a traditional introductory biology course, females in single-gender groups, gender-equal, or groups in which females were the majority spent more time performing hands-on science

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

    Science.gov (United States)

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

    2008-07-01

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

  11. 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

  12. Towards the integration of computational systems biology and high-throughput data: a way to support differential analysis of microarray gene expression data

    OpenAIRE

    Segata, Nicola; Blanzieri, Enrico; Priami, Corrado

    2007-01-01

    The paradigmatic shift occurred in biology that led first to high-throughput experimental techniques and later to computational systems biology must be applied also to the analysis paradigm of the relation between local models and data to obtain an effective prediction framework. In this work we show that the new relation between systems biology models and high-throughput data permits new integrations on the systemic scale like the use of in silico predictions to support the mining of gene ex...

  13. Biomimetic approaches in bone tissue engineering: Integrating biological and physicomechanical strategies.

    Science.gov (United States)

    Fernandez-Yague, Marc A; Abbah, Sunny Akogwu; McNamara, Laoise; Zeugolis, Dimitrios I; Pandit, Abhay; Biggs, Manus J

    2015-04-01

    The development of responsive biomaterials capable of demonstrating modulated function in response to dynamic physiological and mechanical changes in vivo remains an important challenge in bone tissue engineering. To achieve long-term repair and good clinical outcomes, biologically responsive approaches that focus on repair and reconstitution of tissue structure and function through drug release, receptor recognition, environmental responsiveness and tuned biodegradability are required. Traditional orthopedic materials lack biomimicry, and mismatches in tissue morphology, or chemical and mechanical properties ultimately accelerate device failure. Multiple stimuli have been proposed as principal contributors or mediators of cell activity and bone tissue formation, including physical (substrate topography, stiffness, shear stress and electrical forces) and biochemical factors (growth factors, genes or proteins). However, optimal solutions to bone regeneration remain elusive. This review will focus on biological and physicomechanical considerations currently being explored in bone tissue engineering. PMID:25236302

  14. Improving biological understanding and complex trait prediction by integrating prior information in genomic feature models

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon

    In this thesis we investigate an approach to integrate external data into the analysis of genetic variants. The goal is similar to that of gene-set enrichment tests, but relies on the robust statistical framework of linear mixed models. This approach has allowed us to integrate virtually any......, we also use cross validations to estimate the predictive ability of a set. --- The thesis consists of 3 chapters introducing the methodology of linear mixed models, their application, and evaluation by means of test statistics. Then 3 manuscripts in which we investigate the usage of our approach in...... demonstrates the successful application of an integrative approach for enhancing the systems genetics analysis of complex traits. The results shows that by using informed subsets of genetic variants, it is possible to increase the predictive ability in populations of low relatedness; a valuable prospect for...

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

    OpenAIRE

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

    2016-01-01

    Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded b...

  16. Integrative Chemical-Biological Read-Across Approach for Chemical Hazard Classification

    OpenAIRE

    Low, Yen; Sedykh, Alexander; Fourches, Denis; Golbraikh, Alexander; Whelan, Maurice; Rusyn, Ivan; Tropsha, Alexander

    2013-01-01

    Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (”biological” similarity). The Che...

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

    OpenAIRE

    Kurita, Kenji Long

    2015-01-01

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

  18. 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....

  19. Disrupted seasonal biology impacts health, food security, and ecosystems: a call for integrated research

    OpenAIRE

    Stevenson, T. J.; Visser, M.E; Arnold, W; Barrett, P; Biello, S; Dawson, A.; Denlinger, D. L.; Dominoni, D.; Ebling, F.J.; Elton, S.; Evans, N.; Ferguson, H M; Foster, R G; Hau, M.; Haydon, D.T.

    2015-01-01

    The rhythm of life on earth is shaped by seasonal changes in the environment. Plants and animals show profound annual cycles in physiology, health, morphology, behaviour and demography in response to environmental cues. Seasonal biology impacts ecosystems and agriculture, with consequences for humans and biodiversity. Human populations show robust annual rhythms in health and well-being, and the birth month can have lasting effects that persist throughout life. This review emphasizes the need...

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

    OpenAIRE

    GALLAMPOIS Christine

    2012-01-01

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

  1. Integration of 'omics' data in aging research:From biomarkers to systems biology

    OpenAIRE

    Zierer, Jonas; Menni, Cristina; Kastenmüller, Gabi; Spector, Tim D.

    2015-01-01

    Summary Age is the strongest risk factor for many diseases including neurodegenerative disorders, coronary heart disease, type 2 diabetes and cancer. Due to increasing life expectancy and low birth rates, the incidence of age‐related diseases is increasing in industrialized countries. Therefore, understanding the relationship between diseases and aging and facilitating healthy aging are major goals in medical research. In the last decades, the dimension of biological data has drastically incr...

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

    OpenAIRE

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

    2015-01-01

    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...

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

    OpenAIRE

    Mancuso, James J.; Jie Cheng

    2014-01-01

    Comprising 1011 neurons with 1014 synaptic connections the human brain is the ultimate systems biology puzzle. An increasing body of evidence highlights the observation that changes in brain function, both normal and pathological, consistently correlate with dynamic changes in neuronal anatomy. Anatomical changes occur on a full range of scales from the trafficking of individual proteins, to alterations in synaptic morphology both individually and on a systems level, to reductions in long d...

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

    DEFF Research Database (Denmark)

    Brunak, Søren

    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....

  5. 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. PMID:26721187

  6. 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.

  7. 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

  8. 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.

  9. Towards instantaneous cellular level bio diagnosis: laser extraction and imaging of biological entities with conserved integrity and activity.

    Science.gov (United States)

    Ren, L; Robertson, W D; Reimer, R; Heinze, C; Schneider, C; Eggert, D; Truschow, P; Hansen, N-O; Kroetz, P; Zou, J; Miller, R J D

    2015-07-17

    The prospect for spatial imaging with mass spectroscopy at the level of the cell requires new means of cell extraction to conserve molecular structure. To this aim, we demonstrate a new laser extraction process capable of extracting intact biological entities with conserved biological function. The method is based on the recently developed picosecond infrared laser (PIRL), designed specifically to provide matrix-free extraction by selectively exciting the water vibrational modes under the condition of ultrafast desorption by impulsive vibrational excitation (DIVE). The basic concept is to extract the constituent protein structures on the fastest impulsive limit for ablation to avoid excessive thermal heating of the proteins and to use strongly resonant 1-photon conditions to avoid multiphoton ionization and degradation of the sample integrity. With various microscope imaging and biochemical analysis methods, nanoscale single protein molecules, viruses, and cells in the ablation plume are found to be morphologically and functionally identical with their corresponding controls. This method provides a new means to resolve chemical activity within cells and is amenable to subcellular imaging with near-field approaches. The most important finding is the conserved nature of the extracted biological material within the laser ablation plume, which is fully consistent with in vivo structures and characteristics. PMID:26111866

  10. Application study of nuclear technologies for integration chemical, biological and radiological technology

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jae Kon; Han, M. H.; Kim, Y. H.; Yang, J. E.; Jung, K. S.; Cha, H. K.; Moon, J.; La, K. H

    2001-02-01

    The projects are suggested the method to maximize the technology and research results which are being carried out by KAERI on the nuclear field. The study presents 1)the technology to rapidly and accurately determine and the nature of contamination, 2) the technology to predict the spread of contaminant and the magnitude of damage, and 3) the expert-aided decision making technology to identify the optimum counter-measures. And the solutions are also suggested the application to military technology in Chemical, Biological and Radiation field. In addition, I hope this kind of cooperation model come to be the good case of military civilian research harmony to improve the national competition capability.

  11. Application study of nuclear technologies for integration chemical, biological and radiological technology

    International Nuclear Information System (INIS)

    The projects are suggested the method to maximize the technology and research results which are being carried out by KAERI on the nuclear field. The study presents 1)the technology to rapidly and accurately determine and the nature of contamination, 2) the technology to predict the spread of contaminant and the magnitude of damage, and 3) the expert-aided decision making technology to identify the optimum counter-measures. And the solutions are also suggested the application to military technology in Chemical, Biological and Radiation field. In addition, I hope this kind of cooperation model come to be the good case of military civilian research harmony to improve the national competition capability

  12. Neurobiological underpinnings of suicidal behavior: Integrating data from clinical and biological studies

    Directory of Open Access Journals (Sweden)

    Juan J. Carballo

    2009-12-01

    Full Text Available Background and Objectives: Every year, suicide accounts for approximately one million preventable deaths worldwide. Suicidal behavior is complex and multi-determined with risk factors identified in multiple domains including clinical, genetic, environmental, behavioral, neurophysiological, and neurocognitive. Modeling causal pathways that integrate these factors may assist in better identification of high-risk individuals would allow for effective preventive intervention. Methods: Published literature in the English language was reviewed to identify evidence supporting a multi-dimensional model of putative causal pathways for suicidal behavior. Results: There is evidence that clinical, neurochemical, neuroendocrine, neurocognitive, and neurophysiological contributory factors may be useful as intermediate phenotypes in describing putative causal pathways from genetics and early-life adversity to suicidal acts. Conclusions: Determining the causes of suicidal behavior involves integrating risk factors from multiple domains.

  13. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

    OpenAIRE

    Kempa Stefan; Christian Jan-Ole; May Patrick; Walther Dirk

    2009-01-01

    Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the fra...

  14. Comparing two forms of concept map critique activities to support knowledge integration in biology education.

    OpenAIRE

    Schwendimann, Beat

    2014-01-01

    Concept map activities often lack a subsequent revision step that facilitates knowledge integration. This study compares two kinds of concept map critique activities embedded in an evolution unit: Student dyads in one group compared their concept maps against an expert map while dyads in the other group conducted a peer-review. Analysis of the concept maps suggests that both treatment groups significantly improved their understanding of evolution. However, the two groups developed different c...

  15. Biochemoinformatics: integrative computational tools at the interface between chemistry and biology

    OpenAIRE

    Garc??a Serna, Ricard

    2010-01-01

    The work on this thesis has focused on the development of integrated databases and visualization tools for three related areas of biomedical sciences involved in the drug discovery process. An annotated chemical library including drugs and other bioactive compounds with reported affinities over protein targets has been extended and optimized for its use in different knowledge based analysis and virtual profiling methodologies. A second database relating drugs with their side effects has also ...

  16. 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....

  17. 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.

  18. Novel fluorescence-based integrated sensor for chemical and biological agent detection

    Science.gov (United States)

    Frye-Mason, Greg; Leuschen, Martin; Wald, Lara; Paul, Kateri; Hancock, Lawrence F.; Fagan, Steve; Krouse, Justin; Hutchinson, Kira D.

    2004-12-01

    There is a renewed interest in the development of chemical and biological agent sensors due to the increased threat of weapons deployment by terrorist organizations and rogue states. Optically based sensors address the needs of military and homeland security forces in that they are reliable, rapidly deployed, and can provide continuous monitoring with little to no operator involvement. Nomadics has developed optically based chemical weapons sensors that utilize reactive fluorescent chromophores initially developed by Professor Tim Swager at MIT. The chromophores provide unprecedented sensitivity and selectivity toward toxic industrial chemicals and certain chemical weapon agents. The selectivity is based upon the reactivity of the G-class nerve agents (phosphorylation of acetylcholinesterase enzyme) that makes them toxic. Because the sensor recognizes the reactivity of strong electrophiles and not molecular weight, chemical affinity or ionizability, our system detects a specific class of reactive agents and will be able to detect newly developed or modified agents that are not currently known. We have recently extended this work to pursue a combined chemical/biological agent sensor system incorporating technologies based upon novel deep ultraviolet (UV) light emitting diodes (LEDs) developed out of the DARPA Semiconductor UV Optical Sources (SUVOS) program.

  19. 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. PMID:18575108

  20. Integrity testing of Planova™ BioEX virus removal filters used in the manufacture of biological products.

    Science.gov (United States)

    Sekine, Shinya; Komuro, Masayasu; Sohka, Takayuki; Sato, Terry

    2015-05-01

    Confirmation of virus filter integrity is crucial for ensuring the safety of biological products. Two main types of virus filter defects may produce inconsistent and undesirable performance in virus removal: improper pore-size distribution across the membrane; and specific damage, such as tears, broken fibers, or pinholes. Two integrity tests are performed on each individual filter manufactured by Asahi Kasei Medical to ensure the absence of these defects prior to shipment. In this study, we verified that typical usage of Planova™ BioEX filters would not improperly shift the pore-size distribution. Damage occurring during shipment and use (e.g., broken fibers or pinholes) can be detected by end-users with sufficient sensitivity using air-water diffusion based leakage tests. We prepared and tested filters with model pinhole defects of various sizes to develop standard acceptance criteria for the leakage test relative to porcine parvovirus infectivity logarithmic reduction values (LRVs). Our results demonstrate that pinhole defects at or below a certain size for each effective filter surface area have no significant impact on the virus LRV. In conclusion the leakage test is sufficiently sensitive to serve as the sole end-user integrity test for Planova™ BioEX filters, facilitating their use in biopharmaceuticals manufacturing. PMID:25753822

  1. Integrated quantification and identification of aldehydes and ketones in biological samples.

    Science.gov (United States)

    Siegel, David; Meinema, Anne C; Permentier, Hjalmar; Hopfgartner, Gérard; Bischoff, Rainer

    2014-05-20

    The identification of unknown compounds remains to be a bottleneck of mass spectrometry (MS)-based metabolomics screening experiments. Here, we present a novel approach which facilitates the identification and quantification of analytes containing aldehyde and ketone groups in biological samples by adding chemical information to MS data. Our strategy is based on rapid autosampler-in-needle-derivatization with p-toluenesulfonylhydrazine (TSH). The resulting TSH-hydrazones are separated by ultrahigh-performance liquid chromatography (UHPLC) and detected by electrospray ionization-quadrupole-time-of-flight (ESI-QqTOF) mass spectrometry using a SWATH (Sequential Window Acquisition of all Theoretical Fragment-Ion Spectra) data-independent high-resolution mass spectrometry (HR-MS) approach. Derivatization makes small, poorly ionizable or retained analytes amenable to reversed phase chromatography and electrospray ionization in both polarities. Negatively charged TSH-hydrazone ions furthermore show a simple and predictable fragmentation pattern upon collision induced dissociation, which enables the chemo-selective screening for unknown aldehydes and ketones via a signature fragment ion (m/z 155.0172). By means of SWATH, targeted and nontargeted application scenarios of the suggested derivatization route are enabled in the frame of a single UHPLC-ESI-QqTOF-HR-MS workflow. The method's ability to simultaneously quantify and identify molecules containing aldehyde and ketone groups is demonstrated using 61 target analytes from various compound classes and a (13)C labeled yeast matrix. The identification of unknowns in biological samples is detailed using the example of indole-3-acetaldehyde. PMID:24745975

  2. Integrating economic costs and biological traits into global conservation priorities for carnivores.

    Directory of Open Access Journals (Sweden)

    Rafael Dias Loyola

    Full Text Available BACKGROUND: Prioritization schemes usually highlight species-rich areas, where many species are at imminent risk of extinction. To be ecologically relevant these schemes should also include species biological traits into area-setting methods. Furthermore, in a world of limited funds for conservation, conservation action is constrained by land acquisition costs. Hence, including economic costs into conservation priorities can substantially improve their conservation cost-effectiveness. METHODOLOGY/PRINCIPAL FINDINGS: We examined four global conservation scenarios for carnivores based on the joint mapping of economic costs and species biological traits. These scenarios identify the most cost-effective priority sets of ecoregions, indicating best investment opportunities for safeguarding every carnivore species, and also establish priority sets that can maximize species representation in areas harboring highly vulnerable species. We compared these results with a scenario that minimizes the total number of ecoregions required for conserving all species, irrespective of other factors. We found that cost-effective conservation investments should focus on 41 ecoregions highlighted in the scenario that consider simultaneously both ecoregion vulnerability and economic costs of land acquisition. Ecoregions included in priority sets under these criteria should yield best returns of investments since they harbor species with high extinction risk and have lower mean land cost. CONCLUSIONS/SIGNIFICANCE: Our study highlights ecoregions of particular importance for the conservation of the world's carnivores defining global conservation priorities in analyses that encompass socioeconomic and life-history factors. We consider the identification of a comprehensive priority-set of areas as a first step towards an in-situ biodiversity maintenance strategy.

  3. Integration of multiple biological features yields high confidence human protein interactome.

    Science.gov (United States)

    Karagoz, Kubra; Sevimoglu, Tuba; Arga, Kazim Yalcin

    2016-08-21

    The biological function of a protein is usually determined by its physical interaction with other proteins. Protein-protein interactions (PPIs) are identified through various experimental methods and are stored in curated databases. The noisiness of the existing PPI data is evident, and it is essential that a more reliable data is generated. Furthermore, the selection of a set of PPIs at different confidence levels might be necessary for many studies. Although different methodologies were introduced to evaluate the confidence scores for binary interactions, a highly reliable, almost complete PPI network of Homo sapiens is not proposed yet. The quality and coverage of human protein interactome need to be improved to be used in various disciplines, especially in biomedicine. In the present work, we propose an unsupervised statistical approach to assign confidence scores to PPIs of H. sapiens. To achieve this goal PPI data from six different databases were collected and a total of 295,288 non-redundant interactions between 15,950 proteins were acquired. The present scoring system included the context information that was assigned to PPIs derived from eight biological attributes. A high confidence network, which included 147,923 binary interactions between 13,213 proteins, had scores greater than the cutoff value of 0.80, for which sensitivity, specificity, and coverage were 94.5%, 80.9%, and 82.8%, respectively. We compared the present scoring method with others for evaluation. Reducing the noise inherent in experimental PPIs via our scoring scheme increased the accuracy significantly. As it was demonstrated through the assessment of process and cancer subnetworks, this study allows researchers to construct and analyze context-specific networks via valid PPI sets and one can easily achieve subnetworks around proteins of interest at a specified confidence level. PMID:27196966

  4. 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. PMID:26130662

  5. Integrated chemical/biological treatment of paint stripper mixed waste: Metals toxicity and separation

    International Nuclear Information System (INIS)

    The DOE complex has generated vast quantities of complex heterogeneous mixed wastes. Paint stripper waste (PSW) is a complex waste that arose from decontamination and decommissioning activities. It contains paint stripper, cheesecloth, cellulose-based paints with Pb and Cr, and suspect Pu. Los Alamos National Laboratory has 150--200 barrels of PSW and other national laboratories such as Rocky Flats Plant have many more barrels of heterogeneous waste. Few technologies exist that can treat this complex waste. Our approach to solving this problem is the integration of two established technologies: biodegradation and metals chelation

  6. 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.

  7. 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

  8. Integrative activities content (aic: an auxiliary tool for the teaching of Biochemistry in the course of biological sciences at UFRN

    Directory of Open Access Journals (Sweden)

    F. D. Silva

    2015-08-01

    Full Text Available There are constant changes in the development of science, technology, politics, culture and society; the need for change is also evident in the training of teachers. The ease of access to information makes us realize that traditional teaching needs to be updated.The increasing demotivation of students,followed by high reprobation rates, has become a real challenge to the teaching practice.The objective of this work was to awaken in students enrolled in the discipline of MOLECULAR DIVERSITY (MD, a required curricular component in the Course of Biological Sciences at UFRN, an interest in studying the chemistry and functions of biomolecules, better relating the two to each other, and the content already studied in the course, in order to improve the teaching-learning process. This work was developed in a tutoring project registered at PROGRAD/UFRN. This discipline, MD, addresses chemical and structural features of the main organic molecules.The methodology focused on applying problem integrators called INTEGRATIVE ACTIVITIES OF CONTENT. This refers specifically to the application of problems that integrate the topics taught in the discipline, and also those administered in the disciplines processed in parallel, or even in previous semesters. In this way students realize that molecules relate and interact in all bodies; this gives rise to life through metabolism. The discipline is expected to promote meaningful and inter-related learning. We obtained the following results: greater participation and involvement of students in answering the questions posed; greater interest in the discipline;positive changes regarding the number of students who dropped the class, and in reprobation;and greater integration between teachers, students, and teaching assistants. The methodology used in this work was extremely important to achieve the proposed objectives, helping to facilitate the process of teaching-learning, as also to important relate content.

  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

    2016-01-01

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

  10. 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.

    2016-01-01

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

  11. Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts.

    Science.gov (United States)

    Parages, María L; Gutiérrez-Barranquero, José A; Reen, F Jerry; Dobson, Alan D W; O'Gara, Fergal

    2016-03-01

    In recent years, the marine environment has been the subject of increasing attention from biotechnological and pharmaceutical industries as a valuable and promising source of novel bioactive compounds. Marine biodiscovery programmes have begun to reveal the extent of novel compounds encoded within the enormous bacterial richness and diversity of the marine ecosystem. A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally novel biocatalytic activities. With the growing need for green alternatives to industrial processes, and the unique transformations which nature is capable of performing, marine biocatalysts have the potential to markedly improve current industrial pipelines. Furthermore, biocatalysts are known to possess chiral selectivity and specificity, a key focus of pharmaceutical drug design. In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and subsequent improvement of a new generation of marine biocatalysts. PMID:27007381

  12. Integrated (Meta Genomic and Synthetic Biology Approaches to Develop New Biocatalysts

    Directory of Open Access Journals (Sweden)

    María L. Parages

    2016-03-01

    Full Text Available In recent years, the marine environment has been the subject of increasing attention from biotechnological and pharmaceutical industries as a valuable and promising source of novel bioactive compounds. Marine biodiscovery programmes have begun to reveal the extent of novel compounds encoded within the enormous bacterial richness and diversity of the marine ecosystem. A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally novel biocatalytic activities. With the growing need for green alternatives to industrial processes, and the unique transformations which nature is capable of performing, marine biocatalysts have the potential to markedly improve current industrial pipelines. Furthermore, biocatalysts are known to possess chiral selectivity and specificity, a key focus of pharmaceutical drug design. In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and subsequent improvement of a new generation of marine biocatalysts.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    James J Mancuso

    2014-11-01

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

  15. 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. PMID:27293150

  16. 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. PMID:11542554

  17. Integrating clinical and biological information in a shanghai biobank: an introduction to the sample repository and information sharing platform project.

    Science.gov (United States)

    Cui, Wenbin; Zheng, Peiyong; Yang, Jiahong; Zhao, Rong; Gao, Jiechun; Yu, Guangjun

    2015-02-01

    Biobanks are important resources and central tools for translational medicine, which brings scientific research outcomes to clinical practice. The key purpose of biobanking in translational medicine and other medical research is to provide biological samples that are integrated with clinical information. In 2008, the Shanghai Municipal Government launched the "Shanghai Tissue Bank" in an effort to promote research in translational medicine. Now a sharing service platform has been constructed to integrate clinical practice and biological information that can be used in diverse medical and pharmaceutical research studies. The platform collects two kinds of data: sample data and clinical data. The sample data are obtained from the hospital biobank management system, and mainly include the donors' age, gender, marital status, sample source, sample type, collection time, deposit time, and storage method. The clinical data are collected from the "Hospital-Link" system (a medical information sharing system that connects 23 tertiary hospitals in Shanghai). The main contents include donors' corresponding medication information, test reports, inspection reports, and hospital information. As of the end of September 2014, the project has a collection of 16,020 donors and 148,282 samples, which were obtained from 12 medical institutions, and automatically acquired donors' corresponding clinical data from the "Hospital-Link" system for 6830 occurrences. This project will contribute to scientific research at medical institutions in Shanghai, and will also support the development of the biopharmaceutical industry. In this article, we will describe the significance, the construction phases, the application prospects, and benefits of the sample repository and information sharing service platform. PMID:25686046

  18. 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.

  19. 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.

  20. 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. PMID:26234364

  1. Microbial metabolism fuels ecosystem-scale organic matter transformations: an integrated biological and chemical perspective

    Science.gov (United States)

    Wrighton, K. C.; Narrowe, A. B.; Angle, J.; Stefanik, K. S.; Daly, R. A.; Johnston, M.; Miller, C. S.

    2014-12-01

    Freshwater saturated sediments and soils represent vital ecosystems due to their nutrient cycling capacities and their prominent contribution to global greenhouse gas emissions. However, the diversity of microorganisms and metabolic pathways involved in carbon cycling, and the impacts of these processes on other biogeochemical cycles remain poorly understood. Major advances in DNA sequencing have helped forge linkages between the previously disconnected biological and chemical components of these systems. Here, we present data on the use of assembly-based metagenomics to generate hypotheses on microbial carbon degradation and biogeochemical cycling in waterlogged sediments and soils. DNA sequencing from a fresh water aquifer adjacent to the Colorado River in Rifle, CO yielded extensive genome recovery from multiple previously unknown bacterial lineages. Fermentative metabolisms encoded by these genomes drive nitrogen, hydrogen, and sulfur cycling in this subsurface system. We are also applying a similar approach to identify microbial processes in a freshwater wetland on Lake Erie, OH. Given the increased diversity (increased richness, decreased evenness, and strain variation) of wetland sediment microbial communities, we modified methods for specialized assembly of long taxonomic marker gene amplicons (EMIRGE) to create a biogeographical map of Fungi, Archaea, and Bacteria along depth and hydrological transects. This map reveals that the microbial community associated with the top two depths (>7 cm) is significantly different from bottom depths (7-40 cm). Dissolved organic matter (DOM) molecular weight and the presence of oxidized terminal electron acceptors best predict differences in microbial community structure. Laboratory mesocosms amended with pore-water DOM, in situ soil communities, and variable oxygen conditions link DOM composition and redox to microbial metabolic networks, biogeochemical cycles, and green house gas emission. Organism identities from

  2. 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.

  3. 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. PMID:26426153

  4. Ecohydrology of biological soil crusts in arid sand dunes - integration from the micro-scale to the landscape

    Science.gov (United States)

    Veste, M.; Yair, A.; Breckle, S.-W.; Littmann, T.

    2012-04-01

    Biological soil crusts are distributed in many ecosystems from the polar, boreal, temperate, and mediterranean to the tropical regions. They are typical in habitats where the vegetation cover is sparse and microclimatic conditions permit their development. They play an important role for ecosystem processes, enhancing surface stability, changing surface properties and influencing hydrological processes and water re-distribution. The spatial distribution and availability of the water resources are the important factors for the vegetation in drylands. Key questions are (i) how the hydrological processes of the BSC are triggering the vegetation pattern on the landscape level and (ii) how we can integrate the hydrological processes on the micro-scale into the landscape processes and patterns? We studied the interrelations between biological soil crusts and vegetation pattern in arid sand dunes of the north-western Negev. Most of the dunes are covered by biological soil crusts and various types can be distinguished in different exposition and along a 40 km geo-ecological gradient. Rainfall increases from approx. 90 mm in the south to 170 mm in the northern dunes. Biological crusts cover nearly 90% of the sand dunes of the northern Haluza sand field, whereas the parts of the southern dune crests are still mobile. Furthermore, soil lichens plays an important role in the northern dunes, covering 30%-90% of the interdune area as well as of the stable north-/northwest slopes. The surrounding dune slopes are covered by a biological crust with cyanobacteria, green algae, mosses. Upon wetting, infiltration decreases and runoff can be observed in crust cover areas, even in sand dunes. Runoff depends on rainfall intensity, soil thickness and composition. The change of surface properties counteracts the effects of increasing rainfall on the vegetation along the geo-ecological gradient. Because of the increase in soil crust thickness the infiltration rates decrease in the dune area

  5. 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

    2016-03-01

    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. PMID:26820531

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

    Science.gov (United States)

    Rojas, Ana M; Santamaria, Anna; Malik, Rainer; Jensen, Thomas Skøt; Körner, Roman; Morilla, Ian; de Juan, David; Krallinger, Martin; Hansen, Daniel Aaen; Hoffmann, Robert; Lees, Jonathan; Reid, Adam; Yeats, Corin; Wehner, Anja; Elowe, Sabine; Clegg, Andrew B; Brunak, Søren; Nigg, Erich A; Orengo, Christine; Valencia, Alfonso; Ranea, Juan A G

    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 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. PMID:22427808

  7. 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

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

    OpenAIRE

    Toprak, E.; Schnaiter, M.

    2012-01-01

    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, performance of WIBS-4 for discrimination of several types of aerosols, and the detection and identificat...

  9. Biology and integrated control of Pestalotiopsis on container-grown ericaceous crops.

    Science.gov (United States)

    McQuilken, Mark P; Hopkins, K E

    2004-02-01

    Pestalotiopsis isolates obtained from the foliage, stem-base and roots of diseased container-grown ericaceous crops (Calluna, Erica, Pieris and Rhododendron) collected from UK nurseries were identified as Pestalotiopsis sydowiana (Bresad) B Sutton on the basis of conidia morphology. Inoculum sources of the pathogen included diseased stock plants, crop debris, nursery soils, used growing media, pots and floor covering, and dust collected from greenhouse walkways. Isolates were not host-specific and infected other species of ericaceous plants, with typical symptoms including browning of foliage, stems and roots, and the presence of black or greenish black acervuli on diseased tissue. The optimum temperature for growth of three selected isolates of the pathogen was 20-25 degrees C, with little or no growth occurring below 5 or above 30 degrees C. Growth occurred over pH 2.6-8.6, with optimum at 5.5. Decreases in matric potential from -0.3 to -4.0 MPa reduced growth, which was totally inhibited at -6.5 MPa. Greenhouse trials were conducted to evaluate the effects of disease management methods (irrigation, flooring/pot disinfection and fungicide application) on control of the pathogen on potted plants of C vulgaris. Disease incidence and foliar browning caused by P sydowiana were less on fungicide-treated (five-spray programme of alternating prochloraz and carbendazim) potted plants watered by sub-irrigation compared with watering from overhead. Single and combined treatments of flooring/pot disinfection (hydrogen peroxide/peracetic acid) and the five-spray fungicide programme significantly reduced disease incidence and severity compared with dipping pots in water. The combined disinfection and fungicide programme significantly reduced disease incidence and severity, compared to disinfection or fungicide application alone. The importance of these findings for the integrated control of P sydowiana on ericaceous plant nurseries is discussed. PMID:14971679

  10. 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. PMID:26584070

  11. 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. PMID:26921849

  12. 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.

  13. Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology

    Science.gov (United States)

    Körner, Roman; Morilla, Ian; de Juan, David; Krallinger, Martin; Hansen, Daniel Aaen; Hoffmann, Robert; Lees, Jonathan; Reid, Adam; Yeats, Corin; Wehner, Anja; Elowe, Sabine; Clegg, Andrew B.; Brunak, Søren; Nigg, Erich A.; Orengo, Christine; Valencia, Alfonso; Ranea, Juan A. G.

    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 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. PMID:22427808

  14. 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)

    TimothyJamesKinsella

    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.

  15. 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…

  16. 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...

  17. 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...

  18. Quercetin Improved Biological Membrane Integrity and Decreased Protein Oxidation as Induced in Rats by Ionizing Radiation Exposure

    International Nuclear Information System (INIS)

    After radiation exposure at certain levels, harmful changes in the living cell metabolic activities may occur. These changes include oxidation of lipid and protein as well as membrane permeability disorders. Gamma glutamyl transferase (GGT) is recently believed to be important in protecting against oxidative stress and is considered as good indicator of it. In the present study Spague Dawely rats (140-150 g) were exposed to whole body gamma irradiation (shot dose, 5 Gy), samples of blood and liver were taken 1 and 10 days post exposure. Quercetin (pentahydroxy flavone) presented in most vegetables, was administered orally (1.064 mmol/kg body wt.)up to 10 days before radiation exposure to evaluate its anti oxidative role. he data revealed serious effects of radiation exposure on the membrane integrity as reflected by increased serum potassium associated with decreased sodium levels. Oxidation of lipid and protein with antioxidant disorders were recorded after radiation exposure as reflected by increased contents of malondialdehyde, carbonyl and GGT activity. Quercetin administration before radiation exposure attenuated the harmful effects of irradiation in the most chosen parameters. The beneficial role of quercetin may be related to its ability in quenching free radicals and scavenging reactive oxygen species thus improving regeneration in the biological tissues

  19. 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. PMID:26523481

  20. Stress-sensitive neurosignalling in depression: an integrated network biology approach to candidate gene selection for genetic association analysis

    Directory of Open Access Journals (Sweden)

    J. Anke M. van Eekelen

    2012-07-01

    Full Text Available Genetic risk for depressive disorders is poorly understood despite consistent suggestions of a high heritable component. Most genetic studies have focused on risk associated with single variants, a strategy which has so far only yielded small (often non-replicable risks for depressive disorders. In this paper we argue that more substantial risks are likely to emerge from genetic variants acting in synergy within and across larger neurobiological systems (polygenic risk factors. We show how knowledge of major integrated neurobiological systems provides a robust basis for defining and testing theoretically defensible polygenic risk factors. We do this by describing the architecture of the overall stress response. Maladaptation via impaired stress responsiveness is central to the aetiology of depression and anxiety and provides a framework for a systems biology approach to candidate gene selection. We propose principles for identifying genes and gene networks within the neurosystems involved in the stress response and for defining polygenic risk factors based on the neurobiology of stress-related behaviour. We conclude that knowledge of the neurobiology of the stress response system is likely to play a central role in future efforts to improve genetic prediction of depression and related disorders.

  1. Potential for the integration of biological and chemical control of sheath blight disease caused by Rhizoctonia solani on rice.

    Science.gov (United States)

    Boukaew, Sawai; Klinmanee, Chanasirin; Prasertsan, Poonsuk

    2013-10-01

    Biological control using antagonistic microbes to minimize the use of chemical pesticides has recently become more prevalent. In an attempt to find an integrated control system for sheath blight, caused by Rhizoctonia solani in rice, Streptomyces philanthi RM-1-138, commercial formulations of Bacillus subtilis as Larminar® and B. subtilis strain NSRS 89-24+MK-007 as Biobest® and chemical fungicides including carbendazim®, validamycin®, propiconazole® and mancozeb® were applied alone and in combination with S. philanthi RM-1-138. In vitro experiments showed that all treatments tested did provide some control against mycelial growth and sclerotia production by R. solani PTRRS-9. In addition, the four chemical fungicides had no detrimental effects on S. philanthi RM-1-138 even at high concentrations (up to 100 μg/ml). The efficacy of S. philanthi RM-1-138, the commercial formulations of B. subtilis, chemical fungicides alone or in combination with S. philanthi RM-1-138 was also tested in a greenhouse experiment against sheath blight disease on rice plants. All treatments showed some protection of rice for sheath blight by 47-60 % when carbendazim® was applied alone and up to 74 % when combined with S. philanthi RM-1-138. PMID:23653261

  2. Integrated Assessment of PAH Contamination in the Czech Rivers Using a Combination of Chemical and Biological Monitoring

    Directory of Open Access Journals (Sweden)

    Jana Blahova

    2014-01-01

    Full Text Available This study investigated polycyclic aromatic hydrocarbons (PAH pollution of selected rivers in the Czech Republic. Integrated evaluation was carried out using combination of chemical and biological monitoring, in which we measured content of 1-hydroxypyrene (1-OHP in chub bile and priority PAH in water samples obtained by exposing the semipermeable membrane devices at each location. The concentrations of 1-OHP in bile samples and sum of priority PAH in water sampler ranged from 6.8 ng mg protein−1 to 106.6 ng mg protein−1 and from 5.2 ng L−1 to 173.9 ng L−1, respectively. The highest levels of biliary metabolite and PAH in water were measured at the Odra River (the Bohumín site, which is located in relatively heavily industrialized and polluted region. Statistically significant positive correlation between biliary 1-OHP and sum of PAH in water was also obtained (P<0.01, rs=0.806.

  3. Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation.

    Science.gov (United States)

    Hériché, Jean-Karim; Lees, Jon G; Morilla, Ian; Walter, Thomas; Petrova, Boryana; Roberti, M Julia; Hossain, M Julius; Adler, Priit; Fernández, José M; Krallinger, Martin; Haering, Christian H; Vilo, Jaak; Valencia, Alfonso; Ranea, Juan A; Orengo, Christine; Ellenberg, Jan

    2014-08-15

    The advent of genome-wide RNA interference (RNAi)-based screens puts us in the position to identify genes for all functions human cells carry out. However, for many functions, assay complexity and cost make genome-scale knockdown experiments impossible. Methods to predict genes required for cell functions are therefore needed to focus RNAi screens from the whole genome on the most likely candidates. Although different bioinformatics tools for gene function prediction exist, they lack experimental validation and are therefore rarely used by experimentalists. To address this, we developed an effective computational gene selection strategy that represents public data about genes as graphs and then analyzes these graphs using kernels on graph nodes to predict functional relationships. To demonstrate its performance, we predicted human genes required for a poorly understood cellular function-mitotic chromosome condensation-and experimentally validated the top 100 candidates with a focused RNAi screen by automated microscopy. Quantitative analysis of the images demonstrated that the candidates were indeed strongly enriched in condensation genes, including the discovery of several new factors. By combining bioinformatics prediction with experimental validation, our study shows that kernels on graph nodes are powerful tools to integrate public biological data and predict genes involved in cellular functions of interest. PMID:24943848

  4. 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. PMID:24303294

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

    International Nuclear Information System (INIS)

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

  6. A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

    OpenAIRE

    ThomasEissing

    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 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 co...

  7. Integration of behavioral and biological control for the management of cotton insect pests: Significance and cost benefits

    International Nuclear Information System (INIS)

    Earias pheromones. The pheromones were applied once in a season at the start of square formation stage of the cotton crop. The fourth block was treated with conventional insecticides. The farmer applied organophosphate (confidor) and Pyrethroid (Polytrin-C) insecticides in two sprays each. The infestation of pink bollworm and Earias spp. was recorded at weekly intervals. Establishment of the parasitoids was determined by placing Angoumois grain moth eggs in the field. These cards were brought into the laboratory after 24 hours exposure in the differently treated blocks and parasitoid emergence was recorded. For the control of sucking pests, insecticide (confidor) was sprayed uniformly in all the treatments in the third week of June during both years. The cost of the treatments was worked out and the cost benefit ratio for each treatment was calculated. Integration of parasitoids and pheromones, suppressed the bollworms infestation below the economic injury level (5-10%). Separate treatment of pheromones or parasitoids was less effective, and required supplemental measures. The population of the parasitoids in the field was low in the hot months of June and July and thereafter it gradually increased in the succeeding months. Maximum number of the parasitoids was observed in the month of October. The cost of integrated treatment with parasitoids and pheromones was also less than that of insecticide treatment alone. Potential of behavioural and biological control tactics for launching the integrated approach on an area-wide basis is discussed

  8. 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

  9. [Establishment of three-dimensional integrated "serum pharmacochemistry-pharmacokinetics (pharmacodynamics)-systems biology" for research of traditional Chinese medicine prescription and its application in Yinchenhao Tang].

    Science.gov (United States)

    Zhang, Ai-Hua; Sun, Hui; Yan, Guang-Li; Han, Ying; Wang, Xi-Jun

    2013-11-01

    Traditional Chinese medicine (TCM) prescription is a valuable asset for clinical medication, has multi-component and multi-target characteristics. However, due to the complex ingredients of prescription, the unclear mechanism, the lack of scientific data to support the dose-response relationship, it has become the bottleneck for the in-depth study for the process of modernization and internationalization of TCM. It requires the integration of Chinese medicine theory, modern analysis and data mining technology to build new research model for characteristic of TCM prescription. This paper provides an overview of TCM serum pharmacochemistry, pharmacokinetics (pharmacodynamics) and systems biology theory and practice, to establish the integrated three-dimensional "serum pharmacochemistry-pharmacokinetics (pharmacodynamics)-systems biology" for the research of TCM prescription to reveal the pharma-material basis and action mechanism and the compatibility scientific connotation, with a prescription Yinchenhao Tang as a case study. PMID:24494574

  10. 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

  11. 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

  12. Report of the Working Group on Integrative Physical - biological and Ecosystem Modelling (WGIPEM). 16–19 March 2015, Plymouth Marine Laboratory, UK

    OpenAIRE

    ICES

    2015-01-01

    The Working Group on Integrative Physical-Biological and Ecosystem Modelling held their fourth meeting at Plymouth Marine Laboratory, Plymouth, UK. Scientists from Belgium, Denmark, France, Germany, Italy, UK, Netherlands, and USA joined the meeting either directly or by correspondence. The focus of the group is to advance state-of-the-art ecosystem-, individual-based and population modelling of marine sys-tems within the ICES areas. It further addresses effective ways of model coupling and k...

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

    OpenAIRE

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

    2016-01-01

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

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

    OpenAIRE

    Benassi Marcello; Pedrini Massimo; Abate Armando; Bruzzaniti Vicente; Strigari Lidia

    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....

  15. The Interaction Between Pubertal Timing and Peer Popularity for Boys and Girls: An Integration of Biological and Interpersonal Perspectives on Adolescent Depression

    OpenAIRE

    Teunissen, Hanneke A.; Adelman, Caroline B.; Prinstein, Mitchell J.; Spijkerman, Renske; Poelen, Evelien A. P.; Engels, Rutger C. M. E.; Scholte, Ron H. J.

    2010-01-01

    The transition to adolescence marks a time of sharply increased vulnerability to the development of depression, particularly among girls. Past research has examined isolated risk factors from individual theoretical models (e.g., biological, interpersonal, and cognitive) of depression, but few have examined integrative models. This study investigated the conjoint effects of early pubertal timing and popularity in the longitudinal prediction of depressive symptoms. A total of 319 girls and 294 ...

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

    International Nuclear Information System (INIS)

    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

  17. 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, and...

  18. '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)

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

    International Nuclear Information System (INIS)

    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)

  20. 'Integration'

    DEFF Research Database (Denmark)

    Olwig, Karen Fog

    2011-01-01

    , 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...

  1. 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.…

  2. The brain and somatic integration: insights into the standard biological rationale for equating "brain death" with death.

    Science.gov (United States)

    Shewmon, A D

    2001-10-01

    The mainstream rationale for equating "brain death" (BD) with death is that the brain confers integrative unity upon the body, transforming it from a mere collection of organs and tissues to an "organism as a whole." In support of this conclusion, the impressive list of the brain's myriad integrative functions is often cited. Upon closer examination, and after operational definition of terms, however, one discovers that most integrative functions of the brain are actually not somatically integrating, and, conversely, most integrative functions of the body are not brain-mediated. With respect to organism-level vitality, the brain's role is more modulatory than constitutive, enhancing the quality and survival potential of a presupposedly living organism. Integrative unity of a complex organism is an inherently nonlocalizable, holistic feature involving the mutual interaction among all the parts, not a top-down coordination imposed by one part upon a passive multiplicity of other parts. Loss of somatic integrative unity is not a physiologically tenable rationale for equating BD with death of the organism as a whole. PMID:11588655

  3. Biological Stress Response Terminology: Integrating the Concepts of Adaptive Response and Preconditioning Stress Within a Hormetic Dose-Response Framework

    Science.gov (United States)

    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 stres...

  4. 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

  5. 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.…

  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...

  7. 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...

  8. And So It Grows: Using a Computer-Based Simulation of a Population Growth Model to Integrate Biology & Mathematics

    Science.gov (United States)

    Street, Garrett M.; Laubach, Timothy A.

    2013-01-01

    We provide a 5E structured-inquiry lesson so that students can learn more of the mathematics behind the logistic model of population biology. By using models and mathematics, students understand how population dynamics can be influenced by relatively simple changes in the environment.

  9. Integrating Math & Computer Skills in the Biology Classroom: An Example Using Spreadsheet Simulations to Teach Fundamental Sampling Concepts

    Science.gov (United States)

    Ray, Darrell L.

    2013-01-01

    Students often enter biology programs deficient in the math and computational skills that would enhance their attainment of a deeper understanding of the discipline. To address some of these concerns, I developed a series of spreadsheet simulation exercises that focus on some of the mathematical foundations of scientific inquiry and the benefits…

  10. The PlaNet Consortium: A Network of European Plant Databases Connecting Plant Genome Data in an Integrated Biological Knowledge Resource

    Directory of Open Access Journals (Sweden)

    K. F. X. Mayer

    2006-04-01

    Full Text Available The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project.

  11. 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

  12. 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

  13. Pathway of FeEDTA transformation and its impact on performance of NOx removal in a chemical absorption-biological reduction integrated process

    OpenAIRE

    Wei Li; Jingkai Zhao; Lei Zhang; Yinfeng Xia; Nan Liu; Sujing Li; Shihan Zhang

    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 NO x removal from the flue gas. Previous work showed that the Fe(II)EDTA concentration was critical for the NO x 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 NO x removal in a biofilter. Experimental results re...

  14. Integrated biological and chemical control of damping-off caused by Rhizoctonia solani using Bacillus subtilis RB14-C and flutolanil.

    Science.gov (United States)

    Kondoh, M; Hirai, M; Shoda, M

    2001-01-01

    Bacillus subtilis RB14-C was isolated as a potential biological agent to control the occurrence of various plant diseases. Integrated control of damping-off in tomato plants caused by Rhizoctonia solani was carried out in pots using B. subtilis RB14-C and chemical pesticide, flutolanil. The growth of RB14-C was the same in both the flutolanil-containing and the flutolanil-free media, indicating the resistance of RB14-C to flutolanil. Although the productivity of surfactin decreased to one-third in the flutolanil-containing medium, compared with that in the flutolanil-free medium, the productivity of iturin A which is mainly associated with the suppressive ability of RB14-C against plant pathogens was unaffected. The integration of RB14-C and flutolanil reduced the amount of flutolanil used to one-fourth of that of the single use of flutolanil, with the same efficacy of reducing disease occurrence. PMID:16232970

  15. 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.

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

    OpenAIRE

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

    2013-01-01

    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 res...

  17. Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines

    OpenAIRE

    Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

    2010-01-01

    Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research proj...

  18. Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

    International Nuclear Information System (INIS)

    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

  19. 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.

  20. 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.

  1. Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology

    OpenAIRE

    Donner, Erica; Punshon, Tracy; Guerinot, Mary Lou; Lombi, Enzo

    2011-01-01

    Functional characterisation of the genes regulating metal(loid) homeostasis in plants is a major focus of crop biofortification, phytoremediation, and food security research. This paper focuses on the potential for advancing plant metal(loid) research by combining molecular biology and synchrotron-based techniques. Recent advances in x-ray focussing optics and fluorescence detection have greatly improved the potential of synchrotron techniques for plant science research, allowing metal(loids)...

  2. Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes

    OpenAIRE

    Price Jennifer; Dakhallah Duaa; Batte Kara; Piper Melissa G; Wang Kai; Etheridge Alton; Gelinas Richard; Cho Ji-Hoon; Bornman Dan; Zhang Shile; Marsh Clay; Galas David

    2011-01-01

    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...

  3. The Principle of Integration in International Sustainable Development Law (ISDL) with Reference to the Biological Weapons Convention (BWC)

    OpenAIRE

    Marina Abdul Majid; Nor Anita Abdullah; Siti Nurani Mohd Noor; Chan Kok Gan

    2016-01-01

    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) ...

  4. Integrative analyses of miRNA and proteomics identify potential biological pathways associated with onset of pulmonary fibrosis in the bleomycin rat model

    International Nuclear Information System (INIS)

    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

  5. 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.

  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. Endangered and potentially endangered wildlife on John F. Kennedy Space Center and faunal integrity as a goal for maintaining biological diversity

    Science.gov (United States)

    Breininger, David R.; Barkaszi, Mary JO; Smith, Rebecca B.; Oddy, Donna M.; Provancha, Jane A.

    1994-01-01

    Buffer zones for space operations provide for a wildlife diversity unsurpassed among most federal facilities in the continental U.S. demonstrating the coexistence possible with one of man's greatest technological achievements. This document ranks 119 resident or migratory wildlife species that are endangered or declining. The ranking system herein was based on species' vulnerability to extinction and the relevance of Kennedy Space Center (KSC) for maintaining populations in the U.S. and Florida. One amphibian, 19 reptiles, 80 birds, and 19 mammals were considered endangered or declining. KSC is an integral area for regional species diversity being the focus of the Merritt Island/Cape Canaveral/Turnbull Ecosystem which is part of the Indian River Lagoon watershed, an estuary of national significance. Many species that use this system also use the nearby St. Johns River Basin ecosystem. These two ecosystems are biological corridors between temperate Carolinian and tropical/subtropical Caribbean biotic provinces. Threats to biological diversity on KSC were also reviewed. Traditional environmental assessments, resulting from environmental regulation guidelines, focus on environmental contaminants and habitat lost due to construction. However, this review suggested that small population sizes, isolation of populations, ecosystem and habitat fragmentation, road mortality, and other edge effects may represent more critical threats to biological diversity than the traditional topics.

  8. 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.

  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. PMID:27423566

  10. 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

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

    OpenAIRE

    Chih-Chin Oh-Yang; Min-Hsien Wu; Jr-Lung Lin; Shih-Siou Wang

    2011-01-01

    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 pumpin...

  12. 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.

  13. 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...... and sedimentation. Chemical pretreatment resulted in 60% COD-reduction and 75% phosphorus reduction. The chemically precipitated primary sludge was exposed to anaerobic sludge hydrolysis at retention times of 1 and 2 days at temperatures in the range of 15-30°C. At a retention time of two days at 20°C, resulting......, 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...

  14. Evaluation of an index of biotic integrity approach used to assess biological condition in western U.S. streams and rivers at varying spatial scales

    Science.gov (United States)

    Meador, M.R.; Whittier, T.R.; Goldstein, R.M.; Hughes, R.M.; Peck, D.V.

    2008-01-01

    Consistent assessments of biological condition are needed across multiple ecoregions to provide a greater understanding of the spatial extent of environmental degradation. However, consistent assessments at large geographic scales are often hampered by lack of uniformity in data collection, analyses, and interpretation. The index of biotic integrity (IBI) has been widely used in eastern and central North America, where fish assemblages are complex and largely composed of native species, but IBI development has been hindered in the western United States because of relatively low fish species richness and greater relative abundance of alien fishes. Approaches to developing IBIs rarely provide a consistent means of assessing biological condition across multiple ecoregions. We conducted an evaluation of IBIs recently proposed for three ecoregions of the western United States using an independent data set covering a large geographic scale. We standardized the regional IBIs and developed biological condition criteria, assessed the responsiveness of IBIs to basin-level land uses, and assessed their precision and concordance with basin-scale IBIs. Standardized IBI scores from 318 sites in the western United States comprising mountain, plains, and xeric ecoregions were significantly related to combined urban and agricultural land uses. Standard deviations and coefficients of variation revealed relatively low variation in IBI scores based on multiple sampling reaches at sites. A relatively high degree of corroboration with independent, locally developed IBIs indicates that the regional IBIs are robust across large geographic scales, providing precise and accurate assessments of biological condition for western U.S. streams. ?? Copyright by the American Fisheries Society 2008.

  15. The GLOBE 3D Genome Platform - towards a novel system-biological paper tool to integrate the huge complexity of genome organization and function.

    Science.gov (United States)

    Knoch, Tobias A; Lesnussa, Michael; Kepper, Nick; Eussen, Hubert B; Grosveld, Frank G

    2009-01-01

    Genomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the general sequential, three-dimensional and regulatory organization. Here, we present the GLOBE 3D Genome Platform a completely novel grid based virtual "paper" tool and in fact the first system-biological genome browser integrating the holistic complexity of genomes in a single easy comprehensible platform: Based on a detailed study of biophysical and IT requirements, every architectural level from sequence to morphology of one or several genomes can be approached in a real and in a symbolic representation simultaneously and navigated by continuous scale-free zooming within a unique three-dimensional OpenGL and grid driven environment. In principle an unlimited number of multi-dimensional data sets can be visualized, customized in terms of arrangement, shape, colour, and texture etc. as well as accessed and annotated individually or in groups using internal or external data bases/facilities. Any information can be searched and correlated by importing or calculating simple relations in real-time using grid resources. A general correlation and application platform for more complex correlative analysis and a front-end for system-biological simulations both using again the huge capabilities of grid infrastructures is currently under development. Hence, the GLOBE 3D Genome Platform is an example of a grid based approach towards a virtual desktop for genomic work combining the three fundamental distributed resources: i) visual data representation, ii) data access and management, and iii) data analysis and creation. Thus, the GLOBE 3D Genome Platform is the novel system-biology oriented information system urgently needed to access, present, annotate, and to simulate the holistic genome

  16. 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?

  17. 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.

  18. 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. PMID:23057183

  19. 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

  20. Advanced treatment of oilfield production wastewater by an integration of coagulation/flotation, catalytic ozonation and biological processes.

    Science.gov (United States)

    Chen, Ke-Yong; Zhang, Xiao-Bing; Li, Jun

    2016-10-01

    In this study, advanced treatment of heavily polluted oilfield production wastewater (OPW) was investigated employing the combination of coagulation/dissolved air flotation, heterogeneous catalytic ozonation and sequencing batch reactor (SBR) processes. Two SBR reactors were separately set up before and after the ozonation unit. The results show that microbubble flotation was more efficient than macrobubble flotation in pollutant removal. Catalytic ozonation with the prepared Fe/activated carbon catalyst significantly enhanced pollutant removal in the second SBR by improving wastewater biodegradability and reducing wastewater microtoxicity. The treatment technique decreased oil, chemical oxygen demand and NH3-N by about 97%, 88% and 91%, respectively, allowing the discharge limits to be met. Therefore, the integrated process with efficient, economical and sustainable advantages was suitable for advanced treatment of real OPW. PMID:26936286

  1. Adaptive plasticity of Laguncularia racemosa in response to different environmental conditions: integrating chemical and biological data by chemometrics.

    Science.gov (United States)

    da Souza, Iara; Bonomo, Marina Marques; Morozesk, Mariana; Rocha, Lívia Dorsch; Duarte, Ian Drumond; Furlan, Larissa Maria; Arrivabene, Hiulana Pereira; Monferrán, Magdalena Victoria; Matsumoto, Silvia Tamie; Milanez, Camilla Rozindo Dias; Wunderlin, Daniel Alberto; Fernandes, Marisa Narciso

    2014-04-01

    Mangroves are dynamic environments under constant influence of anthropic contaminants. The correlation between environmental contamination levels and possible changes in the morphology of plants, evaluated by multivariate statistics helps to highlight matching between these variables. This study aimed to evaluate the uptake and translocation of metals and metalloids in roots and leaves as well as the changes induced in both anatomy and histochemistry of roots of Laguncularia racemosa inhabiting two estuaries of Espírito Santo (Brazil) with different pollution degrees. The analysis of 14 elements in interstitial water, sediments and plants followed by multivariate statistics, allowed the differentiation of studied sites, showing good match between levels of elements in the environment with the corresponding in plants. L. racemosa showed variations in their root anatomy in different collection areas, with highest values of cortex/vascular cylinder ratio, periderm thickness and air gap area in Vitória Bay, the most polluted sampling area. These three parameters were also important to differentiate the mangrove areas by linear discriminant analysis. The development stage of aerenchyma in roots reflected the oxygen availability in the water, being found a negative correlation between these variables. The combined use of chemical and biological analyses responded quite well to different pollution scenarios, matching morphological responses to physical and chemical parameters, measured at different partitions within the estuary. Thus, L. racemosa can be confirmed as a reliable sentinel plant for biomonitoring of estuaries impacted by anthropic pollution. PMID:24445776

  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. 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.

  4. 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.

  5. 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.

  6. A Molecular Biology Database Digest

    OpenAIRE

    Bry, François; Kröger, Peer

    2000-01-01

    Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration...

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Integrated photochemical and biological treatment of a commercial textile surfactant: Process optimization, process kinetics and COD fractionation

    International Nuclear Information System (INIS)

    The biodegradability of surfactants is a frequent and complex issue arising both at domestic as well as industrial treatment facilities. In the present experimental study, the integrated photochemical (H2O2/UV-C) and biochemical (activated sludge) treatment of a commercial grade nonionic/anionic textile surfactant formulation was investigated. Photochemical baseline experiments have shown that once the initial pH and H2O2 dose were optimized, practically complete COD removal (CODo = 500 ± 30 mg L-1) could be achieved. Once the COD was elevated to values being typical for the textile fabric preparation stage, treatment efficiency was seriously retarded provided that the photochemical treatment conditions remained constant. Moreover, a definite relationship existed between H2O2 consumption and COD removal for H2O2/UV-C advanced oxidation of the textile surfactant. In the second part of the study, COD abatement was modeled for the biodegradation of untreated and photochemically pretreated textile surfactant formulation according to their COD fractions. Results have indicated that the readily biodegradable and rapidly hydrolysable COD fractions of the textile surfactant solution could be appreciably increased upon exposure to an optimum H2O2 concentration (60 mM; i.e. 2.1 g H2O2 (g CODo)-1) and extended UV-C irradiation times (i.e. 90 and 120 min)

  12. Evaluation of an integrated approach involving chemical and biological processes for the detoxification of gold tailings effluent in Ghana

    International Nuclear Information System (INIS)

    Chemical and bio-remediation measures for the detoxification of pollutants such as cyanide and heavy metals in mine tailings effluent have been developed over the years. The study sought to evaluate the decrease in the concentrations of Cu, Zn, Fe, Cd, As and Pb through the integration of the processes involving photo-oxidation, activated carbon, hydrogen peroxide and bacterial degradation to decontaminate wastewater from the gold ore treatment plant until release into the environment in Ghana. The levels of trace metals Cu (0.345 mg l-1), Zn (0.07 mg l-1) and Fe (0.146 mg l-1 ) in treated effluent released into natural water bodies after bacterial degradation was generally within international and local standards for effluent discharges. Except for As, the levels of Cd and Pb which are hazardous heavy metals that may pose adverse health and environmental effects were within acceptable limits. The toxicity of these metals were in the increasing order Pb < Cd < As. The anthropogenic source of As in the chemically processed arseno-pyritic rock ores of the study area and the marginal 14–49% efficiency of As of the different detoxification processes could have contributed to the high levels of As in the effluent. If optimal conditions are attained for the decontamination processes used, the multi-remediation approach could be an effective solution for the decontamination of mine tailings effluent. (au)

  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. 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

  15. 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

  16. 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

  17. Integrated chemical and biological analysis to explain estrogenic potency in bile extracts of red mullet (Mullus barbatus)

    International Nuclear Information System (INIS)

    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

  18. 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.

  19. 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.

  20. Biological evaluation of a technetium-99m-labeled integrated tropane-BAT and its piperidine congener as potential dopamine transporter imaging agents

    Energy Technology Data Exchange (ETDEWEB)

    Kieffer, Davy M. [Laboratory of Radiopharmaceutical Chemistry, University of Leuven, UZ Gasthuisberg, B-3000 Leuven (Belgium); Vanbilloen, Hubert P. [Radiopharmacy, UZ Gasthuisberg, B-3000 Leuven (Belgium); Cleynhens, Bernard J. [Radiopharmacy, UZ Gasthuisberg, B-3000 Leuven (Belgium); Terwinghe, Christelle Y. [Radiopharmacy, UZ Gasthuisberg, B-3000 Leuven (Belgium); Mortelmans, Luc [Nuclear Medicine, UZ Gasthuisberg, B-3000 Leuven (Belgium); Bormans, Guy M. [Laboratory of Radiopharmaceutical Chemistry, University of Leuven, UZ Gasthuisberg, B-3000 Leuven (Belgium); Verbruggen, Alfons M. [Laboratory of Radiopharmaceutical Chemistry, University of Leuven, UZ Gasthuisberg, B-3000 Leuven (Belgium)]. E-mail: alfons.verbruggen@uz.kuleuven.ac.be

    2006-01-15

    Introduction: Recently, we have reported modification of {sup 99m}Tc-TRODAT-1 by integrating the N2S2 metal chelating unit and the tropane skeleton. Results of a preliminary biodistribution study in rats were promising with respect to brain uptake. The present report deals with the further biological characterization of the {sup 99m}Tc-labelled integrated TRODAT derivatives ({sup 99m}Tc-TropaBAT and {sup 99m}Tc-norchloro-TropaBAT) and with the synthesis and biological evaluation of a novel {sup 99m}Tc-labelled piperidine-based derivative ({sup 99m}Tc-PipBAT). Methods: Biodistribution of all radiolabelled complexes was studied in normal mice. A more detailed ex vivo intracerebral distribution study of the two {sup 99m}Tc-TropaBAT complexes was additionally performed in normal rats. Autoradiography of brain sections of normal mice (with or without pretreatment with FP-{beta}-CIT or haloperidol) and rats was performed. Affinity for the dopamine transporter (DAT) was also assessed in vitro in the presence or absence of cocaine. Results: Both {sup 99m}Tc-TropaBAT complexes show a slightly higher brain uptake than {sup 99m}Tc-TRODAT-1, but the striatum/cerebellum activity ratio is less favourable. Nevertheless, significant striatal uptake was detected after ex vivo autoradiography, but this uptake was also observed after pretreatment with FP-{beta}-CIT. Unexpectedly, no striatal uptake was detected after in vitro incubation of mouse brain sections with the tracer agents. For {sup 99m}Tc-PipBAT, neither brain uptake nor in vitro striatal uptake was found. Conclusion: Both {sup 99m}Tc-TropaBAT complexes exhibit similar diffusion into brain as {sup 99m}Tc-TRODAT-1, and ex vivo autoradiography shows significant striatal uptake. However, the inferior striatum/cerebellum activity ratio, the striatal uptake in mice pretreated with FP-{beta}-CIT or haloperidol, and the lack of striatal uptake during in vitro incubation prove that the DAT is not targeted. Brain uptake disappears

  1. How to integrate geology, biology, and modern wireless technologies to assess biotic-abiotic interactions on coastal dune systems: a new multidisciplinary approach

    Science.gov (United States)

    Sarti, Giovanni; Bertoni, Duccio; Bini, Monica; Ciccarelli, Daniela; Ribolini, Adriano; Ruocco, Matteo; Pozzebon, Alessandro; Alquini, Fernanda; Giaccari, Riccardo; Tordella, Stefano

    2014-05-01

    Coastal dune systems are arguably one of the most dynamic environments because their evolution is controlled by many factors, both natural and human-related. Hence, they are often exposed to processes leading to erosion, which in turn determine serious naturalistic and economic losses. Most recent studies carried out on different dune fields worldwide emphasized the notion that a better definition of this environment needs an approach that systematically involves several disciplines, striving to merge every data collected from any individual analyses. Therefore, a new multidisciplinary method to study coastal dune systems has been conceived in order to integrate geology, biology, and modern wireless technologies. The aim of the work is threefold: i) to check the reliability of this new approach; ii) to provide a dataset as complete as ever about the factors affecting the evolution of coastal dunes; and iii) to evaluate the influence of any biotic and abiotic factors on plant communities. The experimentation site is located along the Pisa coast within the Migliarino - S. Rossore - Massaciuccoli Regional Park, a protected area where human influence is low (Tuscany, Italy). A rectangle of 100 x 200 m containing 50 grids of 20 x 20 m was established along the coastal dune systems from the coastline to the pinewood at the landward end of the backdune area. Sampling from each grid determined grain-size analysis carried out on surface sediment samples such as geologic aspects; topographic surveys performed by means of DGPS-RTK instruments; geophysical surveys conducted with a GPR equipment, which will be matched with core drilling activities; digital image analysis of high definition pictures taken by means of a remote controlled aircraft drone flying over the study area; biological data obtained by percent cover of each vascular plant species recorded in the sampling unit. Along with geologic and biologic methodologies, this research implemented the use of informatics

  2. Feasibility of integrating radiation-induced F1 sterility and biological control for population suppression of the pink bollworm, Pectinophora gossypiella, in Pakistan

    International Nuclear Information System (INIS)

    Substitution of casein and wheat germ with locally available ingredients (chickpea flour, soybean flour, wheat husk and sawdust) in the specified casein-wheat germ diet affected various biological parameters of pink bollworm (PBW), Pectinophora gossypiella. The diet containing chickpea flour performed significantly better and is more economical than the other diets tested. The highest PBW field populations were recorded in the month of October when large numbers of fruiting bodies were present in the cotton. Field behavioural observations revealed that mating and other sexual activities of treated and native moths varied significantly with time of night and peak activity was during 03:00-04:00 hours. Male moths treated with 100 Gy as mature pupae responded well to gossyplure baited traps. The attraction of male moths to irradiated virgin females decreased significantly with increasing doses of radiation. Male moths responded more readily to virgin untreated females than to irradiated females. Field-cage studies demonstrated that irradiated moths (100 Gy) released at a 50:1 treated to normal ratio at three week intervals reduced larval infestations inside the cages to subeconomic level. Studies suggested that there is a great potential for integrating the egg parasitoid, Trichogramma chilonis, with the sterile insect technique to control cotton bollworms. (author)

  3. 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.

  4. Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck).

    Science.gov (United States)

    Huang, Dingquan; Zhao, Yihong; Cao, Minghao; Qiao, Liang; Zheng, Zhi-Liang

    2016-01-01

    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 AHA10), 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. PMID:27092171

  5. 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

    2016-05-01

    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. PMID:26855186

  6. Integrative Biological Analysis For Neuropsychopharmacology

    OpenAIRE

    Emmett, Mark R.; Kroes, Roger A; Moskal, Joseph R.; Conrad, Charles A.; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L.

    2013-01-01

    Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain ...

  7. Integrating phosphoproteomics in systems biology

    OpenAIRE

    Yu Liu; Chance, Mark R.

    2014-01-01

    Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundam...

  8. 2K09 and Thereafter : The Coming Era of Integrative Bioinformatics, Systems Biology and Intelligent Computing for Functional Genomics and Personalized Medicine Research

    OpenAIRE

    2010-01-01

    Abstract 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 Co...

  9. 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.

  10. 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. PMID:26152902

  11. Biological Threats

    Science.gov (United States)

    ... Workplace Plans School Emergency Plans Main Content Biological Threats Biological agents are organisms or toxins that can ... for Disease Control and Prevention . Before a Biological Threat Unlike an explosion, a biological attack may or ...

  12. The ESF Programme on Functional Genomics Workshop on ‘Data Integration in Functional Genomics: Application to Biological Pathways’

    Directory of Open Access Journals (Sweden)

    Paul van der Vet

    2006-04-01

    Full Text Available We report from the second ESF Programme on Functional Genomics workshop on Data Integration, which covered topics including the status of biological pathways databases in existing consortia; pathways as part of bioinformatics infrastructures; design, creation and formalization of biological pathways databases; generating and supporting pathway data and interoperability of databases with other external databases and standards. Key issues emerging from the discussions were the need for continued funding to cover maintenance and curation of databases, the importance of quality control of the data in these resources, and efforts to facilitate the exchange of data and to ensure the interoperability of databases.

  13. 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...

  14. 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

  15. Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology

    OpenAIRE

    Leuba, Sanford H.; Carney, Sean M; Dahlburg, Elizabeth M; Eells, Rebecca J; Ghodke, Harshad; Yanamala, Naveena; Schauer, Grant; Klein-Seetharaman, Judith

    2014-01-01

    Background A key challenge in interdisciplinary research is choosing the best approach from a large number of techniques derived from different disciplines and their interfaces. Results To address this challenge in the area of Biophysics and Structural Biology, we have designed a graduate level course to teach students insightful use of experimental biophysical approaches in relationship to addressing biological questions related to biomolecular interactions and dynamics. A weekly seminar and...

  16. 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...

  17. 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."

  18. BiologicalNetworks: visualization and analysis tool for systems biology

    OpenAIRE

    Baitaluk, Michael; Sedova, Mayya; Ray, Animesh; Gupta, Amarnath

    2006-01-01

    Systems level investigation of genomic scale information requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properties of genes or other database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes. Towards that goal, we recently constructed PathSys, a data integration platform for systems biology, which provides dynamic integration over a diverse set of dat...

  19. A Usages of Herb Extracts by Stream Integrated with Micro-organism to Control Insect Pests and Phytophagus Mites by Biological Control

    International Nuclear Information System (INIS)

    A usages of herb extracts by stream integrated rith micro-organism to control insect pests and phytophagus mites by biological control was compared with insecticide to investigate the responses of chili tree and kieffer lime tree. Moreover, herb extracts were tested in controlling insect pests. Herb extracts were selected from many effective kinds such as: Azadirachta indica, Hyptis suaveolens, Citronella grass, Eucalyptus, Stemona, Galangal, Zingiber, cassumunar Roxb. Chronmolaena oderatum, Derris elyptica, Ginger, Annona seed, Malueraca sp., Andrographis paniculata, Veronia aquarrosa, Garlic, Thevetia peruviana, and Tobacco. The experiment was set at Herb Laboratory Ayutthaya Campus, Rajamangala University of Technology, Suvarnabhumi during August 2004 to June 2006. From testing herb extracts at 100 ppm. On Chili germination, the result was that the Chromolaena extracts made highest germination of 69.50%, Citronella grass at 500 ppm., made highest germination of chili seed at 86.00% within 12 days. Garlic extracts could kill 75.90% of aphids in 24 hrs., maximized in this experiments. Malueraca extracts at 500 ppm. Could kill 92.65% of chili aphids similar to the activity of insecticides action in 24 hrs. However at 5,000 ppm. It found that chemical treatment gave difference results from herbal treatments. Annona extracts could kill 64.58% of chili aphids better that others treatments. There are 18 treatment of time at 6 hrs. , 15 hrs., and 24 hrs., respectively. The results found that at 6 hrs., Kelthane could kill 93.75% of red spider mite. At 15 hrs. Stemona could kill 95.50% of red spider mite. At 24 hrs. Stemona or Chromolaena could kill 100% of red spider mite equally, Chrolaena could kill more than 83% of chili thrips at 24 hrs. Annona extracts could harvest the maximum of fruit fresh weight and numbers of fruits. After cutting leaves for producing new leaves, spraying herbal extracts was not different in statistic; however, Eucalyptus extracts, Neem plus

  20. 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...

  1. Multidisciplinary Assessment and Treatment of Self-Injurious Behavior in Autism Spectrum Disorder and Intellectual Disability: Integration of Psychological and Biological Theory and Approach

    Science.gov (United States)

    Minshawi, Noha F.; Hurwitz, Sarah; Morriss, Danielle; McDougle, Christopher J.

    2015-01-01

    The objective of this review is to consider the psychological (largely behavioral) and biological [neurochemical, medical (including genetic), and pharmacological] theories and approaches that contribute to current thinking about the etiology and treatment of self-injurious behavior (SIB) in individuals with autism spectrum disorder and/or…

  2. 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...

  3. 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.

  4. 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.

  5. 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. PMID:21903154

  6. The Role of Biology in Environmental Education

    Science.gov (United States)

    Xingcun, Lu

    2004-01-01

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

  7. Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control

    OpenAIRE

    Krug, Patrick J.; Vendetti, Jann E.; Rodriguez, Albert K.; Retana, Jennifer N.; Hirano, Yayoi M.; Trowbridge, Cynthia D.

    2013-01-01

    DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discover...

  8. The PlaNet Consortium: A Network of European Plant Databases Connecting Plant Genome Data in an Integrated Biological Knowledge Resource

    OpenAIRE

    Schoof, H.; Ernst, R; Mayer, K.F.X.

    2004-01-01

    The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort amo...

  9. 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.

  10. BIOZON: a hub of heterogeneous biological data

    OpenAIRE

    Birkland, Aaron; Yona, Golan

    2005-01-01

    Biological entities are strongly related and mutually dependent on each other. Therefore, there is a growing need to corroborate and integrate data from different resources and aspects of biological systems in order to analyze them effectively. Biozon is a unified biological database that integrates heterogeneous data types such as proteins, structures, domain families, protein–protein interactions and cellular pathways, and establishes the relationships between them. All data are integrated ...

  11. Answering biological questions: querying a systems biology database for nutrigenomics

    OpenAIRE

    Evelo, Chris T.; van Bochove, Kees; Saito, Jahn-Takeshi

    2010-01-01

    The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A particularly urgent objective in coping with the data avalanche is making biologically meaningful information accessible to the researcher. This contribution describes how we intend to meet this objective ...

  12. Teaching evolutionary biology

    Directory of Open Access Journals (Sweden)

    Tidon Rosana

    2004-01-01

    Full Text Available Evolutionary Biology integrates several disciplines of Biology in a complex and interactive manner, where a deep understanding of the subject demands knowledge in diverse areas. Since this knowledge is often inaccessible to the majority of specialized professionals, including the teachers, we present some reflections in order to stimulate discussions aimed at the improvement of the conditions of education in this area. We examine the profile of evolutionary teaching in Brazil, based on questionnaires distributed to teachers in Secondary Education in the Federal District, on data provided by the "National Institute for Educational Studies and Research", and on information collected from teachers working in various regions of this country. Issues related to biological misconceptions, curriculum and didactic material are discussed, and some proposals are presented with the objective of aiding discussions aimed at the improvement of the teaching of evolutionary biology.

  13. Integrated analysis of noncoding RNAs and mRNAs reveals their potential roles in the biological activities of the growth hormone receptor.

    Science.gov (United States)

    Chang, Lei; Qi, Haolong; Xiao, Yusha; Li, Changsheng; Wang, Yitao; Guo, Tao; Liu, Zhisu; Liu, Quanyan

    2016-08-01

    Accumulating evidence has indicated that noncoding RNAs (ncRNAs) have important regulatory potential in various biological processes. The molecular mechanisms by which growth hormone receptor (GHR) deficiency protects against age-related pathologies, reduces the incidence and delays the occurrence of fatal neoplasms are unclear. The aim of this study was to investigate miRNA, lncRNA and mRNA expression profiles and the potential functional roles of these RNA molecules in GHR knockout (GHR-KO) mice. Microarray expression profiles of miRNAs, lncRNAs and mRNAs were determined in wild type control mice and in GHR-KO mice. Differential expression, pathway and gene network analyses were developed to identify the possible biological roles of functional RNA molecules. Compared to wild type control mice, 1695 lncRNAs, 914 mRNAs and 9 miRNAs were upregulated and 1747 lncRNAs, 786 mRNAs and 21 miRNAs were downregulated in female GHR-KO mice. Moreover, 1265 lncRNAs, 724 mRNAs and 41 miRNAs were upregulated and 1377 lncRNAs, 765 mRNAs and 16 miRNAs were downregulated in male GHR-KO mice compared to wild type mice. Co-expression analysis of mRNAs, lncRNAs, and miRNAs showed that mRNAs including Hemxi2, Ero1Ib, 4933434i20RIK, Pde7a and Lgals1, lncRNAs including ASMM9PARTA014848, EL605414-P1, ASMM9PARTA051724, ASMM9PARTA045378 and ASMM9PARTA049185, and miRNAs including miR-188-3p, miR-690, miR-709 and miR-710 are situated at the core position of a three-dimensional lncRNA-mRNA-miRNA regulatory network. KEGG analysis showed that the most significantly regulated pathway was steroid hormone biosynthesis. We identified a set of lncRNAs, miRNAs and mRNAs that were aberrantly expressed in GHR-KO mice. Our results provide a foundation and an expansive view of the biological activities of the GHR. PMID:27064376

  14. An integrated model for interaction of electromagnetic fields with biological systems; Un modello integrato per l'interazione dei campi elettromagnetici con i sistemi biologici

    Energy Technology Data Exchange (ETDEWEB)

    Apollonio, F.; Liberti, M.; Cavagnaro, M.; D' Inzeo, G. [Rome Univ. (Italy). Dipt. di Ingegneria Elettronica; Tarricone, L. [Perugia Univ. (Italy). Dipt. di Ingegneria Elettronica e dell' Informazione

    1999-08-01

    In this work is described a methodology for evaluation of interaction of high frequency electromagnetic field. Biological systems via connection of many macroscopic models. In particular the analysis of neuronal membrane exposed to electromagnetic fields. [Italian] In questo lavoro viene descritta una metologia per affrontare lo studio dei meccanismi di interazione dei campi elettromagnetici ad alta frequenza con i sistemi biologici tramite la connessione di diversi modelli microscopici. In particolare si presenta una metodologia integrata di analisi di una membrana neuronale esposta a campi elettromagnetici. Questa metodologia prevede piu' passi: la valutazione della distribuzione di campo elettromagnetico nella cellula, l'analisi, tramite modelli stocastici, dell'attivita' dei canali proteici in condizione di esposizione, l'analisi del comportamento della tensione transmembranale attraverso un modello dell'intera membrana.

  15. Modeling formalisms in Systems Biology

    OpenAIRE

    Machado, C. D.; Costa, Rafael S.; Rocha, Miguel; Ferreira, E. C.; Tidor, Bruce; Rocha, I.

    2011-01-01

    Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological proc...

  16. 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…

  17. 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.

  18. 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.

  19. Biology Notes.

    Science.gov (United States)

    School Science Review, 1982

    1982-01-01

    Presents procedures, exercises, demonstrations, and information on a variety of biology topics including labeling systems, biological indicators of stream pollution, growth of lichens, reproductive capacity of bulbous buttercups, a straw balance to measure transpiration, interaction of fungi, osmosis, and nitrogen fixation and crop production. (DC)

  20. Amylase and blood cell-count hematological radiation-injury biomarkers in a rhesus monkey radiation model-use of multiparameter and integrated biological dosimetry

    International Nuclear Information System (INIS)

    Effective medical management of suspected radiation exposure incidents requires the recording of dynamic medical data (clinical signs and symptoms), biological assessments of radiation exposure, and physical dosimetry in order to provide diagnostic information to the treating physician and dose assessment for personnel radiation protection records. The need to rapidly assess radiation dose in mass-casualty and population-monitoring scenarios prompted an evaluation of suitable biomarkers that can provide early diagnostic information after exposure. We investigated the utility of serum amylase and hematological blood-cell count biomarkers to provide early assessment of severe radiation exposures in a non-human primate model (i.e., rhesus macaques; n=8) exposed to whole-body radiation of 60Co-gamma rays (6.5 Gy, 40cGymin-1). Serum amylase activity was significantly elevated (12.3±3.27- and 2.6±0.058-fold of day zero samples) at 1 and 2-days, respectively, after radiation. Lymphocyte cell counts decreased (≤15% of day zero samples) 1 and 2 days after radiation exposure. Neutrophil cell counts increased at day one by 1.9(±0.38)-fold compared with levels before irradiation. The ratios of neutrophil to lymphocyte cell counts increased by 13(±2.66)- and 4.23(±0.95)-fold at 1 and 2 days, respectively, after irradiation. These results demonstrate that increases in serum amylase activity along with decreases of lymphocyte counts, increases in neutrophil cell counts, and increases in the ratio of neutrophil to lymphocyte counts 1 day after irradiation can provide enhanced early triage discrimination of individuals with severe radiation exposure and injury. Use of the biodosimetry assessment tool (BAT) application is encouraged to permit dynamic recording of medical data in the management of a suspected radiological casualty

  1. 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. PMID:27568982

  2. Integrating geochemical (surface waters, stream sediments) and biological (diatoms) approaches to assess AMD environmental impact in a pyritic mining area: Aljustrel (Alentejo, Portugal).

    Science.gov (United States)

    Luís, Ana Teresa; Durães, Nuno; de Almeida, Salomé Fernandes Pinheiro; da Silva, Eduardo Ferreira

    2016-04-01

    Aljustrel mines were classified as having high environmental hazard due to their large tailings volume and high metal concentrations in waters and sediments. To assess acid mine drainage impacted systems whose environmental conditions change quickly, the use of biological indicators with short generation time such as diatoms is advantageous. This study combined geochemical and diatom data, whose results were highlighted in 3 groups: Group 1, with low pH (1.9-5.1) and high metal/metalloid (Al, As, Cd, Co, Cu, Fe, Mn, Ni, Pb, Zn; 0.65-1032mg/L) and SO4 (405-39124mg/L) concentrations. An acidophilic species, Pinnularia aljustrelica, was perfectly adapted to the adverse conditions; in contrast, teratological forms of Eunotia exigua were found, showing that metal toxicity affected this species. The low availability of metals/metalloids in sediments of this group indicates that metals/metalloids of the exchangeable fractions had been solubilized, which in fact enables metal/metalloid diatom uptake and consequently the occurrence of teratologies; Group 2, with sites of near neutral pH (5.0-6.8) and intermediate metal/metalloid (0.002-6mg/L) and SO4 (302-2179mg/L) concentrations; this enabled the existence of typical species of uncontaminated streams (Brachysira neglectissima, Achnanthidium minutissimum); Group 3, with samples from unimpacted sites, showing low metal/metalloid (0-0.8mg/L) and SO4 (10-315mg/L) concentrations, high pH (7.0-8.4) and Cl contents (10-2119mg/L) and the presence of brackish to marine species (Entomoneis paludosa). For similar conditions of acidity, differences in diversity, abundance and teratologies of diatoms can be explained by the levels of metals/metalloids. PMID:27090714

  3. 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

    2015-01-01

    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. PMID:26560501

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

    Science.gov (United States)

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

    2016-09-01

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

  5. 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. PMID:25099630

  6. 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.

  7. Using the Biodatamation(TM) strategy to learn introductory college biology: Value-added effects on selected students' conceptual understanding and conceptual integration of the processes of photosynthesis and cellular respiration

    Science.gov (United States)

    Reuter, Jewel Jurovich

    The purpose of this exploratory research was to study how students learn photosynthesis and cellular respiration and to determine the value added to the student's learning by each of the three technology-scaffolded learning strategy components (animated concept presentations and WebQuest-style activities, data collection, and student-constructed animations) of the BioDatamation(TM) (BDM) Program. BDM learning strategies utilized the Theory of Interacting Visual Fields(TM) (TIVF) (Reuter & Wandersee, 2002a, 2002b; 2003a, 2003b) which holds that meaningful knowledge is hierarchically constructed using the past, present, and future visual fields, with visual metacognitive components that are derived from the principles of Visual Behavior (Jones, 1995), Human Constructivist Theory (Mintzes & Wandersee, 1998a), and Visual Information Design Theory (Tufte, 1990, 1997, 2001). Student alternative conceptions of photosynthesis and cellular respiration were determined by the item analysis of 263,267 Biology Advanced Placement Examinations and were used to develop the BDM instructional strategy and interview questions. The subjects were 24 undergraduate students of high and low biology prior knowledge enrolled in an introductory-level General Biology course at a major research university in the Deep South. Fifteen participants received BDM instruction which included original and innovative learning materials and laboratories in 6 phases; 8 of the 15 participants were the subject of in depth, extended individual analysis. The other 9 participants received traditional, non-BDM instruction. Interviews which included participants' creation of concept maps and visual field diagrams were conducted after each phase. Various content analyses, including Chi's Verbal Analysis and quantitizing/qualitizing were used for data analysis. The total value added to integrative knowledge during BDM instruction with the three visual fields was an average increase of 56% for cellular respiration

  8. 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.

  9. Quantum Biology

    CERN Document Server

    Sergi, Alessandro

    2009-01-01

    A critical assessment of the recent developments of molecular biology is presented. The thesis that they do not lead to a conceptual understanding of life and biological systems is defended. Maturana and Varela's concept of autopoiesis is briefly sketched and its logical circularity avoided by postulating the existence of underlying {\\it 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 interpretation of quantum dispersion forces (van der Waals, hydrogen bonding, and so on) as quantum coherence effects hints at the necessity of including long-ranged forces (or mechanisms for them) in condensed matter theories of biological processes. Some quantum effects in biology are reviewed and quantum mechanics is acknowledge...

  10. Bridging the gap between systems biology and synthetic biology

    Directory of Open Access Journals (Sweden)

    FuzhongZhang

    2013-07-01

    Full Text Available 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.

  11. Biological Oceanography

    Science.gov (United States)

    Abbott, M. R.

    1984-01-01

    Within the framework of global biogeochemical cycles and ocean productivity, there are two areas that will be of particular interest to biological oceanography in the 1990s. The first is the mapping in space time of the biomass and productivity of phytoplankton in the world ocean. The second area is the coupling of biological and physical processes as it affects the distribution and growth rate of phytoplankton biomass. Certainly other areas will be of interest to biological oceanographers, but these two areas are amenable to observations from satellites. Temporal and spatial variability is a regular feature of marine ecosystems. The temporal and spatial variability of phytoplankton biomass and productivity which is ubiquitous at all time and space scales in the ocean must be characterized. Remote sensing from satellites addresses these problems with global observations of mesocale (2 to 20 days, 10 to 200 km) features over a long period of time.

  12. 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)

  13. Biology Notes.

    Science.gov (United States)

    School Science Review, 1983

    1983-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including water relation exercise on auxin-treated artichoke tuber tissue; aerobic respiration in yeast; an improved potometer; use of mobiles in biological classification, and experiments on powdery mildews and banana polyphenol oxidase. Includes reading lists…

  14. 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......-ulose dehydratase from the wood-decay fungus Phanerochaete chrysosporium BKM-F-1767. This enzymatically derived cortalcerone is converted in one pot to FA in a methanol/water solvent over an Al-containing Sn-beta zeolite possessing both Bronsted and Lewis acid sites, achieving 42% selectivity to FA at...

  15. 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

  16. Integrative computational biology for cancer research

    OpenAIRE

    Fortney, Kristen; Jurisica, Igor

    2011-01-01

    Over the past two decades, high-throughput (HTP) technologies such as microarrays and mass spectrometry have fundamentally changed clinical cancer research. They have revealed novel molecular markers of cancer subtypes, metastasis, and drug sensitivity and resistance. Some have been translated into the clinic as tools for early disease diagnosis, prognosis, and individualized treatment and response monitoring. Despite these successes, many challenges remain: HTP platforms are often noisy and ...

  17. Integrative systems biology approaches in asthma pharmacogenomics

    OpenAIRE

    Dahlin, Amber; Tantisira, Kelan G.

    2012-01-01

    In order to improve therapeutic outcomes, there is a tremendous need to identify patients who are likely to respond to a given asthma treatment. Pharmacogenomic studies have explained a portion of the variability in drug response and provided an increasing list of candidate genes and SNPs. However, as phenotypic variation arises from a network of complex interactions among genetic and environmental factors, rather than individual genes or SNPs, a multidisciplinary, systems-level approach is r...

  18. FORGETFULNESS DURING AGING: AN INTEGRATED BIOLOGY

    OpenAIRE

    Gold, Paul E.; Korol, Donna L.

    2014-01-01

    Age-related impairments in memory are often attributed to failures, at either systems or molecular levels, of memory storage processes. A major characteristic of changes in memory with increasing age is the advent of forgetfulness in old vs. young animals. This review examines the contribution of a dysfunction of the mechanisms responsible for modulating the maintenance of memory in aged rats. A memory-modulating system that includes epinephrine, acting through release of glucose from liver g...

  19. 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.

  20. Biological programming

    OpenAIRE

    Ramsden, Jeremy J.; Bándi, Gergely

    2010-01-01

    Biology offers a tremendous set of concepts that are potentially very powerfully usable for the software engineer, but they have been barely exploited hitherto. In this position paper we propose a fresh attempt to create the building blocks of a programming technology that could be as successful as life. A key guiding principle is to develop and make use of unambiguous definitions of the essential features of life.

  1. Biological radioprotector

    International Nuclear Information System (INIS)

    According to the patent description, the biological radioprotector is deuterium depleted water, DDW, produced by vacuum distillation with an isotopic content lower than natural value. It appears as such or in a mixture with natural water and carbon dioxide. It can be used for preventing and reducing the ionizing radiation effects upon humans or animal organisms, exposed therapeutically, professionally or accidentally to radiation. The most significant advantage of using DDW as biological radioprotector results from its way of administration. Indeed no one of the radioprotectors currently used today can be orally administrated, what reduces the patients' compliance to prophylactic administrations. The biological radioprotector is an unnoxious product obtained from natural water, which can be administrated as food additive instead of drinking water. Dose modification factor is according to initial estimates around 1.9, what is a remarkable feature when one takes into account that the product is toxicity-free and side effect-free and can be administrated prophylactically as a food additive. A net radioprotective action of the deuterium depletion was evidenced experimentally in laboratory animals (rats) hydrated with DDW of 30 ppm D/(D+H) concentration as compared with normally hydrated control animals. Knowing the effects of irradiation and mechanisms of the acute radiation disease as well as the effects of administration of radiomimetic chemicals upon cellular lines of fast cell division, it appears that the effects of administrating DDW result from stimulation of the immunity system. In conclusion, the biological radioprotector DDW presents the following advantages: - it is obtained from natural products without toxicity; - it is easy to be administrated as a food additive, replacing the drinking water; - besides radioprotective effects, the product has also immunostimulative and antitumoral effects

  2. Marine biology

    International Nuclear Information System (INIS)

    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

  3. 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.

  4. 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…

  5. 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....

  6. 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.

  7. 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)

  8. 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.

  9. 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.

  10. Biological effects

    International Nuclear Information System (INIS)

    Following an introduction into the field of cellular radiation effect considering the most important experimental results, the biological significance of the colony formation ability is brought out. The inactivation concept of stem cells does not only prove to be good, according to the present results, in the interpretation of the pathogenesis of acute radiation effects on moult tissue, it also enables chronicle radiation injuries to be interpreted through changes in the fibrous part of the organs. Radiation therapy of tumours can also be explained to a large extent by the radiation effect on the unlimited reproductiveness of tumour cells. The more or less similar dose effect curves for healthy and tumour tissue in practice lead to intermittent irradiation. The dependence of the intermittent doses and intervals on factors such as Elkind recovery, synchronisation, redistribution, reoxygenation, repopulation and regeneration are reviewed. (ORU/LH)

  11. The relativity of biological function.

    Science.gov (United States)

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

    2015-12-01

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

  12. Creating biological nanomaterials using synthetic biology

    International Nuclear Information System (INIS)

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

  13. Creating biological nanomaterials using synthetic biology

    Directory of Open Access Journals (Sweden)

    MaryJoe K Rice

    2014-01-01

    Full Text Available Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  14. 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…

  15. 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…

  16. 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 ...

  17. 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…

  18. 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.

  19. Integrative metabolic engineering

    Directory of Open Access Journals (Sweden)

    George H McArthur IV

    2015-07-01

    Full Text Available Recent advances in experimental and computational synthetic biology are extremely useful for achieving metabolic engineering objectives. The integration of synthetic biology and metabolic engineering within an iterative design-build-test framework will improve the practice of metabolic engineering by relying more on efficient design strategies. Computational tools that aid in the design and in silico simulation of metabolic pathways are especially useful. However, software helpful for constructing, implementing, measuring and characterizing engineered pathways and networks should not be overlooked. In this review, we highlight computational synthetic biology tools relevant to metabolic engineering, organized in the context of the design-build-test cycle.

  20. Study on Biological Phosphorus Removal in Improved Integrated Alternative Reactor%改良型一体化交替反应池工艺的生物除磷研究

    Institute of Scientific and Technical Information of China (English)

    吴魏刚

    2011-01-01

    Improved integrated alternative reactor combines A2/O process and SBR process, and achieves good nitrogen and phosphorus removal with compact structure arrangement and low running costs. Combined with the production operation of Loujiang WWTP in Suzhou, the operation conditions of the reactor for achieving good phosphorus removal were investigated. The results show that adequate nitrate nitrogen to provide electron acceptors for DPBs is crucial to improve denitrifying phosphorus removal efficiency. At the same time, COD/TP ratio in influent, DO in aerobic tank, MLSS and SRT are main factors affecting biological phosphorus removal. In addition, for non-ideal phosphorus removal efficiency due to low-load operation in rainy season, the corresponding measures are proposed, namely reducing aeration rate, decreasing recycle ratio from aerobic tank to anoxic tank or adding flocculants for chemical phosphorus removal.%改良型一体化交替反应池结合了A2/O工艺和SBR法的特点,构筑物布置紧凑,运行成本较低,同时又实现了良好的脱氮除磷性能.结合苏州娄江污水处理厂的生产运行,研究了改良型一体化交替反应池实现良好除磷效果的运行工况.结果表明,提高反硝化除磷效果的关键是要有充足的硝态氮为DPB提供电子受体;同时,进水COD/TP值、好氧池DO、MLSS以及SRT也是影响生物除磷效果的重要因素.此外,针对雨季低负荷运行时除磷效果不理想的现象提出了相关措施,即降低曝气量、减少好氧边池至缺氧池的回流比,或投加混凝剂进行化学除磷.

  1. Creating biological nanomaterials using synthetic biology

    OpenAIRE

    MaryJoe K Rice; Ruder, Warren C.

    2014-01-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic bi...

  2. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-06-01

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

  3. 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

  4. Platelets in Lung Biology

    Science.gov (United States)

    Weyrich, Andrew S.; Zimmerman, Guy A.

    2013-01-01

    Platelets and the lungs have an intimate relationship. Platelets are anucleate mammalian blood cells that continuously circulate through pulmonary vessels and that have major effector activities in hemostasis and inflammation. The lungs are reservoirs for megakaryocytes, the requisite precursor cell in thrombopoiesis, which is the intricate process by which platelets are generated. Platelets contribute to basal barrier integrity of the alveolar capillaries, which selectively restricts the transfer of water, proteins, and red blood cells out of the vessels. Platelets also contribute to pulmonary vascular repair. Although platelets bolster hemostatic and inflammatory defense of the healthy lung, experimental evidence and clinical evidence indicate that these blood cells are effectors of injury in a variety of pulmonary disorders and syndromes. Newly discovered biological capacities of platelets are being explored in the context of lung defense, disease, and remodeling. PMID:23043249

  5. 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.

  6. Biological effects of radiation

    International Nuclear Information System (INIS)

    This fourth chapter presents: cell structure and metabolism; radiation interaction with biological tissues; steps of the production of biological effect of radiation; radiosensitivity of tissues; classification of biological effects; reversibility, transmissivity and influence factors; pre-natal biological effects; biological effects in therapy and syndrome of acute irradiation

  7. 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.

  8. Towards a heterarchical approach to biology and cognition

    DEFF Research Database (Denmark)

    Bruni, Luis Emilio; Giorgi, Franco

    2015-01-01

    different scientific disciplines working towards a multilevel integrative perspective of biological and cognitive processes, such as systems and integrative biology and neuroscience, social and cultural neuroscience, social signal transduction and psychoneuroimmunology, for instance. We argue that...... structures and substrates are by necessity organized hierarchically, while communication processes – and their embeddedness – are rather organized heterarchically. Before getting into the implications of the heterarchical approach and its congeniality with the semiotic perspective to biology and cognition...... empirical systemic approaches to biology and integrative neuroscience, and conclude with a reflection on its implications to the understanding of the emergence of pathological conditions in multi-level semiotic systems....

  9. [Knowledgebases in postgenomic molecular biology].

    Science.gov (United States)

    Lisitsa, A V; Shilov, B V; Evdokimov, P A; Gusev, S A

    2010-01-01

    Knowledgebases can become an effective tool essentially raising quality of information retrieval in molecular biology, promoting the development of new methods of education and forecasting of the biomedical R&D. Knowledge-based technologies should induce "paradigm shift" in the life science due to integrative focusing of research groups towards the challenges of postgenomic era. This paper debates concept of the knowledgebase, which exploits web usage mining to personalize the access of molecular biologist to the Internet resources. PMID:21328913

  10. Lipidomics Investigations in Cell Biology

    OpenAIRE

    YU, Yang

    2014-01-01

    Cell membrane is the biological barrier serving as both territorial defense and the communication hinge for the interior of cell from its surroundings. As building blocks of cellular membranes and also precursor for second messengers, a variety of lipids play essential roles in cellular membrane dynamics as well as important functions such as cell proliferation, apoptosis, signal transduction and membrane trafficking modulation. Lipidomics, representing the systematic and integrative studies ...

  11. Biologically-inspired machine vision

    OpenAIRE

    Tsitiridis, A

    2013-01-01

    This thesis summarises research on the improved design, integration and expansion of past cortex-like computer vision models, following biologically-inspired methodologies. By adopting early theories and algorithms as a building block, particular interest has been shown for algorithmic parameterisation, feature extraction, invariance properties and classification. Overall, the major original contributions of this thesis have been: 1. The incorporation of a salient feature-based method for sem...

  12. 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...

  13. Teaching Systems Biology: An Active-Learning Approach

    Science.gov (United States)

    Kumar, Anuj

    2005-01-01

    With genomics well established in modern molecular biology, recent studies have sought to further the discipline by integrating complementary methodologies into a holistic depiction of the molecular mechanisms underpinning cell function. This genomic subdiscipline, loosely termed "systems biology," presents the biology educator with both…

  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. 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. PMID:12522106

  16. Mathematical models in biological discovery

    CERN Document Server

    Walter, Charles

    1977-01-01

    When I was asked to help organize an American Association for the Advancement of Science symposium about how mathematical models have con­ tributed to biology, I agreed immediately. The subject is of immense importance and wide-spread interest. However, too often it is discussed in biologically sterile environments by "mutual admiration society" groups of "theoreticians", many of whom have never seen, and most of whom have never done, an original scientific experiment with the biolog­ ical materials they attempt to describe in abstract (and often prejudiced) terms. The opportunity to address the topic during an annual meeting of the AAAS was irresistable. In order to try to maintain the integrity ;,f the original intent of the symposium, it was entitled, "Contributions of Mathematical Models to Biological Discovery". This symposium was organized by Daniel Solomon and myself, held during the 141st annual meeting of the AAAS in New York during January, 1975, sponsored by sections G and N (Biological and Medic...

  17. Microbial Degradation and Carbon Biosequestration Potential of Biochar in Contrasting Soils

    Science.gov (United States)

    Tas, N.; Castanha, C.; Reichl, K.; Fischer, M. L.; Brodie, E. L.; Torn, M. S.; Jansson, J. K.

    2012-12-01

    Biochar is a carbon-rich product that is produced by high-temperature and low-oxygen pyrolysis of biomass, whose addition to soil has been proposed as a promising method for carbon sequestration. Biochar carbon has been assumed to be stable in soil, but recent research shows that it is at least partly degradable by soil microbes. However, the influence of environmental conditions on microbial transformation of biochar is poorly understood. Our overall goal is to determine the factors that regulate microbial decomposition of biochar in soils. We performed laboratory incubation experiments to compare the potential for biochar decomposition in soils from contrasting ecosystems (tropical forest from Puerto Rico and Mediterranean grassland from California), varied temperatures (ambient and +6°C) and depths (A and B horizons). Soil incubations with pyrolyzed 13C-enriched wood were continuously monitored for heterotrophic respiration using an online Cavity Ringdown Spectrometer. Samples collected after 10 and 150 days of incubation were analyzed for the activity of extracellular enzymes while changes in microbial community composition were assessed via pyrotag sequencing of both 16S rRNA and 16S rRNA genes. 13C-CO2 measurements confirmed that a fraction of added biochar was degraded in both soils during the one-year incubation period. Biochar addition was associated with a decline in cellulose and hemicellulose degrading enzyme activity in grassland soils, although not in tropical soils. In both soils, native soil organic carbon decomposition was not significantly impacted by biochar addition. Principle coordinates analysis of microbial composition showed that both soils harbored different microbial communities and those communities at different depths were distinct. The main bacterial groups enriched by biochar addition were Actinobacteria in the grassland soil, and α-Proteobacteria, Actinobacteria and Acidobacteria in the tropical soil. Analysis of 16S rRNA transcripts showed that the most abundant microbes were also the most active and in both soils Actinobacterial activity was significantly influenced by biochar addition. In summary, the addition of biochar to both soils preferentially enhanced the growth and activity of several microbial groups with little impact on native organic carbon decomposition. Quantitative predictions of the stability of biochar in these soils will require an understanding of how the environment regulates metabolism of these bacterial groups. To this end we are currently using the isotopic label to trace biochar-derived metabolites into microbial cells and soil organic matter fractions.

  18. BIOLOGICAL NANOROBOT ARCHITECTURE FOR MEDICAL TARGET IDENTIFICATION

    Directory of Open Access Journals (Sweden)

    S. Paul and Dipti*

    2012-07-01

    Full Text Available This work has an innovative approach for the development of biological nanorobots with sensors for medicine. The biological nanorobots operate in a virtual environment based on random, thermal and chemical control techniques. The biological nanorobot architecture model has biological nano bioelectronics as the basis for manufacturing integrated system devices with embedded biological nano biosensors and actuators, which facilitates its application for medical target identification and drug delivery. The biological nanorobot interaction with the described workspace shows how these biological nanorobots detect the target area and supply the drug. Therefore, our work addresses the control and the architecture design for developing practical molecular machines. Advances in nanotechnology are enabling manufacturing nanosensors and actuators through nano bioelectronics and biologically inspired devices. Analysis of integrated system modeling is one important aspect for supporting nanotechnology in the fast development towards one of the most challenging new fields of science: molecular machines. The use of 3D simulation can provide interactive tools for addressing nanorobot choices on sensing, hardware architecture design, manufacturing approaches, and control methodology investigation.

  19. Systems biology driven software design for the research enterprise

    OpenAIRE

    Killcoyne Sarah; Cavnor Christopher; Boyle John; Shmulevich Ilya

    2008-01-01

    Abstract Background In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the...

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

    OpenAIRE

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

    2015-01-01

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

  1. Implementing Recommendations for Introductory Biology by Writing a New Textbook

    OpenAIRE

    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 ideas (information, evolution, cells, emergent properties, homeostasis), addressing each at five levels of organization (molecules, cells, organisms, popu...

  2. Integrated Documents

    OpenAIRE

    Sawitzki, Günther

    2000-01-01

    An introduction to integrated documents in statistics. Integrated documents allow a seamless integration of interactive statistics and data analysis components in 'life' documents while keeping the full computational power needed for simulation or resampling.

  3. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

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

  4. Shaping Biological Knowledge: Applications in Proteomics

    Directory of Open Access Journals (Sweden)

    R. Appel

    2006-04-01

    Full Text Available The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa and a hypothesis-driven (focus on whole bacterial proteomes approach. These applications are potentially the source of specialized complements to classical biological ontologies.

  5. Radiation induced sterility to control tsetse flies. The effect of ionising radiation and hybridisation on tsetse biology and the use of the sterile insect technique in integrated tsetse control.

    OpenAIRE

    Vreysen, M. J. B.

    1995-01-01

    The induction of dominant lethal mutations by exposing tsetse flies as pupae or adult insects to ionising radiation and the use of hybrid sterility resulting from crosses of closely related tsetse species or subspecies, are potential methods of genetic control of tsetse flies. In this thesis the effects of radiation and hybridisation on the reproductive biology and fitness of several species of tsetse flies has been examined. In addition, aspects of field releases of sterile insects have also...

  6. Computational Systems Chemical Biology

    OpenAIRE

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

    2011-01-01

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

  7. Pictures of Synthetic Biology

    OpenAIRE

    Cserer, Amelie; Seiringer, Alexandra

    2009-01-01

    This article is concerned with the representation of Synthetic Biology in the media and by biotechnology experts. An analysis was made of German-language media articles published between 2004 and 2008, and interviews with biotechnology-experts at the Synthetic Biology conference SB 3.0 in Zurich 2007. The results have been reflected in terms of the definition of Synthetic Biology, applications of Synthetic Biology and the perspectives of opportunities and risks. In the media, Synthetic Biolog...

  8. Opportunities for Merging Chemical and Biological Synthesis

    OpenAIRE

    Wallace, Stephen; Balskus, Emily P.

    2014-01-01

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

  9. Towards Systems Biology of Human Pulmonary Fibrosis

    OpenAIRE

    Studer, Sean M.; Kaminski, Naftali

    2007-01-01

    The integrated effect of multiple pathways, molecules, genetic polymorphisms, environmental stimuli, and possible infection determines the lung phenotype in idiopathic pulmonary fibrosis (IPF), a chronic progressive and often lethal lung disease. Systems biology approaches aim to provide a systemwide view of biological process using computational tools and high-throughput technologies. Although much of the analysis of genome-level transcriptional high-resolution profiles of IPF was reductioni...

  10. A Circular Bioeconomy with Biobased Products from CO2 Sequestration.

    Science.gov (United States)

    Venkata Mohan, S; Modestra, J Annie; Amulya, K; Butti, Sai Kishore; Velvizhi, G

    2016-06-01

    The unprecedented climate change influenced by elevated concentrations of CO2 has compelled the research world to focus on CO2 sequestration. Although existing natural and anthropogenic CO2 sinks have proven valuable, their ability to further assimilate CO2 is now questioned. Thus, we highlight here the importance of biological sequestration methods as alternate and viable routes for mitigating climate change while simultaneously synthesizing value-added products that could sustainably fuel the circular bioeconomy. Four conceptual models for CO2 biosequestration and the synthesis of biobased products, as well as an integrated CO2 biorefinery model, are proposed. Optimizing and implementing this biorefinery model might overcome the limitations of existing sequestration methods and could help realign the carbon balance. PMID:27048926

  11. The Current State and Perspectives of Systems Biology

    Institute of Scientific and Technical Information of China (English)

    Tielui Shi; Yixue Li

    2006-01-01

    Emerging as a new field in biology recently, Systems Biology provides a branch new way to study the biological activities in organisms. In order to decode the complexity of life systematically,systems biology integrates the "-omics" and uses the high throughput methods from transcriptomics,protomics and metabonomics to detect the dynamic activities in cell; and then, it incorporates bioinformatics methods to integrate and analyze those data, and simulate the biological processes based on the model built from those integrated data. In this paper, the current state, the research field and the methods for the Systems Biology are introduced briefly, and then, several ideas about future development in this field are also proposed.

  12. Grand challenges in migration biology.

    Science.gov (United States)

    Bowlin, Melissa S; Bisson, Isabelle-Anne; Shamoun-Baranes, Judy; Reichard, Jonathan D; Sapir, Nir; Marra, Peter P; Kunz, Thomas H; Wilcove, David S; Hedenström, Anders; Guglielmo, Christopher G; Åkesson, Susanne; Ramenofsky, Marilyn; Wikelski, Martin

    2010-09-01

    Billions of animals migrate each year. To successfully reach their destination, migrants must have evolved an appropriate genetic program and suitable developmental, morphological, physiological, biomechanical, behavioral, and life-history traits. Moreover, they must interact successfully with biotic and abiotic factors in their environment. Migration therefore provides an excellent model system in which to address several of the "grand challenges" in organismal biology. Previous research on migration, however, has often focused on a single aspect of the phenomenon, largely due to methodological, geographical, or financial constraints. Integrative migration biology asks 'big questions' such as how, when, where, and why animals migrate, which can be answered by examining the process from multiple ecological and evolutionary perspectives, incorporating multifaceted knowledge from various other scientific disciplines, and using new technologies and modeling approaches, all within the context of an annual cycle. Adopting an integrative research strategy will provide a better understanding of the interactions between biological levels of organization, of what role migrants play in disease transmission, and of how to conserve migrants and the habitats upon which they depend. PMID:21558203

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

    Science.gov (United States)

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

    2013-12-01

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

  14. BIOZON: a hub of heterogeneous biological data.

    Science.gov (United States)

    Birkland, Aaron; Yona, Golan

    2006-01-01

    Biological entities are strongly related and mutually dependent on each other. Therefore, there is a growing need to corroborate and integrate data from different resources and aspects of biological systems in order to analyze them effectively. Biozon is a unified biological database that integrates heterogeneous data types such as proteins, structures, domain families, protein-protein interactions and cellular pathways, and establishes the relationships between them. All data are integrated on to a single graph schema centered around the non-redundant set of biological objects that are shared by each source. This integration results in a highly connected graph structure that provides a more complete picture of the known context of a given object that cannot be determined from any one source. Currently, Biozon integrates roughly 2 million protein sequences, 42 million DNA or RNA sequences, 32,000 protein structures, 150,000 interactions and more from sources such as GenBank, UniProt, Protein Data Bank (PDB) and BIND. Biozon augments source data with locally derived data such as 5 billion pairwise protein alignments and 8 million structural alignments. The user may form complex cross-type queries on the graph structure, add similarity relations to form fuzzy queries and rank the results based on analysis of the edge structure similar to Google PageRank, online at Biozon.org. PMID:16381854

  15. Are we ready to move beyond the reductionist approach of classical synergy control?. 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)

    Lacquaniti, Francesco; Ivanenko, Yuri P.; Zago, Myrka

    2016-07-01

    Starting from the classical concepts introduced by Sherrington [1] and considerably elaborated by Bernstein [2], much has been learned about motor synergies in the last several years. The contributions of the group funded by the European project "The Hand Embodied" are remarkable in the field of biological and robotic control of the hand based on synergies, and they are reflected in this enjoyable review [3]. There, Santello et al. adopt Bernstein's definition of motor synergies as multiple elements working together towards a common goal, with the result that multiple degrees of freedom are controlled within a lower-dimensional space than the available number of dimensions.

  16. Biological imaging in radiation oncology

    Energy Technology Data Exchange (ETDEWEB)

    Grosu, A.L.; Wiedenmann, N.; Molls, M. [Klinik und Poliklinik fuer Strahlentherapie und Radiologische Onkologie Klinikum rechts der Isar, Technical Univ. of Munich (Germany)

    2005-07-01

    The goal of this study was to discuss the value of integrating biological imaging (PET, SPECT, MRS etc.) in radiation treatment planning and monitoring. Studies in patients with brain tumors have shown that, compared to CT and MRI alone, the image fusion of CT/MRI and amino acid SPECT or PET allows a more correct delineation of gross tumor volume (GTV) and planning target volume (PTV). For FDG-PET, comparable results with different techniques are reported in the literature also for bronchial carcinoma, ear-nose-and-throat tumors, and cervical carcinoma, or, in the case of MRS, for prostate cancer. Imaging of hypoxia, cell proliferation, apoptosis, tumor angiogenesis, and gene expression leads to the identification of differently aggressive areas of a biologically inhomogeneous tumor mass that can be individually and more appropriately targeted using innovative IMRT. Thus, a biological, inhomogeneous dose distribution can be generated, the so-called dose painting. In addition, the biological imaging can play a significant role in the evaluation of the therapy response after radiochemotherapy. Clinical studies in ear-nose-and-throat tumors, bronchial carcinoma, esophagus carcinoma, and cervical carcinoma suggest that the sensitivity and specificity of FDG-PET for the therapy response are higher compared to anatomical imaging (CT and MRI). Clinical and experimental studies are required to define the real impact of these investigations in radiation treatment planning, and especially in the evaluation of therapy response. (orig.)

  17. Integrated parasite management

    DEFF Research Database (Denmark)

    Clausen, Jesper Hedegaard; Madsen, Henry; Van, Phan Thi;

    2015-01-01

    Fishborne zoonotic trematodes (FZT) are an emerging problem and there is now a consensus that, in addition to wild-caught fish, fish produced in aquaculture present a major food safety risk, especially in Southeast Asia where aquaculture is important economically. Current control programs target ...... that target critical control points in the aquaculture production cycle identified from a thorough understanding of FZT and host biology and epidemiology. We present recommendations for an integrated parasite management (IPM) program for aquaculture farms....

  18. Infobiotics : computer-aided synthetic systems biology

    OpenAIRE

    Blakes, Jonathan

    2013-01-01

    Until very recently Systems Biology has, despite its stated goals, been too reductive in terms of the models being constructed and the methods used have been, on the one hand, unsuited for large scale adoption or integration of knowledge across scales, and on the other hand, too fragmented. The thesis of this dissertation is that better computational languages and seamlessly integrated tools are required by systems and synthetic biologists to enable them to meet the significant challenges inv...

  19. From ozone depletion to biological UV damage

    Energy Technology Data Exchange (ETDEWEB)

    Tamm, E.; Thomalla, E.; Koepke, P. [Munich Univ. (Germany). Meteorological Inst.

    1995-12-31

    Based on the ozone data from the Meteorological Observatory Hohenpeissenberg (MOHP: 47.8 deg N, 11.01 deg E) and corresponding mean atmospheric conditions, high resolution UV spectra are calculated with a complex radiation transfer model STAR. Biologically weighted UV spectra are investigated as integrated irradiances (dose rates) for maximum zenith angles and as daily integrals for selected days of the year. Ozone variation and uncertainty of action spectra are investigated

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

    Science.gov (United States)

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

    2016-01-01

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters. PMID:27311441