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Sample records for understand complex biological

  1. Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.

    Science.gov (United States)

    Kastrup, Christian J; Runyon, Matthew K; Lucchetta, Elena M; Price, Jessica M; Ismagilov, Rustem F

    2008-04-01

    Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to

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

    DEFF Research Database (Denmark)

    Green, Sara; Serban, Maria; Scholl, Raphael

    2018-01-01

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

  3. The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

    Science.gov (United States)

    Pollard, Thomas D

    2014-12-02

    This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Circulating immune complexes – reviewing the biological roles in ...

    African Journals Online (AJOL)

    Circulating immune complexes – reviewing the biological roles in human immune function and exercise. ... studies that have investigated CIC's following exercise and proposes that a comprehensive understanding and interpretation of immune system responses to exercise should take these complexes into consideration.

  5. Using multi-criteria analysis of simulation models to understand complex biological systems

    Science.gov (United States)

    Maureen C. Kennedy; E. David. Ford

    2011-01-01

    Scientists frequently use computer-simulation models to help solve complex biological problems. Typically, such models are highly integrated, they produce multiple outputs, and standard methods of model analysis are ill suited for evaluating them. We show how multi-criteria optimization with Pareto optimality allows for model outputs to be compared to multiple system...

  6. Understanding the biological underpinnings of ecohydrological processes

    Science.gov (United States)

    Huxman, T. E.; Scott, R. L.; Barron-Gafford, G. A.; Hamerlynck, E. P.; Jenerette, D.; Tissue, D. T.; Breshears, D. D.; Saleska, S. R.

    2012-12-01

    Climate change presents a challenge for predicting ecosystem response, as multiple factors drive both the physical and life processes happening on the land surface and their interactions result in a complex, evolving coupled system. For example, changes in surface temperature and precipitation influence near-surface hydrology through impacts on system energy balance, affecting a range of physical processes. These changes in the salient features of the environment affect biological processes and elicit responses along the hierarchy of life (biochemistry to community composition). Many of these structural or process changes can alter patterns of soil water-use and influence land surface characteristics that affect local climate. Of the many features that affect our ability to predict the future dynamics of ecosystems, it is this hierarchical response of life that creates substantial complexity. Advances in the ability to predict or understand aspects of demography help describe thresholds in coupled ecohydrological system. Disentangling the physical and biological features that underlie land surface dynamics following disturbance are allowing a better understanding of the partitioning of water in the time-course of recovery. Better predicting the timing of phenology and key seasonal events allow for a more accurate description of the full functional response of the land surface to climate. In addition, explicitly considering the hierarchical structural features of life are helping to describe complex time-dependent behavior in ecosystems. However, despite this progress, we have yet to build an ability to fully account for the generalization of the main features of living systems into models that can describe ecohydrological processes, especially acclimation, assembly and adaptation. This is unfortunate, given that many key ecosystem services are functions of these coupled co-evolutionary processes. To date, both the lack of controlled measurements and experimentation

  7. Towards the understanding of network information processing in biology

    Science.gov (United States)

    Singh, Vijay

    Living organisms perform incredibly well in detecting a signal present in the environment. This information processing is achieved near optimally and quite reliably, even though the sources of signals are highly variable and complex. The work in the last few decades has given us a fair understanding of how individual signal processing units like neurons and cell receptors process signals, but the principles of collective information processing on biological networks are far from clear. Information processing in biological networks, like the brain, metabolic circuits, cellular-signaling circuits, etc., involves complex interactions among a large number of units (neurons, receptors). The combinatorially large number of states such a system can exist in makes it impossible to study these systems from the first principles, starting from the interactions between the basic units. The principles of collective information processing on such complex networks can be identified using coarse graining approaches. This could provide insights into the organization and function of complex biological networks. Here I study models of biological networks using continuum dynamics, renormalization, maximum likelihood estimation and information theory. Such coarse graining approaches identify features that are essential for certain processes performed by underlying biological networks. We find that long-range connections in the brain allow for global scale feature detection in a signal. These also suppress the noise and remove any gaps present in the signal. Hierarchical organization with long-range connections leads to large-scale connectivity at low synapse numbers. Time delays can be utilized to separate a mixture of signals with temporal scales. Our observations indicate that the rules in multivariate signal processing are quite different from traditional single unit signal processing.

  8. Understanding Biological Regulation Through Synthetic Biology.

    Science.gov (United States)

    Bashor, Caleb J; Collins, James J

    2018-03-16

    Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function. Expected final online publication date for the Annual Review of Biophysics Volume 47 is May 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  9. Finding optimal interaction interface alignments between biological complexes

    KAUST Repository

    Cui, Xuefeng

    2015-06-13

    Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

  10. Complex biological and bio-inspired systems

    Energy Technology Data Exchange (ETDEWEB)

    Ecke, Robert E [Los Alamos National Laboratory

    2009-01-01

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

  11. Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds.

    Science.gov (United States)

    Fang, Lingzhao; Sahana, Goutam; Ma, Peipei; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

    2017-08-10

    A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes grouped on the basis of "Gene Ontology" (GO), and that incorporating this independent biological information into genomic prediction models might improve their predictive ability. Four complex traits (i.e., milk, fat and protein yields, and mastitis) together with imputed sequence variants in Holstein (HOL) and Jersey (JER) cattle were analysed. We first carried out a post-GWAS analysis in a HOL training population to assess the degree of enrichment of the association signals in the gene regions defined by each GO term. We then extended the genomic best linear unbiased prediction model (GBLUP) to a genomic feature BLUP (GFBLUP) model, including an additional genomic effect quantifying the joint effect of a group of variants located in a genomic feature. The GBLUP model using a single random effect assumes that all genomic variants contribute to the genomic relationship equally, whereas GFBLUP attributes different weights to the individual genomic relationships in the prediction equation based on the estimated genomic parameters. Our results demonstrate that the immune-relevant GO terms were more associated with mastitis than milk production, and several biologically meaningful GO terms improved the prediction accuracy with GFBLUP for the four traits, as compared with GBLUP. The improvement of the genomic prediction between breeds (the average increase across the four traits was 0.161) was more apparent than that it was within the HOL (the average increase across the four traits was 0.020). Our genomic feature modelling approaches provide a framework to simultaneously explore the genetic architecture and genomic prediction of complex traits by taking advantage of

  12. Exploitation of complex network topology for link prediction in biological interactomes

    KAUST Repository

    Alanis Lobato, Gregorio

    2014-06-01

    The network representation of the interactions between proteins and genes allows for a holistic perspective of the complex machinery underlying the living cell. However, the large number of interacting entities within the cell makes network construction a daunting and arduous task, prone to errors and missing information. Fortunately, the structure of biological networks is not different from that of other complex systems, such as social networks, the world-wide web or power grids, for which growth models have been proposed to better understand their structure and function. This means that we can design tools based on these models in order to exploit the topology of biological interactomes with the aim to construct more complete and reliable maps of the cell. In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable and biologically meaningful information that enriches the datasets to which we have access today.

  13. From structure of the complex to understanding of the biology

    Energy Technology Data Exchange (ETDEWEB)

    Rossmann, Michael G., E-mail: mr@purdue.edu [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)

    2007-01-01

    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

  14. From structure of the complex to understanding of the biology

    International Nuclear Information System (INIS)

    Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Morais, Marc C.; Leiman, Petr G.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan

    2007-01-01

    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle

  15. Linking structural features of protein complexes and biological function.

    Science.gov (United States)

    Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

    2015-09-01

    Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

  16. Systematic synergy modeling: understanding drug synergy from a systems biology perspective.

    Science.gov (United States)

    Chen, Di; Liu, Xi; Yang, Yiping; Yang, Hongjun; Lu, Peng

    2015-09-16

    Owing to drug synergy effects, drug combinations have become a new trend in combating complex diseases like cancer, HIV and cardiovascular diseases. However, conventional synergy quantification methods often depend on experimental dose-response data which are quite resource-demanding. In addition, these methods are unable to interpret the explicit synergy mechanism. In this review, we give representative examples of how systems biology modeling offers strategies toward better understanding of drug synergy, including the protein-protein interaction (PPI) network-based methods, pathway dynamic simulations, synergy network motif recognitions, integrative drug feature calculations, and "omic"-supported analyses. Although partially successful in drug synergy exploration and interpretation, more efforts should be put on a holistic understanding of drug-disease interactions, considering integrative pharmacology and toxicology factors. With a comprehensive and deep insight into the mechanism of drug synergy, systems biology opens a novel avenue for rational design of effective drug combinations.

  17. Understanding the biology of urothelial cancer metastasis

    Directory of Open Access Journals (Sweden)

    Takashi Kobayashi

    2016-10-01

    Full Text Available Management of unresectable urothelial cancer (UC has been a clinical challenge for decades. While drug resistance is a key issue, precise understanding of biology of UC metastasis is another challenge for the improvement of treatment outcome of UC patients. Introduction of the cell biology concepts including epithelial-mesenchymal transition (EMT and cancer stemness seems to explain UC metastasis. Molecular genetics based on gene expression profiling, next generation sequencing, and explosion of non-coding RNA world has opened the door to intrinsic molecular subtyping of UC. Next steps include, based on the recently accumulated understanding, the establishment of novel disease models representing UC metastasis in various experimental platforms, particularly in vivo animal systems. Indeed, novel knowledge molecular genetics has not been fully linked to the modeling of UC metastasis. Further understanding of bladder carcinogenesis is needed particularly with regard to cell of origin related to tumor characteristics including driver gene alterations, pathological differentiations, and metastatic ability. Then we will be able to establish better disease models, which will consequently lead us to further understanding of biology and eventually the development of novel therapeutic strategies for UC metastasis.

  18. Chemometric and Statistical Analyses of ToF-SIMS Spectra of Increasingly Complex Biological Samples

    Energy Technology Data Exchange (ETDEWEB)

    Berman, E S; Wu, L; Fortson, S L; Nelson, D O; Kulp, K S; Wu, K J

    2007-10-24

    Characterizing and classifying molecular variation within biological samples is critical for determining fundamental mechanisms of biological processes that will lead to new insights including improved disease understanding. Towards these ends, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to examine increasingly complex samples of biological relevance, including monosaccharide isomers, pure proteins, complex protein mixtures, and mouse embryo tissues. The complex mass spectral data sets produced were analyzed using five common statistical and chemometric multivariate analysis techniques: principal component analysis (PCA), linear discriminant analysis (LDA), partial least squares discriminant analysis (PLSDA), soft independent modeling of class analogy (SIMCA), and decision tree analysis by recursive partitioning. PCA was found to be a valuable first step in multivariate analysis, providing insight both into the relative groupings of samples and into the molecular basis for those groupings. For the monosaccharides, pure proteins and protein mixture samples, all of LDA, PLSDA, and SIMCA were found to produce excellent classification given a sufficient number of compound variables calculated. For the mouse embryo tissues, however, SIMCA did not produce as accurate a classification. The decision tree analysis was found to be the least successful for all the data sets, providing neither as accurate a classification nor chemical insight for any of the tested samples. Based on these results we conclude that as the complexity of the sample increases, so must the sophistication of the multivariate technique used to classify the samples. PCA is a preferred first step for understanding ToF-SIMS data that can be followed by either LDA or PLSDA for effective classification analysis. This study demonstrates the strength of ToF-SIMS combined with multivariate statistical and chemometric techniques to classify increasingly complex biological samples

  19. Characterising the Development of the Understanding of Human Body Systems in High-School Biology Students--A Longitudinal Study

    Science.gov (United States)

    Snapir, Zohar; Eberbach, Catherine; Ben-Zvi-Assaraf, Orit; Hmelo-Silver, Cindy; Tripto, Jaklin

    2017-01-01

    Science education today has become increasingly focused on research into complex natural, social and technological systems. In this study, we examined the development of high-school biology students' systems understanding of the human body, in a three-year longitudinal study. The development of the students' system understanding was evaluated…

  20. Simple, complex and hyper-complex understanding - enhanced sensitivity in observation of information

    DEFF Research Database (Denmark)

    Bering Keiding, Tina

    for construction and analysis of empirical information. A quick overview on empirical research drawing on Luhmann reveals a diverse complex of analytical strategies and empirical methods. Despite differences between strategies and methods they have in common that understanding of uttered information is crucial...... in their production of empirically founded knowledge. However research generally seems to pay more attention to production of uttered information than to selection of understanding. The aim of this contribution is to sketch out a suggestion to how selection of understanding can be systematized in order to produce...... enhanced transparency in selection of understanding as well as enhanced sensitivity and definition in dept. The contribution suggest that we distinguish between three types of understanding; simple, complex and hyper-complex understanding. Simple understanding is the simultaneous selection of understanding...

  1. Emergence of biological complexity: Criticality, renewal and memory

    International Nuclear Information System (INIS)

    Grigolini, Paolo

    2015-01-01

    The key purpose of this article is to establish a connection between two emerging fields of research in theoretical biology. The former focuses on the concept of criticality borrowed from physics that is expected to be extensible to biology through a robust theoretical approach that although not yet available shall eventually shed light into the origin of cognition. The latter, largely based on the tracking of single molecules diffusing in biological cells, is bringing to the general attention the need to go beyond the ergodic assumption currently done in the traditional statistical physics. We show that replacing critical slowing down with temporal complexity explains why biological systems at criticality are resilient and why long-range correlations are compatible with the free-will condition necessary for the emergence of cognition. Temporal complexity generates ergodicity breakdown and requires new forms of response of complex systems to external stimuli. We concisely illustrate these new forms of information transport and we also address the challenging issue of combining temporal complexity with coherence and renewal with infinite memory.

  2. Complexity, Analysis and Control of Singular Biological Systems

    CERN Document Server

    Zhang, Qingling; Zhang, Xue

    2012-01-01

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

  3. Finding optimal interaction interface alignments between biological complexes

    KAUST Repository

    Cui, Xuefeng; Naveed, Hammad; Gao, Xin

    2015-01-01

    Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which

  4. Predictive modelling of complex agronomic and biological systems.

    Science.gov (United States)

    Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J

    2013-09-01

    Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.

  5. Characterising the development of the understanding of human body systems in high-school biology students - a longitudinal study

    Science.gov (United States)

    Snapir, Zohar; Eberbach, Catherine; Ben-Zvi-Assaraf, Orit; Hmelo-Silver, Cindy; Tripto, Jaklin

    2017-10-01

    Science education today has become increasingly focused on research into complex natural, social and technological systems. In this study, we examined the development of high-school biology students' systems understanding of the human body, in a three-year longitudinal study. The development of the students' system understanding was evaluated using the Components Mechanisms Phenomena (CMP) framework for conceptual representation. We coded and analysed the repertory grid personal constructs of 67 high-school biology students at 4 points throughout the study. Our data analysis builds on the assumption that systems understanding entails a perception of all the system categories, including structures within the system (its Components), specific processes and interactions at the macro and micro levels (Mechanisms), and the Phenomena that present the macro scale of processes and patterns within a system. Our findings suggest that as the learning process progressed, the systems understanding of our students became more advanced, moving forward within each of the major CMP categories. Moreover, there was an increase in the mechanism complexity presented by the students, manifested by more students describing mechanisms at the molecular level. Thus, the 'mechanism' category and the micro level are critical components that enable students to understand system-level phenomena such as homeostasis.

  6. Biological significance of complex N-glycans in plants and their impact on plant physiology.

    Science.gov (United States)

    Strasser, Richard

    2014-01-01

    Asparagine (N)-linked protein glycosylation is a ubiquitous co- and post-translational modification which can alter the biological function of proteins and consequently affects the development, growth, and physiology of organisms. Despite an increasing knowledge of N-glycan biosynthesis and processing, we still understand very little about the biological function of individual N-glycan structures in plants. In particular, the N-glycan-processing steps mediated by Golgi-resident enzymes create a structurally diverse set of protein-linked carbohydrate structures. Some of these complex N-glycan modifications like the presence of β1,2-xylose, core α1,3-fucose or the Lewis a-epitope are characteristic for plants and are evolutionary highly conserved. In mammals, complex N-glycans are involved in different cellular processes including molecular recognition and signaling events. In contrast, the complex N-glycan function is still largely unknown in plants. Here, in this short review, I focus on important recent developments and discuss their implications for future research in plant glycobiology and plant biotechnology.

  7. Improved understanding of protein complex offers insight into DNA

    Science.gov (United States)

    Summer Science Writing Internship Improved understanding of protein complex offers insight into DNA clearer understanding of the origin recognition complex (ORC) - a protein complex that directs DNA replication - through its crystal structure offers new insight into fundamental mechanisms of DNA replication

  8. Beyond disease susceptibility-Leveraging genome-wide association studies for new insights into complex disease biology.

    Science.gov (United States)

    Lee, J C

    2017-12-01

    Genetic studies in complex diseases have been highly successful, but have also been largely one-dimensional: predominantly focusing on the genetic contribution to disease susceptibility. While this is undoubtedly important-indeed it is a pre-requisite for understanding the mechanisms underlying disease development-there are many other important aspects of disease biology that have received comparatively little attention. In this review, I will discuss how existing genetic data can be leveraged to provide new insights into other aspects of disease biology, why such insights could change the way we think about complex disease, and how this could provide opportunities for better therapies and/or facilitate personalised medicine. To do this, I will use the example of Crohn's disease-a chronic form of inflammatory bowel disease that has been one of the main success stories in complex disease genetics. Indeed, thanks to genetic studies, we now have a much more detailed understanding of the processes involved in Crohn's disease development, but still know relatively little about what determines the subsequent disease course (prognosis) and why this differs so considerably between individuals. I will discuss how we came to realise that genetic variation plays an important role in determining disease prognosis and how this has changed the way we think about Crohn's disease genetics. This will illustrate how phenotypic data can be used to leverage new insights from genetic data and will provide a broadly applicable framework that could yield new insights into the biology of multiple diseases. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Mössbauer study of some biological iron complexes

    Indian Academy of Sciences (India)

    Abstract. Some biological complexes containing iron are investigated experimentally at room temperature using the Mössbauer resonance. The complexes show quadrupole doublet and Kramer's degeneracy is found to exist. The electric field gradient, difference in s-electron densities and quadrupole coupling constant ...

  10. Drosophila melanogaster--the model organism of choice for the complex biology of multi-cellular organisms

    Science.gov (United States)

    Beckingham, Kathleen M.; Armstrong, J. Douglas; Texada, Michael J.; Munjaal, Ravi; Baker, Dean A.

    2005-01-01

    Drosophila melanogaster has been intensely studied for almost 100 years. The sophisticated array of genetic and molecular tools that have evolved for analysis of gene function in this organism are unique. Further, Drosophila is a complex multi-cellular organism in which many aspects of development and behavior parallel those in human beings. These combined advantages have permitted research in Drosophila to make seminal contributions to the understanding of fundamental biological processes and ensure that Drosophila will continue to provide unique insights in the genomic era. An overview of the genetic methodologies available in Drosophila is given here, together with examples of outstanding recent contributions of Drosophila to our understanding of cell and organismal biology. The growing contribution of Drosophila to our knowledge of gravity-related responses is addressed.

  11. Understanding the biological and environmental implications of nanomaterials

    Science.gov (United States)

    Lin, Sijie

    quantified by UV-vis spectrophotometry and fitted with the Freundlich isothem. Effects of the adsorption of QDs on the photosynthetic activities of the algae are evaluated using O2 evolution and CO2 depletion assays, and the ecological impact of such adsorption is discussed. To understand the effects of nanomaterials on the cell membrane, nanoparticles (Au, TiO2, and QDs) of different surface charges and chemical compositions are introduced to HT-29 mammalian cells in Chapter 4. The polarization of the cell membrane is investigated using a FLIPR membrane potential kit. The phase of the cell membrane, in the presence of both positively and negatively charged nanoparticles, are examined using laurden, a lipophilic dye that serves as a molecular reporter on the fluidic or gel phase of the host membrane. To address the effects of nanomaterials on biological and ecological systems within the same context, Chapter 5 offers a first parallel comparison between mammalian and plant cell responses to nanomaterials. This study is conducted using a plant cell viability assay, complimented by bright field, fluorescence, and electron microscopy imaging. Discussions of this study are presented based on the hydrophobicity and solubility of C60(OH) 20 and of supramolecular complex C70-NOM, hydrophobicity and porous structure of the plant Allium cepa cell wall, and the amphiphilic structure and endocytosis of the plasma cell membrane of both Allium cepa and HT-29 cells. Chapter 6 summarizes and rationalizes results obtained from the entire dissertation research. Future work inspired by this research is presented at the end of the chapter. Specifically, this dissertation is structured to embody the following essential and complementary chapters: (1) Chapter 1: Literature review (2) Chapter 2: Nano-Eco interactions at the whole organism level; (3) Chapter 3: Nano-Eco interactions at the cellular level; (4) Chapter 4: Nano-Bio interactions at the cellular level; (5) Chapter 5: Parallel comparison

  12. Parental Understanding of Tuberous Sclerosis Complex.

    Science.gov (United States)

    Samia, Pauline; Donald, Kirsten A; Schlegel, Birgit; Wilmshurst, Jo M

    2015-09-01

    Tuberous sclerosis complex is a genetic disorder with multisystem involvement that poses significant challenges to the affected child and family. Caregiver knowledge in the South African population has not previously been reported. A prospective study of the parents of 21 children with tuberous sclerosis complex was undertaken. Median parental age was 38 (interquartile range 34.5-45) years. Parents were randomly allocated to receive written information about the condition, or to receive verbal counseling already established in clinic. A significant difference (P = .001) was observed in the change in the mean knowledge scores for the parent group that received written information (34.2 at baseline, 51.7 at the second visit. This impact was higher in parents with an education level of at least grade 8 (P = .003). Parental understanding of tuberous sclerosis complex can be improved by provision of written information and should be routinely available in a readily understandable format. © The Author(s) 2014.

  13. Complex fluids in biological systems experiment, theory, and computation

    CERN Document Server

    2015-01-01

    This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world’s foremost experts explore key topics such as: Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood The motility of microorganisms in complex fluids and the dynamics of active suspensions Challenges and solut...

  14. Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

    Science.gov (United States)

    Liang, Jie; Qian, Hong

    2010-01-01

    Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

  15. Effect of Process-Oriented Guided-Inquiry Learning on Non-majors Biology Students' Understanding of Biological Classification

    Science.gov (United States)

    Wozniak, Breann M.

    The purpose of this study was to examine the effect of process-oriented guided-inquiry learning (POGIL) on non-majors college biology students' understanding of biological classification. This study addressed an area of science instruction, POGIL in the non-majors college biology laboratory, which has yet to be qualitatively and quantitatively researched. A concurrent triangulation mixed methods approach was used. Students' understanding of biological classification was measured in two areas: scores on pre and posttests (consisting of 11 multiple choice questions), and conceptions of classification as elicited in pre and post interviews and instructor reflections. Participants were Minnesota State University, Mankato students enrolled in BIOL 100 Summer Session. One section was taught with the traditional curriculum (n = 6) and the other section in the POGIL curriculum (n = 10) developed by the researcher. Three students from each section were selected to take part in pre and post interviews. There were no significant differences within each teaching method (p familiar animal categories and aquatic habitats, unfamiliar organisms, combining and subdividing initial groupings, and the hierarchical nature of classification. The POGIL students were the only group to surpass these challenges after the teaching intervention. This study shows that POGIL is an effective technique at eliciting students' misconceptions, and addressing these misconceptions, leading to an increase in student understanding of biological classification.

  16. Proteomics Improves the New Understanding of Honeybee Biology.

    Science.gov (United States)

    Hora, Zewdu Ararso; Altaye, Solomon Zewdu; Wubie, Abebe Jemberie; Li, Jianke

    2018-04-11

    The honeybee is one of the most valuable insect pollinators, playing a key role in pollinating wild vegetation and agricultural crops, with significant contribution to the world's food production. Although honeybees have long been studied as model for social evolution, honeybee biology at the molecular level remained poorly understood until the year 2006. With the availability of the honeybee genome sequence and technological advancements in protein separation, mass spectrometry, and bioinformatics, aspects of honeybee biology such as developmental biology, physiology, behavior, neurobiology, and immunology have been explored to new depths at molecular and biochemical levels. This Review comprehensively summarizes the recent progress in honeybee biology using proteomics to study developmental physiology, task transition, and physiological changes in some of the organs, tissues, and cells based on achievements from the authors' laboratory in this field. The research advances of honeybee proteomics provide new insights for understanding of honeybee biology and future research directions.

  17. Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.

    Science.gov (United States)

    Speijer, Dave

    2011-05-01

    Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.

  18. Understanding Complex Construction Systems Through Modularity

    DEFF Research Database (Denmark)

    Jensen, Tor Clarke; Bekdik, Baris; Thuesen, Christian

    2014-01-01

    This paper develops a framework for understanding complexity in construction projects by combining theories of complexity management and modularization. The framework incorporates three dimensions of product, process, and organizational modularity with the case of gypsum wall elements. The analysis...... system, rather than a modular, although the industry forces modular organizational structures. This creates a high complexity degree caused by the non-alignment of building parts and organizations and the frequent swapping of modules....... finds that the main driver of complexity is the fragmentation of the design and production, which causes the production modules to construct and install new product types and variants for each project as the designers are swapped for every project. The many interfaces are characteristics of an integral...

  19. Neuroanthropological Understanding of Complex Cognition – Numerosity and Arithmetics

    Directory of Open Access Journals (Sweden)

    Zarja Mursic

    2013-10-01

    Full Text Available Humankind has a long evolutionary history. When we are trying to understand human complex cognition, it is as well important to look back to entire evolution. I will present the thesis that our biological predispositions and culture, together with natural and social environment, are tightly connected. During ontogenetically development we are shaped by various factors, and they enabled humans to develop some aspects of complex cognition, such as mathematics.In the beginning of the article I present the importance of natural and cultural evolution in other animals. In the following part, I briefly examine the field of mathematics – numerosity and arithmetic. Presentation of comparative animal studies, mainly made on primates, provides some interesting examples in animals’ abilities to separate between different quantities. From abilities for numerosity in animals I continue to neuroscientific studies of humans and our ability to solve simple arithmetic tasks. I also mention cross-cultural studies of arithmetic skills. In the final part of the text I present the field neuroanthropology as a possible new pillar of cognitive science. Finally, it is important to connect human evolution and development with animal cognition studies, but as well with cross-cultural studies in shaping of human ability for numerosity and arithmetic.

  20. Understanding complex urban systems multidisciplinary approaches to modeling

    CERN Document Server

    Gurr, Jens; Schmidt, J

    2014-01-01

    Understanding Complex Urban Systems takes as its point of departure the insight that the challenges of global urbanization and the complexity of urban systems cannot be understood – let alone ‘managed’ – by sectoral and disciplinary approaches alone. But while there has recently been significant progress in broadening and refining the methodologies for the quantitative modeling of complex urban systems, in deepening the theoretical understanding of cities as complex systems, or in illuminating the implications for urban planning, there is still a lack of well-founded conceptual thinking on the methodological foundations and the strategies of modeling urban complexity across the disciplines. Bringing together experts from the fields of urban and spatial planning, ecology, urban geography, real estate analysis, organizational cybernetics, stochastic optimization, and literary studies, as well as specialists in various systems approaches and in transdisciplinary methodologies of urban analysis, the volum...

  1. Analysis of undergraduate students' conceptual models of a complex biological system across a diverse body of learners

    Science.gov (United States)

    Dirnbeck, Matthew R.

    Biological systems pose a challenge both for learners and teachers because they are complex systems mediated by feedback loops; networks of cause-effect relationships; and non-linear, hierarchical, and emergent properties. Teachers and scientists routinely use models to communicate ideas about complex systems. Model-based pedagogies engage students in model construction as a means of practicing higher-order reasoning skills. One such modeling paradigm describes systems in terms of their structures, behaviors, and functions (SBF). The SBF framework is a simple modeling language that has been used to teach about complex biological systems. Here, we used student-generated SBF models to assess students' causal reasoning in the context of a novel biological problem on an exam. We compared students' performance on the modeling problem, their performance on a set of knowledge/comprehension questions, and their performance on a set of scientific reasoning questions. We found that students who performed well on knowledge and understanding questions also constructed more networked, higher quality models. Previous studies have shown that learners' mental maps increase in complexity with increased expertise. We wanted to investigate if biology students with varying levels of training in biology showed a similar pattern when constructing system models. In a pilot study, we administered the same modeling problem to two additional groups of students: 1) an animal physiology course for students pursuing a major in biology (n=37) and 2) an exercise physiology course for non-majors (n=27). We found that there was no significant difference in model organization across the three student populations, but there was a significant difference in the ability to represent function between the three populations. Between the three groups the non-majors had the lowest function scores, the introductory majors had the middle function scores, and the upper division majors had the highest function

  2. Comprehension of complex biological processes by analytical methods: how far can we go using mass spectrometry?

    International Nuclear Information System (INIS)

    Gerner, C.

    2013-01-01

    Comprehensive understanding of complex biological processes is the basis for many biomedical issues of great relevance for modern society including risk assessment, drug development, quality control of industrial products and many more. Screening methods provide means for investigating biological samples without research hypothesis. However, the first boom of analytical screening efforts has passed and we again need to ask whether and how to apply screening methods. Mass spectrometry is a modern tool with unrivalled analytical capacities. This applies to all relevant characteristics of analytical methods such as specificity, sensitivity, accuracy, multiplicity and diversity of applications. Indeed, mass spectrometry qualifies to deal with complexity. Chronic inflammation is a common feature of almost all relevant diseases challenging our modern society; these diseases are apparently highly diverse and include arteriosclerosis, cancer, back pain, neurodegenerative diseases, depression and other. The complexity of mechanisms regulating chronic inflammation is the reason for the practical challenge to deal with it. The presentation shall give an overview of capabilities and limitations of the application of this analytical tool to solve critical questions with great relevance for our society. (author)

  3. Epistemological Predictors of Prospective Biology Teachers' Nature of Science Understandings

    Science.gov (United States)

    Köseoglu, Pinar; Köksal, Mustafa Serdar

    2015-01-01

    The purpose of this study was to investigate epistemological predictors of nature of science understandings of 281 prospective biology teachers surveyed using the Epistemological Beliefs Scale Regarding Science and the Nature of Science Scale. The findings on multiple linear regression showed that understandings about definition of science and…

  4. Synthesis, Physical Characterization and Biological Activity of Some Schiff Base Complexes

    Directory of Open Access Journals (Sweden)

    R. Rajavel

    2008-01-01

    Full Text Available Structural modification of organic molecule has considerable biological relevance. Further, coordination of a biomolecules to the metal ions significantly alters the effectiveness of the biomolecules. In view of the antimicrobial activity ligand [bis-(2-aminobenzaldehyde] malonoyl dihydrazone], metal complexes with Cu(II, Ni(II, Zn(II and oxovanadium(IV have been synthesized and found to be potential antimicrobial agents. An attempt is also made to correlate the biological activities with geometry of the complexes. The complexes have been characterized by elemental analysis, molar conductance, spectra and cyclicvoltammetric measurements. The structural assessment of the complexes has been carried out based on electronic, infrared and molar conductivity values.

  5. EPR spectroscopy of complex biological iron-sulfur systems.

    Science.gov (United States)

    Hagen, Wilfred R

    2018-02-21

    From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

  6. How do precision medicine and system biology response to human body's complex adaptability?

    Science.gov (United States)

    Yuan, Bing

    2016-12-01

    In the field of life sciences, although system biology and "precision medicine" introduce some complex scientifific methods and techniques, it is still based on the "analysis-reconstruction" of reductionist theory as a whole. Adaptability of complex system increase system behaviour uncertainty as well as the difficulties of precise identifification and control. It also put systems biology research into trouble. To grasp the behaviour and characteristics of organism fundamentally, systems biology has to abandon the "analysis-reconstruction" concept. In accordance with the guidelines of complexity science, systems biology should build organism model from holistic level, just like the Chinese medicine did in dealing with human body and disease. When we study the living body from the holistic level, we will fifind the adaptability of complex system is not the obstacle that increases the diffificulty of problem solving. It is the "exceptional", "right-hand man" that helping us to deal with the complexity of life more effectively.

  7. Complex systems of biological interest stability under ionising radiations

    International Nuclear Information System (INIS)

    Maclot, Sylvain

    2014-01-01

    This PhD work presents the study of stability of molecular systems of biological interest in the gas phase after interaction with ionising radiations. The use of ionising radiation can probe the physical chemistry of complex systems at the molecular scale and thus consider their intrinsic properties. Beyond the fundamental aspect, this work is part of the overall understanding of radiation effects on living organisms and in particular the use of ionizing radiation in radiotherapy. Specifically, this study focused on the use of low-energy multiply charged ions (tens of keV) provided by the GANIL (Caen), which includes most of the experiments presented. In addition, experiments using VUV photons were also conducted at synchrotron ELETTRA (Trieste, Italy). The bio-molecular systems studied are amino acids and nucleic acid constituents. Using an experimental crossed beams device allows interaction between biomolecules and ionising radiation leads mainly to the ionization and fragmentation of the system. The study of its relaxation dynamics is by time-of-flight mass spectrometry coupled to a coincidences measurements method. It is shown that an approach combining experiment and theory allows a detailed study of the fragmentation dynamics of complex systems. The results indicate that fragmentation is generally governed by the Coulomb repulsion but the intramolecular rearrangements involve specific relaxation mechanisms. (author) [fr

  8. Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

    NARCIS (Netherlands)

    Bosse, T.; Jonker, C.M.; Treur, J.

    2005-01-01

    This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics

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

    Science.gov (United States)

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

    2017-07-05

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

  10. Understanding Learner Agency as a Complex Dynamic System

    Science.gov (United States)

    Mercer, Sarah

    2011-01-01

    This paper attempts to contribute to a fuller understanding of the nature of language learner agency by considering it as a complex dynamic system. The purpose of the study was to explore detailed situated data to examine to what extent it is feasible to view learner agency through the lens of complexity theory. Data were generated through a…

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

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

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

  12. A Thai pre-service teacher's understanding of nature of science in biology teaching

    Science.gov (United States)

    Srisawat, Akkarawat; Aiemsum-ang, Napapan; Yuenyong, Chokchai

    2018-01-01

    This study was conducted on the effect of understanding and instruction of the nature of science of Ms. Wanida, a pre-service student under science education program in biology, Faculty of Education, Khon Kaen University. Wanida was a teaching practicum student majoring in biology at Khon Kaen University Demonstration School (Modindaeng). She was teaching biology for 38 Grade 10 students. Methodology regarded interpretive paradigm. The study aimed to examine 1) Wanida's understanding of the nature of science, 2) Wanida's instruction of the nature of science, 3 students' understanding of the nature of science from Wanida's instruction, and 4) the effects of Wanida's understanding and instruction of the nature of science on students' understanding of the nature of science from Wanida's instruction. Tools of interpretation included teaching observation, a semi-structured interview, open-ended questionnaire, and an observation record form for the instruction of the nature of science. The data obtained was interpreted, encoded, and classified, using the descriptive statistics. The findings indicated that Wanida held good understanding of the nature of science. She could apply the deficient nature of science approach mostly, followed by the implicit nature of science approach. Unfortunately, she could not show her teaching as explicit nature of science. However, her students' the understanding of the nature of science was good.

  13. Complex network problems in physics, computer science and biology

    Science.gov (United States)

    Cojocaru, Radu Ionut

    lattice at zero temperature and then we apply this formalism to the K-SAT problem defined in Chapter 1. The phase transition which physicists study often corresponds to a change in the computational complexity of the corresponding computer science problem. Chapter 3 presents phase transitions which are specific to the problems discussed in Chapter 1 and also known results for the K-SAT problem. We discuss the replica method and experimental evidences of replica symmetry breaking. The physics approach to hard problems is based on replica methods which are difficult to understand. In Chapter 4 we develop novel methods for studying hard problems using methods similar to the message passing techniques that were discussed in Chapter 2. Although we concentrated on the symmetric case, cavity methods show promise for generalizing our methods to the un-symmetric case. As has been highlighted by John Hopfield, several key features of biological systems are not shared by physical systems. Although living entities follow the laws of physics and chemistry, the fact that organisms adapt and reproduce introduces an essential ingredient that is missing in the physical sciences. In order to extract information from networks many algorithm have been developed. In Chapter 5 we apply polynomial algorithms like minimum spanning tree in order to study and construct gene regulatory networks from experimental data. As future work we propose the use of algorithms like min-cut/max-flow and Dijkstra for understanding key properties of these networks.

  14. Using synthetic biology to make cells tomorrow's test tubes.

    Science.gov (United States)

    Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

    2016-04-18

    The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

  15. Biological Principles and Threshold Concepts for Understanding Natural Selection. Implications for Developing Visualizations as a Pedagogic Tool

    Science.gov (United States)

    Tibell, Lena A. E.; Harms, Ute

    2017-11-01

    Modern evolutionary theory is both a central theory and an integrative framework of the life sciences. This is reflected in the common references to evolution in modern science education curricula and contexts. In fact, evolution is a core idea that is supposed to support biology learning by facilitating the organization of relevant knowledge. In addition, evolution can function as a pivotal link between concepts and highlight similarities in the complexity of biological concepts. However, empirical studies in many countries have for decades identified deficiencies in students' scientific understanding of evolution mainly focusing on natural selection. Clearly, there are major obstacles to learning natural selection, and we argue that to overcome them, it is essential to address explicitly the general abstract concepts that underlie the biological processes, e.g., randomness or probability. Hence, we propose a two-dimensional framework for analyzing and structuring teaching of natural selection. The first—purely biological—dimension embraces the three main principles variation, heredity, and selection structured in nine key concepts that form the core idea of natural selection. The second dimension encompasses four so-called thresholds, i.e., general abstract and/or non-perceptual concepts: randomness, probability, spatial scales, and temporal scales. We claim that both of these dimensions must be continuously considered, in tandem, when teaching evolution in order to allow development of a meaningful understanding of the process. Further, we suggest that making the thresholds tangible with the aid of appropriate kinds of visualizations will facilitate grasping of the threshold concepts, and thus, help learners to overcome the difficulties in understanding the central theory of life.

  16. From globally coupled maps to complex-systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, Kunihiko, E-mail: kaneko@complex.c.u-tokyo.ac.jp [Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, The University of Tokyo 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2015-09-15

    Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

  17. Using biological networks to improve our understanding of infectious diseases

    Directory of Open Access Journals (Sweden)

    Nicola J. Mulder

    2014-08-01

    Full Text Available Infectious diseases are the leading cause of death, particularly in developing countries. Although many drugs are available for treating the most common infectious diseases, in many cases the mechanism of action of these drugs or even their targets in the pathogen remain unknown. In addition, the key factors or processes in pathogens that facilitate infection and disease progression are often not well understood. Since proteins do not work in isolation, understanding biological systems requires a better understanding of the interconnectivity between proteins in different pathways and processes, which includes both physical and other functional interactions. Such biological networks can be generated within organisms or between organisms sharing a common environment using experimental data and computational predictions. Though different data sources provide different levels of accuracy, confidence in interactions can be measured using interaction scores. Connections between interacting proteins in biological networks can be represented as graphs and edges, and thus studied using existing algorithms and tools from graph theory. There are many different applications of biological networks, and here we discuss three such applications, specifically applied to the infectious disease tuberculosis, with its causative agent Mycobacterium tuberculosis and host, Homo sapiens. The applications include the use of the networks for function prediction, comparison of networks for evolutionary studies, and the generation and use of host–pathogen interaction networks.

  18. Top-down models in biology: explanation and control of complex living systems above the molecular level.

    Science.gov (United States)

    Pezzulo, Giovanni; Levin, Michael

    2016-11-01

    It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

  19. Perspectives of a systems biology of the brain: the big data conundrum understanding psychiatric diseases.

    Science.gov (United States)

    Mewes, H W

    2013-05-01

    Psychiatric diseases provoke human tragedies. Asocial behaviour, mood imbalance, uncontrolled affect, and cognitive malfunction are the price for the biological and social complexity of neurobiology. To understand the etiology and to influence the onset and progress of mental diseases remains of upmost importance, but despite the much improved care for the patients, more then 100 years of research have not succeeded to understand the basic disease mechanisms and enabling rationale treatment. With the advent of the genome based technologies, much hope has been created to join the various dimension of -omics data to uncover the secrets of mental illness. Big Data as generated by -omics do not come with explanations. In this essay, I will discuss the inherent, not well understood methodological foundations and problems that seriously obstacle in striving for a quick success and may render lucky strikes impossible. © Georg Thieme Verlag KG Stuttgart · New York.

  20. Biological and social understanding of human nature: biopolitical dimension

    Directory of Open Access Journals (Sweden)

    S. K. Kostiuchkov

    2014-07-01

    Full Text Available This paper examines the position of the biopolitical nature of man as a biosocial being given supplies of both the two spheres of life – natural, biological and social. The necessity of understanding of human nature, which by definition are bio-social importance of the approach to the definition of man as an integral, binary-konnotovanoyi of the «social individual – a species» which is characterized by symmetrical opposition – upposition social and biological. It was found that the main task of modern political science, and in particular bio-political studies presented appeals to rethink the political picture of the world in order to predict the development of a new order or a new chaos. Understanding the formation of a new global civilization worldview is today one of the most important problems, which is connected with the main problem of the modern world – the task of preserving life on the planet. It is concluded that the contradictions of human nature – between the biological and the social, physical and spiritual, universal and the particular, natural and artificial, rational and emotional – in today’s conditions are extremely sharp. The said situation requires more in-depth scientific analysis of human nature, the study of the structural level as human biosocial system.

  1. Understanding pathologic variants of renal cell carcinoma: distilling therapeutic opportunities from biologic complexity.

    Science.gov (United States)

    Shuch, Brian; Amin, Ali; Armstrong, Andrew J; Eble, John N; Ficarra, Vincenzo; Lopez-Beltran, Antonio; Martignoni, Guido; Rini, Brian I; Kutikov, Alexander

    2015-01-01

    Once believed to represent a uniform malignant phenotype, renal cell carcinoma (RCC) is now viewed as a diverse group of cancers that arise from the nephron. To review the pathologic characteristics, clinical behavior, molecular biology, and systemic therapy options of recognized RCC histologic subtypes. A systematic review of English-language articles was performed using the Medline and Web of Science databases. Manuscripts were selected with consensus of the coauthors and evaluated using the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) criteria. The major findings of the evaluated manuscripts are discussed with an emphasis on the description of the pathologic features, clinical behavior, prognosis, and therapeutic strategies. Classification schemes for kidney cancer have undergone dramatic changes over the past two decades. Improvements in these classification schemes are important, as pathologic variants differ not only in disease biology, but also in clinical behavior, prognosis, and response to systemic therapy. In the era of genomic medicine, further refinements in characterization of RCC subtypes will be critical to the progress of this burgeoning clinical space. Kidney cancer can be subdivided into related but different cancers that arise from the kidney's tubules. In this article we review current classifications for kidney cancer, discuss their characteristics, and provide an overview of each subtype's clinical behavior and treatment. We stress that each subtype harbors unique biology and thus responds differently to available treatment strategies. Copyright © 2014 European Association of Urology. Published by Elsevier B.V. All rights reserved.

  2. From Molecules to Life: Quantifying the Complexity of Chemical and Biological Systems in the Universe.

    Science.gov (United States)

    Böttcher, Thomas

    2018-01-01

    Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms. Entities with a certain level of information complexity directly require a functionally complex mechanism for their production or replication and are hence indicative for life-like systems. In order to describe entities combining molecular and information complexity, the term biogenic unit was introduced. Exemplified biogenic unit complexities were calculated for ribozymes, protein enzymes, multimeric protein complexes, and even an entire virus particle. Complexities of prokaryotic and eukaryotic cells, as well as multicellular organisms, were estimated. Thereby distinct evolutionary stages in complexity space were identified. The here developed approach to compare the complexity of biogenic units allows for the first time to address the gradual characteristics of prebiotic and life-like systems without the need for a definition of life. This operational concept may guide our search for life in the Universe, and it may direct the investigations of prebiotic trajectories that lead towards the evolution of complexity at the origins of life.

  3. Applying a complex adaptive system's understanding of health to primary care [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Johannes Bircher

    2016-09-01

    Full Text Available This paper explores the diagnostic and therapeutic potential of a new concept of health. Investigations into the nature of health have led to a new definition that explains health as a complex adaptive system (CAS and is based on five components (a-e. Humans like all biological creatures must satisfactorily respond to (a the demands of life. For this purpose they need (b a biologically given potential (BGP and (c a personally acquired potential (PAP. These properties of individuals are embedded within (d social and (e environmental determinants of health. Between these five components of health there are 10 complex interactions that justify viewing health as a CAS. In each patient, the current state of health as a CAS evolved from the past, will move forward to a new future, and has to be analyzed and treated as an autonomous whole. A diagnostic procedure is suggested as follows: together with the patient, the five components and 10 complex interactions are assessed. This may help patients to better understand their situations and to recognize possible next steps that may be useful in order to evolve toward better health by themselves. In this process mutual trust in the patient-physician interaction is critical. The described approach offers new possibilities for helping patients improve their health prospects.

  4. Physics and biology

    International Nuclear Information System (INIS)

    Frauenfelder, H.

    1988-01-01

    The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

  5. Context dependence of students' views about the role of equations in understanding biology.

    Science.gov (United States)

    Watkins, Jessica; Elby, Andrew

    2013-06-01

    Students' epistemological views about biology--their ideas about what "counts" as learning and understanding biology--play a role in how they approach their courses and respond to reforms. As introductory biology courses incorporate more physics and quantitative reasoning, student attitudes about the role of equations in biology become especially relevant. However, as documented in research in physics education, students' epistemologies are not always stable and fixed entities; they can be dynamic and context-dependent. In this paper, we examine an interview with an introductory student in which she discusses the use of equations in her reformed biology course. In one part of the interview, she expresses what sounds like an entrenched negative stance toward the role equations can play in understanding biology. However, later in the interview, when discussing a different biology topic, she takes a more positive stance toward the value of equations. These results highlight how a given student can have diverse ways of thinking about the value of bringing physics and math into biology. By highlighting how attitudes can shift in response to different tasks, instructional environments, and contextual cues, we emphasize the need to attend to these factors, rather than treating students' beliefs as fixed and stable.

  6. Screening the efficient biological prospects of triazole allied mixed ligand metal complexes

    Science.gov (United States)

    Utthra, Ponnukalai Ponya; Kumaravel, Ganesan; Raman, Natarajan

    2017-12-01

    Triazole appended mixed ligand complexes (1-8) of the general formula [ML (bpy/phen)2]Cl2, where M = Cu(II), Co(II), Ni(II) and Zn(II), L = triazole appended Schiff base (E)sbnd N-(4-nitrobenzylidene)-1H-1,2,4-triazol-3-amine and bpy/phen = 2,2‧-bipyridine/1,10-phenanthroline, have been synthesized. The design and synthesis of this elaborate ligand has been performed with the aim of increasing stability and conjugation of 1,2,4 triazole, whose Schiff base derivatives are known as biologically active compounds thereby exploring their DNA binding affinity and other biological applications. The compounds have been comprehensively characterized by elemental analysis, spectroscopic methods (IR, UV-Vis, EPR, 1H and 13C NMR spectroscopy), ESI mass spectrometry and magnetic susceptibility measurements. The complexes were found to exhibit octahedral geometry. The complexes 1-8 were subjected to DNA binding techniques evaluated using UV-Vis absorption, CV, CD, Fluorescence spectroscopy and hydrodynamic measurements. Complex 5 showed a Kb value of 3.9 × 105 M-1. The DNA damaging efficacy for the complexes was observed to be high compared to the ligand. The antimicrobial screening of the compounds against bacterial and fungal strains indicates that the complexes possess excellent antimicrobial activity than the ligand. The overall biological activity of the complexes with phen as a co-ligand possessed superior potential than the ligand.

  7. 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’.

  8. Temperature-dependent phase transitions in zeptoliter volumes of a complex biological membrane

    International Nuclear Information System (INIS)

    Nikiforov, Maxim P; Jesse, Stephen; Kalinin, Sergei V; Hohlbauch, Sophia; Proksch, Roger; King, William P; Voitchovsky, Kislon; Contera, Sonia Antoranz

    2011-01-01

    Phase transitions in purple membrane have been a topic of debate for the past two decades. In this work we present studies of a reversible transition of purple membrane in the 50-60 deg. C range in zeptoliter volumes under different heating regimes (global heating and local heating). The temperature of the reversible phase transition is 52 ± 5 deg. C for both local and global heating, supporting the hypothesis that this transition is mainly due to a structural rearrangement of bR molecules and trimers. To achieve high resolution measurements of temperature-dependent phase transitions, a new scanning probe microscopy-based method was developed. We believe that our new technique can be extended to other biological systems and can contribute to the understanding of inhomogeneous phase transitions in complex systems.

  9. Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds

    DEFF Research Database (Denmark)

    Fang, Lingzhao; Sahana, Goutam; Ma, Peipei

    2017-01-01

    sequence variants in Holstein (HOL) and Jersey (JER) cattle were analysed. We first carried out a post-GWAS analysis in a HOL training population to assess the degree of enrichment of the association signals in the gene regions defined by each GO term. We then extended the genomic best linear unbiased......BACKGROUND: A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic...

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

    Science.gov (United States)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-06-01

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

  11. A microfluidic dialysis device for complex biological mixture SERS analysis

    KAUST Repository

    Perozziello, Gerardo; Candeloro, Patrizio; Gentile, Francesco T.; Coluccio, Maria Laura; Tallerico, Marco; De Grazia, Antonio; Nicastri, Annalisa; Perri, Angela Mena; Parrotta, Elvira; Pardeo, Francesca; Catalano, Rossella; Cuda, Giovanni; Di Fabrizio, Enzo M.

    2015-01-01

    In this paper, we present a microfluidic device fabricated with a simple and inexpensive process allowing rapid filtering of peptides from a complex mixture. The polymer microfluidic device can be used for sample preparation in biological

  12. Degeneracy: a link between evolvability, robustness and complexity in biological systems

    Directory of Open Access Journals (Sweden)

    Whitacre James M

    2010-02-01

    Full Text Available Abstract A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability.

  13. Review of Biological Network Data and Its Applications

    Directory of Open Access Journals (Sweden)

    Donghyeon Yu

    2013-12-01

    Full Text Available Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

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

    Science.gov (United States)

    Jalili, Mahdi

    2018-03-01

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

  15. Increasing process understanding by analyzing complex interactions in experimental data

    DEFF Research Database (Denmark)

    Naelapaa, Kaisa; Allesø, Morten; Kristensen, Henning Gjelstrup

    2009-01-01

    understanding of a coating process. It was possible to model the response, that is, the amount of drug released, using both mentioned techniques. However, the ANOVAmodel was difficult to interpret as several interactions between process parameters existed. In contrast to ANOVA, GEMANOVA is especially suited...... for modeling complex interactions and making easily understandable models of these. GEMANOVA modeling allowed a simple visualization of the entire experimental space. Furthermore, information was obtained on how relative changes in the settings of process parameters influence the film quality and thereby drug......There is a recognized need for new approaches to understand unit operations with pharmaceutical relevance. A method for analyzing complex interactions in experimental data is introduced. Higher-order interactions do exist between process parameters, which complicate the interpretation...

  16. Ecosystemic Complexity Theory of Conflict: Understanding the Fog of Conflict

    Science.gov (United States)

    Brack, Greg; Lassiter, Pamela S.; Hill, Michele B.; Moore, Sarah A.

    2011-01-01

    Counselors often engage in conflict mediation in professional practice. A model for understanding the complex and subtle nature of conflict resolution is presented. The ecosystemic complexity theory of conflict is offered to assist practitioners in navigating the fog of conflict. Theoretical assumptions are discussed with implications for clinical…

  17. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.

    Science.gov (United States)

    Sudhir, Putty-Reddy; Chen, Chung-Hsuan

    2016-03-22

    A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

  18. Students' Energy Understanding Across Biology, Chemistry, and Physics Contexts

    Science.gov (United States)

    Opitz, S. T.; Neumann, K.; Bernholt, S.; Harms, U.

    2017-07-01

    Energy is considered both as a disciplinary core idea and as a concept cutting across science disciplines. Most previous approaches studied progressing energy understanding in specific disciplinary contexts, while disregarding the relation of understanding across them. Hence, this study provides a systematic analysis of cross-disciplinary energy learning. On the basis of a cross-sectional study with n = 742 students from grades 6, 8, and 10, we analyze students' progression in understanding energy across biology, chemistry, and physics contexts. The study is guided by three hypothetical scenarios that describe how the connection between energy understanding in the three disciplinary contexts changes across grade levels. These scenarios are compared using confirmatory factor analysis (CFA). The results suggest that, from grade 6 to grade 10, energy understanding in the three disciplinary contexts is highly interrelated, thus indicating a parallel progression of energy understanding in the three disciplinary contexts. In our study, students from grade 6 onwards appeared to have few problems to apply one energy understanding across the three disciplinary contexts. These findings were unexpected, as previous research concluded that students likely face difficulties in connecting energy learning across disciplinary boundaries. Potential reasons for these results and the characteristics of the observed cross-disciplinary energy understanding are discussed in the light of earlier findings and implications for future research, and the teaching of energy as a core idea and a crosscutting concept are addressed.

  19. Towards a Unified Understanding of Lithium Action in Basic Biology and its Significance for Applied Biology.

    Science.gov (United States)

    Jakobsson, Eric; Argüello-Miranda, Orlando; Chiu, See-Wing; Fazal, Zeeshan; Kruczek, James; Nunez-Corrales, Santiago; Pandit, Sagar; Pritchet, Laura

    2017-12-01

    about the nature of this competition and suggest using and extending this knowledge towards the goal of a unified understanding of lithium in biology and the application of that understanding in medicine and nutrition.

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

    Science.gov (United States)

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

    2017-11-01

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

  1. Complexity and simplification in understanding recruitment in benthic populations

    KAUST Repository

    Pineda, Jesús

    2008-11-13

    Research of complex systems and problems, entities with many dependencies, is often reductionist. The reductionist approach splits systems or problems into different components, and then addresses these components one by one. This approach has been used in the study of recruitment and population dynamics of marine benthic (bottom-dwelling) species. Another approach examines benthic population dynamics by looking at a small set of processes. This approach is statistical or model-oriented. Simplified approaches identify "macroecological" patterns or attempt to identify and model the essential, "first-order" elements of the system. The complexity of the recruitment and population dynamics problems stems from the number of processes that can potentially influence benthic populations, including (1) larval pool dynamics, (2) larval transport, (3) settlement, and (4) post-settlement biotic and abiotic processes, and larval production. Moreover, these processes are non-linear, some interact, and they may operate on disparate scales. This contribution discusses reductionist and simplified approaches to study benthic recruitment and population dynamics of bottom-dwelling marine invertebrates. We first address complexity in two processes known to influence recruitment, larval transport, and post-settlement survival to reproduction, and discuss the difficulty in understanding recruitment by looking at relevant processes individually and in isolation. We then address the simplified approach, which reduces the number of processes and makes the problem manageable. We discuss how simplifications and "broad-brush first-order approaches" may muddle our understanding of recruitment. Lack of empirical determination of the fundamental processes often results in mistaken inferences, and processes and parameters used in some models can bias our view of processes influencing recruitment. We conclude with a discussion on how to reconcile complex and simplified approaches. Although it

  2. First-Year Biology Students' Understandings of Meiosis: An Investigation Using a Structural Theoretical Framework

    Science.gov (United States)

    Quinn, Frances; Pegg, John; Panizzon, Debra

    2009-01-01

    Meiosis is a biological concept that is both complex and important for students to learn. This study aims to explore first-year biology students' explanations of the process of meiosis, using an explicit theoretical framework provided by the Structure of the Observed Learning Outcome (SOLO) model. The research was based on responses of 334…

  3. Patient Understanding of the Risks and Benefits of Biologic Therapies in Inflammatory Bowel Disease: Insights from a Large-scale Analysis of Social Media Platforms.

    Science.gov (United States)

    Martinez, Bibiana; Dailey, Francis; Almario, Christopher V; Keller, Michelle S; Desai, Mansee; Dupuy, Taylor; Mosadeghi, Sasan; Whitman, Cynthia; Lasch, Karen; Ursos, Lyann; Spiegel, Brennan M R

    2017-07-01

    Few studies have examined inflammatory bowel disease (IBD) patients' knowledge and understanding of biologic therapies outside traditional surveys. Here, we used social media data to examine IBD patients' understanding of the risks and benefits associated with biologic therapies and how this affects decision-making. We collected posts from Twitter and e-forum discussions from >3000 social media sites posted between June 27, 2012 and June 27, 2015. Guided by natural language processing, we identified posts with specific IBD keywords that discussed the risks and/or benefits of biologics. We then manually coded the resulting posts and performed qualitative analysis using ATLAS.ti software. A hierarchical coding structure was developed based on the keyword list and relevant themes were identified through manual coding. We examined 1598 IBD-related posts, of which 452 (28.3%) centered on the risks and/or benefits of biologics. There were 5 main themes: negative experiences and concerns with biologics (n = 247; 54.6%), decision-making surrounding biologic use (n = 169; 37.4%), positive experiences with biologics (n = 168; 37.2%), information seeking from peers (n = 125; 27.7%), and cost (n = 38; 8.4%). Posts describing negative experiences primarily commented on side effects from biologics, concerns about potential side effects and increased cancer risk, and pregnancy safety concerns. Posts on decision-making focused on nonbiologic treatment options, hesitation to initiate biologics, and concerns about changing or discontinuing regimens. Social media reveals a wide range of themes governing patients' experience and choice with IBD biologics. The complexity of navigating their risk-benefit profiles suggests merit in creating online tailored decision tools to support IBD patients' decision-making with biologic therapies.

  4. Practical approaches to biological inorganic chemistry

    CERN Document Server

    Louro, Ricardo O

    2012-01-01

    The book reviews the use of spectroscopic and related methods to investigate the complex structures and mechanisms of biological inorganic systems that contain metals. Each chapter presents an overview of the technique including relevant theory, clearly explains what it is and how it works and then presents how the technique is actually used to evaluate biological structures. Practical examples and problems are included to illustrate each technique and to aid understanding. Designed for students and researchers who want to learn both the basics, and more advanced aspects of bioinorganic chemistry. It includes many colour illustrations enable easier visualization of molecular mechanisms and structures. It provides worked examples and problems that are included to illustrate and test the reader's understanding of each technique. It is written by a multi-author team who use and teach the most important techniques used today to analyse complex biological structures.

  5. Reflecting on complexity of biological systems: Kant and beyond?

    Science.gov (United States)

    Van de Vijver, Gertrudis; Van Speybroeck, Linda; Vandevyvere, Windy

    2003-01-01

    Living organisms are currently most often seen as complex dynamical systems that develop and evolve in relation to complex environments. Reflections on the meaning of the complex dynamical nature of living systems show an overwhelming multiplicity in approaches, descriptions, definitions and methodologies. Instead of sustaining an epistemic pluralism, which often functions as a philosophical armistice in which tolerance and so-called neutrality discharge proponents of the burden to clarify the sources and conditions of agreement and disagreement, this paper aims at analysing: (i) what has been Kant's original conceptualisation of living organisms as natural purposes; (ii) how the current perspectives are to be related to Kant's viewpoint; (iii) what are the main trends in current complexity thinking. One of the basic ideas is that the attention for structure and its epistemological consequences witness to a great extent of Kant's viewpoint, and that the idea of organisational stratification today constitutes a different breeding ground within which complexity issues are raised. The various approaches of complexity in biological systems are captured in terms of two different styles, universalism and (weak and strong) constructivism, between which hybrid forms exist.

  6. Life: An Introduction to Complex Systems Biology

    CERN Document Server

    Kaneko, Kunihiko

    2006-01-01

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

  7. Exploitation of complex network topology for link prediction in biological interactomes

    KAUST Repository

    Alanis Lobato, Gregorio

    2014-01-01

    In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable

  8. Complexity: the organizing principle at the interface of biological (dis ...

    Indian Academy of Sciences (India)

    RAMRAY BHAT

    2017-07-05

    Jul 5, 2017 ... opment of complexity theory in the context of biological systems. ... (DST), a mathematical enterprise that deals with the behaviour of ... and application of programming to trace the dynamical .... with the resultant organization being regulated by the ... more regular the pattern, the smaller the program needed.

  9. Understanding Biological Roles of Venoms Among the Caenophidia: The Importance of Rear-Fanged Snakes.

    Science.gov (United States)

    Mackessy, Stephen P; Saviola, Anthony J

    2016-11-01

    Snake venoms represent an adaptive trophic response to the challenges confronting a limbless predator for overcoming combative prey, and this chemical means of subduing prey shows several dominant phenotypes. Many front-fanged snakes, particularly vipers, feed on various vertebrate and invertebrate prey species, and some of their venom components (e.g., metalloproteinases, cobratoxin) appear to have been selected for "broad-brush" incapacitation of different prey taxa. Using proteomic and genomic techniques, the compositional diversity of front-fanged snakes is becoming well characterized; however, this is not the case for most rear-fanged colubroid snakes. Because these species consume a high diversity of prey, and because venoms are primarily a trophic adaptation, important clues for understanding specific selective pressures favoring venom component composition will be found among rear-fanged snake venoms. Rear-fanged snakes typically (but not always) produce venoms with lower complexity than front-fanged snakes, and there are even fewer dominant (and, arguably, biologically most relevant) venom protein families. We have demonstrated taxon-specific toxic effects, where lizards and birds show high susceptibility while mammals are largely unaffected, for both Old World and New World rear-fanged snakes, strongly indicating a causal link between toxin evolution and prey preference. New data are presented on myotoxin a, showing that the extremely rapid paralysis induced by this rattlesnake toxin is specific for rodents, and that myotoxin a is ineffectual against lizards. Relatively few rear-fanged snake venoms have been characterized, and basic natural history data are largely lacking, but directed sampling of specialized species indicates that novel compounds are likely among these specialists, particularly among those species feeding on invertebrate prey such as scorpions and centipedes. Because many of the more than 2200 species of colubroid snakes are rear

  10. The complexity of DNA damage: relevance to biological consequences

    International Nuclear Information System (INIS)

    Ward, J.F.

    1994-01-01

    Ionizing radiation causes both singly and multiply damaged sites in DNA when the range of radical migration is limited by the presence of hydroxyl radical scavengers (e.g. within cells). Multiply damaged sites are considered to be more biologically relevant because of the challenges they present to cellular repair mechanisms. These sites occur in the form of DNA double-strand breaks (dsb) but also as other multiple damages that can be converted to dsb during attempted repair. The presence of a dsb can lead to loss of base sequence information and/or can permit the two ends of a break to separate and rejoin with the wrong partner. (Multiply damaged sites may also be the biologically relevant type of damage caused by other agents, such as UVA, B and/or C light, and some antitumour antibiotics). The quantitative data available from radiation studies of DNA are shown to support the proposed mechanisms for the production of complex damage in cellular DNA, i.e. via scavengable and non-scavengable mechanisms. The yields of complex damages can in turn be used to support the conclusion that cellular mutations are a consequence of the presence of these damages within a gene. (Author)

  11. Do Zoo Visitors Need Zoology Knowledge to Understand Conservation Messages? An Exploration of the Public Understanding of Animal Biology and of the Conservation of Biodiversity in a Zoo Setting

    Science.gov (United States)

    Dove, Tracy; Byrne, Jenny

    2014-01-01

    This study explores the current knowledge and understanding about animal biology of zoo visitors and investigates whether knowledge of animal biology influences the ability of people to understand how human activity affects biodiversity. Zoos can play a role in the development of scientific literacy in the fields of animal biology and biodiversity…

  12. Understanding Biological Rates and their Temperature Dependence, from Enzymes to Ecosystems

    Science.gov (United States)

    Prentice, E.; Arcus, V. L.

    2017-12-01

    Temperature responses over various scales in biological systems follow a similar pattern; negative curvature results in an optimum temperature (Topt) for activity/growth/turnover, with decreases in rates on either side of Topt. Previously this downturn in rates at high temperatures has been attributed to enzyme denaturation, where a failing of the basic driving units of metabolism was used to describe curvature at the enzyme and organism level. However, recent developments in our understanding of the factors governing enzyme rates at different temperatures have guided a new understanding of the responses of biological systems. Enzymes catalyse reactions by driving the substrate through a high energy species, which is tightly bound to the enzyme. Macromolecular rate theory (MMRT) has recently been developed to account for the changes in the system brought about by this tight binding, specifically the change in the physical parameter heat capacity (ΔCǂp), and the effect this has on the temperature dependence of enzyme reactions. A negative ΔCǂp imparts the signature negative curvature to rates in the absence of denaturation, and finds that Topt, ΔCǂp and curvature are all correlated, placing constraints on biological systems. The simplest of cells comprise thousands of enzymatically catalysed reactions, functioning in series and in parallel in metabolic pathways to determine the overall growth rate of an organism. Intuitively, the temperature effects of enzymes play a role in determining the overall temperature dependence of an organism, in tandem with cellular level regulatory responses. However, the effect of individual Topt values and curvature on overall pathway behaviour is less apparent. Here, this is investigated in the context of MMRT through the in vitro characterisation of a six-step metabolic pathway to understand the steps in isolation and functioning in series. Pathway behaviour is found to be approximately an average of the properties of the

  13. The effects of academic literacy instruction on engagement and conceptual understanding of biology of ninth-grade students

    Science.gov (United States)

    Larson, Susan C.

    Academic language, discourse, vocabulary, motivation, and comprehension of complex texts and concepts are keys to learning subject-area content. The need for a disciplinary literacy approach in high school classrooms accelerates as students become increasing disengaged in school and as content complexity increases. In the present quasi-experimental mixed-method study, a ninth-grade biology unit was designed with an emphasis on promoting academic literacy skills, discourse, meaningful constructivist learning, interest development, and positive learning experiences in order to learn science content. Quantitative and qualitative analyses on a variety of measures completed by 222 students in two high schools revealed that those who received academic literacy instruction in science class performed at significantly higher levels of conceptual understanding of biology content, academic language and vocabulary use, reasoned thought, engagement, and quality of learning experience than control-group students receiving traditionally-organized instruction. Academic literacy was embedded into biology instruction to engage students in meaning-making discourses of science to promote learning. Academic literacy activities were organized according the phases of interest development to trigger and sustain interest and goal-oriented engagement throughout the unit. Specific methods included the Generative Vocabulary Matrix (GVM), scenario-based writing, and involvement in a variety of strategically-placed discourse activities to sustain or "boost" engagement for learning. Traditional instruction for the control group included teacher lecture, whole-group discussion, a conceptual organizer, and textbook reading. Theoretical foundations include flow theory, sociocultural learning theory, and interest theory. Qualitative data were obtained from field notes and participants' journals. Quantitative survey data were collected and analyzed using the Experience Sampling Method (ESM) to

  14. Understanding complex urban systems integrating multidisciplinary data in urban models

    CERN Document Server

    Gebetsroither-Geringer, Ernst; Atun, Funda; Werner, Liss

    2016-01-01

    This book is devoted to the modeling and understanding of complex urban systems. This second volume of Understanding Complex Urban Systems focuses on the challenges of the modeling tools, concerning, e.g., the quality and quantity of data and the selection of an appropriate modeling approach. It is meant to support urban decision-makers—including municipal politicians, spatial planners, and citizen groups—in choosing an appropriate modeling approach for their particular modeling requirements. The contributors to this volume are from different disciplines, but all share the same goal: optimizing the representation of complex urban systems. They present and discuss a variety of approaches for dealing with data-availability problems and finding appropriate modeling approaches—and not only in terms of computer modeling. The selection of articles featured in this volume reflect a broad variety of new and established modeling approaches such as: - An argument for using Big Data methods in conjunction with Age...

  15. A comparison of the application of a biological and phenetic species concept in the Hebeloma crustuliniforme complex within a phylogenetic framework

    DEFF Research Database (Denmark)

    Aanen, Duur Kornelis; Kuyper, T.W.

    2004-01-01

    a major factor. Intercompatibility tests and DNA based phylogenies indicate that most biological species are very closely related and hence provide support for the claim that correspondence between a biological species concept and a phenetic species concept in the H. crustuliniforme complex is not likely...... biological species in that complex. Based on two nuclear sequences, we present a best estimate of the phylogeny of biological species within the complex. Using this phylogeny, on the basis of strict monophyly only two species can be morphologically recognised among 22 biological species. Relaxing......A method is presented to derive an operational phenetic species concept for the Hebeloma crustuliniforme complex in northwestern Europe. The complex was found to consist of at least 22 biological species (intercompatibility groups; ICGs). Almost none of these biological species could be recognised...

  16. Kirigami artificial muscles with complex biologically inspired morphologies

    International Nuclear Information System (INIS)

    Sareh, Sina; Rossiter, Jonathan

    2013-01-01

    In this paper we present bio-inspired smart structures which exploit the actuation of flexible ionic polymer composites and the kirigami design principle. Kirigami design is used to convert planar actuators into active 3D structures capable of large out-of-plane displacement and that replicate biological mechanisms. Here we present the burstbot, a fluid control and propulsion mechanism based on the atrioventricular cuspid valve, and the vortibot, a spiral actuator based on Vorticella campanula, a ciliate protozoa. Models derived from biological counterparts are used as a platform for design optimization and actuator performance measurement. The symmetric and asymmetric fluid interactions of the burstbot are investigated and the effectiveness in fluid transport applications is demonstrated. The vortibot actuator is geometrically optimized as a camera positioner capable of 360° scanning. Experimental results for a one-turn spiral actuator show complex actuation derived from a single degree of freedom control signal. (paper)

  17. Using an adaptive expertise lens to understand the quality of teachers' classroom implementation of computer-supported complex systems curricula in high school science

    Science.gov (United States)

    Yoon, Susan A.; Koehler-Yom, Jessica; Anderson, Emma; Lin, Joyce; Klopfer, Eric

    2015-05-01

    Background: This exploratory study is part of a larger-scale research project aimed at building theoretical and practical knowledge of complex systems in students and teachers with the goal of improving high school biology learning through professional development and a classroom intervention. Purpose: We propose a model of adaptive expertise to better understand teachers' classroom practices as they attempt to navigate myriad variables in the implementation of biology units that include working with computer simulations, and learning about and teaching through complex systems ideas. Sample: Research participants were three high school biology teachers, two females and one male, ranging in teaching experience from six to 16 years. Their teaching contexts also ranged in student achievement from 14-47% advanced science proficiency. Design and methods: We used a holistic multiple case study methodology and collected data during the 2011-2012 school year. Data sources include classroom observations, teacher and student surveys, and interviews. Data analyses and trustworthiness measures were conducted through qualitative mining of data sources and triangulation of findings. Results: We illustrate the characteristics of adaptive expertise of more or less successful teaching and learning when implementing complex systems curricula. We also demonstrate differences between case study teachers in terms of particular variables associated with adaptive expertise. Conclusions: This research contributes to scholarship on practices and professional development needed to better support teachers to teach through a complex systems pedagogical and curricular approach.

  18. Pedagogy of complex relationality exploring complexity theory, neuro-phenomenology, and attentiveness for education

    Science.gov (United States)

    Khattar, Randa

    What do the new sciences of complex relationality offer education? This work draws on complexity theory, neurological understandings of biology and phenomenology, and attentiveness to study what the new sciences might offer education and the possibilities of a pedagogical understanding of embodied knowing. Complexity theory provides understandings of local-global relationality, self-organization, far-from-equilibrium conditions, and emergent dynamics that are important for describing pedagogical relationality. In itself, however, complexity theory is lacking an attention to issues of embodiment that respond directly to an ethical understanding of relationality. Phenomenology provides important views on the human experience of perception, for example, Merleau-Ponty's, whose research opens up possibilities for embodiment and attentiveness. At the level of pedagogical practice, I will pose, following biologists Humberto Maturana and Francisco Varela's autopoietic self-making understanding of life, that attentiveness perspectives, which have been largely absent from western pedagogical theory and practice, are crucial to promoting embodied knowing for education. Maturana and Varela's autopoietic perspective offers an embodied understanding of living---and therefore education---which opens up necessary attentive spaces to listen to one another in non judgmental awareness in the present moment of experience. I offer insights into a relationally complex conception of education drawing on this biological and autopoietically-grounded framework. These insights are framed in the context of five clusters of relations: (1) emergence, far-from-equilibrium, and local-global relationality; (2) autopoietic autonomy, structural determination and sensory-motor coupling; (3) triggering perturbations, structural plasticity, and autopoietic organization; (4) knowing as adequate action, domains of interaction, and blind spots; and (5) attentiveness and responsive relationality. Four

  19. How to make a complex story understandable. Communication on nitrogen

    International Nuclear Information System (INIS)

    Bleeker, A.; Hensen, A.; Erisman, J.W.

    2011-01-01

    Understanding is the first step towards solving the nitrogen problem. Various applications have been developed to gain insight in the complex interactions between the nitrogen cycle and the social-economic and environmental aspects. Experience has learned that many users have not only gained a clearer picture of the urgency and complexity of the problem; now they also have options for dealing with the nitrogen problem. [nl

  20. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    These discussions included, among others, the possible consequences of nonDNA-based inheritance—epigenetics and cultural evolution, niche construction, and developmental mechanisms on our understanding of the evolutionary process, speciation, complexity in biology, and constructing a formal evolutionary theory.

  1. Understanding the biological responses of nanostructured metals and surfaces

    Science.gov (United States)

    Lowe, Terry C.; Reiss, Rebecca A.

    2014-08-01

    Metals produced by Severe Plastic Deformation (SPD) offer distinct advantages for medical applications such as orthopedic devices, in part because of their nanostructured surfaces. We examine the current theoretical foundations and state of knowledge for nanostructured biomaterials surface optimization within the contexts that apply to bulk nanostructured metals, differentiating how their microstructures impact osteogenesis, in particular, for Ultrafine Grained (UFG) titanium. Then we identify key gaps in the research to date, pointing out areas which merit additional focus within the scientific community. For example, we highlight the potential of next-generation DNA sequencing techniques (NGS) to reveal gene and non-coding RNA (ncRNA) expression changes induced by nanostructured metals. While our understanding of bio-nano interactions is in its infancy, nanostructured metals are already being marketed or developed for medical devices such as dental implants, spinal devices, and coronary stents. Our ability to characterize and optimize the biological response of cells to SPD metals will have synergistic effects on advances in materials, biological, and medical science.

  2. Understanding the biological responses of nanostructured metals and surfaces

    International Nuclear Information System (INIS)

    Lowe, Terry C; A Reiss, Rebecca

    2014-01-01

    Metals produced by Severe Plastic Deformation (SPD) offer distinct advantages for medical applications such as orthopedic devices, in part because of their nanostructured surfaces. We examine the current theoretical foundations and state of knowledge for nanostructured biomaterials surface optimization within the contexts that apply to bulk nanostructured metals, differentiating how their microstructures impact osteogenesis, in particular, for Ultrafine Grained (UFG) titanium. Then we identify key gaps in the research to date, pointing out areas which merit additional focus within the scientific community. For example, we highlight the potential of next-generation DNA sequencing techniques (NGS) to reveal gene and non-coding RNA (ncRNA) expression changes induced by nanostructured metals. While our understanding of bio-nano interactions is in its infancy, nanostructured metals are already being marketed or developed for medical devices such as dental implants, spinal devices, and coronary stents. Our ability to characterize and optimize the biological response of cells to SPD metals will have synergistic effects on advances in materials, biological, and medical science

  3. Perceptual Influence of Ugandan Biology Students' Understanding of HIV/AIDS

    Science.gov (United States)

    Mutonyi, Harriet; Nashon, Samson; Nielsen, Wendy S.

    2010-08-01

    In Uganda, curbing the spread of HIV/AIDS has largely depended on public and private media messages about the disease. Media campaigns based on Uganda’s cultural norms of communication are metaphorical, analogical and simile-like. The topic of HIV/AIDS has been introduced into the Senior Three (Grade 11) biology curriculum in Uganda. To what extent do students’ pre-conceptions of the disease, based on these media messages influence students’ development of conceptual understanding of the disease, its transmission and prevention? Of significant importance is the impact the conceptions students have developed from the indirect media messages on classroom instruction on HIV/AIDS. The study is based in a theoretical framework of conceptual change in science learning. An interpretive case study to determine the impact of Ugandan students’ conceptions or perceptions on classroom instruction about HIV/AIDS, involving 160 students aged 15-17, was conducted in four different Ugandan high schools: girls boarding, boys boarding, mixed boarding, and mixed day. Using questionnaires, focus group discussions, recorded biology lessons and informal interviews, students’ preconceptions of HIV/AIDS and how these impact lessons on HIV/AIDS were discerned. These preconceptions fall into four main categories: religious, political, conspiracy and traditional African worldviews. Results of data analysis suggest that students’ prior knowledge is persistent even after biology instructions. This has implications for current teaching approaches, which are mostly teacher-centred in Ugandan schools. A rethinking of the curriculum with the intent of offering science education programs that promote understanding of the science of HIV/AIDS as opposed to what is happening now—insensitivity to misconceptions about the disease—is needed.

  4. Conceptions of Memorizing and Understanding in Learning, and Self-Efficacy Held by University Biology Majors

    Science.gov (United States)

    Lin, Tzu-Chiang; Liang, Jyh-Chong; Tsai, Chin-Chung

    2015-01-01

    This study aims to explore Taiwanese university students' conceptions of learning biology as memorizing or as understanding, and their self-efficacy. To this end, two questionnaires were utilized to survey 293 Taiwanese university students with biology-related majors. A questionnaire for measuring students' conceptions of memorizing and…

  5. Large, dynamic, multi-protein complexes: a challenge for structural biology

    Czech Academy of Sciences Publication Activity Database

    Rozycki, B.; Bouřa, Evžen

    2014-01-01

    Roč. 26, č. 46 (2014), 463103/1-463103/11 ISSN 0953-8984 R&D Projects: GA MŠk LO1302 EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : protein structure * multi-protein complexes * hybrid methods of structural biology Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.346, year: 2014

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

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon

    externally founded information, such as KEGG pathways, Gene Ontology gene sets, or genomic features, and estimate the joint contribution of the genetic variants within these sets to complex trait phenotypes. The analysis of complex trait phenotypes is hampered by the myriad of genes that control the trait...

  7. Understanding Parkinson Disease: A Complex and Multifaceted Illness.

    Science.gov (United States)

    Gopalakrishna, Apoorva; Alexander, Sheila A

    2015-12-01

    Parkinson disease is an incredibly complex and multifaceted illness affecting millions of people in the United States. Parkinson disease is characterized by progressive dopaminergic neuronal dysfunction and loss, leading to debilitating motor, cognitive, and behavioral symptoms. Parkinson disease is an enigmatic illness that is still extensively researched today to search for a better understanding of the disease, develop therapeutic interventions to halt or slow progression of the disease, and optimize patient outcomes. This article aims to examine in detail the normal function of the basal ganglia and dopaminergic neurons in the central nervous system, the etiology and pathophysiology of Parkinson disease, related signs and symptoms, current treatment, and finally, the profound impact of understanding the disease on nursing care.

  8. Using Simple Manipulatives to Improve Student Comprehension of a Complex Biological Process: Protein Synthesis

    Science.gov (United States)

    Guzman, Karen; Bartlett, John

    2012-01-01

    Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

  9. Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

    OpenAIRE

    Shuo Gu; Jianfeng Pei

    2017-01-01

    With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regula...

  10. Quality of Life Philosophy III. Towards a New Biology: Understanding the Biological Connection between Quality of Life, Disease, and Healing

    Directory of Open Access Journals (Sweden)

    Soren Ventegodt

    2003-01-01

    Full Text Available This paper addresses (in a philosophical way the complex and enigmatic interface between matter, life, and consciousness in modern medical science. The problem today in understanding living matter is not at the molecular level, but at the macro level where all molecular activities in the individual cell are coordinated, and especially at a higher level, where the activities of all the organism’s cells are coordinated. Although we understand very much of the body’s chemistry, we have only just started to get the gist of the tremendous organization of living matter. We are just beginning to acknowledge the enormous flow of information that is needed to make everything function in a healthy organism, including consciousness, where every cell does exactly what it has to do to make the organs function.A concept that seems to be able to bridge the scientifically very different domains of matter, life, and consciousness seems to be “biological information”. If a cell is seen as a liquid crystal in which the cell’s molecules constantly connect in firm mutual relationships only to dissolve again and become fluid and free, whenever the cell needs it, the backbone of the cell seems to be the information that organizes the cell. For example, in cell motion a cell is able to crawl with the help of a skeleton of fibers that can be created guided by biological information, whenever the cell needs the solidity provided by the fibers. The moment it has finished crawling or intends to crawl in another direction, these fibers will dissolve again. The fibers are made of millions of molecules that connect in an arranged pattern, and they dissolve when these molecules again let go of each other. How the cell precisely regulates such processes is today a complete mystery. How cells cocreate consciousness is also an enigma. All we can do is describe the cell and the organisms arising from its cells as filled with energy and information as well as an

  11. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

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

    2016-06-01

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

  12. Biological Recovery of Platinum Complexes from Diluted Aqueous Streams by Axenic Cultures.

    Directory of Open Access Journals (Sweden)

    Synthia Maes

    Full Text Available The widespread use of platinum in high-tech and catalytic applications has led to the production of diverse Pt loaded wastewaters. Effective recovery strategies are needed for the treatment of low concentrated waste streams to prevent pollution and to stimulate recovery of this precious resource. The biological recovery of five common environmental Pt-complexes was studied under acidic conditions; the chloro-complexes PtCl42- and PtCl62-, the amine-complex Pt(NH34Cl2 and the pharmaceutical complexes cisplatin and carboplatin. Five bacterial species were screened on their platinum recovery potential; the Gram-negative species Shewanella oneidensis MR-1, Cupriavidus metallidurans CH34, Geobacter metallireducens, and Pseudomonas stutzeri, and the Gram-positive species Bacillus toyonensis. Overall, PtCl42- and PtCl62- were completely recovered by all bacterial species while only S. oneidensis and C. metallidurans were able to recover cisplatin quantitatively (99%, all in the presence of H2 as electron donor at pH 2. Carboplatin was only partly recovered (max. 25% at pH 7, whereas no recovery was observed in the case of the Pt-tetraamine complex. Transmission electron microscopy (TEM revealed the presence of both intra- and extracellular platinum particles. Flow cytometry based microbial viability assessment demonstrated the decrease in number of intact bacterial cells during platinum reduction and indicated C. metallidurans to be the most resistant species. This study showed the effective and complete biological recovery of three common Pt-complexes, and estimated the fate and transport of the Pt-complexes in wastewater treatment plants and the natural environment.

  13. A study of ruthenium complexes of some biologically relevant a-N ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 112; Issue 3. A study of ruthenium complexes of some biologically relevant ∙ -N-heterocyclic ... Author Affiliations. P Sengupta1 S Ghosh1. Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India ...

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  15. Protein scaffolds and higher-order complexes in synthetic biology

    NARCIS (Netherlands)

    den Hamer, A.; Rosier, B.J.H.M.; Brunsveld, L.; de Greef, T.F.A.; Ryadnov, M.; Brunsveld, L.; Suga, H.

    2017-01-01

    Interactions between proteins control molecular functions such as signalling or metabolic activity. Assembly of proteins via scaffold proteins or in higher-order complexes is a key regulatory mechanism. Understanding and functionally applying this concept requires the construction, study, and

  16. [Physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands underlying biological activities of these complexes].

    Science.gov (United States)

    Vanin, A F; Borodulin, R R; Kubrina, L N; Mikoian, V D; Burbaev, D Sh

    2013-01-01

    Current notions and new experimental data of the authors on physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands (glutathione or cysteine), underlying the ability of the complexes to act as NO molecule and nitrosonium ion donors, are considered. This ability determines various biological activities of dinitrosyl iron complexes--inducing long-lasting vasodilation and thereby long-lasting hypotension in human and animals, inhibiting pellet aggregation, increasing red blood cell elasticity, thereby stimulating microcirculation, and reducing necrotic zone in animals with myocardial infarction. Moreover, dinitrosyl iron complexes are capable of accelerating skin wound healing, improving the function of penile cavernous tissue, blocking apoptosis development in cell cultures. When decomposed dinitrosyl iron complexes can exert cytotoxic effect that can be used for curing infectious and carcinogenic pathologies.

  17. Dependency visualization for complex system understanding

    Energy Technology Data Exchange (ETDEWEB)

    Smart, J. Allison Cory [Univ. of California, Davis, CA (United States)

    1994-09-01

    With the volume of software in production use dramatically increasing, the importance of software maintenance has become strikingly apparent. Techniques now sought and developed for reverse engineering and design extraction and recovery. At present, numerous commercial products and research tools exist which are capable of visualizing a variety of programming languages and software constructs. The list of new tools and services continues to grow rapidly. Although the scope of the existing commercial and academic product set is quite broad, these tools still share a common underlying problem. The ability of each tool to visually organize object representations is increasingly impaired as the number of components and component dependencies within systems increases. Regardless of how objects are defined, complex ``spaghetti`` networks result in nearly all large system cases. While this problem is immediately apparent in modem systems analysis involving large software implementations, it is not new. As will be discussed in Chapter 2, related problems involving the theory of graphs were identified long ago. This important theoretical foundation provides a useful vehicle for representing and analyzing complex system structures. While the utility of directed graph based concepts in software tool design has been demonstrated in literature, these tools still lack the capabilities necessary for large system comprehension. This foundation must therefore be expanded with new organizational and visualization constructs necessary to meet this challenge. This dissertation addresses this need by constructing a conceptual model and a set of methods for interactively exploring, organizing, and understanding the structure of complex software systems.

  18. Transition metal complexes of some biologically active ligands; synthesis characterization and bioactivities

    International Nuclear Information System (INIS)

    Rehman, S.; Ali, N.; Nisar, M.

    2009-01-01

    Transition/representative transition metals complexes of biologically active chelating agent 1,2-dipyrolodinoethane were synthesized and characterized through spectral and analytical data. The complexes are of the formula (M(L)X/sub 2/). Where (M = Co (II), Ni (II), Cu (II), Zn (II), Hg (II) and Cd (II) and X = CI, Br, NO/sub 3/). Tetrahedral geometry has been proposed to these-metal complexes with the help of magnetic measurements, elemental analysis, chemical stoichiometry and spectroscopic data Antibacterial activity of the ligand and its metal complexes were screened against Eschereschi coli, Klebsiello pneumonia, Proteus mirabilis, Proteus vulhari, Streptococcus pneumonia, Salmonella Iyphi, Bacilh,s anthrax, Streptococcus fecalis and Staphylococcus aureus. Complexes were found to be active against Eschereschi coli, Klebsiella pneumonia, Proteus mirabilis and Proteus vulharis. (author)

  19. Human Development V: Biochemistry Unable to Explain the Emergence of Biological Form (Morphogenesis and Therefore a New Principle as Source of Biological Information is Needed

    Directory of Open Access Journals (Sweden)

    Søren Ventegodt

    2006-01-01

    Full Text Available Today's biomedicine builds on the conviction that biochemistry can explain the creation of the body, its anatomy and physiology. Unfortunately there are still deep mysteries strangely “fighting back” when we try to define and understand the organism and its creation in the ontogenesis as emerging from biochemistry. In analysing this from a theoretical perspective using a mathematical model focusing on the noise in complex chemical systems we argue that evolving biological structure cannot in principle be a product of chemistry. In this paper we go through the chemical gradient model and argue that this is not able to explain the ontogenesis. We discuss the used gradients as information carriers in chemical self-organizing systems and argue that by use of the “Turing structures” we are only able to modelling the mostly simple biological systems. The bio-chemical model is only able to model simple organization but not to explain the complexity of biological phenomena. We conclude that we seemingly have presented a formal proof (a NO-GO theorem that the self-organizing chemical systems that are using chemical gradients are not able to explain complex biological matters as the ontogenesis. We need a fundamentally new, information-carrying principle to understand biological information and biological order.

  20. Evaluating the biological activity of oil-polluted soils using a complex index

    Science.gov (United States)

    Kabirov, R. R.; Kireeva, N. A.; Kabirov, T. R.; Dubovik, I. Ye.; Yakupova, A. B.; Safiullina, L. M.

    2012-02-01

    A complex index characterizing the biological activity of soils (BAS) is suggested. It is based on an estimate of the level of activity of catalase; the number of heterotrophic and hydrocarbon oxidizing microorganisms, microscopic fungi, algae, and cyanobacteria; and the degree of development of higher plants and insects in the studied soil. The data on using the BAS coefficient for evaluating the efficiency of rehabilitation measures for oil-polluted soils are given. Such measures included introducing the following biological preparations: Lenoil based on a natural consortium of microorganisms Bacillus brevis and Arthrobacter sp.; the Azolen biofertilizer with complex action based on Azotobacter vinelandii; the Belvitamil biopreparation, which is the active silt of pulp and paper production; and a ready-mixed industrial association of aerobic and anaerobic microorganisms that contains hydrocarbon oxidizing microorganisms of the Arthrobacter, Bacillus, Candida, Desulfovibrio, and Pseudomonas genera.

  1. Epidemic processes in complex networks

    OpenAIRE

    Pastor Satorras, Romualdo; Castellano, Claudio; Van Mieghem, Piet; Vespignani, Alessandro

    2015-01-01

    In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world networks have a profound impact on the behavior of equilibrium and nonequilibrium phenomena occurring in various systems, and the study of epidemic spreading is central to our understanding of the unfolding of dynamical processes in complex networks. The t...

  2. Understanding Global Change (UGC) as a Unifying Conceptual Framework for Teaching Ecology: Using UGC in a High School Biology Program to Integrate Earth Science and Biology, and to Demonstrate the Value of Modeling Global Systems in Promoting Conceptual Learning

    Science.gov (United States)

    Levine, J.; Bean, J. R.

    2017-12-01

    Global change science is ideal for NGSS-informed teaching, but presents a serious challenge to K-12 educators because it is complex and interdisciplinary- combining earth science, biology, chemistry, and physics. Global systems are themselves complex. Adding anthropogenic influences on those systems creates a formidable list of topics - greenhouse effect, climate change, nitrogen enrichment, introduced species, land-use change among them - which are often presented as a disconnected "laundry list" of "facts." This complexity, combined with public and mass-media scientific illiteracy, leaves global change science vulnerable to misrepresentation and politicization, creating additional challenges to teachers in public schools. Ample stand-alone, one-off, online resources, many of them excellent, are (to date) underutilized by teachers in the high school science course taken by most students: biology. The Understanding Global Change project (UGC) from the UC Berkeley Museum of Paleontology has created a conceptual framework that organizes, connects, and explains global systems, human and non-human drivers of change in those systems, and measurable changes in those systems. This organization and framework employ core ideas, crosscutting concepts, structure/function relationships, and system models in a unique format that facilitates authentic understanding, rather than memorization. This system serves as an organizing framework for the entire ecology unit of a forthcoming mainstream high school biology program. The UGC system model is introduced up front with its core informational graphic. The model is elaborated, step by step, by adding concepts and processes as they are introduced and explained in each chapter. The informational graphic is thus used in several ways: to organize material as it is presented, to summarize topics in each chapter and put them in perspective, and for review and critical thinking exercises that supplement the usual end-of-chapter lists of

  3. Synchronization in complex networks

    Energy Technology Data Exchange (ETDEWEB)

    Arenas, A.; Diaz-Guilera, A.; Moreno, Y.; Zhou, C.; Kurths, J.

    2007-12-12

    Synchronization processes in populations of locally interacting elements are in the focus of intense research in physical, biological, chemical, technological and social systems. The many efforts devoted to understand synchronization phenomena in natural systems take now advantage of the recent theory of complex networks. In this review, we report the advances in the comprehension of synchronization phenomena when oscillating elements are constrained to interact in a complex network topology. We also overview the new emergent features coming out from the interplay between the structure and the function of the underlying pattern of connections. Extensive numerical work as well as analytical approaches to the problem are presented. Finally, we review several applications of synchronization in complex networks to different disciplines: biological systems and neuroscience, engineering and computer science, and economy and social sciences.

  4. Understanding and Enhancing Soil Biological Health: The Solution for Reversing Soil Degradation

    Directory of Open Access Journals (Sweden)

    R. Michael Lehman

    2015-01-01

    Full Text Available Our objective is to provide an optimistic strategy for reversing soil degradation by increasing public and private research efforts to understand the role of soil biology, particularly microbiology, on the health of our world’s soils. We begin by defining soil quality/soil health (which we consider to be interchangeable terms, characterizing healthy soil resources, and relating the significance of soil health to agroecosystems and their functions. We examine how soil biology influences soil health and how biological properties and processes contribute to sustainability of agriculture and ecosystem services. We continue by examining what can be done to manipulate soil biology to: (i increase nutrient availability for production of high yielding, high quality crops; (ii protect crops from pests, pathogens, weeds; and (iii manage other factors limiting production, provision of ecosystem services, and resilience to stresses like droughts. Next we look to the future by asking what needs to be known about soil biology that is not currently recognized or fully understood and how these needs could be addressed using emerging research tools. We conclude, based on our perceptions of how new knowledge regarding soil biology will help make agriculture more sustainable and productive, by recommending research emphases that should receive first priority through enhanced public and private research in order to reverse the trajectory toward global soil degradation.

  5. Novel synthesis on poly (vinyl alcohol): characterization, complexation a biological activity

    International Nuclear Information System (INIS)

    El-Sawy, N.M.; Elassar, A.Z.; Al-Fulaij, O.

    2002-01-01

    Poly(vinyl alcohol), PVA, readily condensed with phenyl hydrazine and malononitrile in basic medium to give the hydrazone and pyran derivatives, respectively. PVA reacted with chloroacetonitrile, biuet and thiophene carbonyl chloride to give modified polymeric materials. While addition of PVA to acrylonitrile and phenyl isothiocyanate gives the ether and thiocarbamate ester derivatives, respectively. Hydroxylamine hydrochloride reacted with the modified, carbonitrile containing, polymer to give the amidoxime derivative. The amidoximated products of PVA and carbamate ester of polymeric material were complexed with CUCL2 solution. The complex materials were confirmed by using UV and ESDS measurements. The morphology of PVA and complex with CUII was observed by SEM. Biological activity of some of the prepared compounds was investigated toward bacteria and fungi

  6. Encyclopedia of Complexity and Systems Science

    CERN Document Server

    Meyers, Robert A

    2009-01-01

    Encyclopedia of Complexity and Systems Science provides an authoritative single source for understanding and applying the concepts of complexity theory together with the tools and measures for analyzing complex systems in all fields of science and engineering. The science and tools of complexity and systems science include theories of self-organization, complex systems, synergetics, dynamical systems, turbulence, catastrophes, instabilities, nonlinearity, stochastic processes, chaos, neural networks, cellular automata, adaptive systems, and genetic algorithms. Examples of near-term problems and major unknowns that can be approached through complexity and systems science include: The structure, history and future of the universe; the biological basis of consciousness; the integration of genomics, proteomics and bioinformatics as systems biology; human longevity limits; the limits of computing; sustainability of life on earth; predictability, dynamics and extent of earthquakes, hurricanes, tsunamis, and other n...

  7. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna; Oliva, Romina; Cavallo, Luigi; Bonvin, Alexandre M. J. J.

    2017-01-01

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  8. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna

    2017-04-12

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  9. Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

    Directory of Open Access Journals (Sweden)

    Schwieger Michael

    2005-01-01

    Full Text Available Abstract Background Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. Results Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications. Conclusions The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends.

  10. Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

    Science.gov (United States)

    Urrios, Arturo; de Nadal, Eulàlia; Solé, Ricard; Posas, Francesc

    2016-01-01

    Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined. PMID:26829588

  11. Multidisciplinary approaches to understanding collective cell migration in developmental biology.

    Science.gov (United States)

    Schumacher, Linus J; Kulesa, Paul M; McLennan, Rebecca; Baker, Ruth E; Maini, Philip K

    2016-06-01

    Mathematical models are becoming increasingly integrated with experimental efforts in the study of biological systems. Collective cell migration in developmental biology is a particularly fruitful application area for the development of theoretical models to predict the behaviour of complex multicellular systems with many interacting parts. In this context, mathematical models provide a tool to assess the consistency of experimental observations with testable mechanistic hypotheses. In this review, we showcase examples from recent years of multidisciplinary investigations of neural crest cell migration. The neural crest model system has been used to study how collective migration of cell populations is shaped by cell-cell interactions, cell-environmental interactions and heterogeneity between cells. The wide range of emergent behaviours exhibited by neural crest cells in different embryonal locations and in different organisms helps us chart out the spectrum of collective cell migration. At the same time, this diversity in migratory characteristics highlights the need to reconcile or unify the array of currently hypothesized mechanisms through the next generation of experimental data and generalized theoretical descriptions. © 2016 The Authors.

  12. Synthesis, characterization and biological activities of semicarbazones and their copper complexes.

    Science.gov (United States)

    Venkatachalam, Taracad K; Bernhardt, Paul V; Noble, Chris J; Fletcher, Nicholas; Pierens, Gregory K; Thurecht, Kris J; Reutens, David C

    2016-09-01

    Substituted semicarbazones/thiosemicarbazones and their copper complexes have been prepared and several single crystal structures examined. The copper complexes of these semicarbazone/thiosemicarbazones were prepared and several crystal structures examined. The single crystal X-ray structure of the pyridyl-substituted semicarbazone showed two types of copper complexes, a monomer and a dimer. We also found that the p-nitrophenyl semicarbazone formed a conventional 'magic lantern' acetate-bridged dimer. Electron Paramagnetic Resonance (EPR) of several of the copper complexes was consistent with the results of single crystal X-ray crystallography. The EPR spectra of the p-nitrophenyl semicarbazone copper complex in dimethylsulfoxide (DMSO) showed the presence of two species, confirming the structural information. Since thiosemicarbazones and semicarbazones have been reported to exhibit anticancer activity, we examined the anticancer activity of several of the derivatives reported in the present study and interestingly only the thiosemicarbazone showed activity while the semicarbazones were not active indicating that introduction of sulphur atom alters the biological profile of these thiosemicarbazones. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Third International Conference on Complex Systems

    CERN Document Server

    Minai, Ali A; Unifying Themes in Complex Systems

    2006-01-01

    In recent years, scientists have applied the principles of complex systems science to increasingly diverse fields. The results have been nothing short of remarkable: their novel approaches have provided answers to long-standing questions in biology, ecology, physics, engineering, computer science, economics, psychology and sociology. The Third International Conference on Complex Systems attracted over 400 researchers from around the world. The conference aimed to encourage cross-fertilization between the many disciplines represented and to deepen our understanding of the properties common to all complex systems. This volume contains over 35 papers selected from those presented at the conference on topics including: self-organization in biology, ecological systems, language, economic modeling, ecological systems, artificial life, robotics, and complexity and art. ALI MINAI is an Affiliate of the New England Complex Systems Institute and an Associate Professor in the Department of Electrical and Computer Engine...

  14. Recent advances in understanding the biology of marginal zone lymphoma

    Science.gov (United States)

    Zucca, Emanuele

    2018-01-01

    There are three different marginal zone lymphomas (MZLs): the extranodal MZL of mucosa-associated lymphoid tissue (MALT) type (MALT lymphoma), the splenic MZL, and the nodal MZL. The three MZLs share common lesions and deregulated pathways but also present specific alterations that can be used for their differential diagnosis. Although trisomies of chromosomes 3 and 18, deletions at 6q23, deregulation of nuclear factor kappa B, and chromatin remodeling genes are frequent events in all of them, the three MZLs differ in the presence of recurrent translocations, mutations affecting the NOTCH pathway, and the transcription factor Kruppel like factor 2 ( KLF2) or the receptor-type protein tyrosine phosphatase delta ( PTPRD). Since a better understanding of the molecular events underlying each subtype may have practical relevance, this review summarizes the most recent and main advances in our understanding of the genetics and biology of MZLs. PMID:29657712

  15. Diversity of the Cryptococcus neoformans-Cryptococcus gattii species complex.

    NARCIS (Netherlands)

    Bovers, M.; Hagen, F.; Boekhout, T.

    2008-01-01

    More than 110 years of study of the Cryptococcus neoformans and Cryptococcus gattii species complex has resulted in an enormous accumulation of fundamental and applied biological and clinical knowledge. Recent developments in our understanding of the diversity within the species complex are

  16. Next-Generation Sequencing: From Understanding Biology to Personalized Medicine

    Directory of Open Access Journals (Sweden)

    Benjamin Meder

    2013-03-01

    Full Text Available Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.

  17. Bringing content understanding into usability testing in complex application domains—a case study in eHealth

    DEFF Research Database (Denmark)

    Andersen, Simon Bruntse; Rasmussen, Claire Kirchert; Frøkjær, Erik

    2017-01-01

    A usability evaluation technique, Cooperative Usability Testing with Questions of Understanding (CUT with QU) intended to illuminate users’ ability to understand the content information of an application is proposed. In complex application domains as for instance the eHealth domain, this issue...... of users’ content understanding is sometimes crucial, and thus should be carefully evaluated. Unfortunately, conventional usability evaluation techniques do not address challenges of content understanding. In a case study within eHealth, specifically the setting of a rehabilitation clinic involving...... the participation of four physiotherapists and four clients in a period of 3.5 months, it was demonstrated how CUT with QU can complement conventional usability testing and provide insight into users’ challenges with understanding of a new complex eHealth application. More experiments in other complex application...

  18. [New materia medica project: synthetic biology based bioactive metabolites research in medicinal plant].

    Science.gov (United States)

    Wang, Yong

    2017-03-25

    In the last decade, synthetic biology research has been gradually transited from monocellular parts or devices toward more complex multicellular systems. The emerging plant synthetic biology is regarded as the "next chapter" of synthetic biology. The complex and diverse plant metabolism as the entry point, plant synthetic biology research not only helps us understand how real life is working, but also facilitates us to learn how to design and construct more complex artificial life. Bioactive compounds innovation and large-scale production are expected to be breakthrough with the redesigned plant metabolism as well. In this review, we discuss the research progress in plant synthetic biology and propose the new materia medica project to lift the level of traditional Chinese herbal medicine research.

  19. 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...... informatics are seeking to build a holistic model for a better understanding of the drug pharmacology and clinical effects. Here we will present a webserver called ChemProt that can assist, in silico, the drug actions in the context of cellular and disease networks and contribute in the field of disease...... chemical biology, drug repurposing, and off-target effects prediction....

  20. Entropy as a method to investigate complex biological systems. An alternative view on the biological transition from healthy aging to frailty

    Directory of Open Access Journals (Sweden)

    Roberto Siciliano

    2017-07-01

    Full Text Available Everyone is subject to a process of progressive deterioration of control mechanisms, which supervise the complex network of human physiological functions, reducing the individual ability to adapt to emerging situations of stress or change. In the light of results obtained during the last years, it appears that some of the tools of nonlinear dynamics, first developed for the physical sciences are well suited for studies of biological systems. We believe that, considering the level of order or complexity of the anatomical apparatus by measuring a physical quantity, which is the entropy, we can evaluate the health status or vice versa fragility of a biological system. In particular, a reduction in the entropy value, indicates modification of the structural order with a progressive reduction of functional reserve of the individual, which is associated with a failure to adapt to stress conditions, difficult to be analyzed and documented with a unique traditional biochemical or biomolecular vision. Therefore, in this paper, we present a method that, conceptually combines complexity, disease and aging, alloys Poisson statistics, predictive of the personal level of health, to the entropy value indicating the status of bio-dynamic and functional body, seen as a complex and open thermodynamic system.

  1. Understanding schizophrenia as a disorder of consciousness: biological correlates and translational implications from quantum theory perspectives.

    Science.gov (United States)

    Venkatasubramanian, Ganesan

    2015-04-30

    From neurophenomenological perspectives, schizophrenia has been conceptualized as "a disorder with heterogeneous manifestations that can be integrally understood to involve fundamental perturbations in consciousness". While these theoretical constructs based on consciousness facilitate understanding the 'gestalt' of schizophrenia, systematic research to unravel translational implications of these models is warranted. To address this, one needs to begin with exploration of plausible biological underpinnings of "perturbed consciousness" in schizophrenia. In this context, an attractive proposition to understand the biology of consciousness is "the orchestrated object reduction (Orch-OR) theory" which invokes quantum processes in the microtubules of neurons. The Orch-OR model is particularly important for understanding schizophrenia especially due to the shared 'scaffold' of microtubules. The initial sections of this review focus on the compelling evidence to support the view that "schizophrenia is a disorder of consciousness" through critical summary of the studies that have demonstrated self-abnormalities, aberrant time perception as well as dysfunctional intentional binding in this disorder. Subsequently, these findings are linked with 'Orch-OR theory' through the research evidence for aberrant neural oscillations as well as microtubule abnormalities observed in schizophrenia. Further sections emphasize the applicability and translational implications of Orch-OR theory in the context of schizophrenia and elucidate the relevance of quantum biology to understand the origins of this puzzling disorder as "fundamental disturbances in consciousness".

  2. ADAM: analysis of discrete models of biological systems using computer algebra.

    Science.gov (United States)

    Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

    2011-07-20

    Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web

  3. Molecular genetics of glioblastomas: defining subtypes and understanding the biology.

    Science.gov (United States)

    Renault, Ilana Zalcberg; Golgher, Denise

    2015-02-01

    Despite comprehensive therapy, which includes surgery, radiotherapy, and chemotherapy, the prognosis of glioblastoma multiforme is very poor. Diagnosed individuals present an average of 12 to 18 months of life. This article provides an overview of the molecular genetics of these tumors. Despite the overwhelming amount of data available, so far little has been translated into real benefits for the patient. Because this is such a complex topic, the goal is to point out the main alterations in the biological pathways that lead to tumor formation, and how this can contribute to the development of better therapies and clinical care. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Understanding of Leaf Development—the Science of Complexity

    Directory of Open Access Journals (Sweden)

    Robert Malinowski

    2013-06-01

    Full Text Available The leaf is the major organ involved in light perception and conversion of solar energy into organic carbon. In order to adapt to different natural habitats, plants have developed a variety of leaf forms, ranging from simple to compound, with various forms of dissection. Due to the enormous cellular complexity of leaves, understanding the mechanisms regulating development of these organs is difficult. In recent years there has been a dramatic increase in the use of technically advanced imaging techniques and computational modeling in studies of leaf development. Additionally, molecular tools for manipulation of morphogenesis were successfully used for in planta verification of developmental models. Results of these interdisciplinary studies show that global growth patterns influencing final leaf form are generated by cooperative action of genetic, biochemical, and biomechanical inputs. This review summarizes recent progress in integrative studies on leaf development and illustrates how intrinsic features of leaves (including their cellular complexity influence the choice of experimental approach.

  5. Disaster forensics understanding root cause and complex causality

    CERN Document Server

    2016-01-01

    This book aims to uncover the root causes of natural and man-made disasters by going beyond the typical reports and case studies conducted post-disaster. It opens the black box of disasters by presenting ‘forensic analysis approaches’ to disasters, thereby revealing the complex causality that characterizes them and explaining how and why hazards do, or do not, become disasters. This yields ‘systemic’ strategies for managing disasters. Recently the global threat landscape has seen the emergence of high impact, low probability events. Events like Hurricane Katrina, the Great Japan Earthquake and tsunami, Hurricane Sandy, Super Typhoon Haiyan, global terrorist activities have become the new norm. Extreme events challenge our understanding regarding the interdependencies and complexity of the disaster aetiology and are often referred to as Black Swans. Between 2002 and 2011, there were 4130 disasters recorded that resulted from natural hazards around the world. In these, 1,117,527 people perished and a mi...

  6. When physics is not "just physics": complexity science invites new measurement frames for exploring the physics of cognitive and biological development.

    Science.gov (United States)

    Kelty-Stephen, Damian; Dixon, James A

    2012-01-01

    The neurobiological sciences have struggled to resolve the physical foundations for biological and cognitive phenomena with a suspicion that biological and cognitive systems, capable of exhibiting and contributing to structure within themselves and through their contexts, are fundamentally distinct or autonomous from purely physical systems. Complexity science offers new physics-based approaches to explaining biological and cognitive phenomena. In response to controversy over whether complexity science might seek to "explain away" biology and cognition as "just physics," we propose that complexity science serves as an application of recent advances in physics to phenomena in biology and cognition without reducing or undermining the integrity of the phenomena to be explained. We highlight that physics is, like the neurobiological sciences, an evolving field and that the threat of reduction is overstated. We propose that distinctions between biological and cognitive systems from physical systems are pretheoretical and thus optional. We review our own work applying insights from post-classical physics regarding turbulence and fractal fluctuations to the problems of developing cognitive structure. Far from hoping to reduce biology and cognition to "nothing but" physics, we present our view that complexity science offers new explanatory frameworks for considering physical foundations of biological and cognitive phenomena.

  7. Hypothesis: the chaos and complexity theory may help our understanding of fibromyalgia and similar maladies.

    Science.gov (United States)

    Martinez-Lavin, Manuel; Infante, Oscar; Lerma, Claudia

    2008-02-01

    Modern clinicians are often frustrated by their inability to understand fibromyalgia and similar maladies since these illnesses cannot be explained by the prevailing linear-reductionist medical paradigm. This article proposes that new concepts derived from the Complexity Theory may help understand the pathogenesis of fibromyalgia, chronic fatigue syndrome, and Gulf War syndrome. This hypothesis is based on the recent recognition of chaos fractals and complex systems in human physiology. These nonlinear dynamics concepts offer a different perspective to the notion of homeostasis and disease. They propose that the essence of disease is dysfunction and not structural damage. Studies using novel nonlinear instruments have shown that fibromyalgia and similar maladies may be caused by the degraded performance of our main complex adaptive system. This dysfunction explains the multifaceted manifestations of these entities. To understand and alleviate the suffering associated with these complex illnesses, a paradigm shift from reductionism to holism based on the Complexity Theory is suggested. This shift perceives health as resilient adaptation and some chronic illnesses as rigid dysfunction.

  8. Metal-containing Complexes of Lactams, Imidazoles, and Benzimidazoles and Their Biological Activity

    Science.gov (United States)

    Kukalenko, S. S.; Bovykin, B. A.; Shestakova, S. I.; Omel'chenko, A. M.

    1985-07-01

    The results of the latest investigations of the problem of the synthesis of metal-containing complexes of lactams, imidazoles, and benzimidazoles, their structure, and their stability in solutions are surveyed. Some data on their biological activity (pesticide and pharmacological) and the mechanism of their physiological action are presented. The bibliography includes 190 references.

  9. Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from amoxicillin and sugars

    International Nuclear Information System (INIS)

    Naz, N.

    2009-01-01

    Fe (II), Co (II) and Ni (II) metal complexes of new Schiff bases derived from amoxicillin with sugars (D-Glucose, D-Galactose and D-Mannose) have been synthesized and characterized by elemental analysis, FTIR, electronic absorption, and atomic absorption spectroscopy, magnetic moment measurements and thermal analysis. It has been found that Schiff bases behave as bi-dentate ligands forming complexes with 1:2 (metal:ligand) stoichiometry. The complexes were neutral as confirmed by their low conductance values. The biological applications of complexes have been studied on two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and Staphylococcus aureus) microorganisms by Agar diffusion disc method. It has been found that all the complexes have higher biological activities than the pure amoxicillin. (author)

  10. Biologic activity of porphyromonas endodontalis complex lipids.

    Science.gov (United States)

    Mirucki, Christopher S; Abedi, Mehran; Jiang, Jin; Zhu, Qiang; Wang, Yu-Hsiung; Safavi, Kamran E; Clark, Robert B; Nichols, Frank C

    2014-09-01

    Periapical infections secondary to pulpal necrosis are associated with bacterial contamination of the pulp. Porphyromonas endodontalis, a gram-negative organism, is considered to be a pulpal pathogen. P. gingivalis is phylogenetically related to P. endodontalis and synthesizes several classes of novel complex lipids that possess biological activity, including the capacity to promote osteoclastogenesis and osteoclast activation. The purpose of this study was to extract and characterize constituent lipids of P. endodontalis and evaluate their capacity to promote proinflammatory secretory responses in the macrophage cell line, RAW 264.7, as well as their capacity to promote osteoclastogenesis and inhibit osteoblast activity. Constituent lipids of both organisms were fractionated by high-performance liquid chromatography and were structurally characterized using electrospray mass spectrometry or electrospray-mass spectrometry/mass spectrometry. The virulence potential of P. endodontalis lipids was then compared with known biologically active lipids isolated from P. gingivalis. P. endodontalis total lipids were shown to promote tumor necrosis factor alpha secretion from RAW 264.7 cells, and the serine lipid fraction appeared to account for the majority of this effect. P. endodontalis lipid preparations also increased osteoclast formation from RAW 264.7 cells, but osteoblast differentiation in culture was inhibited and appeared to be dependent on Toll-like receptor 2 expression. These effects underscore the importance of P. endodontalis lipids in promoting inflammatory and bone cell activation processes that could lead to periapical pathology. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  11. Understanding the Reading Attributes and Their Cognitive Relationships on a High-Stakes Biology Assessment

    Science.gov (United States)

    Rawlusyk, Kevin James

    Test items used to assess learners' knowledge on high-stakes science examinations contain contextualized questions that unintentionally assess reading skill along with conceptual knowledge. Therefore, students who are not proficient readers are unable to comprehend the text within the test item to demonstrate effectively their level of science knowledge. The purpose of this quantitative study was to understand what reading attributes were required to successfully answer the Biology 30 Diploma Exam. Furthermore, the research sought to understand the cognitive relationships among the reading attributes through quantitative analysis structured by the Attribute Hierarchy Model (AHM). The research consisted of two phases: (1) Cognitive development, where the cognitive attributes of the Biology 30 Exam were specified and hierarchy structures were developed; and (2) Psychometric analysis, that statistically tested the attribute hierarchy using the Hierarchy Consistency Index (HCI), and calculate attribute probabilities. Phase one of the research used January 2011, Biology 30 Diploma Exam, while phase two accessed archival data for the 9985 examinees who took the assessment on January 24th, 2011. Phase one identified ten specific reading attributes, of which five were identified as unique subsets of vocabulary, two were identified as reading visual representations, and three corresponded to general reading skills. Four hierarchical cognitive model were proposed then analyzed using the HCI as a mechanism to explain the relationship among the attributes. Model A had the highest HCI value (0.337), indicating an overall poor data fit, yet for the top achieving examinees the model had an excellent model fit with an HCI value of 0.888, and for examinees that scored over 60% there was a moderate model fit (HCI = 0.592). Linear regressions of the attribute probability estimates suggest that there is a cognitive relationship among six of the ten reading attributes (R2 = 0.958 and 0

  12. Modelling and Simulating Complex Systems in Biology: introducing NetBioDyn : A Pedagogical and Intuitive Agent-Based Software

    OpenAIRE

    Ballet, Pascal; Rivière, Jérémy; Pothet, Alain; Théron, Michaël; Pichavant, Karine; Abautret, Frank; Fronville, Alexandra; Rodin, Vincent

    2017-01-01

    International audience; Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular syst...

  13. Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

    Directory of Open Access Journals (Sweden)

    Shuo Gu

    2017-01-01

    Full Text Available With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

  14. Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective.

    Science.gov (United States)

    Gu, Shuo; Pei, Jianfeng

    2017-01-01

    With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

  15. Understanding the addiction cycle: a complex biology with distinct contributions of genotype vs. sex at each stage.

    Science.gov (United States)

    Wilhelm, C J; Hashimoto, J G; Roberts, M L; Sonmez, M K; Wiren, K M

    2014-10-24

    Ethanol abuse can lead to addiction, brain damage and premature death. The cycle of alcohol addiction has been described as a composite consisting of three stages: intoxication, withdrawal and craving/abstinence. There is evidence for contributions of both genotype and sex to alcoholism, but an understanding of the biological underpinnings is limited. Utilizing both sexes of genetic animal models with highly divergent alcohol withdrawal severity, Withdrawal Seizure-Resistant (WSR) and Withdrawal Seizure-Prone (WSP) mice, the distinct contributions of genotype/phenotype and of sex during addiction stages on neuroadaptation were characterized. Transcriptional profiling was performed to identify expression changes as a consequence of chronic intoxication in the medial prefrontal cortex. Significant expression differences were identified on a single platform and tracked over a behaviorally relevant time course that covered each stage of alcohol addiction; i.e., after chronic intoxication, during peak withdrawal, and after a defined period of abstinence. Females were more sensitive to ethanol with higher fold expression differences. Bioinformatics showed a strong effect of sex on the data structure of expression profiles during chronic intoxication and at peak withdrawal irrespective of genetic background. However, during abstinence, differences were observed instead between the lines/phenotypes irrespective of sex. Confirmation of identified pathways showed distinct inflammatory signaling following intoxication at peak withdrawal, with a pro-inflammatory phenotype in females but overall suppression of immune signaling in males. Combined, these results suggest that each stage of the addiction cycle is influenced differentially by sex vs. genetic background and support the development of stage- and sex-specific therapies for alcohol withdrawal and the maintenance of sobriety. Published by Elsevier Ltd.

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

    Science.gov (United States)

    MacLeod, Miles; Nersessian, Nancy J

    2015-02-01

    In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding." Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. The Mathematical Biology of Human Infections

    Directory of Open Access Journals (Sweden)

    Martin A. Nowak

    1999-12-01

    Full Text Available Humans are constant victims of infectious diseases. Biomedical research during this century has led to important insights into the molecular details of immune defense. Yet, many questions relating to disease require a quantitative understanding of the complex systems that arise from the nonlinear interactions between populations of immune cells and infectious agents. Exploration of such questions has lead to a newly emerging field of mathematical biology describing the spread of infectious agents both within and between infected individuals. This essay will discuss simple and complex models of evolution, and the propagation of virus and prion infections. Such models provide new perspectives for our understanding of infectious disease and provide guidelines for interpreting experimental observation; they also define what needs to be measured to improve understanding.

  18. New insights into pancreatic cancer biology.

    Science.gov (United States)

    Hidalgo, M

    2012-09-01

    Pancreatic cancer remains a devastating disease. Over the last few years, there have been important advances in the molecular and biological understanding of pancreatic cancer. This included understanding of the genomic complexity of the disease, the role of pancreatic cancer stem cells, the relevance of the tumor microenvironment, and the unique metabolic adaptation of pancreas cancer cells to obtain nutrients under hypoxic environment. In this paper, we review the most salient developments in these few areas.

  19. Root Systems Biology: Integrative Modeling across Scales, from Gene Regulatory Networks to the Rhizosphere1

    Science.gov (United States)

    Hill, Kristine; Porco, Silvana; Lobet, Guillaume; Zappala, Susan; Mooney, Sacha; Draye, Xavier; Bennett, Malcolm J.

    2013-01-01

    Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment. PMID:24143806

  20. Assessing the Possibility of Biological Complexity on Other Worlds, with an Estimate of the Occurrence of Complex Life in the Milky Way Galaxy

    Directory of Open Access Journals (Sweden)

    Louis N. Irwin

    2014-05-01

    Full Text Available Rational speculation about biological evolution on other worlds is one of the outstanding challenges in astrobiology. With the growing confirmation that multiplanetary systems abound in the universe, the prospect that life occurs redundantly throughout the cosmos is gaining widespread support. Given the enormous number of possible abodes for life likely to be discovered on an ongoing basis, the prospect that life could have evolved into complex, macro-organismic communities in at least some cases merits consideration. Toward that end, we here propose a Biological Complexity Index (BCI, designed to provide a quantitative estimate of the relative probability that complex, macro-organismic life forms could have emerged on other worlds. The BCI ranks planets and moons by basic, first-order characteristics detectable with available technology. By our calculation only 11 (~1.7% of the extrasolar planets known to date have a BCI above that of Europa; but by extrapolation, the total of such planets could exceed 100 million in our galaxy alone. This is the first quantitative assessment of the plausibility of complex life throughout the universe based on empirical data. It supports the view that the evolution of complex life on other worlds is rare in frequency but large in absolute number.

  1. Herbal medicine, radical scavenger and metal detoxification: bioinorganic, complexity and nano science perspectives

    Science.gov (United States)

    Sumitro, Sutiman B.; Alit, Sukmaningsih

    2018-03-01

    Developing Complexity Science and Nano Biological perspective giving the ideas of interfacing between modern physical and biological sciences for more comprehensive understanding of life. The study of bioinorganic is a trans-disciplinary, and will initiate the way to more comprehensive and better understanding life. We can talk about energy generation, motive forces and energy transfer at the level of macromolecules. We can then develop understanding biological behavior on nano size biological materials and its higher order using modern physics as well as thermodynamic law. This is a necessity to ovoid partial understanding of life that are not match with holism. In animal tissues, the accumulation or overwhelmed production of free radicals can damage cells and are believed to accelerate the progression of cancer, cardiovascular disease, and age-related diseases. Thus a guarded balance of radical species is imperative. Edward Kosower [1] proposed an idea of biradical in an aromatic organic compounds. Each of which having unpaired electrons. The magnetic force of this compound used for making agregation based on their magnetic characters. Bioinorganic low molecular weight complex compounds composing herbal medicine can bind toxic metals. This low molecular weight complex molecules then easily excerted the metals from the body, removing them from their either intracellular or extracellular existences. This bioinorganic chelation potential is now inspiring a new therapeutic strategies.

  2. Managing Complexity

    Energy Technology Data Exchange (ETDEWEB)

    Chassin, David P.; Posse, Christian; Malard, Joel M.

    2004-08-01

    Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today’s most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically-based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This paper explores the state of the art in the use physical analogs for understanding the behavior of some econophysical systems and to deriving stable and robust control strategies for them. In particular we review and discussion applications of some analytic methods based on the thermodynamic metaphor according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood.

  3. PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

    Science.gov (United States)

    Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

    2016-03-10

    Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and

  4. Toward A Better Understanding of Perceived Complexity in Music: A Commentary on Eerola (2016

    Directory of Open Access Journals (Sweden)

    Elizabeth Hellmuth Margulis

    2016-07-01

    Full Text Available Eerola (2016 evaluates models of musical complexity based on expectancy violation and information theory. This commentary notes the deep relationship between these two phenomena, and argues for a more active partnership between computational and psychological approaches in understanding perceptions of musical complexity.

  5. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

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

    2016-01-01

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

  6. A systems biology approach to studying Tai Chi, physiological complexity and healthy aging: design and rationale of a pragmatic randomized controlled trial.

    Science.gov (United States)

    Wayne, Peter M; Manor, Brad; Novak, Vera; Costa, Madelena D; Hausdorff, Jeffrey M; Goldberger, Ary L; Ahn, Andrew C; Yeh, Gloria Y; Peng, C-K; Lough, Matthew; Davis, Roger B; Quilty, Mary T; Lipsitz, Lewis A

    2013-01-01

    Aging is typically associated with progressive multi-system impairment that leads to decreased physical and cognitive function and reduced adaptability to stress. Due to its capacity to characterize complex dynamics within and between physiological systems, the emerging field of complex systems biology and its array of quantitative tools show great promise for improving our understanding of aging, monitoring senescence, and providing biomarkers for evaluating novel interventions, including promising mind-body exercises, that treat age-related disease and promote healthy aging. An ongoing, two-arm randomized clinical trial is evaluating the potential of Tai Chi mind-body exercise to attenuate age-related loss of complexity. A total of 60 Tai Chi-naïve healthy older adults (aged 50-79) are being randomized to either six months of Tai Chi training (n=30), or to a waitlist control receiving unaltered usual medical care (n=30). Our primary outcomes are complexity-based measures of heart rate, standing postural sway and gait stride interval dynamics assessed at 3 and 6months. Multiscale entropy and detrended fluctuation analysis are used as entropy- and fractal-based measures of complexity, respectively. Secondary outcomes include measures of physical and psychological function and tests of physiological adaptability also assessed at 3 and 6months. Results of this study may lead to novel biomarkers that help us monitor and understand the physiological processes of aging and explore the potential benefits of Tai Chi and related mind-body exercises for healthy aging. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. From biological and social network metaphors to coupled bio-social wireless networks

    Science.gov (United States)

    Barrett, Christopher L.; Eubank, Stephen; Anil Kumar, V.S.; Marathe, Madhav V.

    2010-01-01

    Biological and social analogies have been long applied to complex systems. Inspiration has been drawn from biological solutions to solve problems in engineering products and systems, ranging from Velcro to camouflage to robotics to adaptive and learning computing methods. In this paper, we present an overview of recent advances in understanding biological systems as networks and use this understanding to design and analyse wireless communication networks. We expand on two applications, namely cognitive sensing and control and wireless epidemiology. We discuss how our work in these two applications is motivated by biological metaphors. We believe that recent advances in computing and communications coupled with advances in health and social sciences raise the possibility of studying coupled bio-social communication networks. We argue that we can better utilise the advances in our understanding of one class of networks to better our understanding of the other. PMID:21643462

  8. Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases.

    Science.gov (United States)

    Oh, Soo Jin; Choi, Young Ki; Shin, Ok Sarah

    2018-03-01

    Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs. © Copyright: Yonsei University College of Medicine 2018.

  9. Towards a Molecular Understanding of the Fanconi Anemia Core Complex

    Directory of Open Access Journals (Sweden)

    Charlotte Hodson

    2012-01-01

    Full Text Available Fanconi Anemia (FA is a genetic disorder characterized by the inability of patient cells to repair DNA damage caused by interstrand crosslinking agents. There are currently 14 verified FA genes, where mutation of any single gene prevents repair of DNA interstrand crosslinks (ICLs. The accumulation of ICL damage results in genome instability and patients having a high predisposition to cancers. The key event of the FA pathway is dependent on an eight-protein core complex (CC, required for the monoubiquitination of each member of the FANCD2-FANCI complex. Interestingly, the majority of patient mutations reside in the CC. The molecular mechanisms underlying the requirement for such a large complex to carry out a monoubiquitination event remain a mystery. This paper documents the extensive efforts of researchers so far to understand the molecular roles of the CC proteins with regard to its main function in the FA pathway, the monoubiquitination of FANCD2 and FANCI.

  10. Towards a Molecular Understanding of the Fanconi Anemia Core Complex

    Science.gov (United States)

    Hodson, Charlotte; Walden, Helen

    2012-01-01

    Fanconi Anemia (FA) is a genetic disorder characterized by the inability of patient cells to repair DNA damage caused by interstrand crosslinking agents. There are currently 14 verified FA genes, where mutation of any single gene prevents repair of DNA interstrand crosslinks (ICLs). The accumulation of ICL damage results in genome instability and patients having a high predisposition to cancers. The key event of the FA pathway is dependent on an eight-protein core complex (CC), required for the monoubiquitination of each member of the FANCD2-FANCI complex. Interestingly, the majority of patient mutations reside in the CC. The molecular mechanisms underlying the requirement for such a large complex to carry out a monoubiquitination event remain a mystery. This paper documents the extensive efforts of researchers so far to understand the molecular roles of the CC proteins with regard to its main function in the FA pathway, the monoubiquitination of FANCD2 and FANCI. PMID:22675617

  11. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

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

    2017-06-21

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

  12. Understanding complexity in managing agro-pastoral dams ecosystem services in Northern Benin

    NARCIS (Netherlands)

    Kpera, G.N.

    2015-01-01

    Key words: conflict, water quality, crocodile, fish diversity, vegetable, watershed management, institutional changes, innovation system.

    Understanding complexity in managing agro-pastoral dams ecosystem services in Northern Benin

    Gnanki

  13. Understanding Protein Synthesis: An Interactive Card Game Discussion

    Science.gov (United States)

    Lewis, Alison; Peat, Mary; Franklin, Sue

    2005-01-01

    Protein synthesis is a complex process and students find it difficult to understand. This article describes an interactive discussion "game" used by first year biology students at the University of Sydney. The students, in small groups, use the game in which the processes of protein synthesis are actioned by the students during a…

  14. Biological Soft Robotics.

    Science.gov (United States)

    Feinberg, Adam W

    2015-01-01

    In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

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

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

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

  16. BlenX-based compositional modeling of complex reaction mechanisms

    Directory of Open Access Journals (Sweden)

    Judit Zámborszky

    2010-02-01

    Full Text Available Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.

  17. Deconstructing sexual orientation: understanding the phenomena of sexual orientation.

    Science.gov (United States)

    Stein, T S

    1997-01-01

    The very terms of a debate about whether or not sexual orientation is primarily a biological phenomenon fail to consider the complex origins of the phenomenon. Deconstruction of the term "homosexuality" shows that it refers to multiple factors which cannot be studied as or subsumed under a unitary concept. Adequate understanding of sexual orientation must consider the developmental, interpersonal, experiential, and cultural dimensions of sexuality, as well as any biological contributions to sexual attraction, behavior, and identity.

  18. Understanding the Complexities of Communicating Management Decisions on the Subsistence Use of Yukon River Salmon

    Science.gov (United States)

    Brooks, J. F.; Trainor, S.

    2017-12-01

    Over 20,000 residents in Alaska and Yukon Territory rely upon the Yukon River to provide them harvests of Pacific salmon each year. Salmon are a highly valued food resource and the practice of salmon fishing along the Yukon is deep rooted in local cultures and traditions. Potential future impacts of climate change on the health of Yukon River salmon stocks could be significant. Collaborative managerial processes which incorporate the viewpoints of subsistence stakeholders will be crucial in enabling communities and managerial institutions to adapt and manage these impacts. However, the massive extent of the Yukon River makes it difficult for communities rich with highly localized knowledge to situate themselves within a drainage-wide context of resource availability, and to fully understand the implications that management decisions may have for their harvest. Differences in salmon availability and abundance between the upper and lower Yukon, commercial vs. subsistence fishery interests, and enforcement of the international Pacific Salmon Treaty further complicate understanding and makes the topic of salmon as a subsistence resource a highly contentious issue. A map which synthesizes the presence and absence of Pacific salmon throughout the entire Yukon River drainage was requested by both subsistence fishers and natural resource managers in Alaska in order to help facilitate productive conversations about salmon management decisions. Interviews with Alaskan stakeholders with managerial, biological, and subsistence harvest backgrounds were carried out and a literature review was conducted in order to understand what such a map should and could accomplish. During the research process, numerous data gaps concerning the distribution of salmon along the Yukon River were discovered, and insights about the complexities involved in translating science when it is situated within a charged political, economic, and cultural context were revealed. Preliminary maps depicting

  19. The Relationship between Biology Teachers' Understanding of the Nature of Science and the Understanding and Acceptance of the Theory of Evolution

    Science.gov (United States)

    Cofré, Hernán; Cuevas, Emilia; Becerra, Beatriz

    2017-01-01

    Despite the importance of the theory of evolution (TE) to scientific knowledge, a number of misconceptions continue to be found among biology teachers. In this context, the first objective of this study was to identify the impact of professional development programme (PDP) on teachers' understanding of nature of science (NOS) and evolution and on…

  20. The relationship between biology teachers' understanding of the nature of science and the understanding and acceptance of the theory of evolution

    Science.gov (United States)

    Cofré, Hernán; Cuevas, Emilia; Becerra, Beatriz

    2017-11-01

    Despite the importance of the theory of evolution (TE) to scientific knowledge, a number of misconceptions continue to be found among biology teachers. In this context, the first objective of this study was to identify the impact of professional development programme (PDP) on teachers' understanding of nature of science (NOS) and evolution and on the acceptance of this theory. Its second objective was to study the relationship among these variables. Three instruments were used to quantify these variables: the Views of the Nature of Science Version D (VNOS D+), the Assessing Contextual Reasoning about Natural Selection (ACORN), and the Measure of Acceptance of Theory of Evolution (MATE). The results indicate that the PDP had a positive impact on teachers, significantly improving their understanding of the NOS and natural selection, as well as their acceptance of the TE. Furthermore, a positive correlation between the understanding of the NOS obtained by teachers in the first part of the PDP and the understanding and acceptance of evolution that these teachers showed at the end of the programme was determined. However, no relationship between an understanding of the NOS and gains in the understanding and acceptance of evolution was found.

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

    Science.gov (United States)

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

    2015-12-15

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. © 2015 Richardson et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  2. Integrative systems and synthetic biology of cell-matrix adhesion sites.

    Science.gov (United States)

    Zamir, Eli

    2016-09-02

    The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

  3. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Venom Resistance as a Model for Understanding the Molecular Basis of Complex Coevolutionary Adaptations.

    Science.gov (United States)

    Holding, Matthew L; Drabeck, Danielle H; Jansa, Sharon A; Gibbs, H Lisle

    2016-11-01

    SynopsisVenom and venom resistance are molecular phenotypes widely considered to have diversified through coevolution between predators and prey. However, while evolutionary and functional studies on venom have been extensive, little is known about the molecular basis, variation, and complexity of venom resistance. We review known mechanisms of venom resistance and relate these mechanisms to their predicted impact on coevolutionary dynamics with venomous enemies. We then describe two conceptual approaches which can be used to examine venom/resistance systems. At the intraspecific level, tests of local adaptation in venom and resistance phenotypes can identify the functional mechanisms governing the outcomes of coevolution. At deeper evolutionary timescales, the combination of phylogenetically informed analyses of protein evolution coupled with studies of protein function promise to elucidate the mode and tempo of evolutionary change on potentially coevolving genes. We highlight case studies that use each approach to extend our knowledge of these systems as well as address larger questions about coevolutionary dynamics. We argue that resistance and venom are phenotypic traits which hold exceptional promise for investigating the mechanisms, dynamics, and outcomes of coevolution at the molecular level. Furthermore, extending the understanding of single gene-for-gene interactions to the whole resistance and venom phenotypes may provide a model system for examining the molecular and evolutionary dynamics of complex multi-gene interactions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  5. The Effects of Case-Based Instruction on Undergraduate Biology Students' Understanding of the Nature of Science

    Science.gov (United States)

    Burniston, Amy Lucinda

    Undergraduate science education is currently seeing a dramatic pedagogical push towards teaching the philosophies underpinning science as well as an increase in strategies that employ active learning. Many active learning strategies stem from constructivist ideals and have been shown to affect a student's understanding of how science operates and its impact on society- commonly referred to as the nature of science (NOS). One particular constructivist teaching strategy, case-based instruction (CBI), has been recommended by researchers and science education reformists as an effective instructional strategy for teaching NOS. Furthermore, when coupled with explicit-reflective instruction, CBI has been found to significantly increasing understanding of NOS in elementary and secondary students. However, few studies aimed their research on CBI and NOS towards higher education. Thus, this study uses a quasi-experimental, nonequivalent group design to study the effects of CBI on undergraduate science students understandings of NOS. Undergraduate biology student's understanding of NOS were assessed using the Views of Science Education (VOSE) instrument pre and post CBI intervention in Cellular and Molecular Biology and Human Anatomy and Physiology II. Data analysis indicated statistically significant differences between students NOS scores in experimental versus control sections for both courses, with experimental groups obtaining higher posttest scores. The results of this study indicate that undergraduate male and female students have similarly poor understandings of NOS and the use of historical case based instruction can be used as a means to increase undergraduate understanding of NOS.

  6. Spectroscopic, thermal, catalytic and biological studies of Cu(II) azo dye complexes

    Science.gov (United States)

    El-Sonbati, A. Z.; Diab, M. A.; El-Bindary, A. A.; Shoair, A. F.; Hussein, M. A.; El-Boz, R. A.

    2017-08-01

    New complexes of copper(II) with azo compounds of 5-amino-2-(aryl diazenyl)phenol (HLn) are prepared and investigated by elemental analyses, molar conductance, IR, 1H NMR, UV-Visible, mass, ESR spectra, magnetic susceptibility measurements and thermal analyses. The complexes have a square planar structure and general formula [Cu(Ln)(OAc)]H2O. Study the catalytic activities of Cu(II) complexes toward oxidation of benzyl alcohol derivatives to carbonyl compounds were tested using H2O2 as the oxidant. The intrinsic binding constants (Kb) of the ligands (HLn) and Cu(II) complexes (1-4) with CT-DNA are determined. The formed compounds have been tested for biological activity of antioxidants, antibacterial against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria and yeast Candida albicans. Antibiotic (Ampicillin) and antifungal against (Colitrimazole) and cytotoxic compounds HL1, HL2, HL3 and complex (1) showed moderate to good activity against S. aureus, E. coli and Candida albicans, and also to be moderate on antioxidants and toxic substances. Molecular docking is used to predict the binding between the ligands with the receptor of breast cancer (2a91).

  7. Understanding Life : The Evolutionary Dynamics of Complexity and Semiosis

    Science.gov (United States)

    Loeckenhoff, Helmut K.

    2010-11-01

    Post-Renaissance sciences created different cultures. To establish an epistemological base, Physics were separated from the Mental domain. Consciousness was excluded from science. Life Sciences were left in between e.g. LaMettrie's `man—machine' (1748) and 'vitalism' [e.g. Bergson 4]. Causative thinking versus intuitive arguing limited strictly comprehensive concepts. First ethology established a potential shared base for science, proclaiming the `biology paradigm' in the middle of the 20th century. Initially procured by Cybernetics and Systems sciences, `constructivist' models prepared a new view on human perception and thus also of scientific `objectivity when introducing the `observer'. In sequel Computer sciences triggered the ICT revolution. In turn ICT helped to develop Chaos and Complexity sciences, Non-linear Mathematics and its spin-offs in the formal sciences [Spencer-Brown 49] as e.g. (proto-)logics. Models of life systems, as e.g. Anticipatory Systems, integrated epistemology with mathematics and Anticipatory Computing [Dubois 11, 12, 13, 14] connecting them with Semiotics. Seminal ideas laid in the turn of the 19th to the 20th century [J. v. Uexküll 53] detected the co-action and co-evolvement of environments and life systems. Bio-Semiotics ascribed purpose, intent and meaning as essential qualities of life. The concepts of Systems Biology and Qualitative Research enriched and develop also anthropologies and humanities. Brain research added models of (higher) consciousness. An avant-garde is contemplating a science including consciousness as one additional base. New insights from the extended qualitative approach led to re-conciliation of basic assumptions of scientific inquiry, creating the `epistemological turn'. Paradigmatically, resting on macro- micro- and recently on nano-biology, evolution biology sired fresh scripts of evolution [W. Wieser 60,61]. Its results tie to hypotheses describing the emergence of language, of the human mind and of

  8. Treatment of complex biological mixtures with pulsed electric fields An energy transfer characterization

    International Nuclear Information System (INIS)

    Schrive, Luc

    2004-01-01

    Sewage sludge from waste water treatment plants is a complex biological mixture and a problematic by-product because of valorisation restrictions. In order to limit its production, pulsed electric fields (PEF) were studied because of their biological effects and their potentially physico-chemical action. This work demonstrated a paradoxical phenomenon: cell lysis triggered a respirometric activation followed by a delayed lethality. This phenomenon was related to the leakage of internal compounds which were immediately bio-assimilated. At high energy expense, the plasmic membrane permeabilization led to cell death. Practically, with the technical configuration of the equipment, no hydrolysis was detected. This limitation decreases the interest for excess sludge reduction, but for the same reason, PEF cold sterilization technique can be assessed as a promising process. The representation of the electric energy transfer from electrodes to cell was exchanged by the study of mass transfer from the biological cell to the surrounding media under an electromotive force. Thus, the survival rate was modelled by a Sherwood number taking account of electrical, biological and hydraulic parameters. (author) [fr

  9. Use of Graph Database for the Integration of Heterogeneous Biological Data.

    Science.gov (United States)

    Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

    2017-03-01

    Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

  10. Synthesis, characterization, and biological activity of a new palladium(II) complex with deoxyalliin

    Energy Technology Data Exchange (ETDEWEB)

    Corbi, P.P.; Massabni, A.C. [Inst. de Quimica - UNESP, Dept., Dept. de Quimica Geral e Inoganica, Araraquara (Brazil)]. E-mail: pedrocorbi@yahoo.com; Moreira, A.G. [Inst. de Quimica - UNESP, Dept. de Quimica Geral e Inoganica, Araraquara (Brazil); Faculdade de Medicina de Ribeirao Preto - USP, Dept. de Bioquimica e Imunologia, Ribeirao Preto (Brazil); Medrano, F.J. [Laboratorio Nacional de Luz Sincrotron - LNLS, Campinas (Brazil); Jasiulionis, M.G. [Escola Paulista de Medicina - UNIFESP, Dept. de Micro-Imuno-Parasitologia, Sao Paulo (Brazil); Costa-Neto, C.M. [Faculdade de Medicina de Ribeirao Preto - USP, Dept. de Bioquimica e Imunologia, Ribeirao Preto (Brazil)

    2005-02-15

    Synthesis, characterization, and biological activity of a new water-soluble Pd(II)-deoxyalliin (S-allyl-L-cysteine) complex are described in this article. Elemental and thermal analysis for the complex are consistent with the formula [Pd(C{sub 6}H{sub 10}NO{sub 2}S){sub 2}]. {sup 13}C NMR, {sup 1}H NMR, and IR spectroscopy show coordination of the ligand to Pd(II) through S and N atoms in a square planar geometry. Final residue of the thermal treatment was identified as a mixture of PdO and metallic Pd. Antiproliferative assays using aqueous solutions of the complex against HeLa and TM5 tumor cells showed a pronounced activity of the complex even at low concentrations. After incubation for 24 h, the complex induced cytotoxic effect over HeLa cells when used at concentrations higher than 0.40 mmol/L. At lower concentrations, the complex was nontoxic, indicating its action is probably due to cell cycle arrest, rather than cell death. In agreement with these results, the flow cytometric analysis indicated that after incubation for 24 h at low concentrations of the complex cells are arrested in G0/G1. (author)

  11. Micro/nanofabricated environments for synthetic biology.

    Science.gov (United States)

    Collier, C Patrick; Simpson, Michael L

    2011-08-01

    A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions.

    Science.gov (United States)

    Vernon, Ian; Liu, Junli; Goldstein, Michael; Rowe, James; Topping, Jen; Lindsey, Keith

    2018-01-02

    Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs of the analysis, and need to be compared to observed data of various forms. The correct analysis of such models usually requires a global parameter search, over a high dimensional parameter space, that incorporates and respects the most important sources of uncertainty. This can be an extremely difficult task, but it is essential for any meaningful inference or prediction to be made about any biological system. It hence represents a fundamental challenge for the whole of systems biology. Bayesian statistical methodology for the uncertainty analysis of complex models is introduced, which is designed to address the high dimensional global parameter search problem. Bayesian emulators that mimic the systems biology model but which are extremely fast to evaluate are embeded within an iterative history match: an efficient method to search high dimensional spaces within a more formal statistical setting, while incorporating major sources of uncertainty. The approach is demonstrated via application to a model of hormonal crosstalk in Arabidopsis root development, which has 32 rate parameters, for which we identify the sets of rate parameter values that lead to acceptable matches between model output and observed trend data. The multiple insights into the model's structure that this analysis provides are discussed. The methodology is applied to a second related model, and the biological consequences of the resulting comparison, including the evaluation of gene functions, are described. Bayesian uncertainty analysis for complex models using both emulators and history matching is shown to be a powerful technique that can greatly aid the study of a large class of systems biology models. It both provides insight into model behaviour

  13. Analyzing Change in Students' Gene-to-Evolution Models in College-Level Introductory Biology

    Science.gov (United States)

    Dauer, Joseph T.; Momsen, Jennifer L.; Speth, Elena Bray; Makohon-Moore, Sasha C.; Long, Tammy M.

    2013-01-01

    Research in contemporary biology has become increasingly complex and organized around understanding biological processes in the context of systems. To better reflect the ways of thinking required for learning about systems, we developed and implemented a pedagogical approach using box-and-arrow models (similar to concept maps) as a foundational…

  14. An efficient grid layout algorithm for biological networks utilizing various biological attributes

    Directory of Open Access Journals (Sweden)

    Kato Mitsuru

    2007-03-01

    Full Text Available Abstract Background Clearly visualized biopathways provide a great help in understanding biological systems. However, manual drawing of large-scale biopathways is time consuming. We proposed a grid layout algorithm that can handle gene-regulatory networks and signal transduction pathways by considering edge-edge crossing, node-edge crossing, distance measure between nodes, and subcellular localization information from Gene Ontology. Consequently, the layout algorithm succeeded in drastically reducing these crossings in the apoptosis model. However, for larger-scale networks, we encountered three problems: (i the initial layout is often very far from any local optimum because nodes are initially placed at random, (ii from a biological viewpoint, human layouts still exceed automatic layouts in understanding because except subcellular localization, it does not fully utilize biological information of pathways, and (iii it employs a local search strategy in which the neighborhood is obtained by moving one node at each step, and automatic layouts suggest that simultaneous movements of multiple nodes are necessary for better layouts, while such extension may face worsening the time complexity. Results We propose a new grid layout algorithm. To address problem (i, we devised a new force-directed algorithm whose output is suitable as the initial layout. For (ii, we considered that an appropriate alignment of nodes having the same biological attribute is one of the most important factors of the comprehension, and we defined a new score function that gives an advantage to such configurations. For solving problem (iii, we developed a search strategy that considers swapping nodes as well as moving a node, while keeping the order of the time complexity. Though a naïve implementation increases by one order, the time complexity, we solved this difficulty by devising a method that caches differences between scores of a layout and its possible updates

  15. 3D complex: a structural classification of protein complexes.

    Directory of Open Access Journals (Sweden)

    Emmanuel D Levy

    2006-11-01

    Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

  16. Bringing content understanding into usability testing in complex application domains—a case study in eHealth

    DEFF Research Database (Denmark)

    Andersen, Simon Bruntse; Rasmussen, Claire Kirchert; Frøkjær, Erik

    2017-01-01

    A usability evaluation technique, Cooperative Usability Testing with Questions of Understanding (CUT with QU) intended to illuminate users’ ability to understand the content information of an application is proposed. In complex application domains as for instance the eHealth domain, this issue...... the participation of four physiotherapists and four clients in a period of 3.5 months, it was demonstrated how CUT with QU can complement conventional usability testing and provide insight into users’ challenges with understanding of a new complex eHealth application. More experiments in other complex application...... domains involving different kinds of users and evaluators are needed before we can tell whether CUT with QU is an effective usability testing technique of wider applicability. Performing CUT with QU is very demanding by drawing heavily on the evaluators’ ability to respond effectively to openings...

  17. A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

    Directory of Open Access Journals (Sweden)

    Raul Molina

    2014-12-01

    Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

  18. Understanding the physiology of complex congenital heart disease using cardiac magnetic resonance imaging

    International Nuclear Information System (INIS)

    Kappanayil, Mahesh; Kannan, Rajesh; Kumar, Raman Krishna

    2011-01-01

    Complex congenital heart diseases are often associated with complex alterations in hemodynamics. Understanding these key hemodynamic changes is critical to making management decisions including surgery and postoperative management. Existing tools for imaging and hemodynamic assessment like echocardiography, computed tomography and cardiac catheterization have inherent limitations. Cardiac magnetic resonance imaging (MRI) is emerging as a powerful bouquet of tools that allow not only excellent imaging, but also a unique insight into hemodynamics. This article introduces the reader to cardiac MRI and its utility through the clinical example of a child with a complex congenital cyanotic heart disease

  19. Physicochemical and biological study of a renal scintigraphy agent: the DMSA - 99mTc complex

    International Nuclear Information System (INIS)

    Laroche, Dominique

    1979-01-01

    This research thesis deals with the study of the dimercaptosuccinic acid (DMSA) marked with 99m Tc, a recently developed scintigraphy agent used for the kidney isotopic exploration. The author notably studied the relationships between the physicochemical properties of solutions of dimercaptosuccinic acid marked with 99m Tc and the biological distribution of 99m Tc in order to reach a better understanding of the biological mechanism which results in technetium fixation to the kidney

  20. The mathematics and mechanics of biological growth

    CERN Document Server

    Goriely, Alain

    2017-01-01

    This monograph presents a general mechanical theory for biological growth. It provides both a conceptual and a technical foundation for the understanding and analysis of problems arising in biology and physiology. The theory and methods is illustrated on a wide range of examples and applications. A process of extreme complexity, growth plays a fundamental role in many biological processes and is considered to be the hallmark of life itself. Its description has been one of the fundamental problems of life sciences, but until recently, it has not attracted much attention from mathematicians, physicists, and engineers. The author herein presents the first major technical monograph on the problem of growth since D’Arcy Wentworth Thompson’s 1917 book On Growth and Form. The emphasis of the book is on the proper mathematical formulation of growth kinematics and mechanics. Accordingly, the discussion proceeds in order of complexity and the book is divided into five parts. First, a general introduction on the pro...

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

    Science.gov (United States)

    Degrazio, Dominick

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

  2. Land, power and conflict in Afghanistan: seeking to understand complexity

    Directory of Open Access Journals (Sweden)

    Adam Pain

    2013-06-01

    Full Text Available This paper explores the diverse links between land and power under conditions of conflict in Afghanistan, taking into account the complexities of Afghan society. These complexities are structured around interconnecting informal institutions and personalised relationships, culturally specific, diverse and shifting patterns of social relations, and spatially specific patterns of land ownership inequalities. The paper draws on a decade of empirical fieldwork in Afghanistan and recent work on livelihood trajectories and the opium economy. An understanding of the evolution of land ownership and access issues needs to be associated with an appreciation of diverse and potentially contradictory long-term drivers of change in the rural economy. The first of these long-term drivers of change relates to the effects of conflict, not only on land but also of water access under conditions of an increasingly scarce water supply. The second driver relates both to the roles played by village elites and to the structural contrasts between villages located in the mountains and in the plains, with the latter displaying major inequalities in land ownership. The third driver relates to the declining economic role of land in rural livelihoods, given long-term agrarian change and falling farm sizes. An understanding of history is fundamental to explaining these phenomena. How such conflicts play out, and which social groups or individuals they involve, also depend to a large degree on spatial positioning.

  3. The Physics of Proteins An Introduction to Biological Physics and Molecular Biophysics

    CERN Document Server

    Frauenfelder, Hans; Chan, Winnie S

    2010-01-01

    Physics and the life sciences have established new connections within the past few decades, resulting in biological physics as an established subfield with strong groups working in many physics departments. These interactions between physics and biology form a two-way street with physics providing new tools and concepts for understanding life, while biological systems can yield new insights into the physics of complex systems. To address the challenges of this interdisciplinary area, The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics is divided into three interconnected sections. In Parts I and II, early chapters introduce the terminology and describe the main biological systems that physicists will encounter. Similarities between biomolecules, glasses, and solids are stressed with an emphasis on the fundamental concepts of living systems. The central section (Parts III and IV) delves into the dynamics of complex systems. A main theme is the realization that biological sys...

  4. Programming Morphogenesis through Systems and Synthetic Biology.

    Science.gov (United States)

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

    2018-04-01

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

  5. Can complex cellular processes be governed by simple linear rules?

    Science.gov (United States)

    Selvarajoo, Kumar; Tomita, Masaru; Tsuchiya, Masa

    2009-02-01

    Complex living systems have shown remarkably well-orchestrated, self-organized, robust, and stable behavior under a wide range of perturbations. However, despite the recent generation of high-throughput experimental datasets, basic cellular processes such as division, differentiation, and apoptosis still remain elusive. One of the key reasons is the lack of understanding of the governing principles of complex living systems. Here, we have reviewed the success of perturbation-response approaches, where without the requirement of detailed in vivo physiological parameters, the analysis of temporal concentration or activation response unravels biological network features such as causal relationships of reactant species, regulatory motifs, etc. Our review shows that simple linear rules govern the response behavior of biological networks in an ensemble of cells. It is daunting to know why such simplicity could hold in a complex heterogeneous environment. Provided physical reasons can be explained for these phenomena, major advancement in the understanding of basic cellular processes could be achieved.

  6. On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

    Science.gov (United States)

    Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

    2017-12-05

    The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

  7. Scattering methods in complex fluids

    CERN Document Server

    Chen, Sow-Hsin

    2015-01-01

    Summarising recent research on the physics of complex liquids, this in-depth analysis examines the topic of complex liquids from a modern perspective, addressing experimental, computational and theoretical aspects of the field. Selecting only the most interesting contemporary developments in this rich field of research, the authors present multiple examples including aggregation, gel formation and glass transition, in systems undergoing percolation, at criticality, or in supercooled states. Connecting experiments and simulation with key theoretical principles, and covering numerous systems including micelles, micro-emulsions, biological systems, and cement pastes, this unique text is an invaluable resource for graduate students and researchers looking to explore and understand the expanding field of complex fluids.

  8. My Dog's Cheeks: A PBL Project on Collagen for Cell Biology and Genetics Courses

    Science.gov (United States)

    Casla, Alberto Vicario; Zubiaga, Isabel Smith

    2010-01-01

    Students often have an oversimplified view of biological facts, which may hinder subsequent understanding when conceptual complexity gives rise to cognitive conflicts. To avoid this situation here, we present a PBL approach for the analysis of Ehlers-Danlos syndrome (EDS), which integrates a variety of topics in cell biology, genetics, and…

  9. PREFACE: Complex Networks: from Biology to Information Technology

    Science.gov (United States)

    Barrat, A.; Boccaletti, S.; Caldarelli, G.; Chessa, A.; Latora, V.; Motter, A. E.

    2008-06-01

    The field of complex networks is one of the most active areas in contemporary statistical physics. Ten years after seminal work initiated the modern study of networks, interest in the field is in fact still growing, as indicated by the ever increasing number of publications in network science. The reason for such a resounding success is most likely the simplicity and broad significance of the approach that, through graph theory, allows researchers to address a variety of different complex systems within a common framework. This special issue comprises a selection of contributions presented at the workshop 'Complex Networks: from Biology to Information Technology' held in July 2007 in Pula (Cagliari), Italy as a satellite of the general conference STATPHYS23. The contributions cover a wide range of problems that are currently among the most important questions in the area of complex networks and that are likely to stimulate future research. The issue is organised into four sections. The first two sections describe 'methods' to study the structure and the dynamics of complex networks, respectively. After this methodological part, the issue proceeds with a section on applications to biological systems. The issue closes with a section concentrating on applications to the study of social and technological networks. The first section, entitled Methods: The Structure, consists of six contributions focused on the characterisation and analysis of structural properties of complex networks: The paper Motif-based communities in complex networks by Arenas et al is a study of the occurrence of characteristic small subgraphs in complex networks. These subgraphs, known as motifs, are used to define general classes of nodes and their communities by extending the mathematical expression of the Newman-Girvan modularity. The same line of research, aimed at characterising network structure through the analysis of particular subgraphs, is explored by Bianconi and Gulbahce in Algorithm

  10. Understanding valve program complexity in a refurbishment environment - learning from the past

    International Nuclear Information System (INIS)

    Roth, H.E.

    2012-01-01

    The complexity of Valve Program development, planning, execution and management in a refurbishment environment is an enormous undertaking requiring the proper coordination and integration of many moving parts. As such, lack of attention and understanding of this complexity has led to significant cost and schedule overruns in past refurbishment projects in the province. OPEX indicates the challenges in completing valve scope during refurbishments are related but not limited to; lack of detailed condition assessments, improper scope development, insignificant strategic approach to work task planning, scheduling and procurement, absence of contingency planning for common ‘as found’ conditions during execution, lack of proper training requirements, etc. In addition, past contracting strategies to employ numerous companies in collaboration to complete such a complex and specialized program, has resulted in further complications surrounding the management and integration of multiple quality programs and internal company processes. Finally, the aftermath of such fragmented projects results in an absolute closeout nightmare, often times taking years to locate, sift through and re-integrate pertinent information back into customer systems. Valve Program complexity cannot be understood by just anyone, only those that have lived through a refurbishment project and experienced the challenges mentioned above have the knowledge, skill, and ability to appreciate how to tactically apply past learning to realize future improvements. Furthermore, effective contractor-customer collaboration is crucial; true and in-depth knowledge and understanding of the customer quality programs, engineering and work management processes, configuration management requirements, and most importantly the imperative significance of nuclear safety, are all essential components to ensure overall alignment and program success. (author)

  11. Understanding valve program complexity in a refurbishment environment - learning from the past

    Energy Technology Data Exchange (ETDEWEB)

    Roth, H.E. [Babcock & Wilcox Canada Ltd., Cambridge, Ontario (Canada)

    2012-07-01

    The complexity of Valve Program development, planning, execution and management in a refurbishment environment is an enormous undertaking requiring the proper coordination and integration of many moving parts. As such, lack of attention and understanding of this complexity has led to significant cost and schedule overruns in past refurbishment projects in the province. OPEX indicates the challenges in completing valve scope during refurbishments are related but not limited to; lack of detailed condition assessments, improper scope development, insignificant strategic approach to work task planning, scheduling and procurement, absence of contingency planning for common ‘as found’ conditions during execution, lack of proper training requirements, etc. In addition, past contracting strategies to employ numerous companies in collaboration to complete such a complex and specialized program, has resulted in further complications surrounding the management and integration of multiple quality programs and internal company processes. Finally, the aftermath of such fragmented projects results in an absolute closeout nightmare, often times taking years to locate, sift through and re-integrate pertinent information back into customer systems. Valve Program complexity cannot be understood by just anyone, only those that have lived through a refurbishment project and experienced the challenges mentioned above have the knowledge, skill, and ability to appreciate how to tactically apply past learning to realize future improvements. Furthermore, effective contractor-customer collaboration is crucial; true and in-depth knowledge and understanding of the customer quality programs, engineering and work management processes, configuration management requirements, and most importantly the imperative significance of nuclear safety, are all essential components to ensure overall alignment and program success. (author)

  12. Toward understanding the thermodynamics of TALSPEAK process. Medium effects on actinide complexation

    International Nuclear Information System (INIS)

    Zalupski, Peter R.; Martin, Leigh R.; Nash, Ken; Nakamura, Yoshinobu; Yamamoto, Masahiko

    2009-01-01

    The ingenious combination of lactate and diethylenetriamine-N,N,N',N(double p rime),N(double p rime)-pentaacetic acid (DTPA) as an aqueous actinide-complexing medium forms the basis of the successful separation of americium and curium from lanthanides known as the TALSPEAK process. While numerous reports in the prior literature have focused on the optimization of this solvent extraction system, considerably less attention has been devoted to the understanding of the basic thermodynamic features of the complex fluids responsible for the separation. The available thermochemical information of both lactate and DTPA protonation and metal complexation reactions are representative of the behavior of these ions under idealized conditions. Our previous studies of medium effects on lactate protonation suggest that significant departures from the speciation predicted based on reported thermodynamic values should be expected in the TALSPEAK aqueous environment. Thermodynamic parameters describing the separation chemistry of this process thus require further examination at conditions significantly removed from conventional ideal systems commonly employed in fundamental solution chemistry. Such thermodynamic characterization is the key to predictive modelling of TALSPEAK. Improved understanding will, in principle, allow process technologists to more efficiently respond to off-normal conditions during large scale process operation. In this report, the results of calorimetric and potentiometric investigations of the effects of aqueous electrolytes on the thermodynamic parameters for lactate protonation and lactate complexation of americium and neodymium will be presented. Studies on the lactate protonation equilibrium will clearly illustrate distinct thermodynamic variations between strong electrolyte aqueous systems and buffered lactate environment.

  13. Complex formation of blueberry (Vaccinium angustifolium) anthocyanins during freeze-drying and its influence on their biological activity.

    Science.gov (United States)

    Correa-Betanzo, Julieta; Padmanabhan, Priya; Corredig, Milena; Subramanian, Jayasankar; Paliyath, Gopinadhan

    2015-03-25

    Biological activity of polyphenols is influenced by their uptake and is highly influenced by their interactions with the food matrix. This study evaluated the complex formation of blueberry polyphenols with fruit matrixes such as pectin and cellulose and their effect on the biological and antiproliferative properties of human colon cell lines HT-29 and CRL 1790. Free or complexed polyphenols were isolated by dialyzing aqueous or methanolic blueberry homogenates. Seven phenolic compounds and thirteen anthocyanins were identified in blueberry extracts. Blueberry extracts showed varying degrees of antioxidant and antiproliferative activities, as well as α-glucosidase activity. Fruit matrix containing cellulose and pectin, or purified polygalacturonic acid and cellulose, did not retain polyphenols and showed very low antioxidant or antiproliferative activities. These findings suggest that interactions between polyphenols and the food matrix may be more complex than a simple association and may play an important role in the bioefficacy of blueberry polyphenols.

  14. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Directory of Open Access Journals (Sweden)

    Ina Aretz

    2016-04-01

    Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  15. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

    Science.gov (United States)

    Aretz, Ina; Meierhofer, David

    2016-04-27

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  16. Understanding large multiprotein complexes: applying a multiple allosteric networks model to explain the function of the Mediator transcription complex.

    Science.gov (United States)

    Lewis, Brian A

    2010-01-15

    The regulation of transcription and of many other cellular processes involves large multi-subunit protein complexes. In the context of transcription, it is known that these complexes serve as regulatory platforms that connect activator DNA-binding proteins to a target promoter. However, there is still a lack of understanding regarding the function of these complexes. Why do multi-subunit complexes exist? What is the molecular basis of the function of their constituent subunits, and how are these subunits organized within a complex? What is the reason for physical connections between certain subunits and not others? In this article, I address these issues through a model of network allostery and its application to the eukaryotic RNA polymerase II Mediator transcription complex. The multiple allosteric networks model (MANM) suggests that protein complexes such as Mediator exist not only as physical but also as functional networks of interconnected proteins through which information is transferred from subunit to subunit by the propagation of an allosteric state known as conformational spread. Additionally, there are multiple distinct sub-networks within the Mediator complex that can be defined by their connections to different subunits; these sub-networks have discrete functions that are activated when specific subunits interact with other activator proteins.

  17. Application of Biologically Based Lumping To Investigate the Toxicokinetic Interactions of a Complex Gasoline Mixture.

    Science.gov (United States)

    Jasper, Micah N; Martin, Sheppard A; Oshiro, Wendy M; Ford, Jermaine; Bushnell, Philip J; El-Masri, Hisham

    2016-03-15

    People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate the performance of our PBPK model and chemical lumping method. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course toxicokinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 nontarget chemicals. The same biologically based lumping approach can be used to simplify any complex mixture with tens, hundreds, or thousands of constituents.

  18. Biological properties of novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles

    KAUST Repository

    Novak, Maria S.; Bü chel, Gabriel E.; Keppler, Bernhard K.; Jakupec, Michael A.

    2016-01-01

    Since the discovery that nitric oxide (NO) is a physiologically relevant molecule, there has been great interest in the use of metal nitrosyl compounds as antitumor pharmaceuticals. Particularly interesting are those complexes which can deliver NO to biological targets. Ruthenium- and osmium-based compounds offer lower toxicity compared to other metals and show different mechanisms of action as well as different spectra of activity compared to platinum-based drugs. Novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles were studied to elucidate their cytotoxicity and possible interactions with DNA. Apoptosis induction, changes of mitochondrial transmembrane potential and possible formation of reactive oxygen species were investigated as indicators of NO-mediated damage by flow cytometry. Results suggest that ruthenium- and osmium-nitrosyl complexes with the general formula (indazolium)[cis/trans-MCl4(NO)(1H-indazole)] have pronounced cytotoxic potency in cancer cell lines. Especially the more potent ruthenium complexes strongly induce apoptosis associated with depolarization of mitochondrial membranes, and elevated reactive oxygen species levels. Furthermore, a slight yet not unequivocal trend to accumulation of intracellular cyclic guanosine monophosphate attributable to NO-mediated effects was observed.

  19. Biological properties of novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles

    KAUST Repository

    Novak, Maria S.

    2016-03-09

    Since the discovery that nitric oxide (NO) is a physiologically relevant molecule, there has been great interest in the use of metal nitrosyl compounds as antitumor pharmaceuticals. Particularly interesting are those complexes which can deliver NO to biological targets. Ruthenium- and osmium-based compounds offer lower toxicity compared to other metals and show different mechanisms of action as well as different spectra of activity compared to platinum-based drugs. Novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles were studied to elucidate their cytotoxicity and possible interactions with DNA. Apoptosis induction, changes of mitochondrial transmembrane potential and possible formation of reactive oxygen species were investigated as indicators of NO-mediated damage by flow cytometry. Results suggest that ruthenium- and osmium-nitrosyl complexes with the general formula (indazolium)[cis/trans-MCl4(NO)(1H-indazole)] have pronounced cytotoxic potency in cancer cell lines. Especially the more potent ruthenium complexes strongly induce apoptosis associated with depolarization of mitochondrial membranes, and elevated reactive oxygen species levels. Furthermore, a slight yet not unequivocal trend to accumulation of intracellular cyclic guanosine monophosphate attributable to NO-mediated effects was observed.

  20. Simulation of biological flow and transport in complex geometries using embedded boundary/volume-of-fluid methods

    International Nuclear Information System (INIS)

    Trebotich, David

    2007-01-01

    We have developed a simulation capability to model multiscale flow and transport in complex biological systems based on algorithms and software infrastructure developed under the SciDAC APDEC CET. The foundation of this work is a new hybrid fluid-particle method for modeling polymer fluids in irregular microscale geometries that enables long-time simulation of validation experiments. Both continuum viscoelastic and discrete particle representations have been used to model the constitutive behavior of polymer fluids. Complex flow environment geometries are represented on Cartesian grids using an implicit function. Direct simulation of flow in the irregular geometry is then possible using embedded boundary/volume-of-fluid methods without loss of geometric detail. This capability has been used to simulate biological flows in a variety of application geometries including biomedical microdevices, anatomical structures and porous media

  1. Dermal tumorigen PAH and complex mixtures for biological research

    International Nuclear Information System (INIS)

    Griest, W.H.; Guerin, M.R.; Ho, C.

    1985-01-01

    Thirteen commercially available, commonly reported four-five ring dermal tumorigen PAHs, were determined in a set of complex mixtures consisting of crude and upgraded coal liquids, and petroleum crude oils and their distillate fractions. Semi-preparative scale, normal phase high performance liquid chromatographic fractionation followed by capillary column gas chromatography or gas chromatography-mass spectroscopy were used for the measurements. Deuterated or carbon-14 labeled PAH served as internal standards or allowed recovery corrections. Approaches for the preparation and measurement of radiolabeled PAH were examined to provide chemical probes for biological study. Synthetic routes for production of 14 C labeled dihydrobenzo[a]pyrene and 14 C- or 3 H 10-azabenzo[a]pyrene are being studied to provide tracers for fundamental studies in tracheal transplant and skin penetration systems. (DT)

  2. Systematic metabolite annotation and identification in complex biological extracts : combining robust mass spectrometry fragmentation and nuclear magnetic resonance spectroscopy

    NARCIS (Netherlands)

    Hooft, van der J.J.J.

    2012-01-01

    Detailed knowledge of the chemical content of organisms, organs, tissues, and cells is needed to fully characterize complex biological systems. The high chemical variety of compounds present in biological systems is illustrated by the presence of a large variety of compounds, ranging from apolar

  3. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability

    Science.gov (United States)

    Pathak, Rajesh Kumar; Gupta, Sanjay Mohan; Gaur, Vikram Singh; Pandey, Dinesh

    2015-01-01

    Abstract In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes. PMID:26484978

  4. Complex network synchronization of chaotic systems with delay coupling

    International Nuclear Information System (INIS)

    Theesar, S. Jeeva Sathya; Ratnavelu, K.

    2014-01-01

    The study of complex networks enables us to understand the collective behavior of the interconnected elements and provides vast real time applications from biology to laser dynamics. In this paper, synchronization of complex network of chaotic systems has been studied. Every identical node in the complex network is assumed to be in Lur’e system form. In particular, delayed coupling has been assumed along with identical sector bounded nonlinear systems which are interconnected over network topology

  5. How does undergraduate college biology students' level of understanding, in regard to the role of the seed plant root system, relate to their level of understanding of photosynthesis?

    Science.gov (United States)

    Njeng'ere, James Gicheha

    This research study investigated how undergraduate college biology students' level of understanding of the role of the seed plant root system relates to their level of understanding of photosynthesis. This research was conducted with 65 undergraduate non-majors biology who had completed 1 year of biology at Louisiana State University in Baton Rouge and Southeastern Louisiana University in Hammond. A root probe instrument was developed from some scientifically acceptable propositional statements about the root system, the process of photosynthesis, as well as the holistic nature of the tree. These were derived from research reviews of the science education and the arboriculture literature. This was administered to 65 students selected randomly from class lists of the two institutions. Most of the root probe's items were based on the Live Oak tree. An in-depth, clinical interview-based analysis was conducted with 12 of those tested students. A team of root experts participated by designing, validating and answering the same questions that the students were asked. A "systems" lens as defined by a team of college instructors, root experts (Shigo, 1991), and this researcher was used to interpret the results. A correlational coefficient determining students' level of understanding of the root system and their level of understanding of the process of photosynthesis was established by means of Pearson's r correlation (r = 0.328) using the SAS statistical analysis (SAS, 1987). From this a coefficient of determination (r2 = 0.104) was determined. Students' level of understanding of the Live Oak root system (mean score 5.94) was not statistically different from their level of understanding of the process of photosynthesis (mean score 5.54) as assessed by the root probe, t (129) = 0.137, p > 0.05 one tailed-test. This suggests that, to some degree, level of the root system limits level of understanding of photosynthesis and vice versa. Analysis of quantitative and qualitative

  6. Tackling complexities in understanding the social determinants of health: the contribution of ethnographic research.

    Science.gov (United States)

    Bandyopadhyay, Mridula

    2011-11-25

    The complexities inherent in understanding the social determinants of health are often not well-served by quantitative approaches. My aim is to show that well-designed and well-conducted ethnographic studies have an important contribution to make in this regard. Ethnographic research designs are a difficult but rigorous approach to research questions that require us to understand the complexity of people's social and cultural lives. I draw on an ethnographic study to describe the complexities of studying maternal health in a rural area in India. I then show how the lessons learnt in that setting and context can be applied to studies done in very different settings. I show how ethnographic research depends for rigour on a theoretical framework for sample selection; why immersion in the community under study, and rapport building with research participants, is important to ensure rich and meaningful data; and how flexible approaches to data collection lead to the gradual emergence of an analysis based on intense cross-referencing with community views and thus a conclusion that explains the similarities and differences observed. When using ethnographic research design it can be difficult to specify in advance the exact details of the study design. Researchers can encounter issues in the field that require them to change what they planned on doing. In rigorous ethnographic studies, the researcher in the field is the research instrument and needs to be well trained in the method. Ethnographic research is challenging, but nevertheless provides a rewarding way of researching complex health problems that require an understanding of the social and cultural determinants of health.

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

    Science.gov (United States)

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

    2016-10-20

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

  8. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S.; Fredrickson, J. K.; Stevens, R.

    2009-03-01

    Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

  9. Preparation and Characterization Challenges to Understanding Environmental and Biological Impacts of Ceria Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Karakoti, Ajay S.; Munusamy, Prabhakaran; Hostetler, Kasey E.; Kodali, Vamsi K.; Kuchibhatla, Satyanarayana V N T; Orr, Galya; Pounds, Joel G.; Teeguarden, Justin G.; Thrall, Brian D.; Baer, Donald R.

    2012-08-01

    It has been increasingly recognized that understanding and predicting the behaviors of nanoparticles is often limited by the degree to which the particles can be reliably produced and are adequately characterized. Examining data from the literature for ceria nanoparticles suggests that thermal history is one factor that has a strong influence on biological impact. Thermal processing may alter many physicochemical properties of the particles including density, crystal structure and the presence of surface contamination, but these may not be sufficiently recorded or reported to determine the ultimate source of an observed impact. A second example shows the types of difficulties that can be encountered in efforts to apply a well-studied synthesis route to producing well defined particles for biological studies. These examples and others highlight the importance of characterizing particles thoroughly and recording details of particle processing and history that are often not recorded and/or reported.

  10. 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."

  11. "Toward High School Biology": Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems

    Science.gov (United States)

    Herrmann-Abell, Cari F.; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better…

  12. Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

    DEFF Research Database (Denmark)

    Mazzoni, Gianluca; Pedersen, Hanne S.; de Oliveira Junior, Gerson A.

    2017-01-01

    by both conventional and ARTs such as OPU-IVP. The integration of systems biology information across different biological layers generates a complete view of the different molecular networks that control complex traits and can provide a strong contribution to the understanding of traits related to ARTs....

  13. Materiomics: biological protein materials, from nano to macro

    Science.gov (United States)

    Cranford, Steven; Buehler, Markus J

    2010-01-01

    Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics – discovering Nature’s complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature’s materials have been hindered by our lack of fundamental understanding of these materials’ intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties

  14. The molecular biology of WHO grade I astrocytomas.

    Science.gov (United States)

    Marko, Nicholas F; Weil, Robert J

    2012-12-01

    World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood.

  15. Cu(II AND Zn(II COMPLEX COMPOUNDS WITH BIGUANIDES AROMATIC DERIVATIVES. SYNTHESIS, CHARACTERIZATION, BIOLOGICAL ACTIVITY

    Directory of Open Access Journals (Sweden)

    Ticuţa Negreanu-Pîrjol

    2011-05-01

    Full Text Available In this paper we report the synthesis, physical-chemical characterization and antimicrobial activity of some new complex compounds of hetero-aromatic biguanides ligands, chlorhexidine base (CHX and chlorhexidine diacetate (CHXac2 with metallic ions Cu(II and Zn(II, in different molar ratio. The synthesized complexes were characterized by elemental chemical analysis and differential thermal analysis. The stereochemistry of the metallic ions was determined by infrared spectra, UV-Vis, EPR spectroscopy and magnetic susceptibility in the aim to establish the complexes structures. The biological activity of the new complex compounds was identified in solid technique by measuring minimum inhibition diameter of bacterial and fungal culture, against three standard pathogen strains, Escherichia coli ATCC 25922, Staphilococcus aureus ATCC 25923 and Candida albicans ATCC 10231. The results show an increased specific antimicrobial activity for the complexes chlorhexidine:Cu(II 1:1 and 1:2 compared with the one of the Zn(II complexes.

  16. Genome Scale Modeling in Systems Biology: Algorithms and Resources

    Science.gov (United States)

    Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

    2014-01-01

    In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

  17. Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud.

    Science.gov (United States)

    Burns, Malcolm; Wiseman, Gordon; Knight, Angus; Bramley, Peter; Foster, Lucy; Rollinson, Sophie; Damant, Andrew; Primrose, Sandy

    2016-01-07

    Following a report on a significant amount of horse DNA being detected in a beef burger product on sale to the public at a UK supermarket in early 2013, the Elliott report was published in 2014 and contained a list of recommendations for helping ensure food integrity. One of the recommendations included improving laboratory testing capacity and capability to ensure a harmonised approach for testing for food authenticity. Molecular biologists have developed exquisitely sensitive methods based on the polymerase chain reaction (PCR) or mass spectrometry for detecting the presence of particular nucleic acid or peptide/protein sequences. These methods have been shown to be specific and sensitive in terms of lower limits of applicability, but they are largely qualitative in nature. Historically, the conversion of these qualitative techniques into reliable quantitative methods has been beset with problems even when used on relatively simple sample matrices. When the methods are applied to complex sample matrices, as found in many foods, the problems are magnified resulting in a high measurement uncertainty associated with the result which may mean that the assay is not fit for purpose. However, recent advances in the technology and the understanding of molecular biology approaches have further given rise to the re-assessment of these methods for their quantitative potential. This review focuses on important issues for consideration when validating a molecular biology assay and the various factors that can impact on the measurement uncertainty of a result associated with molecular biology approaches used in detection of food fraud, with a particular focus on quantitative PCR-based and proteomics assays.

  18. Dose prescription complexity versus tumor control probability in biologically conformal radiotherapy

    International Nuclear Information System (INIS)

    South, C. P.; Evans, P. M.; Partridge, M.

    2009-01-01

    The technical feasibility and potential benefits of voxel-based nonuniform dose prescriptions for biologically heterogeneous tumors have been widely demonstrated. In some cases, an ''ideal'' dose prescription has been generated by individualizing the dose to every voxel within the target, but often this voxel-based prescription has been discretized into a small number of compartments. The number of dose levels utilized and the methods used for prescribing doses and assigning tumor voxels to different dose compartments have varied significantly. The authors present an investigation into the relationship between the complexity of the dose prescription and the tumor control probability (TCP) for a number of these methods. The linear quadratic model of cell killing was used in conjunction with a number of modeled tumors heterogeneous in clonogen density, oxygenation, or proliferation. Models based on simple mathematical functions, published biological data, and biological image data were investigated. Target voxels were assigned to dose compartments using (i) simple rules based on the initial biological distribution, (ii) iterative methods designed to maximize the achievable TCP, or (iii) methods based on an ideal dose prescription. The relative performance of the simple rules was found to depend on the form of heterogeneity of the tumor, while the iterative and ideal dose methods performed comparably for all models investigated. In all cases the maximum achievable TCP was approached within the first few (typically two to five) compartments. Results suggest that irrespective of the pattern of heterogeneity, the optimal dose prescription can be well approximated using only a few dose levels but only if both the compartment boundaries and prescribed dose levels are well chosen.

  19. Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Son N.; Liyu, Andrey V.; Chu, Rosalie K.; Anderton, Christopher R.; Laskin, Julia

    2017-01-17

    A new approach for constant distance mode mass spectrometry imaging of biological samples using nanospray desorption electrospray ionization (nano-DESI MSI) was developed by integrating a shear-force probe with nano-DESI probe. The technical concept and basic instrumental setup as well as general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enables constant-distance imaging mode via a computer controlled closed feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus Subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites including non-ribosomal peptides (surfactin, plipastatin and iturin) and iron-bound heme on the surface of living bacterial colonies ranging in diameter from 10 mm to 13 mm with height variations of up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Constant-mode nano-DESI MSI is ideally suited for imaging biological samples of complex topography in their native state.

  20. Mammalian synthetic biology for studying the cell.

    Science.gov (United States)

    Mathur, Melina; Xiang, Joy S; Smolke, Christina D

    2017-01-02

    Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

  1. Understanding the implementation of complex interventions in health care: the normalization process model

    Directory of Open Access Journals (Sweden)

    Rogers Anne

    2007-09-01

    Full Text Available Abstract Background The Normalization Process Model is a theoretical model that assists in explaining the processes by which complex interventions become routinely embedded in health care practice. It offers a framework for process evaluation and also for comparative studies of complex interventions. It focuses on the factors that promote or inhibit the routine embedding of complex interventions in health care practice. Methods A formal theory structure is used to define the model, and its internal causal relations and mechanisms. The model is broken down to show that it is consistent and adequate in generating accurate description, systematic explanation, and the production of rational knowledge claims about the workability and integration of complex interventions. Results The model explains the normalization of complex interventions by reference to four factors demonstrated to promote or inhibit the operationalization and embedding of complex interventions (interactional workability, relational integration, skill-set workability, and contextual integration. Conclusion The model is consistent and adequate. Repeated calls for theoretically sound process evaluations in randomized controlled trials of complex interventions, and policy-makers who call for a proper understanding of implementation processes, emphasize the value of conceptual tools like the Normalization Process Model.

  2. Mesoscale modeling: solving complex flows in biology and biotechnology.

    Science.gov (United States)

    Mills, Zachary Grant; Mao, Wenbin; Alexeev, Alexander

    2013-07-01

    Fluids are involved in practically all physiological activities of living organisms. However, biological and biorelated flows are hard to analyze due to the inherent combination of interdependent effects and processes that occur on a multitude of spatial and temporal scales. Recent advances in mesoscale simulations enable researchers to tackle problems that are central for the understanding of such flows. Furthermore, computational modeling effectively facilitates the development of novel therapeutic approaches. Among other methods, dissipative particle dynamics and the lattice Boltzmann method have become increasingly popular during recent years due to their ability to solve a large variety of problems. In this review, we discuss recent applications of these mesoscale methods to several fluid-related problems in medicine, bioengineering, and biotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Mixing and Processing of Complex Biological Fluids

    National Research Council Canada - National Science Library

    Liepmann, Dorian

    2003-01-01

    ... of microfluidic control on the makeup and molecular structure of biological fluids. For this project, we focused on two critical fluids that are biologically significant and that are of critical importance to DoD...

  4. Understanding and quantifying cognitive complexity level in mathematical problem solving items

    Directory of Open Access Journals (Sweden)

    SUSAN E. EMBRETSON

    2008-09-01

    Full Text Available The linear logistic test model (LLTM; Fischer, 1973 has been applied to a wide variety of new tests. When the LLTM application involves item complexity variables that are both theoretically interesting and empirically supported, several advantages can result. These advantages include elaborating construct validity at the item level, defining variables for test design, predicting parameters of new items, item banking by sources of complexity and providing a basis for item design and item generation. However, despite the many advantages of applying LLTM to test items, it has been applied less often to understand the sources of complexity for large-scale operational test items. Instead, previously calibrated item parameters are modeled using regression techniques because raw item response data often cannot be made available. In the current study, both LLTM and regression modeling are applied to mathematical problem solving items from a widely used test. The findings from the two methods are compared and contrasted for their implications for continued development of ability and achievement tests based on mathematical problem solving items.

  5. Y-12 National Security Complex Biological Monitoring and Abatement Program 2007 Calendar Yeare Report

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, M.J.; Greeley, M. S. Jr.; Morris, G. W.; Roy, W. K.; Ryan, M. G.; Smith, J. G.; Southworth, G. R.

    2008-07-01

    The National Pollutant Discharge Elimination System (NPDES) permit issued for the Oak Ridge Y-12 National Security Complex (Y-12 Complex) which became effective May 1, 2006, continued a requirement for a Biological Monitoring and Abatement Program (BMAP). The BMAP was originally developed in 1985 to demonstrate that the effluent limitations established for the Y-12 Complex protected the classified uses of the receiving stream (East Fork Poplar Creek: EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). The objectives of the current BMAP are similar, specifically to assess stream ecological conditions relative to regulatory limits and criteria, to assess ecological impacts as well as recovery in response to Y-12 operations, and to investigate the causes of continuing impacts. The BMAP consists of three tasks that reflect complementary approaches to evaluating the effects of the Y-12 Complex discharges on the biotic integrity of EFPC. These tasks include: (1) bioaccumulation monitoring, (2) benthic macroinvertebrate community monitoring, and (3) fish community monitoring. As required by the NPDES permit, the BMAP benthic macroinvertebrate community monitoring task includes studies to annually evaluate the receiving stream's biological integrity in comparison to TN Water Quality Criteria. BMAP monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) appropriate habitat distribution, and (5) access. The primary sampling sites include upper EFPC at kilometers (EFKs) 24.4 and 23.4 [upstream and downstream of Lake Reality (LR) respectively]; EFK 18.7 (also EFK 18.2 and 19), located

  6. On improved understanding of plasma-chemical processes in complex low-temperature plasmas

    Science.gov (United States)

    Röpcke, Jürgen; Loffhagen, Detlef; von Wahl, Eric; Nave, Andy S. C.; Hamann, Stephan; van Helden, Jean-Piere H.; Lang, Norbert; Kersten, Holger

    2018-05-01

    Over the last years, chemical sensing using optical emission spectroscopy (OES) in the visible spectral range has been combined with methods of mid infrared laser absorption spectroscopy (MIR-LAS) in the molecular fingerprint region from 3 to 20 μm, which contains strong rotational-vibrational absorption bands of a large variety of gaseous species. This optical approach established powerful in situ diagnostic tools to study plasma-chemical processes of complex low-temperature plasmas. The methods of MIR-LAS enable to detect stable and transient molecular species in ground and excited states and to measure the concentrations and temperatures of reactive species in plasmas. Since kinetic processes are inherent to discharges ignited in molecular gases, high time resolution on sub-second timescales is frequently desired for fundamental studies as well as for process monitoring in applied research and industry. In addition to high sensitivity and good temporal resolution, the capacity for broad spectral coverage enabling multicomponent detection is further expanding the use of OES and MIR-LAS techniques. Based on selected examples, this paper reports on recent achievements in the understanding of complex low-temperature plasmas. Recently, a link with chemical modeling of the plasma has been provided, which is the ultimate objective for a better understanding of the chemical and reaction kinetic processes occurring in the plasma. Contribution to the Topical Issue "Fundamentals of Complex Plasmas", edited by Jürgen Meichsner, Michael Bonitz, Holger Fehske, Alexander Piel.

  7. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

    Science.gov (United States)

    Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

    2017-07-03

    Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

  8. Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

    Science.gov (United States)

    Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

    2016-02-01

    The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

  9. Features of Knowledge Building in Biology: Understanding Undergraduate Students' Ideas about Molecular Mechanisms.

    Science.gov (United States)

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. © 2016 K. Southard et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  10. Evolution in students' understanding of thermal physics with increasing complexity

    Science.gov (United States)

    Langbeheim, Elon; Safran, Samuel A.; Livne, Shelly; Yerushalmi, Edit

    2013-12-01

    We analyze the development in students’ understanding of fundamental principles in the context of learning a current interdisciplinary research topic—soft matter—that was adapted to the level of high school students. The topic was introduced in a program for interested 11th grade high school students majoring in chemistry and/or physics, in an off-school setting. Soft matter was presented in a gradual increase in the degree of complexity of the phenomena as well as in the level of the quantitative analysis. We describe the evolution in students’ use of fundamental thermodynamics principles to reason about phase separation—a phenomenon that is ubiquitous in soft matter. In particular, we examine the impact of the use of free energy analysis, a common approach in soft matter, on the understanding of the fundamental principles of thermodynamics. The study used diagnostic questions and classroom observations to gauge the student’s learning. In order to gain insight on the aspects that shape the understanding of the basic principles, we focus on the responses and explanations of two case-study students who represent two trends of evolution in conceptual understanding in the group. We analyze changes in the two case studies’ management of conceptual resources used in their analysis of phase separation, and suggest how their prior knowledge and epistemological framing (a combination of their personal tendencies and their prior exposure to different learning styles) affect their conceptual evolution. Finally, we propose strategies to improve the instruction of these concepts.

  11. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

    Science.gov (United States)

    Transtrum, Mark K; Qiu, Peng

    2016-05-01

    The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior.

  12. Present Day Biology seen in the Looking Glass of Physics of Complexity

    Science.gov (United States)

    Schuster, P.

    Darwin's theory of variation and selection in its simplest form is directly applicable to RNA evolution in vitro as well as to virus evolution, and it allows for quantitative predictions. Understanding evolution at the molecular level is ultimately related to the central paradigm of structural biology: sequence⇒ structure ⇒ function. We elaborate on the state of the art in modeling and understanding evolution of RNA driven by reproduction and mutation. The focus will be laid on the landscape concept—originally introduced by Sewall Wright—and its application to problems in biology. The relation between genotypes and phenotypes is the result of two consecutive mappings from a space of genotypes called sequence space onto a space of phenotypes or structures, and fitness is the result of a mapping from phenotype space into non-negative real numbers. Realistic landscapes as derived from folding of RNA sequences into structures are characterized by two properties: (i) they are rugged in the sense that sequences lying nearby in sequence space may have very different fitness values and (ii) they are characterized by an appreciable degree of neutrality implying that a certain fraction of genotypes and/or phenotypes cannot be distinguished in the selection process. Evolutionary dynamics on realistic landscapes will be studied as a function of the mutation rate, and the role of neutrality in the selection process will be discussed.

  13. Designing and testing a classroom curriculum to teach preschoolers about the biology of physical activity: The respiration system as an underlying biological causal mechanism

    Science.gov (United States)

    Ewing, Tracy S.

    The present study examined young children's understanding of respiration and oxygen as a source of vital energy underlying physical activity. Specifically, the purpose of the study was to explore whether a coherent biological theory, characterized by an understanding that bodily parts (heart and lungs) and processes (oxygen in respiration) as part of a biological system, can be taught as a foundational concept to reason about physical activity. The effects of a biology-based intervention curriculum designed to teach preschool children about bodily functions as a part of the respiratory system, the role of oxygen as a vital substance and how physical activity acts an energy source were examined. Participants were recruited from three private preschool classrooms (two treatment; 1 control) in Southern California and included a total of 48 four-year-old children (30 treatment; 18 control). Findings from this study suggested that young children could be taught relevant biological concepts about the role of oxygen in respiratory processes. Children who received biology-based intervention curriculum made significant gains in their understanding of the biology of respiration, identification of physical and sedentary activities. In addition these children demonstrated that coherence of conceptual knowledge was correlated with improved accuracy at activity identification and reasoning about the inner workings of the body contributing to endurance. Findings from this study provided evidence to support the benefits of providing age appropriate but complex coherent biological instruction to children in early childhood settings.

  14. Telomere biology in aging and cancer: early history and perspectives.

    Science.gov (United States)

    Hayashi, Makoto T

    2018-01-20

    The ends of eukaryotic linear chromosomes are protected from undesired enzymatic activities by a nucleoprotein complex called the telomere. Expanding evidence indicates that telomeres have central functions in human aging and tumorigenesis. While it is undoubtedly important to follow current advances in telomere biology, it is also fruitful to be well informed in seminal historical studies for a comprehensive understanding of telomere biology, and for the anticipation of future directions. With this in mind, I here summarize the early history of telomere biology and current advances in the field, mostly focusing on mammalian studies relevant to aging and cancer.

  15. A CRISPR-based MLST Scheme for Understanding the Population Biology and Epidemiology of Salmonella Enterica

    Science.gov (United States)

    2015-05-26

    N. Shariat, R. E. Timme, J. B. Pettengill, R. Barrangou, E. G. Dudley. Characterization and evolution of Salmonella CRISPR - Cas systems...Barrangou, Edward G. Dudley. Characterization of CRISPR - Cas in Salmonella, 3rd European CRISPR meeting. 14-MAY-14, . : , Margaret K. Kirchner, Nikki... CRISPRs Beyond subtyping approaches, we were motivated to understand the biology of CRISPR - Cas systems in Salmonella. We performed in-depth sequence

  16. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  17. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

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

  18. A chemical-biological evaluation of rhodium(I) N-heterocyclic carbene complexes as prospective anticancer drugs.

    Science.gov (United States)

    Oehninger, Luciano; Küster, Laura Nadine; Schmidt, Claudia; Muñoz-Castro, Alvaro; Prokop, Aram; Ott, Ingo

    2013-12-23

    Rhodium(I) complexes bearing N-heterocyclic carbene (NHC) ligands have been widely used in catalytic chemistry, but there are very few reports of biological properties of these organometallics. A series of Rh(I)-NHC derivatives with 1,5-cyclooctadiene and CO as secondary ligands were synthesized, characterized, and biologically investigated as prospective antitumor drug candidates. Pronounced antiproliferative effects were noted for all complexes, along with moderate inhibitory activity of thioredoxin reductase (TrxR) and efficient binding to biomolecules (DNA, albumin). Biodistribution studies showed that the presence of albumin lowered the cellular uptake and confirmed the transport of rhodium into the nuclei. Changes in the mitochondrial membrane potential (MMP) were observed as well as DNA fragmentation in wild-type and daunorubicin- or vincristine-resistant Nalm-6 leukemia cells. Overall, these studies indicated that Rh(I)-NHC fragments could be used as partial structures of new antitumor agents, in particular in those drugs designed to address resistant malignant tissues. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Thermodynamics of complexity

    DEFF Research Database (Denmark)

    Westerhoff, Hans V.; Jensen, Peter Ruhdal; Snoep, Jacky L.

    1998-01-01

    -called emergent properties. Tendency towards increased entropy is an essential determinant for the behaviour of ideal gas mixtures, showing that even in the simplest physical/chemical systems, (dys)organisation of components is crucial for the behaviour of systems. This presentation aims at illustrating...... that the behaviour of two functionally interacting biological components (molecules, protein domains, pathways, organelles) differs from the behaviour these components would exhibit in isolation from one another, where the difference should be essential for the maintenance and growth of the living state, For a true...... understanding of this BioComplexity, modem thermodynamic concepts and methods (nonequilibrium thermodynamics, metabolic and hierarchical control analysis) will be needed. We shall propose to redefine nonequilibrium thermodynamics as: The science that aims at understanding the behaviour of nonequilibrium systems...

  20. Renal Tumor Anatomic Complexity: Clinical Implications for Urologists.

    Science.gov (United States)

    Joshi, Shreyas S; Uzzo, Robert G

    2017-05-01

    Anatomic tumor complexity can be objectively measured and reported using nephrometry. Various scoring systems have been developed in an attempt to correlate tumor complexity with intraoperative and postoperative outcomes. Nephrometry may also predict tumor biology in a noninvasive, reproducible manner. Other scoring systems can help predict surgical complexity and the likelihood of complications, independent of tumor characteristics. The accumulated data in this new field provide provocative evidence that objectifying anatomic complexity can consolidate reporting mechanisms and improve metrics of comparisons. Further prospective validation is needed to understand the full descriptive and predictive ability of the various nephrometry scores. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies

    Science.gov (United States)

    Smith, John A.

    2013-01-01

    This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

  2. The molecular biology of prostate cancer: current understanding and clinical implications.

    Science.gov (United States)

    Gandhi, Jason; Afridi, Adil; Vatsia, Sohrab; Joshi, Gargi; Joshi, Gunjan; Kaplan, Steven A; Smith, Noel L; Khan, Sardar Ali

    2018-04-01

    With continuous progress over the past few decades in understanding diagnosis, treatment, and genetics, much has been learned about the prostate cancer-diagnosed genome. A comprehensive MEDLINE® and Google scholar literature search was conducted using keyword variations relating to the genetics of prostate cancer such as chromosomal alterations, androgen receptor, castration-resistant, inheritance, polymorphisms, oncogenes, metastasis, biomarkers, and immunotherapy. Traditionally, androgen receptors (AR) have been the focus of research. Recently, identification of recurrent chromosomal alterations that lead to either multiplication of regions (gain-of-function) or deletion of regions (loss-of-function) has opened the door to greater genetic accessibility. These chromosomal aberrations lead to variation in copy number and gene expression. Some of these chromosomal alterations are inherited, while others undergo somatic mutations during disease progression. Inherited gene mutations that make one susceptible to prostate cancer have been identified with familial-linked studies. Somatic genes that progress tumorigenesis have also been identified. Research on the molecular biology of prostate cancer has characterized these genes into tumor suppressor genes or oncogenes. Additionally, genome-wide assay studies have identified many high-risk single-nucleotide polymorphisms recurrent throughout the prostate cancer-diagnosed genome. Castration-resistant prostate cancer is the most aggressive form of prostate cancer, and its research has elucidated many types of mutations associated with AR itself, including enhanced expression and amplification, point mutations, and alternative splicing. Understanding the molecular biology of prostate cancer has permitted more accurate identification using advanced biomarkers and therapy for aggressive forms using immunotherapy. An age-related disease, prostate cancer commands profound attention. With increasing life expectancy and the

  3. Evolution in students’ understanding of thermal physics with increasing complexity

    Directory of Open Access Journals (Sweden)

    Elon Langbeheim

    2013-11-01

    Full Text Available We analyze the development in students’ understanding of fundamental principles in the context of learning a current interdisciplinary research topic—soft matter—that was adapted to the level of high school students. The topic was introduced in a program for interested 11th grade high school students majoring in chemistry and/or physics, in an off-school setting. Soft matter was presented in a gradual increase in the degree of complexity of the phenomena as well as in the level of the quantitative analysis. We describe the evolution in students’ use of fundamental thermodynamics principles to reason about phase separation—a phenomenon that is ubiquitous in soft matter. In particular, we examine the impact of the use of free energy analysis, a common approach in soft matter, on the understanding of the fundamental principles of thermodynamics. The study used diagnostic questions and classroom observations to gauge the student’s learning. In order to gain insight on the aspects that shape the understanding of the basic principles, we focus on the responses and explanations of two case-study students who represent two trends of evolution in conceptual understanding in the group. We analyze changes in the two case studies’ management of conceptual resources used in their analysis of phase separation, and suggest how their prior knowledge and epistemological framing (a combination of their personal tendencies and their prior exposure to different learning styles affect their conceptual evolution. Finally, we propose strategies to improve the instruction of these concepts.

  4. Thai in-service teacher understanding of nature of science in biology teaching: Case of Mali

    Science.gov (United States)

    Aiemsum-ang, Napapan; Yuenyong, Chokchai

    2018-01-01

    This paper aimed to investigate the existing ideas of nature of science (NOS) teaching in Thailand biology classroom. The study reported the existing ideas of nature of science (NOS) teaching of one biology teacher Mrs. Mali who had been teaching for 6 years at in a school in Khon Kaen city. Methodology regarded interpretive paradigm. Tools of interpretation included 2 months of classroom observation, interviewing, and questionnaire of NOS. The findings revealed Mali held good understanding of the nature of science in the aspect of the use of evidence, the aspect of knowledge inquiry through different observation and deduction, the aspect of creativity and imagination influencing science knowledge inquiry, and the aspect of changeable scientific knowledge. Her biology teaching indicated that she used both the deficient nature of science approach and the implicit nature of science approach. The implicit nature of science approach was applied mostly in 7 periods and only 2 periods were arranged using the deficient nature of science approach. The paper has implication for professional development and pre-service program on NOS teaching in Thailand.

  5. Complex and biofluids: From Maxwell to nowadays

    Science.gov (United States)

    Misbah, Chaouqi

    2009-11-01

    Complex fluids are the rule in biology and in many industrial applications. Typical examples are blood, cartilage, and polymer solutions. Unlike water (as well as domestic oils, soft clear drinks, and so on), the law(s) describing the behavior of complex fluids are not yet fully established. The complexity arises from strong coupling between microscopic scales (like the motion of a red blood cell in the case of blood, or a polymer molecule for a polymer solution) and the global scale of the flow (say at the scale of a blood artery, or a channel in laboratory experiments). In this issue entitled Complex and Biofluids a large panel of experimental and theoretical problems of complex fluids is exposed. The topics range from dilute polymer solutions, food products, to biology (blood flow, cell and tissue mechanics). One of the earliest model put forward as an attempt to describe a complex fluid was suggested a long time ago by James Clerk Maxwell (in 1867). Other famous scientists, like Einstein (in 1906), and Taylor (in 1932) have made important contributions to the field, but the topic of complex fluids still continues to pose a formidable challenge to science. This field has known during the past decade an unbelievable upsurge of interest in many branches of science (physics, mechanics, chemistry, biology, medical science, mathematics, and so on). Understanding complex fluids is viewed as one of the biggest challenge of the present century. This synthesis will provide a simple introduction to the topic, summarize the main contribution of this issue, and list major open questions in this field. To cite this article: C. Misbah, C. R. Physique 10 (2009).

  6. Complexity-aware simple modeling.

    Science.gov (United States)

    Gómez-Schiavon, Mariana; El-Samad, Hana

    2018-02-26

    Mathematical models continue to be essential for deepening our understanding of biology. On one extreme, simple or small-scale models help delineate general biological principles. However, the parsimony of detail in these models as well as their assumption of modularity and insulation make them inaccurate for describing quantitative features. On the other extreme, large-scale and detailed models can quantitatively recapitulate a phenotype of interest, but have to rely on many unknown parameters, making them often difficult to parse mechanistically and to use for extracting general principles. We discuss some examples of a new approach-complexity-aware simple modeling-that can bridge the gap between the small-scale and large-scale approaches. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Use of synthetic biology techniques to site-selective introduce posttranslational modifactions in proteins

    NARCIS (Netherlands)

    Bosmans, R.P.G.; Brunsveld, L.; Ryadnov, M.; Brunsveld, L.; Suga, H.

    2014-01-01

    Unravelling the influence of posttranslational modifications (PTMs) on protein functioning is of key interest to get understanding how complex cellular networks are regulated. The current biological toolbox to synthesize these modified proteins in a single form in decent quantities is insufficient,

  8. Synthesis, spectroscopic characterization and in vitro cytotoxicities of new organometallic palladium complexes with biologically active β-diketones; Biological evaluation probing of the interaction mechanism with DNA/Protein and molecular docking

    Science.gov (United States)

    Karami, Kazem; Rafiee, Mina; Lighvan, Zohreh Mehri; Zakariazadeh, Mostafa; Faal, Ali Yeganeh; Esmaeili, Seyed-Alireza; Momtazi-Borojeni, Amir Abbas

    2018-02-01

    [Pd{(C,N)sbnd C6H4CH (CH3)NH}(CUR)] (3) and [Pd2{(C,N)sbnd C6H4CH(CH3)NH2}2(μ-N3CS2)] (4) [cur = 1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dion] novel organometallic complexes with biologically active ligands have been prepared and characterized via elemental analysis, multinuclear spectroscopic techniques (1H, and 13C NMR and IR) and their biological activities, including antitumoral activity and DNA-protein interactions have been investigated. Fluorescence spectroscopy used to study the interaction of the complexes with BSA have shown the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary structure of BSA in the presence of the complexes. In the meantime, spectroscopy and competitive titration have been applied to investigate the interaction of complexes with Warfarin and Ibuprofen site markers for sites I and II, respectively, with BSA. The results have suggested that the locations of complexes 3 and 4 are sites II and I, respectively. UV-Vis spectroscopy, emission titration and helix melting methods have been used to study the interaction of these complexes with CT-DNA, indicating that complexes are bound to CT-DNA by intercalation binding mode. In addition, good cytotoxic activity against MCF-7 (human breast cancer) and JURKAT (human leukemia) cell line has been shown by both complexes whereas low cytotoxicity was exerted on normal peripheral blood mononuclear cells.

  9. A review of human factors challenges of complex adaptive systems: discovering and understanding chaos in human performance.

    Science.gov (United States)

    Karwowski, Waldemar

    2012-12-01

    In this paper, the author explores a need for a greater understanding of the true nature of human-system interactions from the perspective of the theory of complex adaptive systems, including the essence of complexity, emergent properties of system behavior, nonlinear systems dynamics, and deterministic chaos. Human performance, more often than not, constitutes complex adaptive phenomena with emergent properties that exhibit nonlinear dynamical (chaotic) behaviors. The complexity challenges in the design and management of contemporary work systems, including service systems, are explored. Examples of selected applications of the concepts of nonlinear dynamics to the study of human physical performance are provided. Understanding and applications of the concepts of theory of complex adaptive and dynamical systems should significantly improve the effectiveness of human-centered design efforts of a large system of systems. Performance of many contemporary work systems and environments may be sensitive to the initial conditions and may exhibit dynamic nonlinear properties and chaotic system behaviors. Human-centered design of emergent human-system interactions requires application of the theories of nonlinear dynamics and complex adaptive system. The success of future human-systems integration efforts requires the fusion of paradigms, knowledge, design principles, and methodologies of human factors and ergonomics with those of the science of complex adaptive systems as well as modern systems engineering.

  10. Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network

    Directory of Open Access Journals (Sweden)

    Pooja Sharma

    2018-06-01

    Full Text Available Protein complexes are known to play a major role in controlling cellular activity in a living being. Identifying complexes from raw protein protein interactions (PPIs is an important area of research. Earlier work has been limited mostly to yeast. Such protein complex identification methods, when applied to large human PPIs often give poor performance. We introduce a novel method called CSC to detect protein complexes. The method is evaluated in terms of positive predictive value, sensitivity and accuracy using the datasets of the model organism, yeast and humans. CSC outperforms several other competing algorithms for both organisms. Further, we present a framework to establish the usefulness of CSC in analyzing the influence of a given disease gene in a complex topologically as well as biologically considering eight major association factors. Keywords: Protein complex, Connectivity, Semantic similarity, Contribution

  11. MURI: An Integrated Multi-Scale Approach for Understanding Ion Transport in Complex Heterogeneous Organic Materials

    Science.gov (United States)

    2017-09-30

    Thomas A. Witten,f Matthew W. Liberatore,a and Andrew M. Herring,a,* a Department of Chemical and Biological Engineering and bDepartment of Chemistry ...2) To fundamentally understand, with combined experimental and computational approaches, the interplay of chemistry , processing, and morphology on...Society, The International Society of Electrochemistry and The American Institute of Chemical Engineers to give oral and poster presentations. In

  12. [The Biology of Learning].

    Science.gov (United States)

    Campo-Cabal, Gerardo

    2012-01-01

    The effort to relate mental and biological functioning has fluctuated between two doctrines: 1) an attempt to explain mental functioning as a collective property of the brain and 2) as one relatied to other mental processes associated with specific regions of the brain. The article reviews the main theories developed over the last 200 years: phrenology, the psuedo study of the brain, mass action, cellular connectionism and distributed processing among others. In addition, approaches have emerged in recent years that allows for an understanding of the biological determinants and individual differences in complex mental processes through what is called cognitive neuroscience. Knowing the definition of neuroscience, the learning of memory, the ways in which learning occurs, the principles of the neural basis of memory and learning and its effects on brain function, among other things, allows us the basic understanding of the processes of memory and learning and is an important requirement to address the best manner to commit to the of training future specialists in Psychiatry. Copyright © 2012 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

  13. Absence of hydrocortisone from cytoplasmic hormone-protein complexes formed in vivo after administration of biologically active doses of [3H] hydrocortisone

    International Nuclear Information System (INIS)

    Voigt, J.; Grote, H.; Sekeris, C.E.

    1981-01-01

    After administration of [ 3 H] hydrocortisone to adrenalectomized rats, hormone-protein complexes were isolated from liver cytosol by DEAE-cellulose chromatography. After application of biologically active and inactive doses of hydrocortisone five binding components were detected eluting at the same salt concentrations as the hormone-protein complexes observed after incubation of cytosol with [ 3 H] hydrocortisone in vitro. The isolated hormone-protein fractions were acidified and extracted with ethylacetate and the steroids were analyzed by thin-layer chromatography. No significant amount of hydrocortisone could be detected in any of the complexes formed in vivo 5-60 min after administration of biologically active doses of hydrocortisone. 3xi,11β,17α,20xi, 21-Pentahydroxypregnane, steroidal carboxy acids, glucuronides and a very polar conjugate of hydrocortisone were found in the different fractions. After an in vivo dose of hydrocortisone of about 1/5000th of the minimal dose required for enzyme induction, hydrocortisone could be found in all the cytoplasmic hormone-protein complexes formed. In contrast to the cytoplasmic hormone-protein complexes, hydrocortisone could be readily demonstrated in nuclei isolated after the administration of biologically active doses of hormone, although acid metabolites were found to represent the main part of the radioactive compounds present in the nuclei. These acid metabolites were located in the nuclear envelope. (orig.)

  14. Fourth International Conference on Complex Systems

    CERN Document Server

    Minai, Ali A; Unifying Themes in Complex Systems IV

    2008-01-01

    In June of 2002, over 500 professors, students and researchers met in Boston, Massachusetts for the Fourth International Conference on Complex Systems. The attendees represented a remarkably diverse collection of fields: biology, ecology, physics, engineering, computer science, economics, psychology and sociology, The goal of the conference was to encourage cross-fertilization between the many disciplines represented and to deepen understanding of the properties common to all complex systems. This volume contains 43 papers selected from the more than 200 presented at the conference. Topics include: cellular automata, neurology, evolution, computer science, network dynamics, and urban planning. About NECSI: For over 10 years, The New England Complex Systems Institute (NECSI) has been instrumental in the development of complex systems science and its applications. NECSI conducts research, education, knowledge dissemination, and community development around the world for the promotion of the study of complex sys...

  15. Principles of assembly reveal a periodic table of protein complexes.

    Science.gov (United States)

    Ahnert, Sebastian E; Marsh, Joseph A; Hernández, Helena; Robinson, Carol V; Teichmann, Sarah A

    2015-12-11

    Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways. Most assembly transitions can be classified into three basic types, which can then be used to exhaustively enumerate a large set of possible quaternary structure topologies. These topologies, which include the vast majority of observed protein complex structures, enable a natural organization of protein complexes into a periodic table. On the basis of this table, we can accurately predict the expected frequencies of quaternary structure topologies, including those not yet observed. These results have important implications for quaternary structure prediction, modeling, and engineering. Copyright © 2015, American Association for the Advancement of Science.

  16. Biological mineralization of iron: Studies using Moesbauer spectroscopy and complementary techniques

    International Nuclear Information System (INIS)

    Webb, J.; Kim, K.S.; Tran, K.C.; Pierre, T.G.S.

    1988-01-01

    Biological deposition of solid Fe-containing phases can be studied using 57 Fe Moessbauer spectroscopy. Other techniques are needed in order to understand this complex process. These include proton-induced X-ray and γ-ray emission (PIXE/PIGME), electron microscopy, electron and X-ray diffraction, infrared spectroscopy and chemical characterization of organic components. This paper reviews and evaluates the application of these techniques to biological mineralization of Fe, particularly that occurring in the radula teeth of the marine molluscs, chitons and limpets. (orig.)

  17. Materiomics: biological protein materials, from nano to macro

    Directory of Open Access Journals (Sweden)

    Steven Cranford

    2010-11-01

    Full Text Available Steven Cranford, Markus J BuehlerCenter for Materials Science and Engineering, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USAAbstract: Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics – discovering Nature’s complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and

  18. Forty Years of Ebolavirus Molecular Biology: Understanding a Novel Disease Agent Through the Development and Application of New Technologies.

    Science.gov (United States)

    Groseth, Allison; Hoenen, Thomas

    2017-01-01

    Molecular biology is a broad discipline that seeks to understand biological phenomena at a molecular level, and achieves this through the study of DNA, RNA, proteins, and/or other macromolecules (e.g., those involved in the modification of these substrates). Consequently, it relies on the availability of a wide variety of methods that deal with the collection, preservation, inactivation, separation, manipulation, imaging, and analysis of these molecules. As such the state of the art in the field of ebolavirus molecular biology research (and that of all other viruses) is largely intertwined with, if not driven by, advancements in the technical methodologies available for these kinds of studies. Here we review of the current state of our knowledge regarding ebolavirus biology and emphasize the associated methods that made these discoveries possible.

  19. Emerging systems biology approaches in nanotoxicology: Towards a mechanism-based understanding of nanomaterial hazard and risk

    Energy Technology Data Exchange (ETDEWEB)

    Costa, Pedro M.; Fadeel, Bengt, E-mail: Bengt.Fadeel@ki.se

    2016-05-15

    Engineered nanomaterials are being developed for a variety of technological applications. However, the increasing use of nanomaterials in society has led to concerns about their potential adverse effects on human health and the environment. During the first decade of nanotoxicological research, the realization has emerged that effective risk assessment of the multitudes of new nanomaterials would benefit from a comprehensive understanding of their toxicological mechanisms, which is difficult to achieve with traditional, low-throughput, single end-point oriented approaches. Therefore, systems biology approaches are being progressively applied within the nano(eco)toxicological sciences. This novel paradigm implies that the study of biological systems should be integrative resulting in quantitative and predictive models of nanomaterial behaviour in a biological system. To this end, global ‘omics’ approaches with which to assess changes in genes, proteins, metabolites, etc. are deployed allowing for computational modelling of the biological effects of nanomaterials. Here, we highlight omics and systems biology studies in nanotoxicology, aiming towards the implementation of a systems nanotoxicology and mechanism-based risk assessment of nanomaterials. - Highlights: • Systems nanotoxicology is a multi-disciplinary approach to quantitative modelling. • Transcriptomics, proteomics and metabolomics remain the most common methods. • Global “omics” techniques should be coupled to computational modelling approaches. • The discovery of nano-specific toxicity pathways and biomarkers is a prioritized goal. • Overall, experimental nanosafety research must endeavour reproducibility and relevance.

  20. Emerging systems biology approaches in nanotoxicology: Towards a mechanism-based understanding of nanomaterial hazard and risk

    International Nuclear Information System (INIS)

    Costa, Pedro M.; Fadeel, Bengt

    2016-01-01

    Engineered nanomaterials are being developed for a variety of technological applications. However, the increasing use of nanomaterials in society has led to concerns about their potential adverse effects on human health and the environment. During the first decade of nanotoxicological research, the realization has emerged that effective risk assessment of the multitudes of new nanomaterials would benefit from a comprehensive understanding of their toxicological mechanisms, which is difficult to achieve with traditional, low-throughput, single end-point oriented approaches. Therefore, systems biology approaches are being progressively applied within the nano(eco)toxicological sciences. This novel paradigm implies that the study of biological systems should be integrative resulting in quantitative and predictive models of nanomaterial behaviour in a biological system. To this end, global ‘omics’ approaches with which to assess changes in genes, proteins, metabolites, etc. are deployed allowing for computational modelling of the biological effects of nanomaterials. Here, we highlight omics and systems biology studies in nanotoxicology, aiming towards the implementation of a systems nanotoxicology and mechanism-based risk assessment of nanomaterials. - Highlights: • Systems nanotoxicology is a multi-disciplinary approach to quantitative modelling. • Transcriptomics, proteomics and metabolomics remain the most common methods. • Global “omics” techniques should be coupled to computational modelling approaches. • The discovery of nano-specific toxicity pathways and biomarkers is a prioritized goal. • Overall, experimental nanosafety research must endeavour reproducibility and relevance.

  1. Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems

    Science.gov (United States)

    Demongeot, Jacques; Goles, Eric; Morvan, Michel; Noual, Mathilde; Sené, Sylvain

    2010-01-01

    One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally. PMID:20700525

  2. Attraction basins as gauges of robustness against boundary conditions in biological complex systems.

    Directory of Open Access Journals (Sweden)

    Jacques Demongeot

    Full Text Available One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally.

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

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

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

  5. Synthesis, Spectroscopic Characterization and Biological Activities of Transition Metal Complexes Derived from a Tridentate Schiff Base

    Directory of Open Access Journals (Sweden)

    J. Senthil Kumaran

    2013-01-01

    Full Text Available A new series of Cu (II, Ni (II, Co (II and Zn (II complexes have been synthesized from the Schiff base derived from 4-hydroxy-3-methoxybenzylidine-4-aminoantipyrine and 2-aminophenol. The structural features have been determined from their elemental analysis, magnetic susceptibility, molar conductance, Mass, IR, UV-Vis, 1H-NMR, 13C-NMR and ESR spectral studies. The redox behavior of the copper complex has been studied by cyclic voltammetry. The data confirm that the complexes have composition of ML2 type. The electronic absorption spectral data of the complexes propose an octahedral geometry around the central metal ion. All the metal complexes with DNA structure were guided by the presence of inter-molecular C–H⋯O and C–H⋯N hydrogen bonds. The biological activity of the synthesized compounds were tested against the bacterial species such as Bacillus subtilis, Staphylococcus aureus, Proteus vulgaris and fungal species such as Candida albicans by the well-diffusion method.

  6. Atomic switch networks as complex adaptive systems

    Science.gov (United States)

    Scharnhorst, Kelsey S.; Carbajal, Juan P.; Aguilera, Renato C.; Sandouk, Eric J.; Aono, Masakazu; Stieg, Adam Z.; Gimzewski, James K.

    2018-03-01

    Complexity is an increasingly crucial aspect of societal, environmental and biological phenomena. Using a dense unorganized network of synthetic synapses it is shown that a complex adaptive system can be physically created on a microchip built especially for complex problems. These neuro-inspired atomic switch networks (ASNs) are a dynamic system with inherent and distributed memory, recurrent pathways, and up to a billion interacting elements. We demonstrate key parameters describing self-organized behavior such as non-linearity, power law dynamics, and multistate switching regimes. Device dynamics are then investigated using a feedback loop which provides control over current and voltage power-law behavior. Wide ranging prospective applications include understanding and eventually predicting future events that display complex emergent behavior in the critical regime.

  7. Exploring the practicing-connections hypothesis: using gesture to support coordination of ideas in understanding a complex statistical concept.

    Science.gov (United States)

    Son, Ji Y; Ramos, Priscilla; DeWolf, Melissa; Loftus, William; Stigler, James W

    2018-01-01

    In this article, we begin to lay out a framework and approach for studying how students come to understand complex concepts in rich domains. Grounded in theories of embodied cognition, we advance the view that understanding of complex concepts requires students to practice, over time, the coordination of multiple concepts, and the connection of this system of concepts to situations in the world. Specifically, we explore the role that a teacher's gesture might play in supporting students' coordination of two concepts central to understanding in the domain of statistics: mean and standard deviation. In Study 1 we show that university students who have just taken a statistics course nevertheless have difficulty taking both mean and standard deviation into account when thinking about a statistical scenario. In Study 2 we show that presenting the same scenario with an accompanying gesture to represent variation significantly impacts students' interpretation of the scenario. Finally, in Study 3 we present evidence that instructional videos on the internet fail to leverage gesture as a means of facilitating understanding of complex concepts. Taken together, these studies illustrate an approach to translating current theories of cognition into principles that can guide instructional design.

  8. Simulation-based education: understanding the socio-cultural complexity of a surgical training 'boot camp'.

    Science.gov (United States)

    Cleland, Jennifer; Walker, Kenneth G; Gale, Michael; Nicol, Laura G

    2016-08-01

    The focus of simulation-based education (SBE) research has been limited to outcome and effectiveness studies. The effect of social and cultural influences on SBE is unclear and empirical work is lacking. Our objective in this study was to explore and understand the complexity of context and social factors at a surgical boot camp (BC). A rapid ethnographic study, employing the theoretical lenses of complexity and activity theory and Bourdieu's concept of 'capital', to better understand the socio-cultural influences acting upon, and during, two surgical BCs, and their implications for SBE. Over two 4-day BCs held in Scotland, UK, an observer and two preceptors conducted 81 hours of observations, 14 field interviews and 11 formal interviews with faculty members (n = 10, including the lead faculty member, session leaders and junior faculty members) and participants (n = 19 core surgical trainees and early-stage residents). Data collection and inductive analysis for emergent themes proceeded iteratively. This paper focuses on three analytical themes. First, the complexity of the surgical training system and wider health care education context, and how this influenced the development of the BC. Second, participants' views of the BC as a vehicle not just for learning skills but for gaining 'insider information' on how best to progress in surgical training. Finally, the explicit aim of faculty members to use the Scottish Surgical Bootcamp to welcome trainees and residents into the world of surgery, and how this occurred. To the best of our knowledge, this is the first empirical study of a surgical BC that takes a socio-cultural approach to exploring and understanding context, complexities, uncertainties and learning associated with one example of SBE. Our findings suggest that a BC is as much about social and cultural processes as it is about individual, cognitive and acquisitive learning. Acknowledging this explicitly will help those planning similar enterprises and

  9. Soft-Bodied Fossils Are Not Simply Rotten Carcasses - Toward a Holistic Understanding of Exceptional Fossil Preservation: Exceptional Fossil Preservation Is Complex and Involves the Interplay of Numerous Biological and Geological Processes.

    Science.gov (United States)

    Parry, Luke A; Smithwick, Fiann; Nordén, Klara K; Saitta, Evan T; Lozano-Fernandez, Jesus; Tanner, Alastair R; Caron, Jean-Bernard; Edgecombe, Gregory D; Briggs, Derek E G; Vinther, Jakob

    2018-01-01

    Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information. Investigations of fossils preserving non-biomineralized tissues suggest that certain structures that are decay resistant (e.g., the notochord) are rarely preserved (even where carbonaceous components survive), and decay-prone structures (e.g., nervous systems) can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils. © 2017 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  10. Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

    Energy Technology Data Exchange (ETDEWEB)

    Manno, D; Filippo, E; Fiore, R; Serra, A [Dipartimento di Scienza dei Materiali, Universita del Salento, Lecce (Italy); Urso, E; Rizzello, A; Maffia, M [Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita del Salento, Lecce (Italy)

    2010-04-23

    Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP{sup C}. In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP{sup C} at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

  11. Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

    International Nuclear Information System (INIS)

    Manno, D; Filippo, E; Fiore, R; Serra, A; Urso, E; Rizzello, A; Maffia, M

    2010-01-01

    Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP C . In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP C at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

  12. Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

    Science.gov (United States)

    Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

    2016-01-01

    Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

  13. Towards a comprehensive understanding of emerging dynamics and function of pancreatic islets: A complex network approach. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

    Science.gov (United States)

    Loppini, Alessandro

    2018-03-01

    Complex network theory represents a comprehensive mathematical framework to investigate biological systems, ranging from sub-cellular and cellular scales up to large-scale networks describing species interactions and ecological systems. In their exhaustive and comprehensive work [1], Gosak et al. discuss several scenarios in which the network approach was able to uncover general properties and underlying mechanisms of cells organization and regulation, tissue functions and cell/tissue failure in pathology, by the study of chemical reaction networks, structural networks and functional connectivities.

  14. Biological mechanisms, one molecule at a time

    Science.gov (United States)

    Tinoco, Ignacio; Gonzalez, Ruben L.

    2011-01-01

    The last 15 years have witnessed the development of tools that allow the observation and manipulation of single molecules. The rapidly expanding application of these technologies for investigating biological systems of ever-increasing complexity is revolutionizing our ability to probe the mechanisms of biological reactions. Here, we compare the mechanistic information available from single-molecule experiments with the information typically obtained from ensemble studies and show how these two experimental approaches interface with each other. We next present a basic overview of the toolkit for observing and manipulating biology one molecule at a time. We close by presenting a case study demonstrating the impact that single-molecule approaches have had on our understanding of one of life's most fundamental biochemical reactions: the translation of a messenger RNA into its encoded protein by the ribosome. PMID:21685361

  15. Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life

    NARCIS (Netherlands)

    Kaput, J.; Ommen, B. van; Kremer, S.H.A.; Priami, C.; Pontes Monteiro, J.; Morine, M.; Pepping, F.; Diaz, Z.; Fenech, M.; He, Y.; Albers, R.; Drevon, C.A.; Evelo, C.T.; Hancock, R.E.W.; IJsselmuiden, C.; Lumey, L.H.; Minihane, A.M.; Muller, M.; Murgia, C.; Radonjic, M.; Sobral, B.; West, K.P. Jr.

    2014-01-01

    Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum’s one gene—one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of

  16. Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life.

    NARCIS (Netherlands)

    Kaput, J.; Ommen, van B.; Kremer, B.; Priami, C.; Pontes Monteiro, J.; Morine, M.; Pepping, F.; Diaz, Z.; Fenech, M.; He, Y.; Albers, R.; Drevon, C.A.; Evelo, C.T.; Hancock, R.E.W.; Ijsselmuiden, C.; Lumey, L.H.; Minihane, A.M.; Muller, M.R.; Murgia, C.; Radonjic, M.; Sobral, B.W.S.; West Jr., K.P.

    2014-01-01

    Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum’s one gene—one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of

  17. Three-dimensional models of cancer for pharmacology and cancer cell biology: capturing tumor complexity in vitro/ex vivo.

    Science.gov (United States)

    Hickman, John A; Graeser, Ralph; de Hoogt, Ronald; Vidic, Suzana; Brito, Catarina; Gutekunst, Matthias; van der Kuip, Heiko

    2014-09-01

    Cancers are complex and heterogeneous pathological "organs" in a dynamic interplay with their host. Models of human cancer in vitro, used in cancer biology and drug discovery, are generally highly reductionist. These cancer models do not incorporate complexity or heterogeneity. This raises the question as to whether the cancer models' biochemical circuitry (not their genome) represents, with sufficient fidelity, a tumor in situ. Around 95% of new anticancer drugs eventually fail in clinical trial, despite robust indications of activity in existing in vitro pre-clinical models. Innovative models are required that better capture tumor biology. An important feature of all tissues, and tumors, is that cells grow in three dimensions. Advances in generating and characterizing simple and complex (with added stromal components) three-dimensional in vitro models (3D models) are reviewed in this article. The application of stirred bioreactors to permit both scale-up/scale-down of these cancer models and, importantly, methods to permit controlled changes in environment (pH, nutrients, and oxygen) are also described. The challenges of generating thin tumor slices, their utility, and potential advantages and disadvantages are discussed. These in vitro/ex vivo models represent a distinct move to capture the realities of tumor biology in situ, but significant characterization work still remains to be done in order to show that their biochemical circuitry accurately reflects that of a tumor. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Mathematics, structuralism and biology.

    Science.gov (United States)

    Saunders, P T

    1988-01-01

    A new approach is gaining ground in biology, one that has much in common with the structuralist tradition in other fields. It is very much in the spirit of an earlier view of biology and indeed of science in general. It is also, though this is not generally recognized, in the spirit of twentieth century physics. As in modern physics, however, it is not a question of ignoring all the progress that has been made within the former paradigm. On the contrary, the aim is to use it as a basis for setting out in a somewhat different direction. Complex phenomena do not generally lend themselves to reductionist analyses which seek explanation only in terms of detailed mechanisms, but a proper scientific discussion of structure must make full use of what we have already learned - by whatever means - about the processes that underly the phenomena we are trying to understand.

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

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

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

  20. Features of Knowledge Building in Biology: Understanding Undergraduate Students’ Ideas about Molecular Mechanisms

    Science.gov (United States)

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S.

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. PMID:26931398

  1. Complexities of Parental Understanding of Phenylketonuria

    Science.gov (United States)

    Sibinga, Maarten S.; Friedman, C. Jack

    1971-01-01

    Parental understanding of PKU, investigated through a questionnaire, was evaluated as to completeness and with respect to distortion. Education of parents was found to be unrelated to their understanding or tendency to distort. Effectiveness of the pediatrician's communication with parents is discussed. (Author/KW)

  2. Synthetic biology in mammalian cells: Next generation research tools and therapeutics

    Science.gov (United States)

    Lienert, Florian; Lohmueller, Jason J; Garg, Abhishek; Silver, Pamela A

    2014-01-01

    Recent progress in DNA manipulation and gene circuit engineering has greatly improved our ability to programme and probe mammalian cell behaviour. These advances have led to a new generation of synthetic biology research tools and potential therapeutic applications. Programmable DNA-binding domains and RNA regulators are leading to unprecedented control of gene expression and elucidation of gene function. Rebuilding complex biological circuits such as T cell receptor signalling in isolation from their natural context has deepened our understanding of network motifs and signalling pathways. Synthetic biology is also leading to innovative therapeutic interventions based on cell-based therapies, protein drugs, vaccines and gene therapies. PMID:24434884

  3. The role of mathematical models in understanding pattern formation in developmental biology.

    Science.gov (United States)

    Umulis, David M; Othmer, Hans G

    2015-05-01

    In a Wall Street Journal article published on April 5, 2013, E. O. Wilson attempted to make the case that biologists do not really need to learn any mathematics-whenever they run into difficulty with numerical issues, they can find a technician (aka mathematician) to help them out of their difficulty. He formalizes this in Wilsons Principle No. 1: "It is far easier for scientists to acquire needed collaboration from mathematicians and statisticians than it is for mathematicians and statisticians to find scientists able to make use of their equations." This reflects a complete misunderstanding of the role of mathematics in all sciences throughout history. To Wilson, mathematics is mere number crunching, but as Galileo said long ago, "The laws of Nature are written in the language of mathematics[Formula: see text] the symbols are triangles, circles and other geometrical figures, without whose help it is impossible to comprehend a single word." Mathematics has moved beyond the geometry-based model of Galileo's time, and in a rebuttal to Wilson, E. Frenkel has pointed out the role of mathematics in synthesizing the general principles in science (Both point and counter-point are available in Wilson and Frenkel in Notices Am Math Soc 60(7):837-838, 2013). We will take this a step further and show how mathematics has been used to make new and experimentally verified discoveries in developmental biology and how mathematics is essential for understanding a problem that has puzzled experimentalists for decades-that of how organisms can scale in size. Mathematical analysis alone cannot "solve" these problems since the validation lies at the molecular level, but conversely, a growing number of questions in biology cannot be solved without mathematical analysis and modeling. Herein, we discuss a few examples of the productive intercourse between mathematics and biology.

  4. Education science and biological anthropology.

    Science.gov (United States)

    Krebs, Uwe

    2014-01-01

    This contribution states deficits and makes proposals in order to overcome them. First there is the question as to why the Biological Anthropology--despite all its diversifications--hardly ever deals with educational aspects of its subject. Second it is the question as to why Educational Science neglects or even ignores data of Biological Anthropology which are recognizably important for its subject. It is postulated that the stated deficits are caused by several adverse influences such as, the individual identity of each of the involved single sciences; aspects of the recent history of the German Anthropology; a lack of conceptual understanding of each other; methodological differences and, last but not least, the structure of the universities. The necessity to remedy this situation was deduced from two groups of facts. First, more recent data of the Biological Anthropology (e.g. brain functions and learning, sex specificity and education) are of substantial relevance for the Educational Science. Second, the epistemological requirements of complex subjects like education need interdisciplinary approaches. Finally, a few suggestions of concrete topics are given which are related to both, Educational Science and Biological Anthropology.

  5. WE-DE-202-00: Connecting Radiation Physics with Computational Biology

    International Nuclear Information System (INIS)

    2016-01-01

    processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

  6. WE-DE-202-00: Connecting Radiation Physics with Computational Biology

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2016-06-15

    processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

  7. The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria

    Directory of Open Access Journals (Sweden)

    Meghan Zuck

    2017-11-01

    Full Text Available Despite global eradication efforts over the past century, malaria remains a devastating public health burden, causing almost half a million deaths annually (WHO, 2016. A detailed understanding of the mechanisms that control malaria infection has been hindered by technical challenges of studying a complex parasite life cycle in multiple hosts. While many interventions targeting the parasite have been implemented, the complex biology of Plasmodium poses a major challenge, and must be addressed to enable eradication. New approaches for elucidating key host-parasite interactions, and predicting how the parasite will respond in a variety of biological settings, could dramatically enhance the efficacy and longevity of intervention strategies. The field of systems biology has developed methodologies and principles that are well poised to meet these challenges. In this review, we focus our attention on the Liver Stage of the Plasmodium lifecycle and issue a “call to arms” for using systems biology approaches to forge a new era in malaria research. These approaches will reveal insights into the complex interplay between host and pathogen, and could ultimately lead to novel intervention strategies that contribute to malaria eradication.

  8. Complex networks principles, methods and applications

    CERN Document Server

    Latora, Vito; Russo, Giovanni

    2017-01-01

    Networks constitute the backbone of complex systems, from the human brain to computer communications, transport infrastructures to online social systems and metabolic reactions to financial markets. Characterising their structure improves our understanding of the physical, biological, economic and social phenomena that shape our world. Rigorous and thorough, this textbook presents a detailed overview of the new theory and methods of network science. Covering algorithms for graph exploration, node ranking and network generation, among the others, the book allows students to experiment with network models and real-world data sets, providing them with a deep understanding of the basics of network theory and its practical applications. Systems of growing complexity are examined in detail, challenging students to increase their level of skill. An engaging presentation of the important principles of network science makes this the perfect reference for researchers and undergraduate and graduate students in physics, ...

  9. Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from cephradine and sugars

    International Nuclear Information System (INIS)

    Naz, N.; Iqbal, M.Z.

    2011-01-01

    Fe(II), Co(II) and Ni(II) metal complexes of novel schiff bases derived from Cephradine and sugars (D-Glucose, L. Arabinose and D-Galactose) were synthesized and characterized by elemental analysis, magnetic susceptibility, thermal analysis, electronic absorption and FT-IR spectral studies. It has been found that schiff bases behave as bi-dentate-ligands forming complexes with 1:2 (metal:ligand) stoichiometry. the neutral nature of the complexes was confirmed by their low conductance values. The biological activities of complexes have been evaluated against two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and staphylococcus aureus) bacteria by Agar diffusion disc method. It has been found that the complexes have higher activity as compared to the pure Cephradine against the same bacteria. (author)

  10. Complexity in practice: understanding primary care as a complex adaptive system

    Directory of Open Access Journals (Sweden)

    Beverley Ellis

    2010-06-01

    Conclusions The results are real-world exemplars of the emergent properties of complex adaptive systems. Improving clinical governance in primary care requires both complex social interactions and underpinning informatics. The socio-technical lessons learned from this research should inform future management approaches.

  11. Quantification of biopharmaceuticals and biomarkers in complex biological matrices: a comparison of liquid chromatography coupled to tandem mass spectrometry and ligand binding assays

    NARCIS (Netherlands)

    Bults, Peter; van de Merbel, Nico C; Bischoff, Rainer

    2015-01-01

    The quantification of proteins (biopharmaceuticals or biomarkers) in complex biological samples such as blood plasma requires exquisite sensitivity and selectivity, as all biological matrices contain myriads of proteins that are all made of the same 20 proteinogenic amino acids, notwithstanding

  12. Towards physical principles of biological evolution

    Science.gov (United States)

    Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

    2018-03-01

    Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice

  13. Fostering synergy between cell biology and systems biology.

    Science.gov (United States)

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

    2015-08-01

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

  14. Biological contributions to addictions in adolescents and adults: prevention, treatment, and policy implications.

    Science.gov (United States)

    Potenza, Marc N

    2013-02-01

    Despite significant advances in our understanding of the biological bases of addictions, these disorders continue to represent a huge public health burden that is associated with substantial personal suffering. Efforts to target addictions require consideration of how the improved biological understanding of addictions may lead to improved prevention, treatment, and policy initiatives. In this article, we provide a narrative review of current biological models for addictions with a goal of placing existing data and theories within a translational and developmental framework targeting the advancement of prevention, treatment, and policy strategies. Data regarding individual differences, intermediary phenotypes, and main and interactive influences of genetic and environmental contributions in the setting of developmental trajectories that may be influenced by addictive drugs or behavior indicate complex underpinnings of addictions. Consideration and further elucidation of the biological etiologies of addictions hold significant potential for making important gains and reducing the public health impact of addictions. Copyright © 2013 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

  15. The effect of multiple external representations (MERs) worksheets toward complex system reasoning achievement

    Science.gov (United States)

    Sumarno; Ibrahim, M.; Supardi, Z. A. I.

    2018-03-01

    The application of a systems approach to assessing biological systems provides hope for a coherent understanding of cell dynamics patterns and their relationship to plant life. This action required the reasoning about complex systems. In other sides, there were a lot of researchers who provided the proof about the instructional successions. They involved the multiple external representations which improved the biological learning. The researcher conducted an investigation using one shoot case study design which involved 30 students in proving that the MERs worksheets could affect the student's achievement of reasoning about complex system. The data had been collected based on test of reasoning about complex system and student's identification result who worked through MERs. The result showed that only partially students could achieve reasoning about system complex, but their MERs skill could support their reasoning ability of complex system. This study could bring a new hope to develop the MERs worksheet as a tool to facilitate the reasoning about complex system.

  16. Understanding coral reefs as complex systems: degradation and prospects for recovery

    Directory of Open Access Journals (Sweden)

    Raymond T. Dizon

    2006-06-01

    Full Text Available The present century is witness to unprecedented levels of coral reef degradation worldwide. Current understanding based on traditional ideas is unlikely to capture adequately the dynamics of phenomena accompanying this trend. In this regard, the ideas of complexity are reviewed. Some applications to coral reefs as complex systems have already been discussed in the literature although further progress is warranted as the search for new and more effective management tools continues, and the direction towards more holistic, integrative and large scale approaches gains wider acceptance. We distinguish between the concepts of robustness and resilience in the face of disturbance, highlight the various mechanisms that foster these stability properties and provide some coral reef examples. We identify some of the driving forces behind succession that are critical for community assembly and possible reef recovery. Finally, we consider how self-organization arises out of apparently random and chaotic processes and interactions to exhibit certain regularities and patterns especially when moving up on the scale of space and/or time.

  17. A systems biology approach for pathway level analysis

    OpenAIRE

    Draghici, Sorin; Khatri, Purvesh; Tarca, Adi Laurentiu; Amin, Kashyap; Done, Arina; Voichita, Calin; Georgescu, Constantin; Romero, Roberto

    2007-01-01

    A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By usin...

  18. Geometric triangular chiral hexagon crystal-like complexes organization in pathological tissues biological collision order.

    Directory of Open Access Journals (Sweden)

    Jairo A Díaz

    Full Text Available The present study describes and documents self-assembly of geometric triangular chiral hexagon crystal like complex organizations (GTCHC in human pathological tissues. The authors have found this architectural geometric expression at macroscopic and microscopic levels mainly in cancer processes. This study is based essentially on macroscopic and histopathologic analyses of 3000 surgical specimens: 2600 inflammatory lesions and 400 malignant tumours. Geometric complexes identified photographically at macroscopic level were located in the gross surgical specimen, and these areas were carefully dissected. Samples were taken to carry out histologic analysis. Based on the hypothesis of a collision genesis mechanism and because it is difficult to carry out an appropriate methodological observation in biological systems, the authors designed a model base on other dynamic systems to obtain indirect information in which a strong white flash wave light discharge, generated by an electronic device, hits over the lines of electrical conductance structured in helicoidal pattern. In their experimental model, the authors were able to reproduce and to predict polarity, chirality, helicoid geometry, triangular and hexagonal clusters through electromagnetic sequential collisions. They determined that similar events among constituents of extracelular matrix which drive and produce piezoelectric activity are responsible for the genesis of GTCHC complexes in pathological tissues. This research suggests that molecular crystals represented by triangular chiral hexagons derived from a collision-attraction event against collagen type I fibrils emerge at microscopic and macroscopic scales presenting a lateral assembly of each side of hypertrophy helicoid fibers, that represent energy flow in cooperative hierarchically chiral electromagnetic interaction in pathological tissues and arises as a geometry of the equilibrium in perturbed biological systems. Further

  19. Geometric triangular chiral hexagon crystal-like complexes organization in pathological tissues biological collision order.

    Science.gov (United States)

    Díaz, Jairo A; Jaramillo, Natalia A; Murillo, Mauricio F

    2007-12-12

    The present study describes and documents self-assembly of geometric triangular chiral hexagon crystal like complex organizations (GTCHC) in human pathological tissues. The authors have found this architectural geometric expression at macroscopic and microscopic levels mainly in cancer processes. This study is based essentially on macroscopic and histopathologic analyses of 3000 surgical specimens: 2600 inflammatory lesions and 400 malignant tumours. Geometric complexes identified photographically at macroscopic level were located in the gross surgical specimen, and these areas were carefully dissected. Samples were taken to carry out histologic analysis. Based on the hypothesis of a collision genesis mechanism and because it is difficult to carry out an appropriate methodological observation in biological systems, the authors designed a model base on other dynamic systems to obtain indirect information in which a strong white flash wave light discharge, generated by an electronic device, hits over the lines of electrical conductance structured in helicoidal pattern. In their experimental model, the authors were able to reproduce and to predict polarity, chirality, helicoid geometry, triangular and hexagonal clusters through electromagnetic sequential collisions. They determined that similar events among constituents of extracelular matrix which drive and produce piezoelectric activity are responsible for the genesis of GTCHC complexes in pathological tissues. This research suggests that molecular crystals represented by triangular chiral hexagons derived from a collision-attraction event against collagen type I fibrils emerge at microscopic and macroscopic scales presenting a lateral assembly of each side of hypertrophy helicoid fibers, that represent energy flow in cooperative hierarchically chiral electromagnetic interaction in pathological tissues and arises as a geometry of the equilibrium in perturbed biological systems. Further interdisciplinary studies must

  20. Emergent nested systems a theory of understanding and influencing complex systems as well as case studies in urban systems

    CERN Document Server

    Walloth, Christian

    2016-01-01

    This book presents a theory as well as methods to understand and to purposively influence complex systems. It suggests a theory of complex systems as nested systems, i. e. systems that enclose other systems and that are simultaneously enclosed by even other systems. According to the theory presented, each enclosing system emerges through time from the generative activities of the systems they enclose. Systems are nested and often emerge unplanned, and every system of high dynamics is enclosed by a system of slower dynamics. An understanding of systems with faster dynamics, which are always guided by systems of slower dynamics, opens up not only new ways to understanding systems, but also to effectively influence them. The aim and subject of this book is to lay out these thoughts and explain their relevance to the purposive development of complex systems, which are exemplified in case studies from an urban system. The interested reader, who is not required to be familiar with system-theoretical concepts or wit...

  1. Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes

    DEFF Research Database (Denmark)

    Pedersen, Helle Krogh; Gudmundsdottir, Valborg; Brunak, Søren

    2017-01-01

    Type 2 diabetes (T2D) is a complex disease that involves multiple genes. Numerous risk loci have already been associated with T2D, although many susceptibility genes remain to be identified given heritability estimates. Systems biology approaches hold potential for discovering novel T2D genes...... by considering their biological context, such as tissue-specific protein interaction partners. Pancreatic islets are a key T2D tissue and many of the known genetic risk variants lead to impaired islet function, hence a better understanding of the islet-specific dysregulation in the disease-state is essential...... to unveil the full potential of person-specific profiles. Here we identify 3,692 overlapping pancreatic islet protein complexes (containing 10,805 genes) by integrating islet gene and protein expression data with protein interactions. We found 24 of these complexes to be significantly enriched for genes...

  2. Quantum physics meets biology.

    Science.gov (United States)

    Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko

    2009-12-01

    Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a "pedestrian guide" to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future "quantum biology," its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.

  3. Scientific Conceptions of Photosynthesis among Primary School Pupils and Student Teachers of Biology

    Directory of Open Access Journals (Sweden)

    Darja Skribe Dimec

    2017-03-01

    Full Text Available Photosynthesis is the most important biochemical process on Earth. Most living beings depend on it directly or indirectly. Knowledge about photosynthesis enables us to understand how the world functions as an ecosystem and how photosynthesis acts as a bridge between the non-living and living worlds. It is, therefore, understandable that photosynthesis is included in national curricula around the world. The practice unfortunately shows that students at all school levels mostly learn about photosynthesis by rote. Consequently, they have difficulties understanding this vital process. Research also shows many misconceptions in relation to photosynthesis among students of different ages. Based on these, the main aim of our study was to explore the scientific conceptions about photosynthesis held by primary school pupils and student teachers of biology. Data were collected using a questionnaire containing seven biology content questions. The sample consisted of 634 participants, 427 primary school pupils (aged 11–14, and 207 student teachers of biology (aged 20–23. We found that the populations of primary school pupils and student teachers of biology differ greatly concerning scientific conceptions of photosynthesis. The student teachers showed good and complex understanding of photosynthesis, while pupils showed some misconceptions (location of chlorophyll and photosynthesis in a plant, transformation of energy in photosynthesis. Analysis of the development of scientific conceptions about photosynthesis with age showed that there is very little progress among primary school pupils and none among biology student teachers. More involvement of student teachers of biology in practical work at primary schools during their study was suggested to make student teachers aware of, and better understand pupils’ misconceptions.

  4. Cardiac Arrhythmia: In vivo screening in the zebrafish to overcome complexity in drug discovery.

    Science.gov (United States)

    Macrae, Calum A

    2010-07-01

    IMPORTANCE OF THE FIELD: Cardiac arrhythmias remain a major challenge for modern drug discovery. Clinical events are paroxysmal, often rare and may be asymptomatic until a highly morbid complication. Target selection is often based on limited information and though highly specific agents are identified in screening, the final efficacy is often compromised by unanticipated systemic responses, a narrow therapeutic index and substantial toxicities. AREAS COVERED IN THIS REVIEW: Our understanding of complexity of arrhythmogenesis has grown dramatically over the last two decades, and the range of potential disease mechanisms now includes pathways previously thought only tangentially involved in arrhythmia. This review surveys the literature on arrhythmia mechanisms from 1965 to the present day, outlines the complex biology underlying potentially each and every rhythm disturbance, and highlights the problems for rational target identification. The rationale for in vivo screening is described and the utility of the zebrafish for this approach and for complementary work in functional genomics is discussed. Current limitations of the model in this setting and the need for careful validation in new disease areas are also described. WHAT THE READER WILL GAIN: An overview of the complex mechanisms underlying most clinical arrhythmias, and insight into the limits of ion channel conductances as drug targets. An introduction to the zebrafish as a model organism, in particular for cardiovascular biology. Potential approaches to overcoming the hurdles to drug discovery in the face of complex biology including in vivo screening of zebrafish genetic disease models. TAKE HOME MESSAGE: In vivo screening in faithful disease models allows the effects of drugs on integrative physiology and disease biology to be captured during the screening process, in a manner agnostic to potential drug target or targets. This systematic strategy bypasses current gaps in our understanding of disease

  5. The complex jujube genome provides insights into fruit tree biology.

    Science.gov (United States)

    Liu, Meng-Jun; Zhao, Jin; Cai, Qing-Le; Liu, Guo-Cheng; Wang, Jiu-Rui; Zhao, Zhi-Hui; Liu, Ping; Dai, Li; Yan, Guijun; Wang, Wen-Jiang; Li, Xian-Song; Chen, Yan; Sun, Yu-Dong; Liu, Zhi-Guo; Lin, Min-Juan; Xiao, Jing; Chen, Ying-Ying; Li, Xiao-Feng; Wu, Bin; Ma, Yong; Jian, Jian-Bo; Yang, Wei; Yuan, Zan; Sun, Xue-Chao; Wei, Yan-Li; Yu, Li-Li; Zhang, Chi; Liao, Sheng-Guang; He, Rong-Jun; Guang, Xuan-Min; Wang, Zhuo; Zhang, Yue-Yang; Luo, Long-Hai

    2014-10-28

    The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.

  6. Radiosynthesis and biological evaluation of the 99mTc-tricarbonyl moxifloxacin dithiocarbamate complex as a potential Staphylococcus aureus infection radiotracer

    International Nuclear Information System (INIS)

    Shah, Syed Qaiser; Khan, Muhammad Rafiullah

    2011-01-01

    In the present investigation, radiosynthesis of the 99m Tc-tricarbonyl moxifloxacin dithiocarbamate complex ( 99m Tc(CO) 3 -MXND) and its biological evaluation in male Wister rats (MWR) artificially infected with Staphylococcus aureus (S. aureus) was assessed. The 99m Tc(CO) 3 -MXND complex was radiochemically examined in terms of stability in saline and in serum and biologically its in-vitro binding with S. aureus and percent absorption in MWR models. Radiochemically the 99m Tc(CO) 3 -MXND complex showed more than 90% stability in saline up to 240 min and in serum 14.95% undesirable species was appeared within 16 h. In-vitro the 99m Tc(CO) 3 -MXND complex showed saturated binding with S. aureus. In MWR artificially infected with live S. aureus the complex showed about six fold higher uptakes in the infected muscle as compared to the normal muscle. However, insignificant change in the uptake of 99m Tc(CO) 3 -MXND complex in the infected and inflamed or normal muscle was observed in the MWR infected with heat killed S. aureus. The 99m Tc(CO) 3 -MXND complex disappeared from the circulatory system and appeared in the urinary system within 60-90 min followed by excretion through normal route of urinary system. Based on the elevated and stable radiochemical succumb in saline, serum, saturated in-vitro binding with S. aureus and higher accumulation in the target organ of the MWR, we recommend the 99m Tc(CO) 3 -MXND complex for radio-localization of the infection induced by S. aureus in human.

  7. Synthesis, Characterization and Biological Evaluation of Transition Metal Complexes Derived from N, S Bidentate Ligands

    Directory of Open Access Journals (Sweden)

    Enis Nadia Md Yusof

    2015-05-01

    Full Text Available Two bidentate NS ligands were synthesized by the condensation reaction of S-2-methylbenzyldithiocarbazate (S2MBDTC with 2-methoxybenzaldehyde (2MB and 3-methoxybenzaldehyde (3MB. The ligands were reacted separately with acetates of Cu(II, Ni(II and Zn(II yielding 1:2 (metal:ligand complexes. The metal complexes formed were expected to have a general formula of [M(NS2] where M = Cu2+, Ni2+, and Zn2+. These compounds were characterized by elemental analysis, molar conductivity, magnetic susceptibility and various spectroscopic techniques. The magnetic susceptibility measurements and spectral results supported the predicted coordination geometry in which the Schiff bases behaved as bidentate NS donor ligands coordinating via the azomethine nitrogen and thiolate sulfur. The molecular structures of the isomeric S2M2MBH (1 and S2M3MBH (2 were established by X-ray crystallography to have very similar l-shaped structures. The Schiff bases and their metal complexes were evaluated for their biological activities against estrogen receptor-positive (MCF-7 and estrogen receptor-negative (MDA-MB-231 breast cancer cell lines. Only the Cu(II complexes showed marked cytotoxicity against the cancer cell lines. Both Schiff bases and other metal complexes were found to be inactive. In concordance with the cytotoxicity studies, the DNA binding studies indicated that Cu(II complexes have a strong DNA binding affinity.

  8. Nutritional sub-fertility in the dairy cow: towards improved reproductive management through a better biological understanding

    DEFF Research Database (Denmark)

    Friggens, Nic; Disenhaus, C; Petit, H V

    2010-01-01

    for the dairy producer. In this study we focus on understanding the overall biological phenomena associated with nutritional sub-fertility rather than the underlying multiplicity of physiological interactions (already described in a number of recent studies). These phenomena are important because they represent...... the natural adaptations of the animal for dealing with variations in the nutritional environment. They can also be used to monitor and modulate reproductive performance on-farm. There is an underlying trade-off between two aspects of reproduction: investment in the viability of the current calf and investment...... embryos, which are of poorer quality, than do non-lactating cows. The same applies to high- compared to medium-genetic merit cows. Another important biological property is the adaptive use of body reserves in support of reproduction. Orchestrated endocrine changes in pregnancy and lactation facilitate...

  9. Taking the conservation biology perspective to secondary school classrooms.

    Science.gov (United States)

    Wyner, Yael; Desalle, Rob

    2010-06-01

    The influence of conservation biology can be enhanced greatly if it reaches beyond undergraduate biology to students at the middle and high school levels. If a conservation perspective were taught in secondary schools, students who are not interested in biology could be influenced to pursue careers or live lifestyles that would reduce the negative impact of humans on the world. We use what we call the ecology-disrupted approach to transform the topics of conservation biology research into environmental-issue and ecology topics, the major themes of secondary school courses in environmental science. In this model, students learn about the importance and complexity of normal ecological processes by studying what goes wrong when people disrupt them (environmental issues). Many studies published in Conservation Biology are related in some way to the ecological principles being taught in secondary schools. Describing research in conservation biology in the language of ecology curricula in secondary schools can help bring these science stories to the classroom and give them a context in which they can be understood by students. Without this context in the curriculum, a science story can devolve into just another environmental issue that has no immediate effect on the daily lives of students. Nevertheless, if the research is placed in the context of larger ecological processes that are being taught, students can gain a better understanding of ecology and a better understanding of their effect on the world.

  10. Governability Framework for the Evaluation and Implementation of Complex Public Health Functions

    Science.gov (United States)

    Varghese, Joe; Kutty, V. Raman

    2012-01-01

    Background: The dominant theoretical basis of our public health practice originates from a positivist or reductionist paradigm. It fails to take into account the complexity emerging out of public health's multiple influences originating from biological and social worlds. A deeper understanding of the interaction of elements that characterize the…

  11. Influence of the nucleobase on the physicochemical characteristics and biological activities of Sb{sup V}-ribonucleoside complexes

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Claudio S.; Demicheli, Cynthia, E-mail: demichel@netuno.lcc.ufmg.b [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Rocha, Iara C.M. da; Melo, Maria N. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia; Monte Neto, Rubens L.; Frezard, Frederic [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Fisiologia e Biofisica

    2010-07-01

    The influence of the nucleobase (uracyl, U; cytosine, C; adenine, A; guanine, G) on the physicochemical characteristics and in vitro biological activities of Sb{sup V}-ribonucleoside complexes has been investigated. The 1:1 Sb-U and Sb-C complexes were characterized by NMR and ESI-MS spectroscopies and elemental analysis. The stability constant and the apparent association and dissociation rate constants of 1:1 Sb{sup V}-U, Sb{sup V}-C and Sb{sup V}-A complexes were determined. Although Sb{sup V} most probably binds via oxygen atoms to the same 2' and 3' positions in the different nucleosides, the ribose conformational changes and the physicochemical characteristics of the complex depend on the nucleobase. The nucleobase had a strong influence on the cytotoxicity against macrophages and the antileishmanial activity of the Sb{sup V}-ribonucleoside complexes. The Sb{sup V}-purine complexes were more cytotoxic and more effective against Leishmania chagasi than the Sb{sup V}-pyrimidine complexes, supporting the model that the interaction of Sb{sup V} with purine nucleosides may mediate the antileishmanial activity of pentavalent antimonial drugs. (author)

  12. How to Generate Understanding of the Scientific Process in Introductory Biology: A Student-Designed Laboratory Exercise on Yeast Fermentation

    Science.gov (United States)

    Collins, Linda T.; Bell, Rebekah P.

    2004-01-01

    Heavy faculty teaching loads and limited funds biology teachers designed certain objectives in order to increase the understandability of the subject matter of the laboratory exercises they write. In relation to these objectives an old "cookbook" laboratory exercise on yeast fermentation is introduced which involve students asking questions,…

  13. PREFACE: Nanobiology: from physics and engineering to biology

    Science.gov (United States)

    Nussinov, Ruth; Alemán, Carlos

    2006-03-01

    Biological systems are inherently nano in scale. Unlike nanotechnology, nanobiology is characterized by the interplay between physics, materials science, synthetic organic chemistry, engineering and biology. Nanobiology is a new discipline, with the potential of revolutionizing medicine: it combines the tools, ideas and materials of nanoscience and biology; it addresses biological problems that can be studied and solved by nanotechnology; it devises ways to construct molecular devices using biomacromolecules; and it attempts to build molecular machines utilizing concepts seen in nature. Its ultimate aim is to be able to predictably manipulate these, tailoring them to specified needs. Nanobiology targets biological systems and uses biomacromolecules. Hence, on the one hand, nanobiology is seemingly constrained in its scope as compared to general nanotechnology. Yet the amazing intricacy of biological systems, their complexity, and the richness of the shapes and properties provided by the biological polymers, enrich nanobiology. Targeting biological systems entails comprehension of how they work and the ability to use their components in design. From the physical standpoint, ultimately, if we are to understand biology we need to learn how to apply physical principles to figure out how these systems actually work. The goal of nanobiology is to assist in probing these systems at the appropriate length scale, heralding a new era in the biological, physical and chemical sciences. Biology is increasingly asking quantitative questions. Quantitation is essential if we are to understand how the cell works, and the details of its regulation. The physical sciences provide tools and strategies to obtain accurate measurements and simulate the information to allow comprehension of the processes. Nanobiology is at the interface of the physical and the biological sciences. Biology offers to the physical sciences fascinating problems, sophisticated systems and a rich repertoire of

  14. Selection platforms for directed evolution in synthetic biology.

    Science.gov (United States)

    Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

    2016-08-15

    Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).

  15. Synthesis, characterization and biological assay of Salicylaldehyde Schiff base Cu(II) complexes and their precursors

    Science.gov (United States)

    Iftikhar, Bushra; Javed, Kanwal; Khan, Muhammad Saif Ullah; Akhter, Zareen; Mirza, Bushra; Mckee, Vickie

    2018-03-01

    Three new Schiff base ligands were synthesized by the reaction of Salicylaldehyde with semi-aromatic diamines, prepared by the reduction of corresponding dinitro-compounds, and were further used for the formation of complexes with Cu(II) metal ion. The structural features of the synthesized compounds were confirmed by their physical properties and infrared, electronic and NMR spectroscopic techniques. The studies revealed that the synthesized Schiff bases existed as tetradentate ligands and bonded to the metal ion through the phenolic oxygen and azomethine nitrogen. One of the dinitro precursors was also analyzed by single crystal X-ray crystallography, which showed that it crystallizes in monoclinic system with space group P2/n. The thermal behavior of the Cu(II) complexes was determined by thermogravimetric analysis (TGA) and kinetic parameters were evaluated from the data. Schiff base ligands, their precursors and metal complexes were also screened for antibacterial, antifungal, antitumor, Brine shrimp lethality, DPPH free radical scavenging and DNA damage assays. The results of these analyses indicated the substantial potential of the synthesized Schiff bases, their precursors and Cu(II) complexes in biological field as future drugs.

  16. Measuring spatial patterns in floodplains: A step towards understanding the complexity of floodplain ecosystems: Chapter 6

    Science.gov (United States)

    Scown, Murray W.; Thoms, Martin C.; DeJager, Nathan R.; Gilvear, David J.; Greenwood, Malcolm T.; Thoms, Martin C.; Wood, Paul J.

    2016-01-01

    Floodplains can be viewed as complex adaptive systems (Levin, 1998) because they are comprised of many different biophysical components, such as morphological features, soil groups and vegetation communities as well as being sites of key biogeochemical processing (Stanford et al., 2005). Interactions and feedbacks among the biophysical components often result in additional phenomena occuring over a range of scales, often in the absence of any controlling factors (sensu Hallet, 1990). This emergence of new biophysical features and rates of processing can lead to alternative stable states which feed back into floodplain adaptive cycles (cf. Hughes, 1997; Stanford et al., 2005). Interactions between different biophysical components, feedbacks, self emergence and scale are all key properties of complex adaptive systems (Levin, 1998; Phillips, 2003; Murray et al., 2014) and therefore will influence the manner in which we study and view spatial patterns. Measuring the spatial patterns of floodplain biophysical components is a prerequisite to examining and understanding these ecosystems as complex adaptive systems. Elucidating relationships between pattern and process, which are intrinsically linked within floodplains (Ward et al., 2002), is dependent upon an understanding of spatial pattern. This knowledge can help river scientists determine the major drivers, controllers and responses of floodplain structure and function, as well as the consequences of altering those drivers and controllers (Hughes and Cass, 1997; Whited et al., 2007). Interactions and feedbacks between physical, chemical and biological components of floodplain ecosystems create and maintain a structurally diverse and dynamic template (Stanford et al., 2005). This template influences subsequent interactions between components that consequently affect system trajectories within floodplains (sensu Bak et al., 1988). Constructing and evaluating models used to predict floodplain ecosystem responses to

  17. Parameterization and Sensitivity Analysis of a Complex Simulation Model for Mosquito Population Dynamics, Dengue Transmission, and Their Control

    Science.gov (United States)

    Ellis, Alicia M.; Garcia, Andres J.; Focks, Dana A.; Morrison, Amy C.; Scott, Thomas W.

    2011-01-01

    Models can be useful tools for understanding the dynamics and control of mosquito-borne disease. More detailed models may be more realistic and better suited for understanding local disease dynamics; however, evaluating model suitability, accuracy, and performance becomes increasingly difficult with greater model complexity. Sensitivity analysis is a technique that permits exploration of complex models by evaluating the sensitivity of the model to changes in parameters. Here, we present results of sensitivity analyses of two interrelated complex simulation models of mosquito population dynamics and dengue transmission. We found that dengue transmission may be influenced most by survival in each life stage of the mosquito, mosquito biting behavior, and duration of the infectious period in humans. The importance of these biological processes for vector-borne disease models and the overwhelming lack of knowledge about them make acquisition of relevant field data on these biological processes a top research priority. PMID:21813844

  18. Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.

    Science.gov (United States)

    Stéphanou, Angélique; Fanchon, Eric; Innominato, Pasquale F; Ballesta, Annabelle

    2018-05-09

    Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.

  19. SWIM: a computational tool to unveiling crucial nodes in complex biological networks.

    Science.gov (United States)

    Paci, Paola; Colombo, Teresa; Fiscon, Giulia; Gurtner, Aymone; Pavesi, Giulio; Farina, Lorenzo

    2017-03-20

    SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance. Here, we applied SWIM to a large panel of cancer datasets from The Cancer Genome Atlas, in order to highlight switch genes that could be critically associated with the drastic changes in the physiological state of cells or tissues induced by the cancer development. We discovered that switch genes are found in all cancers we studied and they encompass protein coding genes and non-coding RNAs, recovering many known key cancer players but also many new potential biomarkers not yet characterized in cancer context. Furthermore, SWIM is amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human cancer.

  20. Y-12 National Security Complex Biological Monitoring And Abatement Program 2008 Calendar Year Report

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, M. J.; Greeley Jr., M. S.; Mathews, T. J.; Morris, G. W.; Roy, W. K.; Ryon, M. G.; Smith, J. G.; Southworth, G. R.

    2009-07-01

    The National Pollutant Discharge Elimination System (NPDES) permit issued for the Oak Ridge Y-12 National Security Complex (Y-12 Complex) which became effective May 1, 2006, continued a requirement for a Biological Monitoring and Abatement Program (BMAP). The BMAP was originally developed in 1985 to demonstrate that the effluent limitations established for the Y-12 Complex protected the classified uses of the receiving stream (East Fork Poplar Creek: EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). The objectives of the current BMAP are similar, specifically to assess stream ecological conditions relative to regulatory limits and criteria, to assess ecological impacts as well as recovery in response to Y-12 operations, and to investigate the causes of continuing impacts. The BMAP consists of three tasks that reflect complementary approaches to evaluating the effects of the Y-12 Complex discharges on the biotic integrity of EFPC. These tasks include: (1) bioaccumulation monitoring, (2) benthic macroinvertebrate community monitoring, and (3) fish community monitoring. As required by the NPDES permit, the BMAP benthic macroinvertebrate community monitoring task includes studies to annually evaluate the receiving stream's biological integrity in comparison to TN Water Quality Criteria. BMAP monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) appropriate habitat distribution, and (5) access. The primary sampling sites include upper EFPC at kilometers (EFKs) 24.4 and 23.4 [upstream and downstream of Lake Reality (LR) respectively]; EFK 18.7 (also EFK 18.2 and 19), located off

  1. Understanding Crew Decision-Making in the Presence of Complexity: A Flight Simulation Experiment

    Science.gov (United States)

    Young, Steven D.; Daniels, Taumi S.; Evans, Emory; deHaag, Maarten Uijt; Duan, Pengfei

    2013-01-01

    Crew decision making and response have long been leading causal and contributing factors associated with aircraft accidents. Further, it is anticipated that future aircraft and operational environments will increase exposure to risks related to these factors if proactive steps are not taken to account for ever-increasing complexity. A flight simulation study was designed to collect data to help in understanding how complexity can, or may, be manifest. More specifically, an experimental apparatus was constructed that allowed for manipulation of information complexity and uncertainty, while also manipulating operational complexity and uncertainty. Through these manipulations, and the aid of experienced airline pilots, several issues have been discovered, related most prominently to the influence of information content, quality, and management. Flight crews were immersed in an environment that included new operational complexities suggested for the future air transportation system as well as new technological complexities (e.g. electronic flight bags, expanded data link services, synthetic and enhanced vision systems, and interval management automation). In addition, a set of off-nominal situations were emulated. These included, for example, adverse weather conditions, traffic deviations, equipment failures, poor data quality, communication errors, and unexpected clearances, or changes to flight plans. Each situation was based on one or more reference events from past accidents or incidents, or on a similar case that had been used in previous developmental tests or studies. Over the course of the study, 10 twopilot airline crews participated, completing over 230 flights. Each flight consisted of an approach beginning at 10,000 ft. Based on the recorded data and pilot and research observations, preliminary results are presented regarding decision-making issues in the presence of the operational and technological complexities encountered during the flights.

  2. Quantitative chemobiology: a guide into the understanding of plant bioactivity

    Directory of Open Access Journals (Sweden)

    Gottlieb Otto R.

    2002-01-01

    Full Text Available Nothing is more important for human survival today, than understanding nature's mechanisms via a chemo-biological language. This multidisciplinary approach is a complex operation, because it involves integration of several levels of organization, such as chemistry, morphology and ecogeography, expressed by diversification of metabolites, forms and environments, respectively. A comparison among these different expressions of life, in spite of undisputed importance, still remains an arduous research topic. Application of this unified approach would revigorate the study of old and controversial matter, plant bioactivity. To face the major challenge toward this aim: confrontation of traditional knowledge with scientific methodology, required the determination of trends among the uses of angiosperm species independently of empiricisms and regionalities. Thus, incorporation of new codes, expressing biological functions, in the chemo-biological language becomes possible only through evolutionary concepts and patterns.

  3. Breast cancer biology for the radiation oncologist

    Energy Technology Data Exchange (ETDEWEB)

    Strauss, Jonathan [Northwestern Univ., Chicago, IL (United States). Dept. of Radiation Oncology; Small, William [Loyola Univ. Chicago, Maywood, IL (United States). Stritch School of Medicine, Cardianl Bernardin Cancer Center; Woloschak, Gayle E. (ed.) [Northwestern Univ. Feinberg, Chicago, IL (United States). School of Medicine

    2015-10-01

    This is the first textbook of its kind devoted to describing the biological complexities of breast cancer in a way that is relevant to the radiation oncologist. Radiation Oncology has long treated breast cancer as a single biological entity, with all treatment decisions being based on clinical and pathologic risk factors. We are now beginning to understand that biological subtypes of breast cancer may have different risks of recurrence as well as different intrinsic sensitivity to radiotherapy. Multi-gene arrays that have for years been used to predict the risk of distant recurrence and the value of systemic chemotherapy may also have utility in predicting the risk of local recurrence. Additionally, the targeted agents used to treat breast cancer may interact with radiotherapy in ways that can be beneficial or undesirable. All of these emerging issues are extensively discussed in this book, and practical evidence-based treatment recommendations are presented whenever possible.

  4. Breast cancer biology for the radiation oncologist

    International Nuclear Information System (INIS)

    Strauss, Jonathan; Small, William; Woloschak, Gayle E.

    2015-01-01

    This is the first textbook of its kind devoted to describing the biological complexities of breast cancer in a way that is relevant to the radiation oncologist. Radiation Oncology has long treated breast cancer as a single biological entity, with all treatment decisions being based on clinical and pathologic risk factors. We are now beginning to understand that biological subtypes of breast cancer may have different risks of recurrence as well as different intrinsic sensitivity to radiotherapy. Multi-gene arrays that have for years been used to predict the risk of distant recurrence and the value of systemic chemotherapy may also have utility in predicting the risk of local recurrence. Additionally, the targeted agents used to treat breast cancer may interact with radiotherapy in ways that can be beneficial or undesirable. All of these emerging issues are extensively discussed in this book, and practical evidence-based treatment recommendations are presented whenever possible.

  5. Sensor Fusion and Autonomy as a Powerful Combination for Biological Assessment in the Marine Environment

    Directory of Open Access Journals (Sweden)

    Mark A. Moline

    2016-02-01

    Full Text Available The ocean environment and the physical and biological processes that govern dynamics are complex. Sampling the ocean to better understand these processes is difficult given the temporal and spatial domains and sampling tools available. Biological systems are especially difficult as organisms possess behavior, operate at horizontal scales smaller than traditional shipboard sampling allows, and are often disturbed by the sampling platforms themselves. Sensors that measure biological processes have also generally not kept pace with the development of physical counterparts as their requirements are as complex as the target organisms. Here, we attempt to address this challenge by advocating the need for sensor-platform combinations to integrate and process data in real-time and develop data products that are useful in increasing sampling efficiencies. Too often, the data of interest is only garnered after post-processing after a sampling effort and the opportunity to use that information to guide sampling is lost. Here we demonstrate a new autonomous platform, where data are collected, analyzed, and data products are output in real-time to inform autonomous decision-making. This integrated capability allows for enhanced and informed sampling towards improving our understanding of the marine environment.

  6. “Gestaltomics”: Systems Biology Schemes for the Study of Neuropsychiatric Diseases

    Directory of Open Access Journals (Sweden)

    Nora A. Gutierrez Najera

    2017-05-01

    Full Text Available The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the “psychiatric phenotype” is to provide an improved vision of the shape of the phenotype as it is visualized by “Gestalt” psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder will be the result of the integrative composition of every part. Therefore, we propose the term “Gestaltomics” as a term from Systems Biology to integrate data coming from different sources of information (such as the genome, transcriptome, proteome, epigenome, metabolome, phenome, and microbiome. In addition to this biological complexity, the mind is integrated through multiple brain functions that receive and process complex information through channels and perception networks (i.e., sight, ear, smell, memory, and attention that in turn are programmed by genes and influenced by environmental processes (epigenetic. Today, the approach of medical research in human diseases is to isolate one disease for study; however, the presence of an additional disease (co-morbidity or more than one disease (multimorbidity adds complexity to the study of these conditions. This review will present the challenge of integrating psychiatric disorders at different levels of information (Gestaltomics. The implications of increasing the level of complexity, for example, studying the co-morbidity with another disease such as cancer, will also be discussed.

  7. Mediation, moderation, and context: Understanding complex relations among cognition, affect, and health behaviour.

    Science.gov (United States)

    Kiviniemi, Marc T; Ellis, Erin M; Hall, Marissa G; Moss, Jennifer L; Lillie, Sarah E; Brewer, Noel T; Klein, William M P

    2018-01-01

    Researchers have historically treated cognition and affect as separate constructs in motivating health behaviour. We present a framework and empirical evidence for complex relations between cognition and affect in predicting health behaviour. Main Outcome, Design and Results: First, affect and cognition can mediate each other's relation to health behaviour. Second, affect and cognition can moderate the other's impact. Third, context can change the interplay of affect and cognition. Fourth, affect and cognition may be indelibly fused in some psychological constructs (e.g. worry, anticipated regret and reactance). These four propositions in our framework are not mutually exclusive. Examination of the types of complex relations described here can benefit theory development, empirical testing of theories and intervention design. Doing so will advance the understanding of mechanisms involved in regulation of health behaviours and the effectiveness of interventions to change health behaviours.

  8. Beam-time for biology

    CERN Multimedia

    Jordan Juras

    2010-01-01

    There's no question that playing with mercury or handling radioactive cadmium with your bare hands is a risky business. But understanding how these and other toxic metals interact with biomolecules within the body is a challenging feat; one for which the ISOLDE IS488 collaboration hopes to provide valuable insight.   General view of the ISOLDE experimental area. Unlike most of the facilities at CERN's accelerator complex, ISOLDE is not targeted mainly at particle physics. Rather, it produces radioactive nuclei during proton bombardment to study, among other things, physical and biological chemistry. At ISOLDE, the 1.4 GeV proton beam of the PS Booster (an early stage in CERN's accelerator complex) produces nuclear reactions in a thick target, creating a large variety of radioactive nuclei, which are mass-separated for use in experiments. In the case of the IS488 collaboration, the ion beam is directed into ice. "We implant radioactive metal ions into ice", explains Monika Stac...

  9. Third International Conference on Complex Systems

    CERN Document Server

    Minai, Ali A; Unifying Themes in Complex Systems

    2006-01-01

    In recent years, scientists have applied the principles of complex systems science to increasingly diverse fields. The results have been nothing short of remarkable: their novel approaches have provided answers to long-standing questions in biology, ecology, physics, engineering, computer science, economics, psychology and sociology. The Third International Conference on Complex Systems attracted over 400 researchers from around the world. The conference aimed to encourage cross-fertilization between the many disciplines represented and to deepen our understanding of the properties common to all complex systems. This volume contains selected transcripts from presentations given at the conference. Speakers include: Chris Adami, Kenneth Arrow, Michel Baranger, Dan Braha, Timothy Buchman, Michael Caramanis, Kathleen Carley, Greg Chaitin, David Clark, Jack Cohen, Jim Collins, George Cowan, Clay Easterly, Steven Eppinger, Irving Epstein, Dan Frey, Ary Goldberger, Helen Harte, Leroy Hood, Don Ingber, Atlee Jackson,...

  10. Synthesis, Characterization and Spectral Studies of Noble Heterobinuclear Complexes of Transition Metal Ions and their Biological Activity

    Directory of Open Access Journals (Sweden)

    Netra Pal Singh

    2011-01-01

    Full Text Available Some noble heterobinuclear complexes of transition metal ions with bis(salicylaldehydemalonyl-dihydrazone in the presence of 5-nitroindazole Cu(II / Ni(II- chloride of the type [ML1M‘L2Cl2] or [ML1FeL2Cl2]Cl, where M = Ni(II, Cu(II and M' = Mn(II, Co(II, have been prepared. All the complexes have been characterized by IR, UV vis and EPR spectroscopy, elemental analysis, magnetic moment and molar conductance measurement. Spectral studies and magnetic moment measurement in DMF suggest the covalent nature of the complexes, except the [ML1FeL2Cl2]Cl complex which is 1:1 electrolyte. An octahedral geometry is proposed for M‘ and square planer for M for the heterobinuclear complexes. The low value of magnetic moment and overlapping EPR signals are due to spin crossover since both of the metals have unpaired electrons with same molecular symmetry. The lowering of the magnetic moment has been discussed. The biological activity (antifungal and antibacterial of the represented compounds has been studied.

  11. Sustainable Materials Management (SMM) Web Academy Webinar: Compost from Food Waste: Understanding Soil Chemistry and Soil Biology on a College/University Campus

    Science.gov (United States)

    This page contains information about the Sustainable Materials Management (SMM) Web Academy Webinar Series titled Compost from Food Waste:Understanding Soil Chemistry and Soil Biology on a College/University Campus

  12. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  13. Embryonic stem cell interactomics: the beginning of a long road to biological function.

    Science.gov (United States)

    Yousefi, Maram; Hajihoseini, Vahid; Jung, Woojin; Hosseinpour, Batol; Rassouli, Hassan; Lee, Bonghee; Baharvand, Hossein; Lee, KiYoung; Salekdeh, Ghasem Hosseini

    2012-12-01

    Embryonic stem cells (ESCs) are capable of unlimited self-renewal while maintaining pluripotency. They are of great interest in regenerative medicine due to their ability to differentiate into all cell types of the three embryonic germ layers. Recently, induced pluripotent stem cells (iPSCs) have shown similarities to ESCs and thus promise great therapeutic potential in regenerative medicine. Despite progress in stem cell biology, our understanding of the exact mechanisms by which pluripotency and self-renewal are established and maintained is largely unknown. A better understanding of these processes may lead to discovery of alternative ways for reprogramming, differentiation and more reliable applications of stem cells in therapies. It has become evident that proteins generally function as members of large complexes that are part of a more complex network. Therefore, the identification of protein-protein interactions (PPI) is an efficient strategy for understanding protein function and regulation. Systematic genome-wide and pathway-specific PPI analysis of ESCs has generated a network of ESC proteins, including major transcription factors. These PPI networks of ESCs may contribute to a mechanistic understanding of self-renewal and pluripotency. In this review we describe different experimental approaches for the identification of PPIs along with various databases. We discuss biological findings and technical challenges encountered with interactome studies of pluripotent stem cells, and provide insight into how interactomics is likely to develop.

  14. Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films

    Science.gov (United States)

    Heon Kim, Tae; Yoon, Jong-Gul; Hyub Baek, Seung; Park, Woong-Kyu; Mo Yang, Sang; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Won Noh, Tae

    2015-07-01

    Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.

  15. Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films.

    Science.gov (United States)

    Kim, Tae Heon; Yoon, Jong-Gul; Baek, Seung Hyub; Park, Woong-kyu; Yang, Sang Mo; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Noh, Tae Won

    2015-07-01

    Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.

  16. Biologic Drugs: A New Target Therapy in COPD?

    Science.gov (United States)

    Yousuf, Ahmed; Brightling, Christopher E

    2018-04-23

    Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease associated with significant morbidity and mortality. Current diagnostic criteria based on the presence of fixed airflow obstruction and symptoms do not integrate the complex pathological changes occurring within the lung and they do not define different airway inflammatory patterns. The current management of COPD is based on 'one size fits all' approach and does not take the importance of heterogeneity in COPD population into account. The available treatments aim to alleviate symptoms and reduce exacerbation frequency but do not alter the course of the disease. Recent advances in molecular biology have furthered our understanding of inflammatory pathways in pathogenesis of COPD and have led to development of targeted therapies (biologics and small molecules) based on predefined biomarkers. Herein we shall review the trials of biologics in COPD and potential future drug developments in the field.

  17. Building biological foundries for next-generation synthetic biology.

    Science.gov (United States)

    Chao, Ran; Yuan, YongBo; Zhao, HuiMin

    2015-07-01

    Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

  18. Co(II) and Cd(II) Complexes Derived from Heterocyclic Schiff-Bases: Synthesis, Structural Characterisation, and Biological Activity

    Science.gov (United States)

    Ahmed, Riyadh M.; Yousif, Enaam I.; Al-Jeboori, Mohamad J.

    2013-01-01

    New monomeric cobalt and cadmium complexes with Schiff-bases, namely, N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]furan-2-carbohydrazide (L1) and N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]thiophene-2-carbohydrazide (L2) are reported. Schiff-base ligands L1 and L2 were derived from condensation of 3-hydroxy-4-methoxybenzaldehyde (iso-vanillin) with furan-2-carboxylic acid hydrazide and thiophene-2-carboxylic acid hydrazide, respectively. Complexes of the general formula [M(L)2]Cl2 (where M = Co(II) or Cd(II), L = L1 or L2) have been obtained from the reaction of the corresponding metal chloride with the ligands. The ligands and their metal complexes were characterised by spectroscopic methods (FTIR, UV-Vis, 1H, and 13C NMR spectra), elemental analysis, metal content, magnetic measurement, and conductance. These studies revealed the formation of four-coordinate complexes in which the geometry about metal ion is tetrahedral. Biological activity of the ligands and their metal complexes against gram positive bacterial strain Bacillus (G+) and gram negative bacteria Pseudomonas (G−) revealed that the metal complexes become less resistive to the microbial activities as compared to the free ligands. PMID:24027449

  19. Biocellion: accelerating computer simulation of multicellular biological system models.

    Science.gov (United States)

    Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

    2014-11-01

    Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. A Tryptoline Ring-Distortion Strategy Leads to Complex and Diverse Biologically Active Molecules from the Indole Alkaloid Yohimbine.

    Science.gov (United States)

    Paciaroni, Nicholas G; Ratnayake, Ranjala; Matthews, James H; Norwood, Verrill M; Arnold, Austin C; Dang, Long H; Luesch, Hendrik; Huigens, Robert W

    2017-03-28

    High-throughput screening (HTS) is the primary driver to current drug-discovery efforts. New therapeutic agents that enter the market are a direct reflection of the structurally simple compounds that make up screening libraries. Unlike medically relevant natural products (e.g., morphine), small molecules currently being screened have a low fraction of sp 3 character and few, if any, stereogenic centers. Although simple compounds have been useful in drugging certain biological targets (e.g., protein kinases), more sophisticated targets (e.g., transcription factors) have largely evaded the discovery of new clinical agents from screening collections. Herein, a tryptoline ring-distortion strategy is described that enables the rapid synthesis of 70 complex and diverse compounds from yohimbine (1); an indole alkaloid. The compounds that were synthesized had architecturally complex and unique scaffolds, unlike 1 and other scaffolds. These compounds were subjected to phenotypic screens and reporter gene assays, leading to the identification of new compounds that possessed various biological activities, including antiproliferative activities against cancer cells with functional hypoxia-inducible factors, nitric oxide inhibition, and inhibition and activation of the antioxidant response element. This tryptoline ring-distortion strategy can begin to address diversity problems in screening libraries, while occupying biologically relevant chemical space in areas critical to human health. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Understanding the Thermodynamics of Biological Order

    Science.gov (United States)

    Peterson, Jacob

    2012-01-01

    By growth in size and complexity (i.e., changing from more probable to less probable states), plants and animals appear to defy the second law of thermodynamics. The usual explanation describes the input of nutrient and sunlight energy into open thermodynamic systems. However, energy input alone does not address the ability to organize and create…

  2. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments.

    Science.gov (United States)

    Kudoh, Hiroshi

    2016-04-01

    Phenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High-resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature-responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC-mediated long-term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short-term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

  3. Physical biology of human brain development

    Directory of Open Access Journals (Sweden)

    Silvia eBudday

    2015-07-01

    Full Text Available Neurodevelopment is a complex, dynamic process that involves a precisely orchestrated sequence of genetic, environmental, biochemical, and physical events. Developmental biology and genetics have shaped our understanding of the molecular and cellular mechanisms during neurodevelopment. Recent studies suggest that physical forces play a central role in translating these cellular mechanisms into the complex surface morphology of the human brain. However, the precise impact of neuronal differentiation, migration, and connection on the physical forces during cortical folding remains unknown. Here we review the cellular mechanisms of neurodevelopment with a view towards surface morphogenesis, pattern selection, and evolution of shape. We revisit cortical folding as the instability problem of constrained differential growth in a multi-layered system. To identify the contributing factors of differential growth, we map out the timeline of neurodevelopment in humans and highlight the cellular events associated with extreme radial and tangential expansion. We demonstrate how computational modeling of differential growth can bridge the scales-from phenomena on the cellular level towards form and function on the organ level-to make quantitative, personalized predictions. Physics-based models can quantify cortical stresses, identify critical folding conditions, rationalize pattern selection, and predict gyral wavelengths and gyrification indices. We illustrate that physical forces can explain cortical malformations as emergent properties of developmental disorders. Combining biology and physics holds promise to advance our understanding of human brain development and enable early diagnostics of cortical malformations with the ultimate goal to improve treatment of neurodevelopmental disorders including epilepsy, autism spectrum disorders, and schizophrenia.

  4. Bioinstrumentation: Tools for Understanding Life.

    Science.gov (United States)

    Wandersee, James H., Ed.; And Others

    This book was written to help introductory biology teachers gain a basic understanding of contemporary bioinstrumentation and the uses to which it is put in the laboratory. It includes topics that are most basic to understanding the nature of biology. The book is divided into five sections: (1) "Separation and Identification" that includes…

  5. Understanding Federal regulations as guidelines for classical biological control programs

    Science.gov (United States)

    Michael E. Montgomery

    2011-01-01

    This chapter reviews the legislation and rules that provide the foundation for federal regulation of the introduction of natural enemies of insects as biological control agents. It also outlines the steps for complying with regulatory requirements, using biological control of Adelges tsugae Annand, the hemlock woolly adelgid (HWA), as an example. The...

  6. Current theoretical models fail to predict the topological complexity of the human genome

    Directory of Open Access Journals (Sweden)

    Javier eArsuaga

    2015-08-01

    Full Text Available Understanding the folding of the human genome is a key challenge of modern structural biology. The emergence of chromatin conformation capture assays ({it e.g.} Hi-C has revolutionized chromosome biology and provided new insights into the three dimensional structure of the genome. The experimental data are highly complex and need to be analyzed with quantitative tools. It has been argued that the data obtained from Hi-C assays are consistent with a fractal organization of the genome. A key characteristic textcolor{red}{of the fractal globule} is the lack of topological complexity (knotting or inter-linking. However, the absence of topological complexity contradicts results from polymer physics showing that the entanglement of long linear polymers in a confined volume increases rapidly with the length and with decreasing volume. textcolor{red}{{it In vivo} and {it in vitro} assays support this claim in some biological systems. We simulate knotted lattice polygons confined inside a sphere and demonstrate that their contact frequencies agree with the human Hi-C data.} We conclude that the topological complexity of the human genome cannot be inferred from current Hi-C data.

  7. Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems

    Science.gov (United States)

    Cerbino, Roberto; Cicuta, Pietro

    2017-09-01

    Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.

  8. The Mediator Complex and Lipid Metabolism.

    Science.gov (United States)

    Zhang, Yi; Xiaoli; Zhao, Xiaoping; Yang, Fajun

    2013-03-01

    The precise control of gene expression is essential for all biological processes. In addition to DNA-binding transcription factors, numerous transcription cofactors contribute another layer of regulation of gene transcription in eukaryotic cells. One of such transcription cofactors is the highly conserved Mediator complex, which has multiple subunits and is involved in various biological processes through directly interacting with relevant transcription factors. Although the current understanding on the biological functions of Mediator remains incomplete, research in the past decade has revealed an important role of Mediator in regulating lipid metabolism. Such function of Mediator is dependent on specific transcription factors, including peroxisome proliferator-activated receptor-gamma (PPARγ) and sterol regulatory element-binding proteins (SREBPs), which represent the master regulators of lipid metabolism. The medical significance of these findings is apparent, as aberrant lipid metabolism is intimately linked to major human diseases, such as type 2 diabetes and cardiovascular disease. Here, we briefly review the functions and molecular mechanisms of Mediator in regulation of lipid metabolism.

  9. Translational environmental biology: cell biology informing conservation.

    Science.gov (United States)

    Traylor-Knowles, Nikki; Palumbi, Stephen R

    2014-05-01

    Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Regulation of drug-metabolizing enzymes in infectious and inflammatory disease: implications for biologics-small molecule drug interactions.

    Science.gov (United States)

    Mallick, Pankajini; Taneja, Guncha; Moorthy, Bhagavatula; Ghose, Romi

    2017-06-01

    Drug-metabolizing enzymes (DMEs) are primarily down-regulated during infectious and inflammatory diseases, leading to disruption in the metabolism of small molecule drugs (smds), which are increasingly being prescribed therapeutically in combination with biologics for a number of chronic diseases. The biologics may exert pro- or anti-inflammatory effect, which may in turn affect the expression/activity of DMEs. Thus, patients with infectious/inflammatory diseases undergoing biologic/smd treatment can have complex changes in DMEs due to combined effects of the disease and treatment. Areas covered: We will discuss clinical biologics-SMD interaction and regulation of DMEs during infection and inflammatory diseases. Mechanistic studies will be discussed and consequences on biologic-small molecule combination therapy on disease outcome due to changes in drug metabolism will be highlighted. Expert opinion: The involvement of immunomodulatory mediators in biologic-SMDs is well known. Regulatory guidelines recommend appropriate in vitro or in vivo assessments for possible interactions. The role of cytokines in biologic-SMDs has been documented. However, the mechanisms of drug-drug interactions is much more complex, and is probably multi-factorial. Studies aimed at understanding the mechanism by which biologics effect the DMEs during inflammation/infection are clinically important.

  11. Carbon nanomaterials in biological systems

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-09-19

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

  12. Integrative biological analysis for neuropsychopharmacology.

    Science.gov (United States)

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

    2014-01-01

    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 studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches--proteomics, transcriptomics, metabolomics, and glycomics--have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studies that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine.

  13. Carbon nanomaterials in biological systems

    International Nuclear Information System (INIS)

    Pu Chun Ke; Qiao Rui

    2007-01-01

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

  14. Repair Responses of Dental Pulp to Tooth Injury and Biological Properties of Dentin-pulp Complex

    OpenAIRE

    大島, 勇人; Ohshima, Hayato

    2004-01-01

    Regeneration-the creation of a new tissue after the original one has been lost-is the fundamental biological capability in an organism. Numerous organs are considered to contain stem cells referred to as adult stem cells, even in the adult. Adult stem cells can give rise to a limited set of adult tissue types. In the field of clinical dentistry, it is well-known that the dentin-pulp complex is capable of repair after tooth injuries such as tooth replantation/transplantation or restorative pro...

  15. Computations, Complexity, Experiments, and the World Outside Physics

    International Nuclear Information System (INIS)

    Kadanoff, L.P

    2009-01-01

    Computer Models in the Sciences and Social Sciences. 1. Simulation and Prediction in Complex Systems: the Good the Bad and the Awful. This lecture deals with the history of large-scale computer modeling mostly in the context of the U.S. Department of Energy's sponsorship of modeling for weapons development and innovation in energy sources. 2. Complexity: Making a Splash-Breaking a Neck - The Making of Complexity in Physical System. For ages thinkers have been asking how complexity arise. The laws of physics are very simple. How come we are so complex? This lecture tries to approach this question by asking how complexity arises in physical fluids. 3. Forrester, et. al. Social and Biological Model-Making The partial collapse of the world's economy has raised the question of whether we could improve the performance of economic and social systems by a major effort on creating understanding via large-scale computer models. (author)

  16. Bions: a family of biomimetic mineralo-organic complexes derived from biological fluids.

    Directory of Open Access Journals (Sweden)

    Cheng-Yeu Wu

    Full Text Available Mineralo-organic nanoparticles form spontaneously in human body fluids when the concentrations of calcium and phosphate ions exceed saturation. We have shown previously that these mineralo-organic nanoparticles possess biomimetic properties and can reproduce the whole phenomenology of the so-called nanobacteria-mineralized entities initially described as the smallest microorganisms on earth. Here, we examine the possibility that various charged elements and ions may form mineral nanoparticles with similar properties in biological fluids. Remarkably, all the elements tested, including sodium, magnesium, aluminum, calcium, manganese, iron, cobalt, nickel, copper, zinc, strontium, and barium form mineralo-organic particles with bacteria-like morphologies and other complex shapes following precipitation with phosphate in body fluids. Upon formation, these mineralo-organic particles, which we term bions, invariably accumulate carbonate apatite during incubation in biological fluids; yet, the particles also incorporate additional elements and thus reflect the ionic milieu in which they form. Bions initially harbor an amorphous mineral phase that gradually converts to crystals in culture. Our results show that serum produces a dual inhibition-seeding effect on bion formation. Using a comprehensive proteomic analysis, we identify a wide range of proteins that bind to these mineral particles during incubation in medium containing serum. The two main binding proteins identified, albumin and fetuin-A, act as both inhibitors and seeders of bions in culture. Notably, bions possess several biomimetic properties, including the possibility to increase in size and number and to be sub-cultured in fresh culture medium. Based on these results, we propose that bions represent biological, mineralo-organic particles that may form in the body under both physiological and pathological homeostasis conditions. These mineralo-organic particles may be part of a

  17. Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity

    NARCIS (Netherlands)

    Speijer, Dave

    2011-01-01

    Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory

  18. Varieties of noise: analogical reasoning in synthetic biology.

    Science.gov (United States)

    Knuuttila, Tarja; Loettgers, Andrea

    2014-12-01

    The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.

  19. Biological activities of some Fluoroquinolones-metal complexes

    African Journals Online (AJOL)

    McRoy

    DNA cleavage studies of some synthesized metal complexes of fluoroquinolone ... Although the FQs are generally characterized by a broad antimicrobial spectrum ..... six Coordinate 3rd metal complexes with N- (5 –Phenyl-3,4- thiadiazol-2-yl).

  20. Biological design in science classrooms

    Science.gov (United States)

    Scott, Eugenie C.; Matzke, Nicholas J.

    2007-01-01

    Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront “intelligent design” (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older “creation science” movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education. PMID:17494747

  1. Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes.

    Science.gov (United States)

    Herschlag, Daniel; Natarajan, Aditya

    2013-03-26

    Enzymes are remarkable catalysts that lie at the heart of biology, accelerating chemical reactions to an astounding extent with extraordinary specificity. Enormous progress in understanding the chemical basis of enzymatic transformations and the basic mechanisms underlying rate enhancements over the past decades is apparent. Nevertheless, it has been difficult to achieve a quantitative understanding of how the underlying mechanisms account for the energetics of catalysis, because of the complexity of enzyme systems and the absence of underlying energetic additivity. We review case studies from our own work that illustrate the power of precisely defined and clearly articulated questions when dealing with such complex and multifaceted systems, and we also use this approach to evaluate our current ability to design enzymes. We close by highlighting a series of questions that help frame some of what remains to be understood, and we encourage the reader to define additional questions and directions that will deepen and broaden our understanding of enzymes and their catalysis.

  2. Complex Parts, Complex Data: Why You Need to Understand What Radiation Single Event Testing Data Does and Doesn't Show and the Implications Thereof

    Science.gov (United States)

    LaBel, Kenneth A.; Berg, Melanie D.

    2015-01-01

    Electronic parts (integrated circuits) have grown in complexity such that determining all failure modes and risks from single particle event testing is impossible. In this presentation, the authors will present why this is so and provide some realism on what this means. Its all about understanding actual risks and not making assumptions.

  3. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

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

  4. FuturICT: Participatory computing to understand and manage our complex world in a more sustainable and resilient way

    Science.gov (United States)

    Helbing, D.; Bishop, S.; Conte, R.; Lukowicz, P.; McCarthy, J. B.

    2012-11-01

    We have built particle accelerators to understand the forces that make up our physical world. Yet, we do not understand the principles underlying our strongly connected, techno-socio-economic systems. We have enabled ubiquitous Internet connectivity and instant, global information access. Yet we do not understand how it impacts our behavior and the evolution of society. To fill the knowledge gaps and keep up with the fast pace at which our world is changing, a Knowledge Accelerator must urgently be created. The financial crisis, international wars, global terror, the spreading of diseases and cyber-crime as well as demographic, technological and environmental change demonstrate that humanity is facing serious challenges. These problems cannot be solved within the traditional paradigms. Moving our attention from a component-oriented view of the world to an interaction-oriented view will allow us to understand the complex systems we have created and the emergent collective phenomena characterising them. This paradigm shift will enable new solutions to long-standing problems, very much as the shift from a geocentric to a heliocentric worldview has facilitated modern physics and the ability to launch satellites. The FuturICT flagship project will develop new science and technology to manage our future in a complex, strongly connected world. For this, it will combine the power of information and communication technology (ICT) with knowledge from the social and complexity sciences. ICT will provide the data to boost the social sciences into a new era. Complexity science will shed new light on the emergent phenomena in socially interactive systems, and the social sciences will provide a better understanding of the opportunities and risks of strongly networked systems, in particular future ICT systems. Hence, the envisaged FuturICT flagship will create new methods and instruments to tackle the challenges of the 21st century. FuturICT could indeed become one of the most

  5. Biological Screening of Newly Synthesized BIAN N-Heterocyclic Gold Carbene Complexes in Zebrafish Embryos

    Science.gov (United States)

    Farooq, Muhammad; Abu Taha, Nael; Butorac, Rachel R.; Evans, Daniel Anthony; Elzatahry, Ahmed A.; Elsayed, Elsayed Ahmed; Wadaan, Mohammad A. M.; Al-Deyab, Salem S.; Cowley, Alan H.

    2015-01-01

    N-Heterocyclic carbene (NHC) metal complexes possess diverse biological activities but have yet to be extensively explored as potential chemotherapeutic agents. We have previously reported the synthesis of a new class of NHC metal complexes N-heterocyclic with acetate [IPr(BIAN)AuOAc] and chloride [IPr(BIAN)AuCl] ligands. In the experiments reported herein, the zebrafish embryos were exposed to serial dilutions of each of these complexes for 10–12 h. One hundred percent mortality was observed at concentrations ≥50 µM. At sub-lethal concentrations (10–30 µM), both compounds influenced zebrafish embryonic development. However, quite diverse categories of abnormalities were found in exposed embryos with each compound. Severe brain deformation and notochord degeneration were evident in the case of [IPr(BIAN)AuOAc]. The zebrafish embryos treated with [IPr(BIAN)AuCl] exhibited stunted growth and consequently had smaller body sizes. A depletion of 30%–40% glutathione was detected in the treated embryos, which could account for one of the possible mechanism of neurotoxicity. The fact that these compounds are capable of both affecting the growth and also compromising antioxidant systems by elevating intracellular ROS production implies that they could play an important role as a new breed of therapeutic molecules. PMID:26501273

  6. Improving off-line accelerated tryptic digestion. Towards fast-lane proteolysis of complex biological samples.

    Science.gov (United States)

    Vukovic, Jadranka; Loftheim, Håvard; Winther, Bjørn; Reubsaet, J Léon E

    2008-06-27

    Off-line digestion of proteins using immobilized trypsin beads is studied with respect to the format of the digestion reactor, the digestion conditions, the comparison with in-solution digestion and its use in complex biological samples. The use of the filter vial as the most appropriate digestion reactor enables simple, efficient and easy-to-handle off-line digestion of the proteins on trypsin beads. It was shown that complex proteins like bovine serum albumin (BSA) need much longer time (89 min) and elevated temperature (37 degrees C) to be digested to an acceptable level compared to smaller proteins like cytochrome c (5 min, room temperature). Comparing the BSA digestion using immobilized trypsin beads with conventional in-solution digestion (overnight at 37 degrees C), it was shown that comparable results were obtained with respect to sequence coverage (>90%) and amount of missed cleavages (in both cases around 20 peptides with 1 or 2 missed cleavages were detected). However, the digestion using immobilized trypsin beads was considerable less time consuming. Good reproducibility and signal intensities were obtained for the digestion products of BSA in a complex urine sample. In addition to this, peptide products of proteins typically present in urine were identified.

  7. XAS Investigation of bio-relevant cobalt complexes in aqueous media

    International Nuclear Information System (INIS)

    Bresson, C.; Lamouroux, C.; Esnouf, S.; Solari, P.L.; Den Auwer, C.

    2006-01-01

    Cobalt is an essential element of biological cycles involved in numerous metallo-biomolecules, but it becomes a toxic element at high concentration or a radio-toxic element because of its use in the nuclear industry. 'Molecular speciation' in biological media is an essential prerequisite to evaluate its chemical behaviour as well as its toxic or beneficial effects. In this scheme, we have focused on the coordination properties of the thiol-containing amino acid cysteine (Cys) and the pseudo-peptide N-(2-mercapto-propionyl) glycine (MPG) towards the Co 2+ cation in aqueous media. XAS at the Co K edge and traditional spectroscopic techniques have been coupled in order to structurally characterize the cobalt coordination sphere. Oxidation states and geometries of the bis- and tris-cysteinato Co(III) complexes are in agreement with the literature data. In addition, bond lengths between the metallic centre and the donor atoms have been determined. The structure of a new dimeric N-(2-mercapto-propionyl) glycinato Co(II) complex in solution is also reported. The coordination of MPG to Co(II) through the thiolate and carboxylate functions is ascertained. This work provides fundamental structural information about bio-relevant complexes of cobalt, which will contribute to our understanding of the chemical behaviour and the biological role of this radionuclide. (authors)

  8. Understanding the fate and biological effects of Ag- and TiO2-nanoparticles in the environment: The quest for advanced analytics and interdisciplinary concepts

    International Nuclear Information System (INIS)

    Schaumann, Gabriele E.; Philippe, Allan; Bundschuh, Mirco; Metreveli, George; Klitzke, Sondra; Rakcheev, Denis; Grün, Alexandra

    2015-01-01

    Engineered inorganic nanoparticles (EINP) from consumers' products and industrial applications, especially silver and titanium dioxide nanoparticles (NP), are emitted into the aquatic and terrestrial environments in increasing amounts. However, the current knowledge on their environmental fate and biological effects is diverse and renders reliable predictions complicated. This review critically evaluates existing knowledge on colloidal aging mechanisms, biological functioning and transport of Ag NP and TiO 2 NP in water and soil and it discusses challenges for concepts, experimental approaches and analytical methods in order to obtain a comprehensive understanding of the processes linking NP fate and effects. Ag NP undergo dissolution and oxidation with Ag 2 S as a thermodynamically determined endpoint. Nonetheless, Ag NP also undergo colloidal transformations in the nanoparticulate state and may act as carriers for other substances. Ag NP and TiO 2 NP can have adverse biological effects on organisms. Whereas Ag NP reveal higher colloidal stability and mobility, the efficiency of NOM as a stabilizing agent is greater towards TiO 2 NP than towards Ag NP, and multivalent cations can dominate the colloidal behavior over NOM. Many of the past analytical obstacles have been overcome just recently. Single particle ICP-MS based methods in combination with field flow fractionation techniques and hydrodynamic chromatography have the potential to fill the gaps currently hampering a comprehensive understanding of fate and effects also at a low field relevant concentrations. These analytical developments will allow for mechanistically orientated research and transfer to a larger set of EINP. This includes separating processes driven by NP specific properties and bulk chemical properties, categorization of effect-triggering pathways directing the EINP effects towards specific recipients, and identification of dominant environmental parameters triggering fate and effect of

  9. Teaching Trajectories and Students' Understanding of Difficult Concepts in Biology in Obio/Akpor Local Government Area in Rivers State

    Science.gov (United States)

    Mumuni, Abosede Anthonia Olufemi; Dike, John Worlu; Uzoma-Nwogu, Azibaolanari

    2017-01-01

    This study investigated the effects of teaching trajectories on students' understanding of difficult concepts in Biology. Two research questions and two null hypotheses guided the study which was carried out in Obio/Akpor Local Government Area of Rivers State. Two public coeducational schools out of thirteen drawn through purposive sampling…

  10. Advances in the understanding of the BBSome complex structure and function

    Directory of Open Access Journals (Sweden)

    Hernandez-Hernandez V

    2015-10-01

    Full Text Available Victor Hernandez-Hernandez, Dagan JenkinsGenetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UKAbstract: Bardet–Biedl syndrome (BBS is an autosomal recessive condition characterized by important clinical features, including obesity, blindness, renal cystic disease, and intellectual disability. BBS is caused by mutations in >20 genes, a subset of which form the so-called BBSome. The BBSome is a complex that coats intracellular vesicles and interacts with key proteins, such as small GTPases, that regulate the trafficking of these vesicles to the base of cilia. Cilia are microtubular protusions present on the surface of most cells that are defective in a key group of disorders known as ciliopathies, of which BBS is one. BBSome components particularly localize to the basal body of cilia, and also centrosomes, where they interact with pericentriolar material proteins that regulate their function. The BBSome also facilitates the transport of key cargo within cilia by acting as an adaptor protein for intraflagellar transport complexes, and as such BBS mutations lead to a variety of functional defects in cilia in a tissue- and cell-type-specific manner. This might include defects in photoreceptor trafficking linked to the connecting cilium, abnormal hedgehog signaling within bone, and aberrant calcium signaling in response to fluid flow along renal tubules, although the precise mechanisms are still not completely understood. Taken together, the BBSome is an important complex that may be targeted for treatment of a variety of common and important disorders, and understanding the precise function of the BBSome will be essential to capitalize on this translationally.Keywords: retinitis pigmentosa GTPase regulator, polycystin, disrupted in schizophrenia 1, Hedgehog signaling, calcium signaling, photoreceptors

  11. Complex chemistry

    International Nuclear Information System (INIS)

    Kim, Bong Gon; Kim, Jae Sang; Kim, Jin Eun; Lee, Boo Yeon

    2006-06-01

    This book introduces complex chemistry with ten chapters, which include development of complex chemistry on history coordination theory and Warner's coordination theory and new development of complex chemistry, nomenclature on complex with conception and define, chemical formula on coordination compound, symbol of stereochemistry, stereo structure and isomerism, electron structure and bond theory on complex, structure of complex like NMR and XAFS, balance and reaction on solution, an organo-metallic chemistry, biology inorganic chemistry, material chemistry of complex, design of complex and calculation chemistry.

  12. Epigenetic Effects of Diet on Fruit Fly Lifespan: An Investigation to Teach Epigenetics to Biology Students

    Science.gov (United States)

    Billingsley, James; Carlson, Kimberly A.

    2010-01-01

    Do our genes exclusively control us, or are other factors at play? Epigenetics can provide a means for students to use inquiry-based methods to understand a complex biological concept. Students research and design an experiment testing whether dietary supplements affect the lifespan of Drosophila melanogaster over multiple generations.

  13. XIV Mediterranean Conference on Medical and Biological Engineering and Computing

    CERN Document Server

    Christofides, Stelios; Pattichis, Constantinos

    2016-01-01

    This volume presents the proceedings of Medicon 2016, held in Paphos, Cyprus. Medicon 2016 is the XIV in the series of regional meetings of the International Federation of Medical and Biological Engineering (IFMBE) in the Mediterranean. The goal of Medicon 2016 is to provide updated information on the state of the art on Medical and Biological Engineering and Computing under the main theme “Systems Medicine for the Delivery of Better Healthcare Services”. Medical and Biological Engineering and Computing cover complementary disciplines that hold great promise for the advancement of research and development in complex medical and biological systems. Research and development in these areas are impacting the science and technology by advancing fundamental concepts in translational medicine, by helping us understand human physiology and function at multiple levels, by improving tools and techniques for the detection, prevention and treatment of disease. Medicon 2016 provides a common platform for the cross fer...

  14. Alkali Metal Ion Complexes with Phosphates, Nucleotides, Amino Acids, and Related Ligands of Biological Relevance. Their Properties in Solution.

    Science.gov (United States)

    Crea, Francesco; De Stefano, Concetta; Foti, Claudia; Lando, Gabriele; Milea, Demetrio; Sammartano, Silvio

    2016-01-01

    Alkali metal ions play very important roles in all biological systems, some of them are essential for life. Their concentration depends on several physiological factors and is very variable. For example, sodium concentrations in human fluids vary from quite low (e.g., 8.2 mmol dm(-3) in mature maternal milk) to high values (0.14 mol dm(-3) in blood plasma). While many data on the concentration of Na(+) and K(+) in various fluids are available, the information on other alkali metal cations is scarce. Since many vital functions depend on the network of interactions occurring in various biofluids, this chapter reviews their complex formation with phosphates, nucleotides, amino acids, and related ligands of biological relevance. Literature data on this topic are quite rare if compared to other cations. Generally, the stability of alkali metal ion complexes of organic and inorganic ligands is rather low (usually log K  Na(+) > K(+) > Rb(+) > Cs(+). For example, for citrate it is: log K ML = 0.88, 0.80, 0.48, 0.38, and 0.13 at 25 °C and infinite dilution. Some considerations are made on the main aspects related to the difficulties in the determination of weak complexes. The importance of the alkali metal ion complexes was also studied in the light of modelling natural fluids and in the use of these cations as probes for different processes. Some empirical relationships are proposed for the dependence of the stability constants of Na(+) complexes on the ligand charge, as well as for correlations among log K values of NaL, KL or LiL species (L = generic ligand).

  15. Data integration, systems approach and multilevel description of complex biosystems

    International Nuclear Information System (INIS)

    Hernández-Lemus, Enrique

    2013-01-01

    Recent years have witnessed the development of new quantitative approaches and theoretical tenets in the biological sciences. The advent of high throughput experiments in genomics, proteomics and electrophysiology (to cite just a few examples) have provided the researchers with unprecedented amounts of data to be analyzed. Large datasets, however can not provide the means to achieve a complete understanding of the underlying biological phenomena, unless they are supplied with a solid theoretical framework and with proper analytical tools. It is now widely accepted that by using and extending some of the paradigmatic principles of what has been called complex systems theory, some degree of advance in this direction can be attained. We will be presenting ways in which by using data integration techniques (linear, non-linear, combinatorial, graphical), multidimensional-multilevel descriptions (multifractal modeling, dimensionality reduction, computational learning), as well as an approach based in systems theory (interaction maps, probabilistic graphical models, non-equilibrium physics) have allowed us to better understand some problems in the interface of Statistical Physics and Computational Biology

  16. Radiocharacterization of the 99mTc-rufloxacin complex and biological evaluation in Staphylococcus aureus infected rat model

    International Nuclear Information System (INIS)

    Syed Qaiser Shah; Muhammad Rafiullah Khan

    2011-01-01

    99m Tc-rufloxacin ( 99m Tc-RUN) complex was prepared by reaction of different amounts of reduced sodium pertechnetate with different amount of Rufloxacin (RUN) antibiotic for the in vivo scintigraphic localization of the Staphylococcus aureus (S. aureus) infectious foci in Male Wister Rats (MWR) model. The 99m Tc-RUN complex was radiochemically and biologically characterized in terms of radiochemical stability in saline, serum, in vitro binding with S. aureus and biodistribution in artificially infected with S. aureus MWR. The 99m Tc-RUN complex showed stability more than 90% up to 240 min in normal saline with a maximum stability value of 98.10 ± 0.18% at 30 min after reconstitution. At 37 deg C the complex showed in vitro permanence in serum up to 16 h with 13.90% side products during incubation. The 99m Tc-RUN complex showed saturated in vitro binding with S. aureus at different intervals with a maximum uptake value of 71.50%. Infected to normal muscle, infected to inflamed and inflamed to normal muscles ratios were approximately 6.04, 4.31 and 1.40. Based on the stability of the complex in saline, serum, in vitro binding with S. aureus and biodistribution results, the 99m Tc-RUN complex is recommended for in vivo scintigraphic localization of the S. aureus in vivo infectious foci in human. (author)

  17. Syntheses, structural elucidation, thermal properties, theoretical quantum chemical studies (DFT and biological studies of barbituric–hydrazone complexes

    Directory of Open Access Journals (Sweden)

    Amina A. Soayed

    2015-03-01

    Full Text Available Condensation of barbituric acid with hydrazine hydrate yielded barbiturichydrazone (L which was characterized using IR, 1H NMR and mass spectra. The Co(II, Ni(II and Cu(II complexes derived from this ligand have been synthesized and structurally characterized by elemental analyses, spectroscopic methods (IR, UV–Vis and ESR and thermal analyses (TGA, DTG and DTA and the structures were further elucidated using quantum chemical density functional theory. Complexes of L were found to have the ML.nH2O stoichiometry with either tetrahedral or octahedral geometry. The ESR data showed the Cu(II complex to be in a tetragonal geometry. Theoretical investigation of the electronic structure of metal complexes at the TD-DFT/B3LYP level of theory has been carried out and discussed. The fundamental vibrational wavenumbers were calculated and a good agreement between observed and scaled calculated wavenumbers was achieved. Thermal studies were performed to deduce the stabilities of the ligand and complexes. Thermodynamic parameters, such as the order of reactions (n, activation energy ΔE∗, enthalpy of reaction ΔH∗ and entropy ΔS∗ were calculated from DTA curves using Horowitz–Metzger method. The ligand L and its complexes have been screened for their antifungal and antibacterial activities and were found to possess better biological activities compared to those of unsubstituted barbituric acid complexes.

  18. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  19. The Oral Histories of Six African American Males in Their Ecology of Advanced Placement Biology

    Science.gov (United States)

    Halasa, Katrina Bassam

    2012-01-01

    The major purpose of this qualitative study was to examine the past in order to understand the complex phenomenon of students engaging in science (Newman, Ridenour, Newman, & DeMarco, 2003) specifically through the oral histories of six self-identified African American males enrolled in a high school Advanced Placement Biology class and the…

  20. The cell biology of Tobacco mosaic virus replication and movement

    Directory of Open Access Journals (Sweden)

    Chengke eLiu

    2013-02-01

    Full Text Available Successful systemic infection of a plant by Tobacco mosaic virus (TMV requires three processes that repeat over time: initial establishment and accumulation in invaded cells, intercellular movement and systemic transport. Accumulation and intercellular movement of TMV necessarily involves intracellular transport by complexes containing virus and host proteins and virus RNA during a dynamic process that can be visualized. Multiple membranes appear to assist TMV accumulation, while membranes, microfilaments and microtubules appear to assist TMV movement. Here we review cell biological studies that describe TMV-membrane, -cytoskeleton and -other host protein interactions which influence virus accumulation and movement in leaves and callus tissue. The importance of understanding the developmental phase of the infection in relationship to the observed virus-membrane or -host protein interaction is emphasized. Utilizing the latest observations of TMV-membrane and -host protein interactions within our evolving understanding of the infection ontogeny, a model for TMV accumulation and intracellular spread in a cell biological context is provided.

  1. Douglas Hanahan: The daunting complexity of cancer: understanding the battlefield is a step towards winning the war

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    The Inaugural Grace-CERN Lecture The daunting complexity of cancer: understanding the battlefield is a step towards winning the war  Douglas Hanahan, Ph.D. Director, Swiss Institute for Experimental Cancer Research (ISREC)  Professor of Molecular Oncology, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL) Vice Director, Swiss Cancer Center Lausanne Synopsis (version francaise ci-dessous) Cancer is a disease with hundreds of variations, both in affected organs and in responses to different therapies.  Modern human cancer research is producing an avalanche of data about the distinctive genetic aberrations of its specific types, further accentuating the diversity and vast complexity of the disease. There is hope that elucidating its mechanisms will lead to more informed and more effective therapeutic strategies.  Understanding the enemy is paramount, and yet tumors arising in different organs can be so different as to de...

  2. Evolutionary foundations for cancer biology.

    Science.gov (United States)

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

  3. The biology of strigolactones

    KAUST Repository

    Ruyter-Spira, Carolien P.

    2013-02-01

    The strigolactones are rhizosphere signaling molecules as well as a new class of plant hormones with a still increasing number of biological functions being uncovered. Here, we review a recent major breakthrough in our understanding of strigolactone biosynthesis, which has revealed the unexpected simplicity of the originally postulated complex pathway. Moreover, the discovery and localization of a strigolactone exporter sheds new light on putative strigolactone fluxes to the rhizosphere as well as within the plant. The combination of these data with information on the expression and regulation of strigolactone biosynthetic and downstream signaling genes provides new insights into how strigolactones control the many different aspects of plant development and how their rhizosphere signaling role may have evolved. © 2012 Elsevier Ltd.

  4. Toward High School Biology: Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems.

    Science.gov (United States)

    Herrmann-Abell, Cari F; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better foundation, we used research-based design principles and collaborated in the development of a curricular intervention that applies chemistry ideas to living and nonliving contexts. Six eighth grade teachers and their students participated in a test of the unit during the Spring of 2013. Two of the teachers had used an earlier version of the unit the previous spring. The other four teachers were randomly assigned either to implement the unit or to continue teaching the same content using existing materials. Pre- and posttests were administered, and the data were analyzed using Rasch modeling and hierarchical linear modeling. The results showed that, when controlling for pretest score, gender, language, and ethnicity, students who used the curricular intervention performed better on the posttest than the students using existing materials. Additionally, students who participated in the intervention held fewer misconceptions. These results demonstrate the unit's promise in improving students' understanding of the targeted ideas. © 2016 C. F. Herrmann-Abell et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  5. Inverse Problems in Systems Biology: A Critical Review.

    Science.gov (United States)

    Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

    2018-01-01

    Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

  6. A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

    Energy Technology Data Exchange (ETDEWEB)

    Aderem, Alan; Adkins, Joshua N.; Ansong, Charles; Galagan, James; Kaiser, Shari; Korth, Marcus J.; Law, G. L.; McDermott, Jason E.; Proll, Sean; Rosenberger, Carrie; Schoolnik, Gary; Katze, Michael G.

    2011-02-01

    The 20th century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food and water borne illnesses are frequent, multi-drug resistant microbes are on the rise, and the needed drugs and vaccines have not been developed. The scientific approaches of the past—including the intense focus on individual genes and proteins typical of molecular biology—have not been sufficient to address these challenges. The first decade of the 21st century has seen remarkable innovations in technology and computational methods. These new tools provide nearly comprehensive views of complex biological systems and can provide a correspondingly deeper understanding of pathogen-host interactions. To take full advantage of these innovations, the National Institute of Allergy and Infectious Diseases recently initiated the Systems Biology Program for Infectious Disease Research. As participants of the Systems Biology Program we think that the time is at hand to redefine the pathogen-host research paradigm.

  7. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.

    Science.gov (United States)

    Bashor, Caleb J; Horwitz, Andrew A; Peisajovich, Sergio G; Lim, Wendell A

    2010-01-01

    The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by disrupting them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful approach to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. In addition, by building minimal toy networks, one can systematically explore the relationship between network structure and function. Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems.

  8. A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology

    Science.gov (United States)

    Chen, Bor-Sen; Lin, Ying-Po

    2013-01-01

    Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties that are observed in biological systems at many different levels. The underlying principles for robust stabilization and environmental disturbance attenuation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be large enough to confer: intrinsic robustness for tolerating intrinsic parameter fluctuations; genetic robustness for buffering genetic variations; and environmental robustness for resisting environmental disturbances. Network robustness is needed so phenotype stability of biological network can be maintained, guaranteeing phenotype robustness. Synthetic biology is foreseen to have important applications in biotechnology and medicine; it is expected to contribute significantly to a better understanding of functioning of complex biological systems. This paper presents a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation for synthetic gene networks in synthetic biology. Further, from the unifying mathematical framework, we found that the phenotype robustness criterion for synthetic gene networks is the following: if intrinsic robustness + genetic robustness + environmental robustness ≦ network robustness, then the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in synthetic biology can also be investigated through corresponding phenotype robustness criteria from the systematic point of view. Finally, a robust synthetic design that involves network evolution algorithms with desired behavior under intrinsic parameter fluctuations, genetic variations, and environmental

  9. [Biological and neural bases of partner preferences in rodents: models to understand human pair bonds].

    Science.gov (United States)

    Coria-Avila, G A; Hernández-Aguilar, M E; Toledo-Cárdenas, R; García-Hernández, L I; Manzo, J; Pacheco, P; Miquel, M; Pfaus, J G

    To analyse the biological and neural bases of partner preference formation in rodents as models to understand human pair bonding. Rodents are social individuals, capable of forming short- or long-lasting partner preferences that develop slowly by stimuli like cohabitation, or rapidly by stimuli like sex and stress. Dopamine, corticosteroids, oxytocin, vasopressin, and opioids form the neurochemical substrate for pair bonding in areas like the nucleus accumbens, the prefrontal cortex, the piriform cortex, the medial preoptic area, the ventral tegmental area and the medial amygdala, among others. Additional areas may participate depending on the nature of the conditioned stimuli by which and individual recognizes a preferred partner. Animal models help us understand that the capacity of an individual to display long-lasting and selective preferences depends on neural bases, selected throughout evolution. The challenge in neuroscience is to use this knowledge to create new solutions for mental problems associated with the incapacity of an individual to display a social bond, keep one, or cope with the disruption of a consolidated one.

  10. The common extremalities in biology and physics maximum energy dissipation principle in chemistry, biology, physics and evolution

    CERN Document Server

    Moroz, Adam

    2011-01-01

    This book is the first unified systemic description of dissipative phenomena, taking place in biology, and non-dissipative (conservative) phenomena, which is more relevant to physics. Fully updated and revised, this new edition extends our understanding of nonlinear phenomena in biology and physics from the extreme / optimal perspective. The first book to provide understanding of physical phenomena from a biological perspective and biological phenomena from a physical perspective Discusses emerging fields and analysis Provides examples.

  11. Building bridges between cellular and molecular structural biology.

    Science.gov (United States)

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  12. Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes

    DEFF Research Database (Denmark)

    Pedersen, Helle Krogh; Gudmundsdottir, Valborg; Brunak, Søren

    2017-01-01

    Type 2 diabetes (T2D) is a complex disease that involves multiple genes. Numerous risk loci have already been associated with T2D, although many susceptibility genes remain to be identified given heritability estimates. Systems biology approaches hold potential for discovering novel T2D genes by ...... starting point when evaluating an individual's alterations at the genome, transcriptome, or proteome level in relation to T2D in clinical settings.......Type 2 diabetes (T2D) is a complex disease that involves multiple genes. Numerous risk loci have already been associated with T2D, although many susceptibility genes remain to be identified given heritability estimates. Systems biology approaches hold potential for discovering novel T2D genes...... by considering their biological context, such as tissue-specific protein interaction partners. Pancreatic islets are a key T2D tissue and many of the known genetic risk variants lead to impaired islet function, hence a better understanding of the islet-specific dysregulation in the disease-state is essential...

  13. Human biological rhythm in traditional Chinese medicine

    Directory of Open Access Journals (Sweden)

    Tianxing Zhang

    2016-10-01

    Full Text Available Traditional Chinese medicine (TCM has a comprehensive and thorough understanding of biological rhythm. Biological rhythm is an inherent connotation of “harmony between human and nature”, one of the thoughts in TCM. TCM discusses emphatically circadian rhythm, syzygial rhythm and seasonal rhythm, and particularly circadian and seasonal rhythms. Theories of Yin Yang and Five Elements are the principles and methods, with which TCM understands biological rhythms. Based on theories in TCM, biological rhythm in essence is a continuous variation of the human body state synchronized with natural rhythms, and theories of Yin Yang and Five Elements are both language tools to describe this continuous variation and theoretical tools for its investigation and application. The understandings of biological rhythm in TCM can be applied to etiology, health care, disease control and treatment. Many understandings in TCM have been confirmed by modern research and clinical reports, but there are still some pending issues. TCM is distinguished for its holistic viewpoint on biological rhythms.

  14. Organic chemistry and biology: chemical biology through the eyes of collaboration.

    Science.gov (United States)

    Hruby, Victor J

    2009-12-18

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

  15. RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

    Science.gov (United States)

    Ohno, Hirohisa; Saito, Hirohide

    2016-01-01

    Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Understanding the fate and biological effects of Ag- and TiO{sub 2}-nanoparticles in the environment: The quest for advanced analytics and interdisciplinary concepts

    Energy Technology Data Exchange (ETDEWEB)

    Schaumann, Gabriele E., E-mail: schaumann@uni-landau.de [Universität Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstr. 7, D-76829 Landau (Germany); Philippe, Allan, E-mail: philippe@uni-landau.de [Universität Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstr. 7, D-76829 Landau (Germany); Bundschuh, Mirco, E-mail: mirco.bundschuh@slu.se [Universität Koblenz-Landau, Institute for Environmental Sciences, Group of Ecotoxicology and Environment, Fortstr. 7, D-76829 Landau (Germany); Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Lennart Hjelms väg 9, SE-75007 Uppsala (Sweden); Metreveli, George, E-mail: metreveli@uni-landau.de [Universität Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstr. 7, D-76829 Landau (Germany); Klitzke, Sondra, E-mail: sondra.klitzke@tu-berlin.de [Albert-Ludwigs-Universität Freiburg, Institute of Forest Sciences, Chair of Soil Ecology, 79085 Freiburg i.Br. (Germany); Berlin University of Technology, Institute of Ecology, Department of Soil Science, Ernst-Reuter-Platz 1, D-10587 Berlin (Germany); Rakcheev, Denis, E-mail: rakcheev@uni-landau.de [Universität Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstr. 7, D-76829 Landau (Germany); Grün, Alexandra, E-mail: alexg@uni-koblenz.de [Universität Koblenz-Landau, Institute for Integrated Natural Sciences, Dept. of Biology, Universitätsstr. 1, D-56070 Koblenz (Germany); and others

    2015-12-01

    Engineered inorganic nanoparticles (EINP) from consumers' products and industrial applications, especially silver and titanium dioxide nanoparticles (NP), are emitted into the aquatic and terrestrial environments in increasing amounts. However, the current knowledge on their environmental fate and biological effects is diverse and renders reliable predictions complicated. This review critically evaluates existing knowledge on colloidal aging mechanisms, biological functioning and transport of Ag NP and TiO{sub 2} NP in water and soil and it discusses challenges for concepts, experimental approaches and analytical methods in order to obtain a comprehensive understanding of the processes linking NP fate and effects. Ag NP undergo dissolution and oxidation with Ag{sub 2}S as a thermodynamically determined endpoint. Nonetheless, Ag NP also undergo colloidal transformations in the nanoparticulate state and may act as carriers for other substances. Ag NP and TiO{sub 2} NP can have adverse biological effects on organisms. Whereas Ag NP reveal higher colloidal stability and mobility, the efficiency of NOM as a stabilizing agent is greater towards TiO{sub 2} NP than towards Ag NP, and multivalent cations can dominate the colloidal behavior over NOM. Many of the past analytical obstacles have been overcome just recently. Single particle ICP-MS based methods in combination with field flow fractionation techniques and hydrodynamic chromatography have the potential to fill the gaps currently hampering a comprehensive understanding of fate and effects also at a low field relevant concentrations. These analytical developments will allow for mechanistically orientated research and transfer to a larger set of EINP. This includes separating processes driven by NP specific properties and bulk chemical properties, categorization of effect-triggering pathways directing the EINP effects towards specific recipients, and identification of dominant environmental parameters triggering

  17. A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

    Science.gov (United States)

    Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

    2013-01-01

    SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

  18. Uncovering Biological Network Function via Graphlet Degree Signatures

    Directory of Open Access Journals (Sweden)

    Nataša Pržulj

    2008-01-01

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

  19. Understanding life together: A brief history of collaboration in biology

    Science.gov (United States)

    Vermeulen, Niki; Parker, John N.; Penders, Bart

    2013-01-01

    The history of science shows a shift from single-investigator ‘little science’ to increasingly large, expensive, multinational, interdisciplinary and interdependent ‘big science’. In physics and allied fields this shift has been well documented, but the rise of collaboration in the life sciences and its effect on scientific work and knowledge has received little attention. Research in biology exhibits different historical trajectories and organisation of collaboration in field and laboratory – differences still visible in contemporary collaborations such as the Census of Marine Life and the Human Genome Project. We employ these case studies as strategic exemplars, supplemented with existing research on collaboration in biology, to expose the different motives, organisational forms and social dynamics underpinning contemporary large-scale collaborations in biology and their relations to historical patterns of collaboration in the life sciences. We find the interaction between research subject, research approach as well as research organisation influencing collaboration patterns and the work of scientists. PMID:23578694

  20. Excitation energy transfer in natural photosynthetic complexes and chlorophyll trefoils: hole-burning and single complex/trefoil spectroscopic studies

    Energy Technology Data Exchange (ETDEWEB)

    Ryszard Jankowiak, Kansas State University, Department of Chemistry, CBC Bldg., Manhattan KS, 66505; Phone: (785) 532-6785

    2012-09-12

    In this project we studied both natural photosynthetic antenna complexes and various artificial systems (e.g. chlorophyll (Chl) trefoils) using high resolution hole-burning (HB) spectroscopy and excitonic calculations. Results obtained provided more insight into the electronic (excitonic) structure, inhomogeneity, electron-phonon coupling strength, vibrational frequencies, and excitation energy (or electron) transfer (EET) processes in several antennas and reaction centers. For example, our recent work provided important constraints and parameters for more advanced excitonic calculations of CP43, CP47, and PSII core complexes. Improved theoretical description of HB spectra for various model systems offers new insight into the excitonic structure and composition of low-energy absorption traps in very several antenna protein complexes and reaction centers. We anticipate that better understanding of HB spectra obtained for various photosynthetic complexes and their simultaneous fits with other optical spectra (i.e. absorption, emission, and circular dichroism spectra) provides more insight into the underlying electronic structures of these important biological systems. Our recent progress provides a necessary framework for probing the electronic structure of these systems via Hole Burning Spectroscopy. For example, we have shown that the theoretical description of non-resonant holes is more restrictive (in terms of possible site energies) than those of absorption and emission spectra. We have demonstrated that simultaneous description of linear optical spectra along with HB spectra provides more realistic site energies. We have also developed new algorithms to describe both nonresonant and resonant hole-burn spectra using more advanced Redfield theory. Simultaneous description of various optical spectra for complex biological system, e.g. artificial antenna systems, FMO protein complexes, water soluble protein complexes, and various mutants of reaction centers

  1. Phylogenetics and genetic diversity of the Cotesia flavipes complex of parasitoid wasps (Hymenoptera: Braconidae), biological control agents of lepidopteran stemborers.

    Science.gov (United States)

    Muirhead, Kate A; Murphy, Nicholas P; Sallam, Nader; Donnellan, Stephen C; Austin, Andrew D

    2012-06-01

    The Cotesia flavipes complex of parasitoid wasps (Hymenoptera: Braconidae) are economically important for the biological control of lepidopteran stemboring pests associated with gramineous crops. Some members of the complex successfully parasitize numerous stemborer pest species, however certain geographic populations have demonstrated variation in the range of hosts that they parasitize. In addition, the morphology of the complex is highly conserved and considerable confusion surrounds the identity of species and host-associated biotypes. We generated nucleotide sequence data for two mtDNA genes (COI, 16S) and three anonymous nuclear loci (CfBN, CfCN, CfEN) for the C. flavipes complex. To analyze genetic variation and relationships among populations we used (1) concatenated mtDNA and nDNA data, (2) a nDNA multilocus network approach, and (3) two species tree inference methods, i.e. Bayesian estimation of species trees (BEST) and Bayesian inference of species trees from multilocus data with (*)BEAST. All phylogenetic analyses provide strong support for monophyly of the complex and the presence of at least four species, C. chilonis (from China and Japan), C. sesamiae (from Africa), C. flavipes (originating from the Indo-Asia region but introduced into Africa and the New World), and C. nonagriae (from Australia and Papua New Guinea). Haplotype diversity of geographic populations relates to historical biogeographic barriers and biological control introductions, and reflects previous reports of ecological variation in these species. Strong discordance was found between the mitochondrial and nuclear markers in the Papua New Guinea haplotypes, which may be an outcome of hybridization and introgression of C. flavipes and C. nonagriae. The position of Cotesia flavipes from Japan was not well supported in any analysis and was the sister taxon to C. nonagriae (mtDNA, (*)BEAST), C. flavipes (nDNA) or C. flavipes+C. nonagriae (BEST) and, may represent a cryptic species. The

  2. Investigating the Relationship between Instructors' Use of Active-Learning Strategies and Students' Conceptual Understanding and Affective Changes in Introductory Biology: A Comparison of Two Active-Learning Environments

    Science.gov (United States)

    Cleveland, Lacy M.; Olimpo, Jeffrey T.; DeChenne-Peters, Sue Ellen

    2017-01-01

    In response to calls for reform in undergraduate biology education, we conducted research examining how varying active-learning strategies impacted students' conceptual understanding, attitudes, and motivation in two sections of a large-lecture introductory cell and molecular biology course. Using a quasi-experimental design, we collected…

  3. 25 Years of Tension over Actin Binding to the Cadherin Cell Adhesion Complex: The Devil is in the Details.

    Science.gov (United States)

    Nelson, W James; Weis, William I

    2016-07-01

    Over the past 25 years, there has been a conceptual (re)evolution in understanding how the cadherin cell adhesion complex, which contains F-actin-binding proteins, binds to the actin cytoskeleton. There is now good synergy between structural, biochemical, and cell biological results that the cadherin-catenin complex binds to F-actin under force. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. WE-DE-202-03: Modeling of Biological Processes - What Happens After Early Molecular Damage?

    International Nuclear Information System (INIS)

    McMahon, S.

    2016-01-01

    processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

  5. WE-DE-202-03: Modeling of Biological Processes - What Happens After Early Molecular Damage?

    Energy Technology Data Exchange (ETDEWEB)

    McMahon, S. [Massachusetts General Hospital and Harvard Medical School (United States)

    2016-06-15

    processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

  6. Modeling complex biological flows in multi-scale systems using the APDEC framework

    Science.gov (United States)

    Trebotich, David

    2006-09-01

    We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

  7. Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review.

    Science.gov (United States)

    Boyd, Philip W; Collins, Sinead; Dupont, Sam; Fabricius, Katharina; Gattuso, Jean-Pierre; Havenhand, Jonathan; Hutchins, David A; Riebesell, Ulf; Rintoul, Max S; Vichi, Marcello; Biswas, Haimanti; Ciotti, Aurea; Gao, Kunshan; Gehlen, Marion; Hurd, Catriona L; Kurihara, Haruko; McGraw, Christina M; Navarro, Jorge M; Nilsson, Göran E; Passow, Uta; Pörtner, Hans-Otto

    2018-06-01

    Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy-making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain process-oriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science-based policy formulation. © 2018 John Wiley & Sons Ltd.

  8. Inorganic concepts relevant to metal binding, activity, and toxicity in a biological system

    Energy Technology Data Exchange (ETDEWEB)

    Hoeschele, J.D. (Warner-Lambert Co., Ann Arbor, MI (USA). Parke-Davis Pharmaceutical Research Div.); Turner, J.E.; England, M.W. (Oak Ridge National Lab., TN (USA))

    1990-01-01

    The purpose of this paper is to review selected physical and inorganic concepts and factors which might be important in assessing and/or understanding the fact and disposition of a metal system in a biological environment. Hopefully, such inquiries will ultimately permit us to understand, rationalize, and predict differences and trends in biological effects as a function of the basic nature of a metal system and, in optimal cases, serve as input to a system of guidelines for the notion of Chemical Dosimetry.'' The plan of this paper is to first review, in general terms, the basic principles of the Crystal Field Theory (CFT), a unifying theory of bonding in metal complexes. This will provide the necessary theoretical background for the subsequent discussion of selected concepts and factors. 21 refs., 7 figs., 6 tabs.

  9. High stability and biological activity of the copper(II) complexes of alloferon 1 analogues containing tryptophan.

    Science.gov (United States)

    Kadej, Agnieszka; Kuczer, Mariola; Czarniewska, Elżbieta; Urbański, Arkadiusz; Rosiński, Grzegorz; Kowalik-Jankowska, Teresa

    2016-10-01

    Copper(II) complex formation processes between the alloferon 1 (Allo1) (HGVSGHGQHGVHG) analogues where the tryptophan residue is introducing in the place His residue H1W, H6W, H9W and H12W have been studied by potentiometric, UV-visible, CD and EPR spectroscopic, and MS methods. For all analogues of alloferon 1 complex speciation have been obtained for a 1:1 metal-to-ligand molar ratio and 2:1 of H1W because of precipitation at higher (2:1, 3:1 and 4:1) ratios. At physiological pH7.4 and a 1:1 metal-to-ligand molar ratio the tryptophan analogues of alloferon 1 form the CuH -1 L and/or CuH -2 L complexes with the 4N binding mode. The introduction of tryptophan in place of histidine residues changes the distribution diagram of the complexes formed with the change of pH and their stability constants compared to the respective substituted alanine analogues of alloferon 1. The CuH -1 L, CuH -2 L and CuH -3 L complexes of the tryptophan analogues are more stable from 1 to 5 log units in comparison to those of the alanine analogues. This stabilization of the complexes may result from cation(Cu(II))-π and indole/imidazole ring interactions. The induction of apoptosis in vivo, in Tenebrio molitor cells by the ligands and their copper(II) complexes at pH7.4 was studied. The biological results show that copper(II) ions in vivo did not cause any apparent apoptotic features. The most active were the H12W peptide and Cu(II)-H12W complex formed at pH7.4. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. A review on versatile applications of transition metal complexes incorporating Schiff bases

    Directory of Open Access Journals (Sweden)

    Ahmed M. Abu-Dief

    2015-06-01

    Full Text Available Schiff bases and their complexes are versatile compounds synthesized from the condensation of an amino compound with carbonyl compounds and widely used for industrial purposes and also exhibit a broad range of biological activities including antifungal, antibacterial, antimalarial, antiproliferative, anti-inflammatory, antiviral, and antipyretic properties. Many Schiff base complexes show excellent catalytic activity in various reactions and in the presence of moisture. Over the past few years, there have been many reports on their applications in homogeneous and heterogeneous catalysis. The high thermal and moisture stabilities of many Schiff base complexes were useful attributes for their application as catalysts in reactions involving at high temperatures. The activity is usually increased by complexation therefore to understand the properties of both ligands and metal can lead to the synthesis of highly active compounds. The influence of certain metals on the biological activity of these compounds and their intrinsic chemical interest as multidentate ligands has prompted a considerable increase in the study of their coordination behaviour. Development of a new chemotherapeutic Schiff bases and their metal complexes is now attracting the attention of medicinal chemists. This review compiles examples of the most promising applied Schiff bases and their complexes in different areas.

  11. Synthetic Biology: Putting Synthesis into Biology

    Science.gov (United States)

    Liang, Jing; Luo, Yunzi; Zhao, Huimin

    2010-01-01

    The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

  12. Microgravity Fluids for Biology, Workshop

    Science.gov (United States)

    Griffin, DeVon; Kohl, Fred; Massa, Gioia D.; Motil, Brian; Parsons-Wingerter, Patricia; Quincy, Charles; Sato, Kevin; Singh, Bhim; Smith, Jeffrey D.; Wheeler, Raymond M.

    2013-01-01

    Microgravity Fluids for Biology represents an intersection of biology and fluid physics that present exciting research challenges to the Space Life and Physical Sciences Division. Solving and managing the transport processes and fluid mechanics in physiological and biological systems and processes are essential for future space exploration and colonization of space by humans. Adequate understanding of the underlying fluid physics and transport mechanisms will provide new, necessary insights and technologies for analyzing and designing biological systems critical to NASAs mission. To enable this mission, the fluid physics discipline needs to work to enhance the understanding of the influence of gravity on the scales and types of fluids (i.e., non-Newtonian) important to biology and life sciences. In turn, biomimetic, bio-inspired and synthetic biology applications based on physiology and biology can enrich the fluid mechanics and transport phenomena capabilities of the microgravity fluid physics community.

  13. A generic algorithm for layout of biological networks.

    Science.gov (United States)

    Schreiber, Falk; Dwyer, Tim; Marriott, Kim; Wybrow, Michael

    2009-11-12

    Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration. We present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks. The presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.

  14. Systems biology perspectives on minimal and simpler cells.

    Science.gov (United States)

    Xavier, Joana C; Patil, Kiran Raosaheb; Rocha, Isabel

    2014-09-01

    The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  15. Systems Biology Perspectives on Minimal and Simpler Cells

    Science.gov (United States)

    Xavier, Joana C.; Patil, Kiran Raosaheb

    2014-01-01

    SUMMARY The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells. PMID:25184563

  16. EPR Characterization of Dinitrosyl Iron Complexes with Thiol-Containing Ligands as an Approach to Their Identification in Biological Objects: An Overview.

    Science.gov (United States)

    Vanin, Anatoly F

    2018-06-01

    The overview demonstrates how the use of only one physico-chemical approach, viz., the electron paramagnetic resonance method, allowed detection and identification of dinitrosyl iron complexes with thiol-containing ligands in various animal and bacterial cells. These complexes are formed in biological objects in the paramagnetic (electron paramagnetic resonance-active) mononuclear and diamagnetic (electron paramagnetic resonance-silent) binuclear forms and control the activity of nitrogen monoxide, one of the most universal regulators of metabolic processes in the organism. The analysis of electronic and spatial structures of dinitrosyl iron complex sheds additional light on the mechanism whereby dinitrosyl iron complex with thiol-containing ligands function in human and animal cells as donors of nitrogen monoxide and its ionized form, viz., nitrosonium ions (NO + ).

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

    Science.gov (United States)

    Hruby, Victor J.

    2011-01-01

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

  18. From technological advances to biological understanding: The main steps toward high-precision RT in breast cancer.

    Science.gov (United States)

    Leonardi, Maria Cristina; Ricotti, Rosalinda; Dicuonzo, Samantha; Cattani, Federica; Morra, Anna; Dell'Acqua, Veronica; Orecchia, Roberto; Jereczek-Fossa, Barbara Alicja

    2016-10-01

    Radiotherapy improves local control in breast cancer (BC) patients which increases overall survival in the long term. Improvements in treatment planning and delivery and a greater understanding of BC behaviour have laid the groundwork for high-precision radiotherapy, which is bound to further improve the therapeutic index. Precise identification of target volumes, better coverage and dose homogeneity have had a positive impact on toxicity and local control. The conformity of treatment dose due to three-dimensional radiotherapy and new techniques such as intensity modulated radiotherapy makes it possible to spare surrounding normal tissue. The widespread use of dose-volume constraints and histograms have increased awareness of toxicity. Real time image guidance has improved geometric precision and accuracy, together with the implementation of quality assurance programs. Advances in the precision of radiotherapy is also based on the choice of the appropriate fractionation and approach. Adaptive radiotherapy is not only a technical concept, but is also a biological concept based on the knowledge that different types of BC have distinctive patterns of locoregional spread. A greater understanding of cancer biology helps in choosing the treatment best suited to a particular situation. Biomarkers predictive of response play a crucial role. The combination of radiotherapy with molecular targeted therapies may enhance radiosensitivity, thus increasing the cytotoxic effects and improving treatment response. The appropriateness of an alternative fractionation, partial breast irradiation, dose escalating/de-escalating approaches, the extent of nodal irradiation have been examined for all the BC subtypes. The broadened concept of adaptive radiotherapy is vital to high-precision treatments. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Darwin and Reductionisms: Victorian, Neo-Darwinian and Postgenomic Biologies

    Directory of Open Access Journals (Sweden)

    Angelique Richardson

    2010-10-01

    Full Text Available This article compares the open-ended Darwinism of Charles Darwin, George Lewes, George Eliot and Thomas Hardy with reductive post-Weismann and early eugenist views and more recent neo-Darwinian ideas including literary Darwinism. It argues that some Victorians had a clear sense of the complexities of the natural world, and of the centrality of environment to life. This awareness contrasts with the processes of divorce and isolation that underpin neo-Darwinian understandings of evolutionary development. But biologists and philosophers of biology are now emphasising the complex and dynamic relations between organism and environment in ways that would have appealed to Darwin’s contemporaries. The article establishes that there are significant parallels between mid-Victorian and postgenomic thought.

  20. Modeling Power Systems as Complex Adaptive Systems

    Energy Technology Data Exchange (ETDEWEB)

    Chassin, David P.; Malard, Joel M.; Posse, Christian; Gangopadhyaya, Asim; Lu, Ning; Katipamula, Srinivas; Mallow, J V.

    2004-12-30

    Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today's most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This report explores the state-of-the-art physical analogs for understanding the behavior of some econophysical systems and deriving stable and robust control strategies for using them. We review and discuss applications of some analytic methods based on a thermodynamic metaphor, according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood. We apply these methods to the question of how power markets can be expected to behave under a variety of conditions.

  1. Octamer-binding protein 4 affects the cell biology and phenotypic transition of lung cancer cells involving β-catenin/E-cadherin complex degradation.

    Science.gov (United States)

    Chen, Zhong-Shu; Ling, Dong-Jin; Zhang, Yang-De; Feng, Jian-Xiong; Zhang, Xue-Yu; Shi, Tian-Sheng

    2015-03-01

    Clinical studies have reported evidence for the involvement of octamer‑binding protein 4 (Oct4) in the tumorigenicity and progression of lung cancer; however, the role of Oct4 in lung cancer cell biology in vitro and its mechanism of action remain to be elucidated. Mortality among lung cancer patients is more frequently due to metastasis rather than their primary tumors. Epithelial‑mesenchymal transition (EMT) is a prominent biological event for the induction of epithelial cancer metastasis. The aim of the present study was to investigate whether Oct4 had the capacity to induce lung cancer cell metastasis via the promoting the EMT in vitro. Moreover, the effect of Oct4 on the β‑catenin/E‑cadherin complex, associated with EMT, was examined using immunofluorescence and immunoprecipitation assays as well as western blot analysis. The results demonstrated that Oct4 enhanced cell invasion and adhesion accompanied by the downregulation of epithelial marker cytokeratin, and upregulation of the mesenchymal markers vimentin and N‑cadherin. Furthermore, Oct4 induced EMT of lung cancer cells by promoting β‑catenin/E‑cadherin complex degradation and regulating nuclear localization of β‑catenin. In conclusion, the present study indicated that Oct4 affected the cell biology of lung cancer cells in vitro through promoting lung cancer cell metastasis via EMT; in addition, the results suggested that the association and degradation of the β‑catenin/E‑cadherin complex was regulated by Oct4 during the process of EMT.

  2. ICPP: Approach for Understanding Complexity of Plasma

    Science.gov (United States)

    Sato, Tetsuya

    2000-10-01

    In this talk I wish to present an IT system that could promote Science of Complexity. In order to deal with a seemingly `complex' phenomenon, which means `beyond analytical manipulation', computer simulation is a viable powerful tool. However, complexity implies a concept beyond the horizon of reductionism. Therefore, rather than simply solving a complex phenomenon for a given boundary condition, one must establish an intelligent way of attacking mutual evolution of a system and its environment. NIFS-TCSC has been developing a prototype system that consists of supercomputers, virtual reality devices and high-speed network system. Let us explain this by picking up a global atmospheric circulation group, global oceanic circulation group and local weather prediction group. Local weather prediction group predicts the local change of the weather such as the creation of cloud and rain in the near future under the global conditions obtained by the global atmospheric and ocean groups. The global groups run simulations by modifying the local heat source/sink evaluated by the local weather prediction and then obtain the global conditions in the next time step. By repeating such a feedback performance one can predict the mutual evolution of the local system and its environment. Mutual information exchanges among multiple groups are carried out instantaneously by the networked common virtual reality space in which 3-D global and local images of the atmospheric and oceanic circulation and the cloud and rain maps are arbitrarily manipulated by any of the groups and commonly viewed. The present networking system has a great advantage that any simulation groups can freely and arbitrarily change their alignment, so that mutual evolution of any stratum system can become tractable by utilizing this network system.

  3. Biological activities of some Fluoroquinolones-metal complexes

    African Journals Online (AJOL)

    McRoy

    Background: Metal ions play a vital role in the design of more biologically active drugs. Aim: The paper reviewed the .... 2H2O by direct reaction of copper(II) sulphate pentahydrate with ciprofloxacin in distilled water. ... membered ring and the chloride ion completes the seven coordination around the Ca2+ion.[37-39].

  4. Computational systems biology and dose-response modeling in relation to new directions in toxicity testing.

    Science.gov (United States)

    Zhang, Qiang; Bhattacharya, Sudin; Andersen, Melvin E; Conolly, Rory B

    2010-02-01

    The new paradigm envisioned for toxicity testing in the 21st century advocates shifting from the current animal-based testing process to a combination of in vitro cell-based studies, high-throughput techniques, and in silico modeling. A strategic component of the vision is the adoption of the systems biology approach to acquire, analyze, and interpret toxicity pathway data. As key toxicity pathways are identified and their wiring details elucidated using traditional and high-throughput techniques, there is a pressing need to understand their qualitative and quantitative behaviors in response to perturbation by both physiological signals and exogenous stressors. The complexity of these molecular networks makes the task of understanding cellular responses merely by human intuition challenging, if not impossible. This process can be aided by mathematical modeling and computer simulation of the networks and their dynamic behaviors. A number of theoretical frameworks were developed in the last century for understanding dynamical systems in science and engineering disciplines. These frameworks, which include metabolic control analysis, biochemical systems theory, nonlinear dynamics, and control theory, can greatly facilitate the process of organizing, analyzing, and understanding toxicity pathways. Such analysis will require a comprehensive examination of the dynamic properties of "network motifs"--the basic building blocks of molecular circuits. Network motifs like feedback and feedforward loops appear repeatedly in various molecular circuits across cell types and enable vital cellular functions like homeostasis, all-or-none response, memory, and biological rhythm. These functional motifs and associated qualitative and quantitative properties are the predominant source of nonlinearities observed in cellular dose response data. Complex response behaviors can arise from toxicity pathways built upon combinations of network motifs. While the field of computational cell

  5. Protein complex prediction via dense subgraphs and false positive analysis.

    Directory of Open Access Journals (Sweden)

    Cecilia Hernandez

    Full Text Available Many proteins work together with others in groups called complexes in order to achieve a specific function. Discovering protein complexes is important for understanding biological processes and predict protein functions in living organisms. Large-scale and throughput techniques have made possible to compile protein-protein interaction networks (PPI networks, which have been used in several computational approaches for detecting protein complexes. Those predictions might guide future biologic experimental research. Some approaches are topology-based, where highly connected proteins are predicted to be complexes; some propose different clustering algorithms using partitioning, overlaps among clusters for networks modeled with unweighted or weighted graphs; and others use density of clusters and information based on protein functionality. However, some schemes still require much processing time or the quality of their results can be improved. Furthermore, most of the results obtained with computational tools are not accompanied by an analysis of false positives. We propose an effective and efficient mining algorithm for discovering highly connected subgraphs, which is our base for defining protein complexes. Our representation is based on transforming the PPI network into a directed acyclic graph that reduces the number of represented edges and the search space for discovering subgraphs. Our approach considers weighted and unweighted PPI networks. We compare our best alternative using PPI networks from Saccharomyces cerevisiae (yeast and Homo sapiens (human with state-of-the-art approaches in terms of clustering, biological metrics and execution times, as well as three gold standards for yeast and two for human. Furthermore, we analyze false positive predicted complexes searching the PDBe (Protein Data Bank in Europe database in order to identify matching protein complexes that have been purified and structurally characterized. Our analysis shows

  6. Biologically Complex Planar Cell Plasma Membranes Supported on Polyelectrolyte Cushions Enhance Transmembrane Protein Mobility and Retain Native Orientation.

    Science.gov (United States)

    Liu, Han-Yuan; Chen, Wei-Liang; Ober, Christopher K; Daniel, Susan

    2018-01-23

    Reconstituted supported lipid bilayers (SLB) are widely used as in vitro cell-surface models because they are compatible with a variety of surface-based analytical techniques. However, one of the challenges of using SLBs as a model of the cell surface is the limited complexity in membrane composition, including the incorporation of transmembrane proteins and lipid diversity that may impact the activity of those proteins. Additionally, it is challenging to preserve the transmembrane protein native orientation, function, and mobility in SLBs. Here, we leverage the interaction between cell plasma membrane vesicles and polyelectrolyte brushes to create planar bilayers from cell plasma membrane vesicles that have budded from the cell surface. This approach promotes the direct incorporation of membrane proteins and other species into the planar bilayer without using detergent or reconstitution and preserves membrane constituents. Furthermore, the structure of the polyelectrolyte brush serves as a cushion between the planar bilayer and rigid supporting surface, limiting the interaction of the cytosolic domains of membrane proteins with this surface. Single particle tracking was used to analyze the motion of GPI-linked yellow fluorescent proteins (GPI-YFP) and neon-green fused transmembrane P2X2 receptors (P2X2-neon) and shows that this platform retains over 75% mobility of multipass transmembrane proteins in its native membrane environment. An enzyme accessibility assay confirmed that the protein orientation is preserved and results in the extracellular domain facing toward the bulk phase and the cytosolic side facing the support. Because the platform presented here retains the complexity of the cell plasma membrane and preserves protein orientation and mobility, it is a better representative mimic of native cell surfaces, which may find many applications in biological assays aimed at understanding cell membrane phenomena.

  7. Nice to know you: Positive emotions, self-other overlap, and complex understanding in the formation of a new relationship.

    Science.gov (United States)

    Waugh, Christian E; Fredrickson, Barbara L

    2006-04-01

    Based on Fredrickson's ((1998). What good are positive emotions? Review of General Psychology, 2, 300-319.; (2001). The role of positive emotions in positive psychology: The broaden-and-build theory of positive emotions. American Psychologist, 56, 218-226) broaden-and-build theory and Aron and Aron's ((1986). Love as expansion of the self: Understanding attraction and satisfaction. New York: Hemisphere) self-expansion theory, it was hypothesized that positive emotions broaden people's feelings of self-other overlap in the beginning of a new relationship. In a prospective study of first-year college students, we found that, after 1 week in college, positive emotions predicted increased self-other overlap with new roommates, which in turn predicted a more complex understanding of the roommate. In addition, participants who experienced a high ratio of positive to negative emotions throughout the first month of college reported a greater increase in self-other overlap and complex understanding than participants with a low positivity ratio. Implications for the role of positive emotions in the formation of new relationships are discussed.

  8. Nice to know you: Positive emotions, self–other overlap, and complex understanding in the formation of a new relationship

    Science.gov (United States)

    WAUGH, CHRISTIAN E.; FREDRICKSON, BARBARA L.

    2007-01-01

    Based on Fredrickson's ((1998). What good are positive emotions? Review of General Psychology, 2, 300–319.; (2001). The role of positive emotions in positive psychology: The broaden-and-build theory of positive emotions. American Psychologist, 56, 218–226) broaden-and-build theory and Aron and Aron's ((1986). Love as expansion of the self: Understanding attraction and satisfaction. New York: Hemisphere) self-expansion theory, it was hypothesized that positive emotions broaden people's feelings of self–other overlap in the beginning of a new relationship. In a prospective study of first-year college students, we found that, after 1 week in college, positive emotions predicted increased self–other overlap with new roommates, which in turn predicted a more complex understanding of the roommate. In addition, participants who experienced a high ratio of positive to negative emotions throughout the first month of college reported a greater increase in self–other overlap and complex understanding than participants with a low positivity ratio. Implications for the role of positive emotions in the formation of new relationships are discussed. PMID:21691460

  9. Simulating biological processes: stochastic physics from whole cells to colonies

    Science.gov (United States)

    Earnest, Tyler M.; Cole, John A.; Luthey-Schulten, Zaida

    2018-05-01

    The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a ‘minimal cell’. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

  10. The biology of personalized cancer medicine: facing individual complexities underlying hallmark capabilities.

    Science.gov (United States)

    De Palma, Michele; Hanahan, Douglas

    2012-04-01

    It is a time of great promise and expectation for the applications of knowledge about mechanisms of cancer toward more effective and enduring therapies for human disease. Conceptualizations such as the hallmarks of cancer are providing an organizing principle with which to distill and rationalize the abject complexities of cancer phenotypes and genotypes across the spectrum of the human disease. A countervailing reality, however, involves the variable and often transitory responses to most mechanism-based targeted therapies, returning full circle to the complexity, arguing that the unique biology and genetics of a patient's tumor will in the future necessarily need to be incorporated into the decisions about optimal treatment strategies, the frontier of personalized cancer medicine. This perspective highlights considerations, metrics, and methods that may prove instrumental in charting the landscape of evaluating individual tumors so to better inform diagnosis, prognosis, and therapy. Integral to the consideration is remarkable heterogeneity and variability, evidently embedded in cancer cells, but likely also in the cell types composing the supportive and interactive stroma of the tumor microenvironment (e.g., leukocytes and fibroblasts), whose diversity in form, regulation, function, and abundance may prove to rival that of the cancer cells themselves. By comprehensively interrogating both parenchyma and stroma of patients' cancers with a suite of parametric tools, the promise of mechanism-based therapy may truly be realized. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  11. Efficient sample preparation from complex biological samples using a sliding lid for immobilized droplet extractions.

    Science.gov (United States)

    Casavant, Benjamin P; Guckenberger, David J; Beebe, David J; Berry, Scott M

    2014-07-01

    Sample preparation is a major bottleneck in many biological processes. Paramagnetic particles (PMPs) are a ubiquitous method for isolating analytes of interest from biological samples and are used for their ability to thoroughly sample a solution and be easily collected with a magnet. There are three main methods by which PMPs are used for sample preparation: (1) removal of fluid from the analyte-bound PMPs, (2) removal of analyte-bound PMPs from the solution, and (3) removal of the substrate (with immobilized analyte-bound PMPs). In this paper, we explore the third and least studied method for PMP-based sample preparation using a platform termed Sliding Lid for Immobilized Droplet Extractions (SLIDE). SLIDE leverages principles of surface tension and patterned hydrophobicity to create a simple-to-operate platform for sample isolation (cells, DNA, RNA, protein) and preparation (cell staining) without the need for time-intensive wash steps, use of immiscible fluids, or precise pinning geometries. Compared to other standard isolation protocols using PMPs, SLIDE is able to perform rapid sample preparation with low (0.6%) carryover of contaminants from the original sample. The natural recirculation occurring within the pinned droplets of SLIDE make possible the performance of multistep cell staining protocols within the SLIDE by simply resting the lid over the various sample droplets. SLIDE demonstrates a simple easy to use platform for sample preparation on a range of complex biological samples.

  12. Silver nanoparticles in complex biological media: assessment of colloidal stability and protein corona formation

    Energy Technology Data Exchange (ETDEWEB)

    Argentiere, Simona, E-mail: simona.argentiere@fondazionefilarete.com; Cella, Claudia, E-mail: claudia.cella@unimi.it [Fondazione Filarete (Italy); Cesaria, Maura, E-mail: maura.cesaria@le.infn.it [Università del Salento, Dipartimento di Matematica e Fisica “Ennio De Giorgi” (Italy); Milani, Paolo, E-mail: paolo.milani@mi.infn.it; Lenardi, Cristina, E-mail: cristina.lenardi@mi.infn.it [Università degli Studi di Milano, CIMAINA and Dipartimento di Fisica (Italy)

    2016-08-15

    Engineered silver nanoparticles (AgNPs) are among the most used nanomaterials in consumer products, therefore concerns are raised about their potential for adverse effects in humans and environment. Although an increasing number of studies in vitro and in vivo are being reported on the toxicity of AgNPs, most of them suffer from incomplete characterization of AgNPs in the tested biological media. As a consequence, the comparison of toxicological data is troublesome and the toxicity evaluation still remains an open critical issue. The development of a reliable protocol to evaluate interactions of AgNPs with surrounding proteins as well as to assess their colloidal stability is therefore required. In this regard, it is of importance not only to use multiple, easy-to-access and simple techniques but also to understand limitations of each characterization methods. In this work, the morphological and structural behaviour of AgNPs has been studied in two relevant biological media, namely 10 % FBS and MP. Three different techniques (Dynamic Light Scattering, Transmission Electron Microscopy, UV–Vis spectroscopy) were tested for their suitability in detecting AgNPs of three different sizes (10, 40 and 100 nm) coated with either citrate or polyvinylpyrrolidone. Results showed that UV–Vis spectroscopy is the most versatile and informative technique to gain information about interaction between AgNPs and surrounding proteins and to determine their colloidal stability in the tested biological media. These findings are expected to provide useful insights in characterizing AgNPs before performing any further in vitro/in vivo experiment.

  13. Synthetic biology: engineering molecular computers

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

  14. A Method for Selective Depletion of Zn(II) Ions from Complex Biological Media and Evaluation of Cellular Consequences of Zn(II) Deficiency

    Science.gov (United States)

    Richardson, Christopher E. R.; Cunden, Lisa S.; Butty, Vincent L.; Nolan, Elizabeth M.; Lippard, Stephen J.; Shoulders, Matthew D.

    2018-01-01

    We describe the preparation, evaluation, and application of an S100A12 protein-conjugated solid support, hereafter the “A12-resin,” that can remove 99% of Zn(II) from complex biological solutions without significantly perturbing the concentrations of other metal ions. The A12-resin can be applied to selectively deplete Zn(II) from diverse tissue culture media and from other biological fluids, including human serum. To further demonstrate the utility of this approach, we investigated metabolic, transcriptomic, and metallomic responses of HEK293 cells cultured in medium depleted of Zn(II) using S100A12. The resulting data provide insight into how cells respond to acute Zn(II) deficiency. We expect that the A12-resin will facilitate interrogation of disrupted Zn(II) homeostasis in biological settings, uncovering novel roles for Zn(II) in biology. PMID:29334734

  15. The Molecular Biology Capstone Assessment: A Concept Assessment for Upper-Division Molecular Biology Students

    Science.gov (United States)

    Couch, Brian A.; Wood, William B.; Knight, Jennifer K.

    2015-01-01

    Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in…

  16. Research Progress in Oncology. Highlighting and Exploiting the Roles of Several Strategic Proteins in Understanding Cancer Biology

    Directory of Open Access Journals (Sweden)

    Odiba Arome S.

    2016-01-01

    Full Text Available Although almost all biological processes are mediated by a variety of proteins, it is important to bring to spotlight recent experimental and clinical research advances that had their focus on highlighting and taking advantage of the roles of several strategic proteins in order to gain more understanding of cancer biology. Proteins have a major stake in the initiation, progression, sustenance and completion of cellular processes, and have also demonstrated their vital roles in cancer processes. The characteristic functions of proteins and modified proteins have been utilized in the understanding and treatment of cancer. Recent insights in such roles and applications include linker histone H1.2 in the compaction of chromatin and gene silencing via the recognition of H3K27me3; c-Jun with Fra-2/c-Fos in the promotion of aggressive tumour phenotypes in tongue cancer; the use of sodium channelinhibiting agents targeting the transmembrane protein in breast, colon and prostate cancer; SET-mediated activities; protein interaction networks in glioma; Gpnmb significance as a biomarker; β-carbolines inhibition on Wnt/β-catenin signaling; p53 mutants co-opt chromatin pathways; Bone morphogenetic protein 4 as regulator of the behaviors of cancer cell; Brain-Expressed X-linked (BEX proteins in human cancers; targeting CDK4/6 including protein kinases to make a reversal of multidrug resistance in sarcoma. In-depth knowledge of Proteomics will go a long way in helping us uncover a lot more strategies that will help us in the long fight against cancer.

  17. An Integrative Systems Biology Approach to Understanding Pulmonary Diseases

    NARCIS (Netherlands)

    Auffray, Charles; Adcock, Ian M.; Chung, Kian Fan; Djukanovic, Ratko; Pison, Christophe; Sterk, Peter J.

    2010-01-01

    Chronic inflammatory pulmonary diseases such as COPD and asthma are highly prevalent and associated with a major health burden worldwide. Despite a wealth of biologic and clinical information on normal and pathologic airway structure and function, the primary causes and mechanisms of disease remain

  18. Rhodium complexes as therapeutic agents.

    Science.gov (United States)

    Ma, Dik-Lung; Wang, Modi; Mao, Zhifeng; Yang, Chao; Ng, Chan-Tat; Leung, Chung-Hang

    2016-02-21

    The landscape of inorganic medicinal chemistry has been dominated by the investigation of platinum, and to a lesser extent ruthenium, complexes over the past few decades. Recently, complexes based on other metal centers such as rhodium have attracted attention due to their tunable chemical and biological properties as well as distinct mechanisms of action. This perspective highlights recent examples of rhodium complexes that show diverse biological activities against various targets, including enzymes and protein-protein interactions.

  19. 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…

  20. Cancer initiation and progression: an unsimplifiable complexity

    Directory of Open Access Journals (Sweden)

    Frezza Eldo E

    2006-10-01

    Full Text Available Abstract Background Cancer remains one of the most complex diseases affecting humans and, despite the impressive advances that have been made in molecular and cell biology, how cancer cells progress through carcinogenesis and acquire their metastatic ability is still widely debated. Conclusion There is no doubt that human carcinogenesis is a dynamic process that depends on a large number of variables and is regulated at multiple spatial and temporal scales. Viewing cancer as a system that is dynamically complex in time and space will, however, probably reveal more about its underlying behavioural characteristics. It is encouraging that mathematicians, biologists and clinicians continue to contribute together towards a common quantitative understanding of cancer complexity. This way of thinking may further help to clarify concepts, interpret new and old experimental data, indicate alternative experiments and categorize the acquired knowledge on the basis of the similarities and/or shared behaviours of very different tumours.

  1. Complex Time-Delay Systems Theory and Applications

    CERN Document Server

    Atay, Fatihcan M

    2010-01-01

    Time delays in dynamical systems arise as an inevitable consequence of finite speeds of information transmission. Realistic models increasingly demand the inclusion of delays in order to properly understand, analyze, design, and control real-life systems. The goal of this book is to present the state-of-the-art in research on time-delay dynamics in the framework of complex systems and networks. While the mathematical theory of delay equations is quite mature, its application to the particular problems of complex systems and complexity is a newly emerging field, and the present volume aims to play a pioneering role in this perspective. The chapters in this volume are authored by renowned experts and cover both theory and applications in a wide range of fields, with examples extending from neuroscience and biology to laser physics and vehicle traffic. Furthermore, all chapters include sufficient introductory material and extensive bibliographies, making the book a self-contained reference for both students and ...

  2. The mechanics of soft biological composites.

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Thao D. (Sandia National Laboratories, Livermore, CA); Grazier, John Mark; Boyce, Brad Lee; Jones, Reese E. (Sandia National Laboratories, Livermore, CA)

    2007-10-01

    Biological tissues are uniquely structured materials with technologically appealing properties. Soft tissues such as skin, are constructed from a composite of strong fibrils and fluid-like matrix components. This was the first coordinated experimental/modeling project at Sandia or in the open literature to consider the mechanics of micromechanically-based anisotropy and viscoelasticity of soft biological tissues. We have exploited and applied Sandia's expertise in experimentation and mechanics modeling to better elucidate the behavior of collagen fibril-reinforced soft tissues. The purpose of this project was to provide a detailed understanding of the deformation of ocular tissues, specifically the highly structured skin-like tissue in the cornea. This discovery improved our knowledge of soft/complex materials testing and modeling. It also provided insight into the way that cornea tissue is bio-engineered such that under physiologically-relevant conditions it has a unique set of properties which enhance functionality. These results also provide insight into how non-physiologic loading conditions, such as corrective surgeries, may push the cornea outside of its natural design window, resulting in unexpected non-linear responses. Furthermore, this project created a clearer understanding of the mechanics of soft tissues that could lead to bio-inspired materials, such as highly supple and impact resistant body armor, and improve our design of human-machine interfaces, such as micro-electrical-mechanical (MEMS) based prosthetics.

  3. Reduction theories elucidate the origins of complex biological rhythms generated by interacting delay-induced oscillations.

    Directory of Open Access Journals (Sweden)

    Ikuhiro Yamaguchi

    Full Text Available Time delay is known to induce sustained oscillations in many biological systems such as electroencephalogram (EEG activities and gene regulations. Furthermore, interactions among delay-induced oscillations can generate complex collective rhythms, which play important functional roles. However, due to their intrinsic infinite dimensionality, theoretical analysis of interacting delay-induced oscillations has been limited. Here, we show that the two primary methods for finite-dimensional limit cycles, namely, the center manifold reduction in the vicinity of the Hopf bifurcation and the phase reduction for weak interactions, can successfully be applied to interacting infinite-dimensional delay-induced oscillations. We systematically derive the complex Ginzburg-Landau equation and the phase equation without delay for general interaction networks. Based on the reduced low-dimensional equations, we demonstrate that diffusive (linearly attractive coupling between a pair of delay-induced oscillations can exhibit nontrivial amplitude death and multimodal phase locking. Our analysis provides unique insights into experimentally observed EEG activities such as sudden transitions among different phase-locked states and occurrence of epileptic seizures.

  4. Tutorial: Electroporation of cells in complex materials and tissue

    Science.gov (United States)

    Rems, L.; Miklavčič, D.

    2016-05-01

    Electroporation is being successfully used in biology, medicine, food processing, and biotechnology, and in some environmental applications. Recent applications also include in addition to classical electroporation, where cells are exposed to micro- or milliseconds long pulses, exposures to extremely short nanosecond pulses, i.e., high-frequency electroporation. Electric pulses are applied to cells in different structural configurations ranging from suspended cells to cells in tissues. Understanding electroporation of cells in tissues and other complex environments is a key to its successful use and optimization in various applications. Thus, explanation will be provided theoretically/numerically with relation to experimental observations by scaling our understanding of electroporation from the molecular level of the cell membrane up to the tissue level.

  5. Single lipid vesicle assay for characterizing single-enzyme kinetics of phospholipid hydrolysis in a complex biological fluid.

    Science.gov (United States)

    Tabaei, Seyed R; Rabe, Michael; Zetterberg, Henrik; Zhdanov, Vladimir P; Höök, Fredrik

    2013-09-25

    Imaging of individual lipid vesicles is used to track single-enzyme kinetics of phospholipid hydrolysis. The method is employed to quantify the catalytic activity of phospholipase A2 (PLA2) in both pure and complex biological fluids. The measurements are demonstrated to offer a subpicomolar limit of detection (LOD) of human secretory PLA2 (sPLA2) in up to 1000-fold-diluted cerebrospinal fluid (CSF). An additional new feature provided by the single-enzyme sensitivity is that information about both relative concentration variations of active sPLA2 in CSF and the specific enzymatic activity can be simultaneously obtained. When CSF samples from healthy controls and individuals diagnosed with Alzheimer's disease (AD) are analyzed, the specific enzymatic activity is found to be preserved within 7% in the different CSF samples whereas the enzyme concentration differs by up to 56%. This suggests that the previously reported difference in PLA2 activity in CSF samples from healthy and AD individuals originates from differences in the PLA2 expression level rather than from the enzyme activity. Conventional ensemble averaging methods used to probe sPLA2 activity do not allow one to obtain such information. Together with an improvement in the LOD of at least 1 order of magnitude compared to that of conventional assays, this suggests that the method will become useful in furthering our understanding of the role of PLA2 in health and disease and in detecting the pharmacodynamic effects of PLA2-targeting drug candidates.

  6. Evolution of egg coats: linking molecular biology and ecology.

    Science.gov (United States)

    Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

    2015-08-01

    One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation. © 2015 John Wiley & Sons Ltd.

  7. New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems

    Science.gov (United States)

    Aliashkevich, Alena; Alvarez, Laura; Cava, Felipe

    2018-01-01

    In the environment bacteria share their habitat with a great diversity of organisms, from microbes to humans, animals and plants. In these complex communities, the production of extracellular effectors is a common strategy to control the biodiversity by interfering with the growth and/or viability of nearby microbes. One of such effectors relies on the production and release of extracellular D-amino acids which regulate diverse cellular processes such as cell wall biogenesis, biofilm integrity, and spore germination. Non-canonical D-amino acids are mainly produced by broad spectrum racemases (Bsr). Bsr’s promiscuity allows it to generate high concentrations of D-amino acids in environments with variable compositions of L-amino acids. However, it was not clear until recent whether these molecules exhibit divergent functions. Here we review the distinctive biological roles of D-amino acids, their mechanisms of action and their modulatory properties of the biodiversity of complex eco-systems. PMID:29681896

  8. Biological evaluation of transdichloridoplatinum(II) complexes with 3- and 4-acetylpyridine in comparison to cisplatin

    International Nuclear Information System (INIS)

    Filipovic, Lana; Arandelovic, Sandra; Gligorijevic, Nevenka; Krivokuca, Ana; Jankovic, Radmila; Srdic-Rajic, Tatjana; Rakic, Gordana; Tesic, Zivoslav; Radulovic, Sinisa

    2013-01-01

    In our previous study we reported the synthesis and cytotoxicity of two trans-platinum(II) complexes: trans-[PtCl 2 (3-acetylpyridine) 2 ] (1) and trans-[PtCl 2 (4-acetylpyridine) 2 ] (2), revealing significant cytotoxic potential of 2. In order to evaluate the mechanism underlying biological activity of both trans-Pt(II) isomers, comparative studies versus cisplatin were performed in HeLa, MRC-5 and MS1 cells. The cytotoxic activity of the investigated complexes was determined using SRB assay. The colagenolytic activity was determined using gelatin zymography, while the effect of platinum complexes on matrix metalloproteinases 2 and 9 mRNA expression was evaluated by quantitative real-time PCR. Apoptotic potential and cell cycle alterations were determined by FACS analyses. Western blot analysis was used to evaluate the effect on expression of DNA-repair enzyme ERCC1, and quantitative real-time PCR was used for the ERCC1 mRNA expression analysis. In vitro antiangiogenic potential was determined by tube formation assay. Platinum content in intracellular DNA and proteins was determined by inductively coupled plasma-optical emission spectrometry. Compound 2 displayed an apparent cytoselective profile, and flow cytometry analysis in HeLa cells indicated that 2 exerted antiproliferative effect through apoptosis induction, while 1 induced both apoptosis and necrosis. Action of 1 and 2, as analyzed by quantitative real-time PCR and Western blot, was associated with down-regulation of ERCC1. Both trans-complexes inhibited MMP-9 mRNA expression in HeLa, while 2 significantly abrogated in vitro tubulogenesis in MS1 cells. The ability of 2 to induce multiple and selective in vitro cytotoxic effects encourages further investigations of trans-platinum(II) complexes with substituted pyridines

  9. Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

    Science.gov (United States)

    De Domenico, Manlio

    2018-03-01

    Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

  10. Understanding global health governance as a complex adaptive system.

    Science.gov (United States)

    Hill, Peter S

    2011-01-01

    The transition from international to global health reflects the rapid growth in the numbers and nature of stakeholders in health, as well as the constant change embodied in the process of globalisation itself. This paper argues that global health governance shares the characteristics of complex adaptive systems, with its multiple and diverse players, and their polyvalent and constantly evolving relationships, and rich and dynamic interactions. The sheer quantum of initiatives, the multiple networks through which stakeholders (re)configure their influence, the range of contexts in which development for health is played out - all compound the complexity of this system. This paper maps out the characteristics of complex adaptive systems as they apply to global health governance, linking them to developments in the past two decades, and the multiple responses to these changes. Examining global health governance through the frame of complexity theory offers insight into the current dynamics of governance, and while providing a framework for making meaning of the whole, opens up ways of accessing this complexity through local points of engagement.

  11. Characterization and biological activity of Solidago canadensis complex.

    Science.gov (United States)

    Šutovská, M; Capek, P; Kocmálová, M; Fraňová, S; Pawlaczyk, I; Gancarz, R

    2013-01-01

    Polyphenolic-polysaccharide-protein complex has been isolated from flowers of Solidago canadensis L. by hot alkaline extraction procedure. Compositional analyses of S canadensis complex revealed the presence of carbohydrates (43 wt%), protein (27 wt%), phenolics (12 wt%), uronic acids (10 wt%) and inorganic material (8 wt%). The carbohydrate part was rich in neutral sugars (81 wt%) while uronids were determined in lower amount (19 wt%). Monosaccharide analysis of carbohydrate part revealed the presence of five main sugar components, i.e. rhamnose (~23 wt%), arabinose (~20 wt%), uronic acids (~19 wt%), galactose (~17 wt%) and glucose (~14 wt%), and indicated thus the presence of rhamnogalacturonan and arabinogalactan in S. canadensis complex. HPLC analysis of complex showed one single peak of molecule mass at 11.2 kDa. Antitussive activity tests, performed in three doses of Solidago complex, showed the reduction of the number of cough efforts in the dose-dependent manner. Higher doses (50 and 75 mg/kg b.w.) were shown to be by 15 and 20% more effective than that of lower one (25mg/kg b.w.). However, the antitussive effect of the highest dose (75 mg/kg b.w.) was by 10% lower in comparison with that of codeine, the strongest antitussive agent. Besides, the highest dose of the complex (75 mg/kg b.w.) significantly decreased values of specific airways resistance and their effect remained longer as that of salbutamol, a representative of classic antiasthmatic drugs. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Theoretical study of chromophores for biological sensing: Understanding the mechanism of rhodol based multi-chromophoric systems

    Science.gov (United States)

    Rivera-Jacquez, Hector J.; Masunov, Artëm E.

    2018-06-01

    Development of two-photon fluorescent probes can aid in visualizing the cellular environment. Multi-chromophore systems display complex manifolds of electronic transitions, enabling their use for optical sensing applications. Time-Dependent Density Functional Theory (TDDFT) methods allow for accurate predictions of the optical properties. These properties are related to the electronic transitions in the molecules, which include two-photon absorption cross-sections. Here we use TDDFT to understand the mechanism of aza-crown based fluorescent probes for metals sensing applications. Our findings suggest changes in local excitation in the rhodol chromophore between unbound form and when bound to the metal analyte. These changes are caused by a charge transfer from the aza-crown group and pyrazol units toward the rhodol unit. Understanding this mechanism leads to an optimized design with higher two-photon excited fluorescence to be used in medical applications.

  13. Sex matters: The effects of biological sex on adipose tissue biology and energy metabolism

    Directory of Open Access Journals (Sweden)

    Teresa G. Valencak

    2017-08-01

    Full Text Available Adipose tissue is a complex and multi-faceted organ. It responds dynamically to internal and external stimuli, depending on the developmental stage and activity of the organism. The most common functional subunits of adipose tissue, white and brown adipocytes, regulate and respond to endocrine processes, which then determine metabolic rate as well as adipose tissue functions. While the molecular aspects of white and brown adipose biology have become clearer in the recent past, much less is known about sex-specific differences in regulation and deposition of adipose tissue, and the specific role of the so-called pink adipocytes during lactation in females. This review summarises the current understanding of adipose tissue dynamics with a focus on sex-specific differences in adipose tissue energy metabolism and endocrine functions, focussing on mammalian model organisms as well as human-derived data. In females, pink adipocytes trans-differentiate during pregnancy from subcutaneous white adipocytes and are responsible for milk-secretion in mammary glands. Overlooking biological sex variation may ultimately hamper clinical treatments of many aspects of metabolic disorders. Keywords: Body fatness, Adipose tissue, Sex-specific differences, Adipokines, Adipocytes, Obesity, Energy metabolism

  14. Prostaglandins and their receptors in insect biology

    Directory of Open Access Journals (Sweden)

    David eStanley

    2011-12-01

    Full Text Available We treat the biological significance of prostaglandins (PGs and their known receptors in insect biology. PGs and related eicosanoids are oxygenated derivatives of arachidonic acid (AA and two other C20 polyunsaturated fatty acids. PGs are mostly appreciated in the context of biomedicine, but a growing body of literature indicates the biological significance of these compounds extends throughout the animal kingdom, and possibly beyond. PGs act in several crucial areas of insect biology. In reproduction, a specific PG, PGE2, releases oviposition behavior in most crickets and a few other insect species; PGs also mediate events in egg development in some species, which may represent all insects. PGs play major roles in modulating fluid secretion in Malpighian tubules, rectum and salivary glands, although, again, this has been studied in only a few insect species that may represent the Class. Insect immunity is a very complex defense system. PGs and other eicosanoids mediate a large number of immune reactions to infection and invasion. The actions of most PGs are mediated by specific receptors. Biomedical research has discovered a great deal of knowledge about PG receptors in mammals, including their structures, pharmacology, molecular biology and cellular locations. Studies of PG receptors in insects lag behind the biomedical background, however, recent results hold the promise of accelerated research in this area. A PG receptor has been identified in a class of lepidopteran hemocytes and experimentally linked to the release of prophenoloxidase. We conclude that research into PGs and their receptors in insects will lead to important advances in our understanding of insect biology.

  15. Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits

    Science.gov (United States)

    Watson, Emma; MacNeil, Lesley T.; Ritter, Ashlyn D.; Yilmaz, L. Safak; Rosebrock, Adam P.; Caudy, Amy A.; Walhout, Albertha J. M.

    2014-01-01

    SUMMARY Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here we used an interspecies systems biology approach with Caenorhabditis elegans and two if its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal’s gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development and reduces fertility, but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology. PMID:24529378

  16. Photocytotoxic lanthanide complexes

    Indian Academy of Sciences (India)

    Among many applications of lanthanides, gadolinium complexes are used as magnetic resonance imaging (MRI) contrast agents in clinical radiology and luminescent lanthanides for bioanalysis, imaging and sensing. The chemistry of photoactive lanthanide complexes showing biological applications is of recent origin.

  17. Found in translation: understanding the biology and behavior of experimental traumatic brain injury

    Science.gov (United States)

    Bondi, Corina O.; Semple, Bridgette D.; Noble-Haeusslein, Linda J.; Osier, Nicole D.; Carlson, Shaun W.; Dixon, C. Edward; Giza, Christopher C.; Kline, Anthony E.

    2014-01-01

    BONDI, C.O., B.D. Semple, L.J. Noble-Haeusslein, N.D. Osier, S.W. Carlson, C.E. Dixon, C.C. Giza and A.E. Kline. Found in translation: understanding the biology and behavior of experimental traumatic brain injury. NEUROSCI BIOBEHAV REV. The aim of this review is to discuss in greater detail the topics covered in the recent symposium entitled “Traumatic brain injury: laboratory and clinical perspectives,” presented at the 2014 International Behavioral Neuroscience Society annual meeting. Herein we review contemporary laboratory models of traumatic brain injury (TBI) including common assays for sensorimotor and cognitive behavior. New modalities to evaluate social behavior after injury to the developing brain, as well as the attentional set-shifting test (AST) as a measure of executive function in TBI, will be highlighted. Environmental enrichment (EE) will be discussed as a preclinical model of neurorehabilitation, and finally, an evidence-based approach to sports-related concussion will be considered. The review consists predominantly of published data, but some discussion of ongoing or future directions is provided. PMID:25496906

  18. New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Nancy J.; Paša-Tolić, Ljiljana; Bailey, Vanessa L.; Dohnalkova, Alice C.

    2017-06-01

    Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. The aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.

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

    Science.gov (United States)

    Cahill, James F

    2015-10-26

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

  20. The role of socioscientific issues in biology teaching – from the perspective of teachers

    OpenAIRE

    Tidemand, Sofie; Nielsen, Jan Alexis

    2017-01-01

    Previous research has documented that students who engage with socioscientific issues can acquire some of the complex competences and skills typically related to scientific literacy. But an emerging field of research on science teachers’ understanding and use of socioscientific issues, has documented that a range of challenges hinders the uptake of socioscientific issues. In this study we investigated the interpretation and implementation of socioscientific issues among Danish biology teacher...

  1. Seeking simplicity for the understanding of multiphase flows

    Science.gov (United States)

    Stone, Howard A.

    2017-10-01

    Fluid mechanics is a discipline with rich phenomena, with motions occurring over an enormous range of length scales, and spanning a wide range of laminar and turbulent flows, instabilities, and applications in industry, nature, biology, and medicine. The subfield of complex fluids typically refers to those flows where the complexity is introduced, for example, by the presence of suspended particles, multiple phases, soft boundaries, and electrokinetic effects; several distinct multiphase flows of Newtonian fluids make up the examples in this article. Interfaces play a significant role and modify the flow with feedback that further changes the shapes of the interfaces. I will provide examples of our work highlighting (i) new features of classical instabilities triggered by changes in geometry, (ii) multiphase flows relevant to the design of liquid-infused substrates exhibiting effective slip while retaining the trapped liquid, and (iii) unexpected dynamics in flow at a T-junction. The interplay of experiments and mathematical models and/or simulations is critical to the new understanding developed.

  2. Synthetic biology: programming cells for biomedical applications.

    Science.gov (United States)

    Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

    2012-01-01

    The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.

  3. Profil Kompetensi Profesional Guru Mapel Biologi Pasca Sertifikasi di Karesidenan Surakarta

    Directory of Open Access Journals (Sweden)

    Sofyan Anif

    2015-07-01

    Full Text Available As stated in UU No. 14, 2005 and PP No. 74, 2008 that teachers as proffessional educator have to possess four competences, namely: pedagogic, proffessional, character, and social. However the condition in Indonesia is not like that. In general, they are in low category, specifically in pedagogic and proffessional. Those conditions happen in biology teachers and other teacher subjects. Then the aim of this study is to observe the profile of biology teachers especially their proffessional competence pasca sertification in Surakarta residance. The population of this study is all biology teachers (332 persons that have rechieved sertification through direct, portofolio, and PLPG program. Purposive random sampling is used to get 116 teachers. Data are collected by depth interview, documentation, and test, then the collected data are analysed by descriptive qualitative. The result shows that the profile of proffessional competence of biology teachers can be grouped into three: low, middle, and high. The teachers are low in: concept implementation, using tool of measurements, biology experiment planning, using the result of reflection, self reflection, understanding the principles and theories of savety work, doing action research, and understanding the steps of biology experiement correctly. The teachers are middle in: understanding the objective of the study, creative and innovative in implementing and developing science of biology nad correlated sciences, undesrtanding thinking process of biology, using symbolic language, undesrtanding standard competence, and understanding the scoupe of biology. They are high in: understanding the structure biology science and its correlation, selecting the material, cooking the material creatively, understanding the concepts, laws, and biology theories, undesrtanding the history of the natural science, specifically biology, understanding the basic competence of the subject or topic, updating their knowledge from

  4. Toward High School Biology: Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems

    Science.gov (United States)

    Herrmann-Abell, Cari F.; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better foundation, we used research-based design principles and collaborated in the development of a curricular intervention that applies chemistry ideas to living and nonliving contexts. Six eighth grade teachers and their students participated in a test of the unit during the Spring of 2013. Two of the teachers had used an earlier version of the unit the previous spring. The other four teachers were randomly assigned either to implement the unit or to continue teaching the same content using existing materials. Pre- and posttests were administered, and the data were analyzed using Rasch modeling and hierarchical linear modeling. The results showed that, when controlling for pretest score, gender, language, and ethnicity, students who used the curricular intervention performed better on the posttest than the students using existing materials. Additionally, students who participated in the intervention held fewer misconceptions. These results demonstrate the unit’s promise in improving students’ understanding of the targeted ideas. PMID:27909024

  5. Ways of incorporating photographic images in learning and assessing high school biology: A study of visual perception and visual cognition

    Science.gov (United States)

    Nixon, Brenda Chaumont

    This study evaluated the cognitive benefits and costs of incorporating biology-textbook and student-generated photographic images into the learning and assessment processes within a 10th grade biology classroom. The study implemented Wandersee's (2000) 20-Q Model of Image-Based Biology Test-Item Design (20-Q Model) to explore the use of photographic images to assess students' understanding of complex biological processes. A thorough review of the students' textbook using ScaleMaster R with PC Interface was also conducted. The photographs, diagrams, and other representations found in the textbook were measured to determine the percentage of each graphic depicted in the book and comparisons were made to the text. The theoretical framework that guided the research included Human Constructivist tenets espoused by Mintzes, Wandersee and Novak (2000). Physiological and cognitive factors of images and image-based learning as described by Robin (1992), Solso (1997) and Wandersee (2000) were examined. Qualitative case study design presented by Yin (1994), Denzin and Lincoln (1994) was applied and data were collected through interviews, observations, student activities, student and school artifacts and Scale Master IIRTM measurements. The results of the study indicate that although 24% of the high school biology textbook is devoted to photographic images which contribute significantly to textbook cost, the teacher and students paid little attention to photographic images other than as aesthetic elements for creating biological ambiance, wasting valuable opportunities for learning. The analysis of the photographs corroborated findings published by the Association American Association for the Advancement of Science that indicated "While most of the books are lavishly illustrated, these representations are rarely helpful, because they are too abstract, needlessly complicated, or inadequately explained" (Roseman, 2000, p. 2). The findings also indicate that applying the 20-Q

  6. Biological impact of music and software-based auditory training

    Science.gov (United States)

    Kraus, Nina

    2012-01-01

    Auditory-based communication skills are developed at a young age and are maintained throughout our lives. However, some individuals – both young and old – encounter difficulties in achieving or maintaining communication proficiency. Biological signals arising from hearing sounds relate to real-life communication skills such as listening to speech in noisy environments and reading, pointing to an intersection between hearing and cognition. Musical experience, amplification, and software-based training can improve these biological signals. These findings of biological plasticity, in a variety of subject populations, relate to attention and auditory memory, and represent an integrated auditory system influenced by both sensation and cognition. Learning outcomes The reader will (1) understand that the auditory system is malleable to experience and training, (2) learn the ingredients necessary for auditory learning to successfully be applied to communication, (3) learn that the auditory brainstem response to complex sounds (cABR) is a window into the integrated auditory system, and (4) see examples of how cABR can be used to track the outcome of experience and training. PMID:22789822

  7. Biological water-oxidizing complex: a nano-sized manganese-calcium oxide in a protein environment.

    Science.gov (United States)

    Najafpour, Mohammad Mahdi; Moghaddam, Atefeh Nemati; Yang, Young Nam; Aro, Eva-Mari; Carpentier, Robert; Eaton-Rye, Julian J; Lee, Choon-Hwan; Allakhverdiev, Suleyman I

    2012-10-01

    The resolution of Photosystem II (PS II) crystals has been improved using isolated PS II from the thermophilic cyanobacterium Thermosynechococcus vulcanus. The new 1.9 Å resolution data have provided detailed information on the structure of the water-oxidizing complex (Umena et al. Nature 473: 55-61, 2011). The atomic level structure of the manganese-calcium cluster is important for understanding the mechanism of water oxidation and to design an efficient catalyst for water oxidation in artificial photosynthetic systems. Here, we have briefly reviewed our knowledge of the structure and function of the cluster.

  8. Modulation of mutagen-induced biological effects by inhibitors of DNA repair

    International Nuclear Information System (INIS)

    Natarajan, A.T.; Mullenders, L.F.H.; Zwanenburg, T.S.B.

    1986-01-01

    When lesions are induced in the DNA by mutagenic agents, they are subjected to cellular repair. Unrepaired and misrepaired lesions lead to biological effects, such as cell killing, point mutations and chromosomal alterations (aberrations and sister chromatid exchanges - SCEs). It is very difficult to directly correlate any particular type of lesion to a specific biological effect. However, in specific cases, this has been done. For example, short wave UV induced biological effects (cell killing, chromosomal alterations) result predominantly from induced cyclobutane dimers and by photoreactivation experiments, one can demonstrate that with the removal of dimers all types biological effects are diminished. In cases where many types of lesions are considered responsible for the observed biological effects other strategies have been employed to identify the possible lesion. The frequencies of induced chromosomal alterations and point mutations increase with the dose of the mutagen employed and an inhibition of DNA repair following treatment with the mutagen. Prevention of the cells from dividing following mutagen treatment allows them to repair premutational damage, thus reducing the biological effects induced. By comprehensive studies involving quantification of primary DNA lesions, their repair and biological effects will enable us to understand to some extent the complex processes involved in the manifestation of specific biological effects that follow the treatment of cells with mutagenic carcinogens

  9. Understanding complexities of synaptic transmission in medically intractable seizures: A paradigm of epilepsy research

    Directory of Open Access Journals (Sweden)

    Jyotirmoy Banerjee

    2013-01-01

    Full Text Available Investigating the changes associated with the development of epileptic state in humans is complex and requires a multidisciplinary approach. Understanding the intricacies of medically intractable epilepsy still remains a challenge for neurosurgeons across the world. A significant number of patients who has undergone resective brain surgery for epilepsy still continue to have seizures. The reason behind this therapy resistance still eludes us. Thus to develop a cure for the difficult to treat epilepsy, we need to comprehensively study epileptogenesis. Although various animal models are developed but none of them replicate the pathological conditions in humans. So the ideal way to understand epileptogenecity is to examine the tissue resected for the treatment of intractable epilepsy. Advanced imaging and electrical localization procedures are utilized to establish the epileptogenic zone in epilepsy patients. Further molecular and cytological studies are required for the microscopic analysis of brain samples collected from the epileptogenic focus. As alterations in inhibitory as well as excitatory synaptic transmission are key features of epilepsy, understanding the regulation of neurotransmission in the resected surgery zone is of immense importance. Here we summarize various modalities of in vitro slice analysis from the resected brain specimen to understand the changes in GABAergic and glutamatergic synaptic transmission in epileptogenic zone. We also review evidence pertaining to the proposed role of nicotinic receptors in abnormal synaptic transmission which is one of the major causes of epileptiform activity. Elucidation of current concepts in regulation of synaptic transmission will help develop therapies for epilepsy cases that cannot me managed pharmacologically.

  10. Mathematical models in biology bringing mathematics to life

    CERN Document Server

    Ferraro, Maria; Guarracino, Mario

    2015-01-01

    This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy.  The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content...

  11. A stratified myeloid system, the challenge of understanding macrophage diversity.

    Science.gov (United States)

    Geissmann, F; Mass, E

    2015-12-01

    The present issue of 'Seminars in Immunology' addresses the topic of macrophage biology, 100 years after the death of Elie Metchnikoff (May 1845-July 1916). As foreseen by Metchnikoff, the roles of macrophages in the maintenance of homeostasis and immunity against pathogens have become a broad and active area of investigation. We now start to realize that the myeloid system includes a multiplicity of cell types with diverse developmental origins and functions. Therefore, the textbook picture of a plastic and multifunctional macrophage does not meet the requirements of our current knowledge anymore. Further development toward a quantitative and molecular understanding of myeloid cell biology in vivo and their roles in tissue homeostasis and remodeling will benefit from taking this complexity into account. A tentative model to help in this pursuit and account for myeloid cell and macrophage diversity is discussed below. Copyright © 2016. Published by Elsevier Ltd.

  12. Quantifying complexity in metabolic engineering using the LASER database

    Directory of Open Access Journals (Sweden)

    James D. Winkler

    2016-12-01

    Full Text Available We previously introduced the LASER database (Learning Assisted Strain EngineeRing, https://bitbucket.org/jdwinkler/laser_release (Winkler et al. 2015 to serve as a platform for understanding past and present metabolic engineering practices. Over the past year, LASER has been expanded by 50% to include over 600 engineered strains from 450 papers, including their growth conditions, genetic modifications, and other information in an easily searchable format. Here, we present the results of our efforts to use LASER as a means for defining the complexity of a metabolic engineering “design”. We evaluate two complexity metrics based on the concepts of construction difficulty and novelty. No correlation is observed between expected product yield and complexity, allowing minimization of complexity without a performance trade-off. We envision the use of such complexity metrics to filter and prioritize designs prior to implementation of metabolic engineering efforts, thereby potentially reducing the time, labor, and expenses of large-scale projects. Possible future developments based on an expanding LASER database are then discussed. Keywords: Metabolic engineering, Synthetic biology, Standardization, Design tools

  13. Complex systems dynamics in aging: new evidence, continuing questions.

    Science.gov (United States)

    Cohen, Alan A

    2016-02-01

    There have long been suggestions that aging is tightly linked to the complex dynamics of the physiological systems that maintain homeostasis, and in particular to dysregulation of regulatory networks of molecules. This review synthesizes recent work that is starting to provide evidence for the importance of such complex systems dynamics in aging. There is now clear evidence that physiological dysregulation--the gradual breakdown in the capacity of complex regulatory networks to maintain homeostasis--is an emergent property of these regulatory networks, and that it plays an important role in aging. It can be measured simply using small numbers of biomarkers. Additionally, there are indications of the importance during aging of emergent physiological processes, functional processes that cannot be easily understood through clear metabolic pathways, but can nonetheless be precisely quantified and studied. The overall role of such complex systems dynamics in aging remains an important open question, and to understand it future studies will need to distinguish and integrate related aspects of aging research, including multi-factorial theories of aging, systems biology, bioinformatics, network approaches, robustness, and loss of complexity.

  14. Data warehousing in molecular biology.

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    Schönbach, C; Kowalski-Saunders, P; Brusic, V

    2000-05-01

    In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.

  15. The "Performance of Rotavirus and Oral Polio Vaccines in Developing Countries" (PROVIDE) study: description of methods of an interventional study designed to explore complex biologic problems.

    Science.gov (United States)

    Kirkpatrick, Beth D; Colgate, E Ross; Mychaleckyj, Josyf C; Haque, Rashidul; Dickson, Dorothy M; Carmolli, Marya P; Nayak, Uma; Taniuchi, Mami; Naylor, Caitlin; Qadri, Firdausi; Ma, Jennie Z; Alam, Masud; Walsh, Mary Claire; Diehl, Sean A; Petri, William A

    2015-04-01

    Oral vaccines appear less effective in children in the developing world. Proposed biologic reasons include concurrent enteric infections, malnutrition, breast milk interference, and environmental enteropathy (EE). Rigorous study design and careful data management are essential to begin to understand this complex problem while assuring research subject safety. Herein, we describe the methodology and lessons learned in the PROVIDE study (Dhaka, Bangladesh). A randomized clinical trial platform evaluated the efficacy of delayed-dose oral rotavirus vaccine as well as the benefit of an injectable polio vaccine replacing one dose of oral polio vaccine. This rigorous infrastructure supported the additional examination of hypotheses of vaccine underperformance. Primary and secondary efficacy and immunogenicity measures for rotavirus and polio vaccines were measured, as well as the impact of EE and additional exploratory variables. Methods for the enrollment and 2-year follow-up of a 700 child birth cohort are described, including core laboratory, safety, regulatory, and data management practices. Intense efforts to standardize clinical, laboratory, and data management procedures in a developing world setting provide clinical trials rigor to all outcomes. Although this study infrastructure requires extensive time and effort, it allows optimized safety and confidence in the validity of data gathered in complex, developing country settings. © The American Society of Tropical Medicine and Hygiene.

  16. 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.

  17. Metabolomics in Radiation-Induced Biological Dosimetry: A Mini-Review and a Polyamine Study

    Directory of Open Access Journals (Sweden)

    Changhyun Roh

    2018-05-01

    Full Text Available In this study, we elucidate that polyamine metabolite is a powerful biomarker to study post-radiation changes. Metabolomics in radiation biodosimetry, the application of a metabolomics analysis to the field of radiobiology, promises to increase the understanding of biological responses by ionizing radiation (IR. Radiation exposure triggers a complex network of molecular and cellular responses that impacts metabolic processes and alters the levels of metabolites. Such metabolites have potential as biomarkers for radiation dosimetry. Among metabolites, polyamine is one of many potential biomarkers to estimate radiation response. In addition, this review provides an opportunity for the understanding of a radiation metabolomics in biodosimetry and a polyamine case study.

  18. Moving college students to a better understanding of substrate specificity of enzymes through utilizing multimedia pre-training and an interactive enzyme model

    Science.gov (United States)

    Saleh, Mounir R.

    Scientists' progress in understanding enzyme specificity uncovered a complex natural phenomenon. However, not all of the currently available biology textbooks seem to be up to date on this progress. Students' understanding of how enzymes work is a core requirement in biochemistry and biology tertiary education. Nevertheless, current pre-college science education does not provide students with enough biochemical background to enable them to understand complex material such as this. To bridge this gap, a multimedia pre-training presentation was prepared to fuel the learner's prior knowledge with discrete facts necessary to understand the presented concept. This treatment is also known to manage intrinsic cognitive load during the learning process. An interactive instructional enzyme model was also built to motivate students to learn about substrate specificity of enzymes. Upon testing the effect of this combined treatment on 111 college students, desirable learning outcomes were found in terms of cognitive load, motivation, and achievement. The multimedia pre-training group reported significantly less intrinsic cognitive load, higher motivation, and demonstrated higher transfer performance than the control and post-training groups. In this study, a statistical mediation model is also proposed to explain how cognitive load and motivation work in concert to foster learning from multimedia pre-training. This type of research goes beyond simple forms of "what works" to a deeper understanding of "how it works", thus enabling informed decisions for multimedia instructional design. Multimedia learning plays multiple roles in science education. Therefore, science learners would be some of the first to benefit from improving multimedia instructional design. Accordingly, complex scientific phenomena can be introduced to college students in a motivating, informative, and cognitively efficient learning environment.

  19. On the Limitations of Biological Knowledge

    Science.gov (United States)

    Dougherty, Edward R; Shmulevich, Ilya

    2012-01-01

    Scientific knowledge is grounded in a particular epistemology and, owing to the requirements of that epistemology, possesses limitations. Some limitations are intrinsic, in the sense that they depend inherently on the nature of scientific knowledge; others are contingent, depending on the present state of knowledge, including technology. Understanding limitations facilitates scientific research because one can then recognize when one is confronted by a limitation, as opposed to simply being unable to solve a problem within the existing bounds of possibility. In the hope that the role of limiting factors can be brought more clearly into focus and discussed, we consider several sources of limitation as they apply to biological knowledge: mathematical complexity, experimental constraints, validation, knowledge discovery, and human intellectual capacity. PMID:23633917

  20. Positioning genomics in biology education: content mapping of undergraduate biology textbooks.

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    Wernick, Naomi L B; Ndung'u, Eric; Haughton, Dominique; Ledley, Fred D

    2014-12-01

    Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.