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Sample records for biologically relevant metal-based

  1. Making Plant Biology Curricula Relevant.

    ERIC Educational Resources Information Center

    Hershey, David R.

    1992-01-01

    Reviews rationale, purposes, challenges, and relevance of hands-on, plant biology curricula that have been developed in response to the limited use of plants in biology education. Discusses methods to maintain both instructional rigor and student interest in the following topics: cut flowers, container-growing media, fertilizers, hydroponics,…

  2. Biology relevant to space radiation

    SciTech Connect

    Fry, R.J.M.

    1996-08-01

    The biological effects of the radiations to which mankind on earth are exposed are becoming known with an increasing degree of detail. This knowledge is the basis of the estimates of risk that, in turn, fosters a comprehensive and evolving radiation protection system. The substantial body of information has been, and is being, applied to questions about the biological effects of radiation is space and the associated risk estimates. The purpose of this paper is not to recount all the biological effect of radiation but to concentrate on those that may occur as a result from exposure to the radiations encountered in space. In general, the biological effects of radiation in space are the same as those on earth. However, the evidence that the effects on certain tissues by the heaviest-charged particles can be interpreted on the basis of our knowledge about other high-LET radiation is equivocal. This specific question will be discussed in greater detail later. It is important to point out the that there are only limited data about the effects on humans of two components of the radiations in space, namely protons and heavy ions. Thus predictions of effects on space crews are based on experimental systems exposed on earth at rates and fluences that are higher than those in space and one the effects of gamma or x rays with estimates of the equivalent doses using quality factors.

  3. Biology relevant to space radiation

    SciTech Connect

    Fry, R.J.M.

    1997-04-30

    There are only very limited data on the health effects to humans from the two major components of the radiations in space, namely protons and heavy ions. As a result, predictions of the accompanying effects must be based either on (1) data generated through studies of experimental systems exposed on earth at rates and fluences higher than those in space, or (2) extrapolations from studies of gamma and x rays. Better information is needed about the doses, dose rates, and the energy and LET spectra of the radiations at the organ level that are anticipated to be encountered during extended space missions. In particular, there is a need for better estimates of the relationship between radiation quality and biological effects. In the case of deterministic effects, it is the threshold that is important. The possibility of the occurrence of a large solar particle event (SPE) requires that such effects be considered during extended space missions. Analyses suggest, however, that it is feasible to provide sufficient shielding so as to reduce such effects to acceptable levels, particularly if the dose rates can be limited. If these analyses prove correct, the primary biological risks will be the stochastic effects (latent cancer induction). The contribution of one large SPE to the risk of stochastic effects while undesirable will not be large in comparison to the potential total dose on a mission of long duration.

  4. Mammalian lipoxygenases and their biological relevance

    PubMed Central

    Kuhn, Hartmut; Banthiya, Swathi; van Leyen, Klaus

    2015-01-01

    Lipoxygenases (LOXs) form a heterogeneous class of lipid peroxidizing enzymes, which have been implicated in cell proliferation and differentiation but also in the pathogenesis of various diseases with major public health relevance. As other fatty acid dioxygenases LOX oxidize polyunsaturated fatty acids to their corresponding hydroperoxy derivatives, which are further transformed to bioactive lipid mediators (eicosanoids and related substances). On the other hand, lipoxygenases are key players in regulation of the cellular redox homeostasis, which is an important element in gene expression regulation. Although the first mammalian lipoxygenases were discovered 40 years ago and although the enzymes have been well characterized with respect to their structural and functional properties the biological roles of the different lipoxygenase isoforms are not completely understood. This review is aimed at summarizing the current knowledge on the physiological roles of different mammalian LOX-isoforms and their patho-physiological function in inflammatory, metabolic, hyperproliferative, neurodegenerative and infectious disorders. PMID:25316652

  5. Biologically Relevant Glycopeptides: Synthesis and Applications

    NASA Astrophysics Data System (ADS)

    Bennett, Clay S.; Payne, Richard J.; Koeller, Kathryn M.; Wong, Chi-Huey

    Over the past two decades interest in glycopeptides and glycoproteins has intensified, due in part to the development of new and efficient methods for the synthesis of these compounds. This includes a number of chemical and enzymatic techniques for incorporating glycosylation onto the peptide backbone as well as the introduction of powerful peptide ligation methods for the construction of glycoproteins. This review discusses these methods with a special emphasis on biologically relevant glycopeptides and glycoproteins. This includes the development of a number of antigens which hold promise as potential vaccines for HIV, cancer, or a host of other clinically important diseases. In addition the development of new antibiotics aimed at overcoming the problem of resistance will be discussed. Finally, chemical and enzymatic methods for the construction of glycopeptide mimetics will be described.

  6. BioMe: biologically relevant metals.

    PubMed

    Tus, Alan; Rakipovic, Alen; Peretin, Goran; Tomic, Sanja; Sikic, Mile

    2012-07-01

    In this article, we introduce BioMe (biologically relevant metals), a web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal coordination sphere, distribution of coordination numbers, percentage of metal ions coordinated by the combination of selected ligands, distribution of monodentate and bidentate metal-carboxyl, bindings for ASP and GLU, percentage of particular binuclear metal centers, distribution of coordination geometry, descriptive statistics for a metal ion-donor distance and percentage of the selected metal ions coordinated by each of the selected ligands. Statistics is presented in numerical and graphical forms. The underlying database contains information about all contacts within the range of 3 Å from a metal ion found in the asymmetric crystal unit. The stored information for each metal ion includes Protein Data Bank code, structure determination method, types of metal-binding chains [protein, ribonucleic acid (RNA), deoxyribonucleic acid (DNA), water and other] and names of the bounded ligands (amino acid residue, RNA nucleotide, DNA nucleotide, water and other) and the coordination number, the coordination geometry and, if applicable, another metal(s). BioMe is on a regular weekly update schedule. It is accessible at http://metals.zesoi.fer.hr.

  7. The Biological Relevance of Artificial Life: Lessons from Artificial Intelligence

    NASA Technical Reports Server (NTRS)

    Colombano, Silvano

    2000-01-01

    There is no fundamental reason why A-life couldn't simply be a branch of computer science that deals with algorithms that are inspired by, or emulate biological phenomena. However, if these are the limits we place on this field, we miss the opportunity to help advance Theoretical Biology and to contribute to a deeper understanding of the nature of life. The history of Artificial Intelligence provides a good example, in that early interest in the nature of cognition quickly was lost to the process of building tools, such as "expert systems" that, were certainly useful, but provided little insight in the nature of cognition. Based on this lesson, I will discuss criteria for increasing the biological relevance of A-life and the probability that this field may provide a theoretical foundation for Biology.

  8. Predicting hydration propensities of biologically relevant α-ketoamides.

    PubMed

    Wedler, Henry B; Palazzo, Teresa A; Pemberton, Ryan P; Hamann, Christian S; Kurth, Mark J; Tantillo, Dean J

    2015-10-01

    Quantum chemical calculations coupled to experiments were used to predict covalent hydration propensities of biologically relevant α-ketoamides. Experimentally determined hydration equilibrium constants for related ketones and aldehydes were compared to computationally determined values to develop a method for predicting hydration equilibrium constants. This method was used on six newly synthesized α-ketoamides to experimentally verify computational predictions. A correlation between calculation and experiment was observed and applied to models of several pertinent APIs. Our results indicate that the keto form is favored for practically all α-ketoamides in biological environs. PMID:26306983

  9. Behavior of nanoceria in biologically-relevant environments

    SciTech Connect

    Kumar, Amit; Das, Soumen; Munusamy, Prabhakaran; Self, William; Baer, Donald R.; Sayle, Dean C.; Seal, Sudipta

    2014-09-08

    Cerium oxide nanoparticles (CNPs) have gained a considerable attention in biological research due to their anti-oxidant like behaviour and regenerative nature. The current literature on CNPs reports many successful attempts on harnessing the beneficial therapeutic properties in biology. However studies have also shown toxicity effect with some types of CNPs. This review discusses issues associated with the behaviours of CNPs in biological systems and identifies key knowledge gaps. We explore how salient physicochemical properties (size, surface chemistry, surface stabilizers) contribute to the potential positive and negative aspects of nanoceria in biological systems. Based on variations of results reported in the literature, important issues need to be addressed. Are we really studying the same particles with slight variations in size and physicochemical properties or do the particles being examined have fundamentally different behaviours? Are the variations observed in the result of differences in the initial properties of the particles or the results of downstream effects that emerge as the particles are prepared for specific studies and they interact with biological or other environmental moieties? How should particles be appropriately prepared for relevant environmental/toxicology/safety studies? It is useful to recognize that nanoparticles encompass some of the same complexities and variability associated with biological components

  10. Hands-on-Entropy, Energy Balance with Biological Relevance

    NASA Astrophysics Data System (ADS)

    Reeves, Mark

    2015-03-01

    Entropy changes underlie the physics that dominates biological interactions. Indeed, introductory biology courses often begin with an exploration of the qualities of water that are important to living systems. However, one idea that is not explicitly addressed in most introductory physics or biology textbooks is important contribution of the entropy in driving fundamental biological processes towards equilibrium. From diffusion to cell-membrane formation, to electrostatic binding in protein folding, to the functioning of nerve cells, entropic effects often act to counterbalance deterministic forces such as electrostatic attraction and in so doing, allow for effective molecular signaling. A small group of biology, biophysics and computer science faculty have worked together for the past five years to develop curricular modules (based on SCALEUP pedagogy). This has enabled students to create models of stochastic and deterministic processes. Our students are first-year engineering and science students in the calculus-based physics course and they are not expected to know biology beyond the high-school level. In our class, they learn to reduce complex biological processes and structures in order model them mathematically to account for both deterministic and probabilistic processes. The students test these models in simulations and in laboratory experiments that are biologically relevant such as diffusion, ionic transport, and ligand-receptor binding. Moreover, the students confront random forces and traditional forces in problems, simulations, and in laboratory exploration throughout the year-long course as they move from traditional kinematics through thermodynamics to electrostatic interactions. This talk will present a number of these exercises, with particular focus on the hands-on experiments done by the students, and will give examples of the tangible material that our students work with throughout the two-semester sequence of their course on introductory

  11. The allosteric modulation of lipases and its possible biological relevance

    PubMed Central

    Köhler, Jens; Wünsch, Bernhard

    2007-01-01

    Background During the development of an enantioselective synthesis using the lipase from Mucor miehei an unusual reaction course was observed, which was analyzed precisely. For the first time an allosteric modulation of a lipase changing its selectivity was shown. Theory Considering the biological relevance of the discovered regulation mechanism we developed a theory that describes the regulation of energy homeostasis and fat metabolism. Conclusion This theory represents a new approach to explain the cause of the metabolic syndrome and provides an innovative basis for further research activity. PMID:17825093

  12. Biology and Clinical Relevance of Acute Myeloid Leukemia Stem Cells.

    PubMed

    Reinisch, Andreas; Chan, Steven M; Thomas, Daniel; Majeti, Ravindra

    2015-07-01

    Evidence for the cancer stem cell model was first demonstrated in xenotransplanted blood and bone marrow samples from patients with acute myeloid leukemia (AML) almost two decades ago, supporting the concept that a rare clonal and mutated leukemic stem cell (LSC) population is sufficient to drive leukemic growth. The inability to eliminate LSCs with conventional therapies is thought to be the primary cause of disease relapse in AML patients, and as such, novel therapies with the ability to target this population are required to improve patient outcomes. An important step towards this goal is the identification of common immunophenotypic surface markers and biological properties that distinguish LSCs from normal hematopoietic stem and progenitor cells (HSPCs) across AML patients. This work has resulted in the development of a large number of potential LSC-selective therapies that target cell surface molecules, intracellular signaling pathways, and the bone marrow microenvironment. Here, we will review the basic biology, immunophenotypic detection, and clinical relevance of LSCs, as well as emerging biological and small-molecule strategies that either directly target LSCs or indirectly target these cells through modulation of their microenvironment.

  13. Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions.

    PubMed

    Semenov, Sergey N; Kraft, Lewis J; Ainla, Alar; Zhao, Mengxia; Baghbanzadeh, Mostafa; Campbell, Victoria E; Kang, Kyungtae; Fox, Jerome M; Whitesides, George M

    2016-09-28

    Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving

  14. Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions

    NASA Astrophysics Data System (ADS)

    Semenov, Sergey N.; Kraft, Lewis J.; Ainla, Alar; Zhao, Mengxia; Baghbanzadeh, Mostafa; Campbell, Victoria E.; Kang, Kyungtae; Fox, Jerome M.; Whitesides, George M.

    2016-09-01

    Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving

  15. Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions.

    PubMed

    Semenov, Sergey N; Kraft, Lewis J; Ainla, Alar; Zhao, Mengxia; Baghbanzadeh, Mostafa; Campbell, Victoria E; Kang, Kyungtae; Fox, Jerome M; Whitesides, George M

    2016-01-01

    Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving

  16. Novel bio-essential metal based complexes linked by heterocyclic ligand: Synthesis, structural elucidation, biological investigation and docking analysis.

    PubMed

    Arun, T; Subramanian, R; Raman, N

    2016-01-01

    New series of bio-essential metal based complexes linked by Schiff base ligand (L) and 2,2'-bipyridine (bpy) have been synthesized and characterized by diverse spectral techniques such as elemental analysis, magnetic susceptibility, molar conductivity measurements, FT-IR, UV-Vis., (1)H NMR, (13)C NMR, EPR and Mass. The spectral data suggest that the metal complexes espouse octahedral geometry around the metal ions. Interactions of the complexes with CT DNA have been explored by electronic absorption, ethidium bromide displacement assay, viscosity measurements, cyclic voltammetry and differential pulse voltammetry in order to evaluate the possible DNA-binding mode and to calculate the corresponding DNA-binding constants. The DNA interaction studies propose that the intercalative mode of interaction and the complexes exhibit oxidative cleavage of pUC19 DNA in the presence of hydrogen peroxide as activator. The synthesized Schiff base ligand and its metal complexes have been screened for anti-microbial activity by micro dilution method against two Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), two Gram-negative bacteria (Escherichia coli and Salmonella typhi) and three fungi strains (Fusarium solani, Aspergillus niger and Candida albicans) revealing that the complexes are good anti-pathogenic agents than the ligand. Moreover, molecular docking analysis has been performed to confirm the nature of binding of the complexes with DNA.

  17. Identifying Biologically Relevant Cues in the Hydrologic Regime

    NASA Astrophysics Data System (ADS)

    Lovellford, R. M.; Flitcroft, R.; Santelmann, M. V.; Grant, G. E.; Safeeq, M.; Lewis, S.

    2012-12-01

    Seasonal variation in hydrologic discharge and temperature defines the availability, connectivity, and quality of lentic habitats. Native aquatic species are adapted to local hydrologic regimes , eg. magnitudes and rates of change . In recent decades, biologically relevant hydrologic conditions have been identified that are necessary to maintain habitat conditions for aquatic obligate species. Another element of hydrologic regimes important to aquatic species are the cues that inform individuals of seasonal changes that precipitate important physiological or behavioral alterations. There is a need for hydrologists, biologists, and ecologists, to define biologically significant cues within the hydrologic regime. Coho salmon (Onchorhynchus kisutch), an anadromous species of Pacific salmon, offers an example of sensitivity to environmental cues. Examinations of the run-timing of mature adult coho salmon on the North Umpqua River, OR, indicate that migration timing coincides with decreasing fall water temperatures prior to increasing winter discharge. For this species, adults leave the ocean ready to spawn. Adults need to spawn in small headwater streams prior to the onset of intense storm conditions that prohibit effective deposition or fertilization of eggs in redds (salmon nests).Therefore, the timing of spawning must be carefully executed. Understanding the cues that trigger specific behaviors gives insight to the processes that provide ecosystem stability and flexibility over time. Improved understanding of these cues may help us protect freshwater ecosystems and improve management for endangered species.

  18. Characterization of Nanoparticle Aggregation in Biologically Relevant Fluids

    NASA Astrophysics Data System (ADS)

    McEnnis, Kathleen; Lahann, Joerg

    Nanoparticles (NPs) are often studied as drug delivery vehicles, but little is known about their behavior in blood once injected into animal models. If the NPs aggregate in blood, they will be shunted to the liver or spleen instead of reaching the intended target. The use of animals for these experiments is costly and raises ethical questions. Typically dynamic light scattering (DLS) is used to analyze aggregation behavior, but DLS cannot be used because the components of blood also scatter light. As an alternative, a method of analyzing NPs in biologically relevant fluids such as blood plasma has been developed using nanoparticle tracking analysis (NTA) with fluorescent filters. In this work, NTA was used to analyze the aggregation behavior of fluorescent polystyrene NPs with different surface modifications in blood plasma. It was expected that different surface chemistries on the particles will change the aggregation behavior. The effect of the surface modifications was investigated by quantifying the percentage of NPs in aggregates after addition to blood plasma. The use of this characterization method will allow for better understanding of particle behavior in the body, and potential problems, specifically aggregation, can be addressed before investing in in vivo studies.

  19. Biological Relevance and Therapeutic Potential of the Hypusine Modification System*

    PubMed Central

    Pällmann, Nora; Braig, Melanie; Sievert, Henning; Preukschas, Michael; Hermans-Borgmeyer, Irm; Schweizer, Michaela; Nagel, Claus Henning; Neumann, Melanie; Wild, Peter; Haralambieva, Eugenia; Hagel, Christian; Bokemeyer, Carsten; Hauber, Joachim; Balabanov, Stefan

    2015-01-01

    Hypusine modification of the eukaryotic initiation factor 5A (eIF-5A) is emerging as a crucial regulator in cancer, infections, and inflammation. Although its contribution in translational regulation of proline repeat-rich proteins has been sufficiently demonstrated, its biological role in higher eukaryotes remains poorly understood. To establish the hypusine modification system as a novel platform for therapeutic strategies, we aimed to investigate its functional relevance in mammals by generating and using a range of new knock-out mouse models for the hypusine-modifying enzymes deoxyhypusine synthase and deoxyhypusine hydroxylase as well as for the cancer-related isoform eIF-5A2. We discovered that homozygous depletion of deoxyhypusine synthase and/or deoxyhypusine hydroxylase causes lethality in adult mice with different penetrance compared with haploinsufficiency. Network-based bioinformatic analysis of proline repeat-rich proteins, which are putative eIF-5A targets, revealed that these proteins are organized in highly connected protein-protein interaction networks. Hypusine-dependent translational control of essential proteins (hubs) and protein complexes inside these networks might explain the lethal phenotype observed after deletion of hypusine-modifying enzymes. Remarkably, our results also demonstrate that the cancer-associated isoform eIF-5A2 is dispensable for normal development and viability. Together, our results provide the first genetic evidence that the hypusine modification in eIF-5A is crucial for homeostasis in mammals. Moreover, these findings highlight functional diversity of the hypusine system compared with lower eukaryotes and indicate eIF-5A2 as a valuable and safe target for therapeutic intervention in cancer. PMID:26037925

  20. Biomedically relevant circuit-design strategies in mammalian synthetic biology.

    PubMed

    Bacchus, William; Aubel, Dominique; Fussenegger, Martin

    2013-01-01

    The development and progress in synthetic biology has been remarkable. Although still in its infancy, synthetic biology has achieved much during the past decade. Improvements in genetic circuit design have increased the potential for clinical applicability of synthetic biology research. What began as simple transcriptional gene switches has rapidly developed into a variety of complex regulatory circuits based on the transcriptional, translational and post-translational regulation. Instead of compounds with potential pharmacologic side effects, the inducer molecules now used are metabolites of the human body and even members of native cell signaling pathways. In this review, we address recent progress in mammalian synthetic biology circuit design and focus on how novel designs push synthetic biology toward clinical implementation. Groundbreaking research on the implementation of optogenetics and intercellular communications is addressed, as particularly optogenetics provides unprecedented opportunities for clinical application. Along with an increase in synthetic network complexity, multicellular systems are now being used to provide a platform for next-generation circuit design.

  1. Biomedically relevant circuit-design strategies in mammalian synthetic biology

    PubMed Central

    Bacchus, William; Aubel, Dominique; Fussenegger, Martin

    2013-01-01

    The development and progress in synthetic biology has been remarkable. Although still in its infancy, synthetic biology has achieved much during the past decade. Improvements in genetic circuit design have increased the potential for clinical applicability of synthetic biology research. What began as simple transcriptional gene switches has rapidly developed into a variety of complex regulatory circuits based on the transcriptional, translational and post-translational regulation. Instead of compounds with potential pharmacologic side effects, the inducer molecules now used are metabolites of the human body and even members of native cell signaling pathways. In this review, we address recent progress in mammalian synthetic biology circuit design and focus on how novel designs push synthetic biology toward clinical implementation. Groundbreaking research on the implementation of optogenetics and intercellular communications is addressed, as particularly optogenetics provides unprecedented opportunities for clinical application. Along with an increase in synthetic network complexity, multicellular systems are now being used to provide a platform for next-generation circuit design. PMID:24061539

  2. Biologically relevant neural network architectures for support vector machines.

    PubMed

    Jändel, Magnus

    2014-01-01

    Neural network architectures that implement support vector machines (SVM) are investigated for the purpose of modeling perceptual one-shot learning in biological organisms. A family of SVM algorithms including variants of maximum margin, 1-norm, 2-norm and ν-SVM is considered. SVM training rules adapted for neural computation are derived. It is found that competitive queuing memory (CQM) is ideal for storing and retrieving support vectors. Several different CQM-based neural architectures are examined for each SVM algorithm. Although most of the sixty-four scanned architectures are unconvincing for biological modeling four feasible candidates are found. The seemingly complex learning rule of a full ν-SVM implementation finds a particularly simple and natural implementation in bisymmetric architectures. Since CQM-like neural structures are thought to encode skilled action sequences and bisymmetry is ubiquitous in motor systems it is speculated that trainable pattern recognition in low-level perception has evolved as an internalized motor programme.

  3. Streptococcus pyogenes biofilms—formation, biology, and clinical relevance

    PubMed Central

    Fiedler, Tomas; Köller, Thomas; Kreikemeyer, Bernd

    2015-01-01

    Streptococcus pyogenes (group A streptococci, GAS) is an exclusive human bacterial pathogen. The virulence potential of this species is tremendous. Interactions with humans range from asymptomatic carriage over mild and superficial infections of skin and mucosal membranes up to systemic purulent toxic-invasive disease manifestations. Particularly the latter are a severe threat for predisposed patients and lead to significant death tolls worldwide. This places GAS among the most important Gram-positive bacterial pathogens. Many recent reviews have highlighted the GAS repertoire of virulence factors, regulators and regulatory circuits/networks that enable GAS to colonize the host and to deal with all levels of the host immune defense. This covers in vitro and in vivo studies, including animal infection studies based on mice and more relevant, macaque monkeys. It is now appreciated that GAS, like many other bacterial species, do not necessarily exclusively live in a planktonic lifestyle. GAS is capable of microcolony and biofilm formation on host cells and tissues. We are now beginning to understand that this feature significantly contributes to GAS pathogenesis. In this review we will discuss the current knowledge on GAS biofilm formation, the biofilm-phenotype associated virulence factors, regulatory aspects of biofilm formation, the clinical relevance, and finally contemporary treatment regimens and future treatment options. PMID:25717441

  4. Relevance of ammonium oxidation within biological soil crust communities

    USGS Publications Warehouse

    Johnson, S.L.; Budinoff, C.R.; Belnap, J.; Garcia-Pichel, F.

    2005-01-01

    Thin, vertically structured topsoil communities that become ecologically important in arid regions (biological soil crusts or BSCs) are responsible for much of the nitrogen inputs into pristine arid lands. We studied N2 fixation and ammonium oxidation (AO) at subcentimetre resolution within BSCs from the Colorado Plateau. Pools of dissolved porewater nitrate/ nitrite, ammonium and organic nitrogen in wetted BSCs were high in comparison with those typical of aridosoils. They remained stable during incubations, indicating that input and output processes were of similar magnitude. Areal N2 fixation rates (6.5-48 ??mol C2H2 m-2 h -1) were high, the vertical distribution of N2 fixation peaking close to the surface if populations of heterocystous cyanobacteria were present, but in the subsurface if they were absent. Areal AO rates (19-46 ??mol N m-2 h-1) were commensurate with N2 fixation inputs. When considering oxygen availability, AO activity invariably peaked 2-3 mm deep and was limited by oxygen (not ammonium) supply. Most probable number (MPN)-enumerated ammonia-oxidizing bacteria (6.7-7.9 ?? 103 cells g-1 on average) clearly peaked at 2-3 mm depth. Thus, AO (hence nitrification) is a spatially restricted but important process in the nitrogen cycling of BSC, turning much of the biologically fixed nitrogen into oxidized forms, the fate of which remains to be determined.

  5. Student perception of relevance of biology content to everyday life: A study in higher education biology courses

    NASA Astrophysics Data System (ADS)

    Himschoot, Agnes Rose

    The purpose of this mixed method case study was to examine the effects of methods of instruction on students' perception of relevance in higher education non-biology majors' courses. Nearly ninety percent of all students in a liberal arts college are required to take a general biology course. It is proposed that for many of those students, this is the last science course they will take for life. General biology courses are suspected of discouraging student interest in biology with large enrollment, didactic instruction, covering a huge amount of content in one semester, and are charged with promoting student disengagement with biology by the end of the course. Previous research has been aimed at increasing student motivation and interest in biology as measured by surveys and test results. Various methods of instruction have been tested and show evidence of improved learning gains. This study focused on students' perception of relevance of biology content to everyday life and the methods of instruction that increase it. A quantitative survey was administered to assess perception of relevance pre and post instruction over three topics typically taught in a general biology course. A second quantitative survey of student experiences during instruction was administered to identify methods of instruction used in the course lecture and lab. While perception of relevance dropped in the study, qualitative focus groups provided insight into the surprising results by identifying topics that are more relevant than the ones chosen for the study, conveying the affects of the instructor's personal and instructional skills on student engagement, explanation of how active engagement during instruction promotes understanding of relevance, the roll of laboratory in promoting students' understanding of relevance as well as identifying external factors that affect student engagement. The study also investigated the extent to which gender affected changes in students' perception of

  6. Student Perception of Relevance of Biology Content to Everyday Life: A Study in Higher Education Biology Courses

    ERIC Educational Resources Information Center

    Himschoot, Agnes Rose

    2012-01-01

    The purpose of this mixed method case study was to examine the effects of methods of instruction on students' perception of relevance in higher education non-biology majors' courses. Nearly ninety percent of all students in a liberal arts college are required to take a general biology course. It is proposed that for many of those students, this is…

  7. Extracellular Vesicles: Composition, Biological Relevance, and Methods of Study

    PubMed Central

    Zaborowski, MikoŁaj P.; Balaj, Leonora; Breakefield, Xandra O.; Lai, Charles P.

    2015-01-01

    The release of extracellular vesicles (EVs), including exosomes and microvesicles, is a phenomenon shared by many cell types as a means of communicating with other cells and also potentially removing cell contents. The cargo of EVs includes the proteins, lipids, nucleic acids, and membrane receptors of the cells from which they originate. EVs released into the extracellular space can enter body fluids and potentially reach distant tissues. Once taken up by neighboring and/or distal cells, EVs can transfer functional cargo that may alter the status of recipient cells, thereby contributing to both physiological and pathological processes. In this article, we will focus on EV composition, mechanisms of uptake, and their biological effects on recipient cells. We will also discuss established and recently developed methods used to study EVs, including isolation, quantification, labeling and imaging protocols, as well as RNA analysis. PMID:26955082

  8. Terahertz vibrational properties of water nanoclusters relevant to biology.

    PubMed

    Johnson, Keith

    2012-01-01

    Water nanoclusters are shown from first-principles calculations to possess unique terahertz-frequency vibrational modes in the 1-6 THz range, corresponding to O-O-O "bending," "squashing," and "twisting" "surface" distortions of the clusters. The cluster molecular-orbital LUMOs are huge Rydberg-like "S," "P," "D," and "F" orbitals that accept an extra electron via optical excitation, ionization, or electron donation from interacting biomolecules. Dynamic Jahn-Teller coupling of these "hydrated-electron" orbitals to the THz vibrations promotes such water clusters as vibronically active "structured water" essential to biomolecular function such as protein folding. In biological microtubules, confined water-cluster THz vibrations may induce their "quantum coherence" communicated by Jahn-Teller phonons via coupling of the THz electromagnetic field to the water clusters' large electric dipole moments. PMID:23277672

  9. An automated PLS search for biologically relevant QSAR descriptors.

    PubMed

    Olah, Marius; Bologa, Cristian; Oprea, Tudor I

    2004-01-01

    An automated PLS engine, WB-PLS, was applied to 1632 QSAR series with at least 25 compounds per series extracted from WOMBAT (WOrld of Molecular BioAcTivity). WB-PLS extracts a single Y variable per series, as well as pre-computed X variables from a table. The table contained 2D descriptors, the drug-like MDL 320 keys as implemented in the Mesa A&C Fingerprint module, and in-house generated topological-pharmacophore SMARTS counts and fingerprints. Each descriptor type was treated as a block, with or without scaling. Cross-validation, variable importance on projections (VIP) above 0.8 and q2 > or = 0.3 were applied for model significance. Among cross-validation methods, leave-one-in-seven-out (CV7) is a better measure of model significance, compared to leave-one-out (measuring redundancy) and leave-half-out (too restrictive). SMARTS counts overlap with 2D descriptors (having a more quantitative nature), whereas MDL keys overlap with in-house fingerprints (both are more qualitative). The SMARTS counts is the most effective descriptor system, when compared to the other three. At the individual level, size-related descriptors and topological indices (in the 2D property space), and branched SMARTS, aromatic and ring atom types and halogens are found to be most relevant according to the VIP criterion.

  10. MRI probes for sensing biologically relevant metal ions.

    PubMed

    Bonnet, Célia S; Tóth, Eva

    2010-03-01

    Given the important role of metal ions in fundamental biological processes, the visualization of their concentration in living animals by repeatable, noninvasive imaging techniques, such as MRI, would be highly desirable. A large number of metal-responsive MRI contrast agents, the majority based on Gd(3+) complexes, have been reported in recent years. The contrast-enhancing properties (relaxivity) of a Gd(3+) complex can be most conveniently modulated by interaction with the sensed metal cation via changes in the number of water molecules bound directly to Gd(3+) or changes in the size of the complex, which represent the two major strategies to develop metal sensitive MRI probes. Here, we survey paramagnetic lanthanide complexes involving Gd(3+) agents and paramagnetic chemical exchange saturation transfer probes designed to detect the most important endogenous metal ions: calcium, zinc, iron and copper. Future work will likely focus on extending applications of these agents to living animals, as well as on exploring new ways of creating molecular MRI probes in order to meet requirements such as higher specificity or lower detection limits.

  11. IDENTIFICATION OF BIOLOGICALLY RELEVANT GENES USING A DATABASE OF RAT LIVER AND KIDNEY BASELINE GENE EXPRESSION

    EPA Science Inventory

    Microarray data from independent labs and studies can be compared to potentially identify toxicologically and biologically relevant genes. The Baseline Animal Database working group of HESI was formed to assess baseline gene expression from microarray data derived from control or...

  12. FireDB: a compendium of biological and pharmacologically relevant ligands.

    PubMed

    Maietta, Paolo; Lopez, Gonzalo; Carro, Angel; Pingilley, Benjamin J; Leon, Leticia G; Valencia, Alfonso; Tress, Michael L

    2014-01-01

    FireDB (http://firedb.bioinfo.cnio.es) is a curated inventory of catalytic and biologically relevant small ligand-binding residues culled from the protein structures in the Protein Data Bank. Here we present the important new additions since the publication of FireDB in 2007. The database now contains an extensive list of manually curated biologically relevant compounds. Biologically relevant compounds are informative because of their role in protein function, but they are only a small fraction of the entire ligand set. For the remaining ligands, the FireDB provides cross-references to the annotations from publicly available biological, chemical and pharmacological compound databases. FireDB now has external references for 95% of contacting small ligands, making FireDB a more complete database and providing the scientific community with easy access to the pharmacological annotations of PDB ligands. In addition to the manual curation of ligands, FireDB also provides insights into the biological relevance of individual binding sites. Here, biological relevance is calculated from the multiple sequence alignments of related binding sites that are generated from all-against-all comparison of each FireDB binding site. The database can be accessed by RESTful web services and is available for download via MySQL.

  13. Making Biology Learning Relevant to Students: Integrating People, History, and Context into College Biology Teaching

    ERIC Educational Resources Information Center

    Chamany, Katayoun; Allen, Deborah; Tanner, Kimberly

    2008-01-01

    Teaching students to make connections between what they learn in the classroom and what they see in everyday life is imperative. As biology instructors, they may choose to teach biology devoid of social context, believing that students can make these connections on their own. However, students model their instructors' behaviors, and follow their…

  14. Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces.

    PubMed

    Kim, Jonghoon; Kim, Heejun; Park, Seung Bum

    2014-10-22

    In the search for new therapeutic agents for currently incurable diseases, attention has turned to traditionally "undruggable" targets, and collections of drug-like small molecules with high diversity and quality have become a prerequisite for new breakthroughs. To generate such collections, the diversity-oriented synthesis (DOS) strategy was developed, which aims to populate new chemical space with drug-like compounds containing a high degree of molecular diversity. The resulting DOS-derived libraries have been of great value for the discovery of various bioactive small molecules and therapeutic agents, and thus DOS has emerged as an essential tool in chemical biology and drug discovery. However, the key challenge has become how to design and synthesize drug-like small-molecule libraries with improved biological relevancy as well as maximum molecular diversity. This Perspective presents the development of privileged substructure-based DOS (pDOS), an efficient strategy for the construction of polyheterocyclic compound libraries with high biological relevancy. We envisioned the specific interaction of drug-like small molecules with certain biopolymers via the incorporation of privileged substructures into polyheterocyclic core skeletons. The importance of privileged substructures such as benzopyran, pyrimidine, and oxopiperazine in rigid skeletons was clearly demonstrated through the discovery of bioactive small molecules and the subsequent identification of appropriate target biomolecule using a method called "fluorescence difference in two-dimensional gel electrophoresis". Focusing on examples of pDOS-derived bioactive compounds with exceptional specificity, we discuss the capability of privileged structures to serve as chemical "navigators" toward biologically relevant chemical spaces. We also provide an outlook on chemical biology research and drug discovery using biologically relevant compound libraries constructed by pDOS, biology-oriented synthesis, or

  15. Identifying relevant data for a biological database: handcrafted rules versus machine learning.

    PubMed

    Sehgal, Aditya Kumar; Das, Sanmay; Noto, Keith; Saier, Milton H; Elkan, Charles

    2011-01-01

    With well over 1,000 specialized biological databases in use today, the task of automatically identifying novel, relevant data for such databases is increasingly important. In this paper, we describe practical machine learning approaches for identifying MEDLINE documents and Swiss-Prot/TrEMBL protein records, for incorporation into a specialized biological database of transport proteins named TCDB. We show that both learning approaches outperform rules created by hand by a human expert. As one of the first case studies involving two different approaches to updating a deployed database, both the methods compared and the results will be of interest to curators of many specialized databases.

  16. How biologically relevant are interaction-based modules in protein networks?

    PubMed Central

    Poyatos, Juan F; Hurst, Laurence D

    2004-01-01

    By applying a graph-based algorithm to yeast protein-interaction networks we have extracted modular structures and show that they can be validated using information from the phylogenetic conservation of the network components. We show that the module cores, the parts with the highest intramodular connectivity, are biologically relevant components of the networks. These constituents correlate only weakly with other levels of organization. We also discuss how such structures could be used for finding targets for antimicrobial drugs. PMID:15535869

  17. Making developmental biology relevant to undergraduates in an era of economic rationalism in Australia.

    PubMed

    Key, Brian; Nurcombe, Victor

    2003-01-01

    This report describes the road map we followed at our university to accommodate three main factors: financial pressure within the university system; desire to enhance the learning experience of undergraduates; and motivation to increase the prominence of the discipline of developmental biology in our university. We engineered a novel, multi-year undergraduate developmental biology program which was "student-oriented," ensuring that students were continually exposed to the underlying principles and philosophy of this discipline throughout their undergraduate career. Among its key features are introductory lectures in core courses in the first year, which emphasize the relevance of developmental biology to tissue engineering, reproductive medicine, therapeutic approaches in medicine, agriculture and aquaculture. State-of-the-art animated computer graphics and images of high visual impact are also used. In addition, students are streamed into the developmental biology track in the second year, using courses like human embryology and courses shared with cell biology, which include practicals based on modern experimental approaches. Finally, fully dedicated third-year courses in developmental biology are undertaken in conjunction with stand-alone practical courses where students experiencefirst-hand work in a research laboratory. Our philosophy is a "cradle-to-grave" approach to the education of undergraduates so as to prepare highly motivated, enthusiastic and well-educated developmental biologists for entry into graduate programs and ultimately post-doctoral research.

  18. Population distribution models: species distributions are better modeled using biologically relevant data partitions

    PubMed Central

    2011-01-01

    Background Predicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions. Results Despite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit. Conclusions Because the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications. PMID:21929792

  19. Unaffected features of BSA stabilized Ag nanoparticles after storage and reconstitution in biological relevant media.

    PubMed

    Valenti, Laura E; Giacomelli, Carla E

    2015-08-01

    Silver-coated orthopedic implants and silver composite materials have been proposed to produce local biocidal activity at low dose to reduce post-surgery infection that remains one of the major contributions to the patient morbidity. This work presents the synthesis combined with the characterization, colloidal stability in biological relevant media, antimicrobial activity and handling properties of silver nanoparticles (Ag-NP) before and after freeze dry and storage. The nanomaterial was synthesized in aqueous solution with simple, reproducible and low-cost strategies using bovine serum albumin (BSA) as the stabilizing agent. Ag-NP were characterized by means of the size distribution and morphology (UV-vis spectra, dynamic light scattering measurements and TEM images), charge as a function of the pH (zeta potential measurements) and colloidal stability in biological relevant media (UV-vis spectra and dynamic light scattering measurements). Further, the interactions between the protein and Ag-NP were evaluated by surface enhanced Raman spectroscopy (SERS) and the antimicrobial activity was tested with two bacteria strains (namely Staphylococcus aureus and Staphylococcus epidermidis) mainly present in the infections caused by implants and prosthesis in orthopedic surgery. Finally, the Ag-NP dispersed in aqueous solution were dried and stored as long-lasting powders that were easily reconstituted without losing their stability and antimicrobial properties. The proposed methods to stabilize Ag-NP not only produce stable dispersions in media of biological relevance but also long-lasting powders with optimal antimicrobial activity in the nanomolar range. This level is much lower than the cytotoxicity determined in vitro on osteoblasts, osteoclasts and osteoarthritic chondrocytes. The synthesized Ag-NP can be incorporated as additive of biomaterials or pharmaceutical products to confer antimicrobial activity in a powdered form in different formulations, dispersed in

  20. [Microbiological and biological methods of the European Pharmacopoeia. Relevant for each medicinal product].

    PubMed

    Norwig, J

    2014-10-01

    According to the EU Directive 2001/83 the European Pharmacopoeia is the official Pharmacopoeia of the European Union. Therefore the European Pharmacopoeia is one of the legal pharmacopoeial compendia in Germany. Any licensed medicinal product on the German market complies with the requirements of the compendial monographs, if applicable. Because the general monographs of the European Pharmacopoeia on Dosage Forms, Substances for Pharmaceutical Use and Pharmaceutical Preparations refer to the microbiological and biological methods of the Pharmacopoeia, the methods are relevant for medicinal products, too. This article presents a rough summary of the microbiological and biological methods of the European Pharmacopoeia and is intended to be a stimulus for the reader to better understand the original compendia. The short description of the methods mentioned, here, is a summary from the Pharmacopoeia and the non-official collection of comments on the texts of the European Pharmacopoeia. PMID:25200487

  1. On the possible biological relevance of HSNO isomers: a computational investigation.

    PubMed

    Ivanova, Lena V; Anton, Becka J; Timerghazin, Qadir K

    2014-05-14

    Thionitrous acid (HSNO), the smallest S-nitrosothiol, has been identified as a potential biologically active molecule that connects the biochemistries of two important gasotransmitters, nitric oxide (NO) and hydrogen sulfide (H2S). Here, we computationally explore possible isomerization reactions of HSNO that may occur under physiological conditions using high-level coupled-cluster as well as density functional theory and composite CBS-QB3 methodology calculations. Gas-phase calculations show that the formation of the tautomeric form HONS and the Y-isomer SN(H)O is thermodynamically feasible, as they are energetically close, within ∼6 kcal mol(-1), to HSNO, while the recently proposed three-membered ring isomer is not thermodynamically or kinetically accessible. The gas-phase intramolecular proton-transfer reactions required for HSNO isomerization into HONS and SN(H)O are predicted to have prohibitively high reaction barriers, 30-50 kcal mol(-1). However, the polar aqueous environment and water-assisted proton shuttle should decrease these barriers to ∼9 kcal mol(-1), which makes these two isomers kinetically accessible under physiological conditions. Our calculations also support the possibility of an aqueous reaction between the Y-isomer SN(H)O and H2S leading to biologically active nitroxyl HNO. These results suggest that the formation of HSNO in biological milieu can lead to various derivative species with their own, possibly biologically relevant, activity.

  2. Metal based biologically active compounds: design, synthesis, and antibacterial/antifungal/cytotoxic properties of triazole-derived Schiff bases and their oxovanadium(IV) complexes.

    PubMed

    Chohan, Zahid H; Sumrra, Sajjad H; Youssoufi, Moulay H; Hadda, Taibi B

    2010-07-01

    A new series of oxovanadium(IV) complexes have been designed and synthesized with a new class of triazole Schiff bases derived from the reaction of 3,5-diamino-1,2,4-triazole with 2-hydroxy-1-naphthaldehyde, pyrrole-2-carboxaldehyde, pyridine-2-carboxaldehyde and acetyl pyridine-2-carboxaldehyde, respectively. Physical (magnetic susceptibility, molar conductance), spectral (IR, (1)H NMR, (13)C NMR, mass and electronic) and analytical data have established the structures of these synthesized Schiff bases and their oxovanadium(IV) complexes. The Schiff bases, predominantly act as bidentate and coordinate with the vanadium(IV) metal to give a stoichiometric ratio of 1:2 [M:L], forming a general formulae, [M(L-H)(2)] and [M(L)(2)]SO(4) where L = (L(1))-(L(4)) and M = VO(IV) of these complexes in a square-pyramidal geometry. In order to evaluate the biological activity of Schiff bases and to assess the role of vanadium(IV) metal on biological activity, the triazole Schiff bases and their oxovanadium(IV) complexes have been studied for in vitro antibacterial activity against four Gram-negative (Escherichia coli, Shigella flexenari, Pseudomonas aeruginosa, Salmonella typhi) and two Gram-positive (Staphylococcus aureus, Bacillus subtilis) bacterial strains, in vitro antifungal activity against Trichophyton longifucus, Candida albican, Aspergillus flavus, Microscopum canis, Fusarium solani and Candida glaberata. The simple Schiff bases showed weaker to significant activity against one or more bacterial and fungal strains. In most of the cases higher activity was exhibited upon coordination with vanadium(IV) metal. Brine shrimp bioassay was also carried out for in vitro cytotoxic properties against Artemia salina. PMID:20338672

  3. Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions.

    PubMed

    Fedotova, Marina V; Kruchinin, Sergey E

    2014-06-01

    The ion-binding between inorganic ions and charged functional groups of glycine zwitter-ion in NaCl(aq), KCl(aq), MgCl2(aq), and CaCl2(aq) has been investigated over a wide salt concentration range by using integral equation theory in the 3D-RISM approach. These systems mimic biological systems where binding of ions to charged residues at protein surfaces is relevant. It has been found that the stability of ion pairs formed by the carboxylate group and added inorganic cations decreases in the sequence Mg(2+)>Ca(2+)>Na(+)>K(+). However, all formed ion pairs are weak and decrease in stability with increasing salt concentration. On the other hand, at a given salt concentration the stability of (-NH3(+):Cl(-))aq ion pairs is similar in all studied systems. The features of ion-binding and the salt concentration effect on this process are discussed.

  4. Biologically relevant molecular transducer with increased computing power and iterative abilities.

    PubMed

    Ratner, Tamar; Piran, Ron; Jonoska, Natasha; Keinan, Ehud

    2013-05-23

    As computing devices, which process data and interconvert information, transducers can encode new information and use their output for subsequent computing, offering high computational power that may be equivalent to a universal Turing machine. We report on an experimental DNA-based molecular transducer that computes iteratively and produces biologically relevant outputs. As a proof of concept, the transducer accomplished division of numbers by 3. The iterative power was demonstrated by a recursive application on an obtained output. This device reads plasmids as input and processes the information according to a predetermined algorithm, which is represented by molecular software. The device writes new information on the plasmid using hardware that comprises DNA-manipulating enzymes. The computation produces dual output: a quotient, represented by newly encoded DNA, and a remainder, represented by E. coli phenotypes. This device algorithmically manipulates genetic codes. PMID:23706637

  5. Lack of [3H]quinuclidinyl benzylate binding to biologically relevant binding sites on mononuclear cells.

    PubMed

    Adams, E M; Lubrano, T M; Gordon, J; Fields, J Z

    1992-09-01

    We analyzed the binding characteristics of [3H]quinuclidinyl benzylate ([3H]QNB), a muscarinic cholinergic ligand, to rat and human mononuclear cells (MNC). Under various assay conditions, atropine-sensitive, saturable binding occurred with an apparent Kd of 10 nM. Conditions which disrupted the MNC membrane reduced total binding and eliminated specific binding. Muscarinic agonists were unable to inhibit [3H]QNB binding to MNC at concentrations up to 10(-2) M. Stereoisomers dexetimide and levetimide were equipotent inhibitors of binding (IC50 2 x 10(-5) M). We conclude that, although atropine-sensitive binding of [3H]QNB to MNC occurs, the binding is not consistent with the presence of a biologically relevant muscarinic cholinergic receptor. PMID:1392105

  6. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

    PubMed Central

    Yu, Agnès; Lepère, Gersende; Jay, Florence; Wang, Jingyu; Bapaume, Laure; Wang, Yu; Abraham, Anne-Laure; Penterman, Jon; Fischer, Robert L.; Voinnet, Olivier; Navarro, Lionel

    2013-01-01

    DNA methylation is an epigenetic mark that silences transposable elements (TEs) and repeats. Whereas the establishment and maintenance of DNA methylation are relatively well understood, little is known about their dynamics and biological relevance in plant and animal innate immunity. Here, we show that some TEs are demethylated and transcriptionally reactivated during antibacterial defense in Arabidopsis. This effect is correlated with the down-regulation of key transcriptional gene silencing factors and is partly dependent on an active demethylation process. DNA demethylation restricts multiplication and vascular propagation of the bacterial pathogen Pseudomonas syringae in leaves and, accordingly, some immune-response genes, containing repeats in their promoter regions, are negatively regulated by DNA methylation. This study provides evidence that DNA demethylation is part of a plant-induced immune response, potentially acting to prime transcriptional activation of some defense genes linked to TEs/repeats. PMID:23335630

  7. Biological relevance and consequences of chemical- or metal-induced DNA cross-linking

    SciTech Connect

    Paustenbach, D.J.; Finley, B.L.

    1996-03-01

    A vast number of chemicals are known to induce mutagenesis and/or carcinogenesis in mammals. Although disruption of cellular nuclear material resulting ultimately in mutagenesis/carcinogenesis can be accomplished by various mechanisms, the search for biomarkers of chemical-induced toxicity continues. This review focuses on the ability of certain metals or chemicals to bind to DNA in a cross-link fashion in whole animal as well as under in vitro conditions. The methodologies currently used to determine DNA cross-linking are described. The biological relevance of the presence of chemical- or metal-induced DNA cross-linking as a measure of carcinogenesis in humans is still under debate, as there is no clear correlation between the disease and the DNA cross-link reaction. 62 refs., 3 tabs.

  8. Biologically relevant photoacoustic imaging phantoms with tunable optical and acoustic properties.

    PubMed

    Vogt, William C; Jia, Congxian; Wear, Keith A; Garra, Brian S; Joshua Pfefer, T

    2016-10-01

    Established medical imaging technologies such as magnetic resonance imaging and computed tomography rely on well-validated tissue-simulating phantoms for standardized testing of device image quality. The availability of high-quality phantoms for optical-acoustic diagnostics such as photoacoustic tomography (PAT) will facilitate standardization and clinical translation of these emerging approaches. Materials used in prior PAT phantoms do not provide a suitable combination of long-term stability and realistic acoustic and optical properties. Therefore, we have investigated the use of custom polyvinyl chloride plastisol (PVCP) formulations for imaging phantoms and identified a dual-plasticizer approach that provides biologically relevant ranges of relevant properties. Speed of sound and acoustic attenuation were determined over a frequency range of 4 to 9 MHz and optical absorption and scattering over a wavelength range of 400 to 1100 nm. We present characterization of several PVCP formulations, including one designed to mimic breast tissue. This material is used to construct a phantom comprised of an array of cylindrical, hemoglobin-filled inclusions for evaluation of penetration depth. Measurements with a custom near-infrared PAT imager provide quantitative and qualitative comparisons of phantom and tissue images. Results indicate that our PVCP material is uniquely suitable for PAT system image quality evaluation and may provide a practical tool for device validation and intercomparison.

  9. Biologically relevant photoacoustic imaging phantoms with tunable optical and acoustic properties.

    PubMed

    Vogt, William C; Jia, Congxian; Wear, Keith A; Garra, Brian S; Joshua Pfefer, T

    2016-10-01

    Established medical imaging technologies such as magnetic resonance imaging and computed tomography rely on well-validated tissue-simulating phantoms for standardized testing of device image quality. The availability of high-quality phantoms for optical-acoustic diagnostics such as photoacoustic tomography (PAT) will facilitate standardization and clinical translation of these emerging approaches. Materials used in prior PAT phantoms do not provide a suitable combination of long-term stability and realistic acoustic and optical properties. Therefore, we have investigated the use of custom polyvinyl chloride plastisol (PVCP) formulations for imaging phantoms and identified a dual-plasticizer approach that provides biologically relevant ranges of relevant properties. Speed of sound and acoustic attenuation were determined over a frequency range of 4 to 9 MHz and optical absorption and scattering over a wavelength range of 400 to 1100 nm. We present characterization of several PVCP formulations, including one designed to mimic breast tissue. This material is used to construct a phantom comprised of an array of cylindrical, hemoglobin-filled inclusions for evaluation of penetration depth. Measurements with a custom near-infrared PAT imager provide quantitative and qualitative comparisons of phantom and tissue images. Results indicate that our PVCP material is uniquely suitable for PAT system image quality evaluation and may provide a practical tool for device validation and intercomparison. PMID:26886681

  10. Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity.

    PubMed

    Harper, B; McClain, S; Ganko, E W

    2012-08-01

    Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence.

  11. Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry.

    PubMed

    Baker, Stuart G

    2014-01-01

    To gain biological insights, investigators sometimes compare sequences of gene expression measurements under two scenarios (such as two drugs or species). For this situation, we developed an algorithm to fit, identify, and compare biologically relevant response curves in terms of heteromorphy (different curves), heterochrony (different transition times), and heterometry (different magnitudes). The curves are flat, linear, sigmoid, hockey-stick (sigmoid missing a steady state), transient (sigmoid missing two steady states), impulse (with peak or trough), step (with intermediate-level plateau), impulse+ (impulse with an extra parameter), step+ (step with an extra parameter), further characterized by upward or downward trend. To reduce overfitting, we fit the curves to every other response, evaluated the fit in the remaining responses, and identified the most parsimonious curves that yielded a good fit. We measured goodness of fit using a statistic comparable over different genes, namely the square root of the mean squared prediction error as a percentage of the range of responses, which we call the relative prediction error (RPE). We illustrated the algorithm using data on gene expression at 14 times in the embryonic development in two species of frogs. Software written in Mathematica is freely available. PMID:27605029

  12. Phosphate ester hydrolysis of biologically relevant molecules by cerium oxide nanoparticles.

    PubMed

    Kuchma, Melissa Hirsch; Komanski, Christopher B; Colon, Jimmie; Teblum, Andrew; Masunov, Artëm E; Alvarado, Beatrice; Babu, Suresh; Seal, Sudipta; Summy, Justin; Baker, Cheryl H

    2010-12-01

    In an effort to characterize the interaction of cerium oxide nanoparticles (CNPs) in biological systems, we explored the reactivity of CNPs with the phosphate ester bonds of p-nitrophenylphosphate (pNPP), ATP, o-phospho-l-tyrosine, and DNA. The activity of the bond cleavage for pNPP at pH 7 is calculated to be 0.860 ± 0.010 nmol p-nitrophenol/min/μg CNPs. Interestingly, when CNPs bind to plasmid DNA, no cleavage products are detected. While cerium(IV) complexes generally exhibit the ability to break phosphorus-oxygen bonds, the reactions we report appear to be dependent on the availability of cerium(III) sites, not cerium(IV) sites. We investigated the dephosphorylation mechanism from the first principles and find the reaction proceeds through inversion of the phosphate group similar to an S(N)2 mechanism. The ability of CNPs to interact with phosphate ester bonds of biologically relevant molecules has important implications for their use as potential therapeutics.

  13. Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry

    PubMed Central

    Baker, Stuart G.

    2014-01-01

    To gain biological insights, investigators sometimes compare sequences of gene expression measurements under two scenarios (such as two drugs or species). For this situation, we developed an algorithm to fit, identify, and compare biologically relevant response curves in terms of heteromorphy (different curves), heterochrony (different transition times), and heterometry (different magnitudes). The curves are flat, linear, sigmoid, hockey-stick (sigmoid missing a steady state), transient (sigmoid missing two steady states), impulse (with peak or trough), step (with intermediate-level plateau), impulse+ (impulse with an extra parameter), step+ (step with an extra parameter), further characterized by upward or downward trend. To reduce overfitting, we fit the curves to every other response, evaluated the fit in the remaining responses, and identified the most parsimonious curves that yielded a good fit. We measured goodness of fit using a statistic comparable over different genes, namely the square root of the mean squared prediction error as a percentage of the range of responses, which we call the relative prediction error (RPE). We illustrated the algorithm using data on gene expression at 14 times in the embryonic development in two species of frogs. Software written in Mathematica is freely available.

  14. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

    PubMed

    Hastings, Janna; de Matos, Paula; Dekker, Adriano; Ennis, Marcus; Harsha, Bhavana; Kale, Namrata; Muthukrishnan, Venkatesh; Owen, Gareth; Turner, Steve; Williams, Mark; Steinbeck, Christoph

    2013-01-01

    ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.

  15. Is it biologically relevant to measure the structures of small peptides in the gas-phase?

    NASA Astrophysics Data System (ADS)

    Barran, Perdita E.; Polfer, Nick C.; Campopiano, Dominic J.; Clarke, David J.; Langridge-Smith, Patrick R. R.; Langley, Ross J.; Govan, John R. W.; Maxwell, Alison; Dorin, Julia R.; Millar, Robert P.; Bowers, Michael T.

    2005-02-01

    Recent developments in sample introduction of biologically relevant molecules have heralded a new era for gas-phase methods of structural determination. One of the biggest challenges is to relate gas-phase structures, often measured in the absence of water and counter ions, with in vivo biologically active structures. An advantage of gas-phase based techniques is that a given peptide can be analysed in a variety of different forms, for example, as a function of charge state, or with additional water molecules. Molecular modelling can provide insight into experimental findings and help elucidate the differences between structural forms. Combining experiment and theory provides a thorough interrogation of candidate conformations. Here two important naturally occurring peptide systems have been examined in detail and results are assessed in terms of their biological significance. The first of these is gonadotropin-releasing hormone (GnRH), a decapeptide which is the central regulator of the reproductive system in vertebrates. We have examined several naturally occurring variants of this peptide using Ion Mobility Mass Spectrometry and Electron Capture Dissociation (ECD) in conjunction with Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR-MS). Candidate conformations are modelled using the AMBER force field. Single amino acid changes, for example Gly6 --> Ala6, or Ala6 --> D-Ala6, have observable effects on the gas phase structure of GnRH. It has been shown that evolutionary primary sequence variations are key to the biological activity of GnRH, and it is thought that this is due to different binding affinities at target receptors. This work provides strong evidence that this activity is structurally based. The second system examined is the relationship between the quaternary structure and activity of two novel [beta]-defensins. FT-ICR mass spectrometry has been employed to characterize di-sulphide bridging and dissociation based experiments utilised to

  16. Investigation of some biologically relevant redox reactions using electrochemical mass spectrometry interfaced by desorption electrospray ionization.

    PubMed

    Lu, Mei; Wolff, Chloe; Cui, Weidong; Chen, Hao

    2012-04-01

    Recently we have shown that, as a versatile ionization technique, desorption electrospray ionization (DESI) can serve as a useful interface to combine electrochemistry (EC) with mass spectrometry (MS). In this study, the EC/DESI-MS method has been further applied to investigate some aqueous phase redox reactions of biological significance, including the reduction of peptide disulfide bonds and nitroaromatics as well as the oxidation of phenothiazines. It was found that knotted/enclosed disulfide bonds in the peptides apamin and endothelin could be electrochemically cleaved. Subsequent tandem MS analysis of the resulting reduced peptide ions using collision-induced dissociation (CID) and electron-capture dissociation (ECD) gave rise to extensive fragment ions, providing a fast protocol for sequencing peptides with complicated disulfide bond linkages. Flunitrazepam and clonazepam, a class of nitroaromatic drugs, are known to undergo reduction into amines which was proposed to involve nitroso and N-hydroxyl intermediates. Now in this study, these corresponding intermediate ions were successfully intercepted and their structures were confirmed by CID. This provides mass spectrometric evidence for the mechanism of the nitro to amine conversion process during nitroreduction, an important redox reaction involved in carcinogenesis. In addition, the well-known oxidation reaction of chlorpromazine was also examined. The putative transient one-electron transfer product, the chlorpromazine radical cation (m/z 318), was captured by MS, for the first time, and its structure was also verified by CID. In addition to these observations, some features of the DESI-interfaced electrochemical mass spectrometry were discussed, such as simple instrumentation and the lack of background signal. These results further demonstrate the feasibility of EC/DESI-MS for the study of the biology-relevant redox chemistry and would find applications in proteomics and drug development research.

  17. Semi-Supervised Multimodal Relevance Vector Regression Improves Cognitive Performance Estimation from Imaging and Biological Biomarkers

    PubMed Central

    Cheng, Bo; Chen, Songcan; Kaufer, Daniel I.

    2013-01-01

    Accurate estimation of cognitive scores for patients can help track the progress of neurological diseases. In this paper, we present a novel semi-supervised multimodal relevance vector regression (SM-RVR) method for predicting clinical scores of neurological diseases from multimodal imaging and biological biomarker, to help evaluate pathological stage and predict progression of diseases, e.g., Alzheimer’s diseases (AD). Unlike most existing methods, we predict clinical scores from multimodal (imaging and biological) biomarkers, including MRI, FDG-PET, and CSF. Considering that the clinical scores of mild cognitive impairment (MCI) subjects are often less stable compared to those of AD and normal control (NC) subjects due to the heterogeneity of MCI, we use only the multimodal data of MCI subjects, but no corresponding clinical scores, to train a semi-supervised model for enhancing the estimation of clinical scores for AD and NC subjects. We also develop a new strategy for selecting the most informative MCI subjects. We evaluate the performance of our approach on 202 subjects with all three modalities of data (MRI, FDG-PET and CSF) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. The experimental results show that our SM-RVR method achieves a root-mean-square error (RMSE) of 1.91 and a correlation coefficient (CORR) of 0.80 for estimating the MMSE scores, and also a RMSE of 4.45 and a CORR of 0.78 for estimating the ADAS-Cog scores, demonstrating very promising performances in AD studies. PMID:23504659

  18. A Comparison of Biological and Adoptive Mothers and Fathers: The Relevance of Biological Kinship and Gendered Constructs of Parenthood.

    ERIC Educational Resources Information Center

    Miall, Charlene E.; March, Karen

    2003-01-01

    Used qualitative interviews to examine beliefs and values about biological and adoptive parents. Considered how biological kinship, gender, and actual parenting behavior affect the assessments respondents made of the emotional bonding between parents and children. Found that biological and adoptive parents viewed motherhood as instinctive and…

  19. Benchmark interaction energies for biologically relevant noncovalent complexes containing divalent sulfur.

    PubMed

    Mintz, Benjamin J; Parks, Jerry M

    2012-01-26

    Molecules containing divalent sulfur can participate in significant noncovalent interactions. Computing accurate noncovalent interaction energies using ab initio quantum chemical methods requires a proper description of electron correlation effects. Coupled-cluster theory with single and double substitutions and perturbative triple substitutions, CCSD(T), using extrapolation to the complete basis set (CBS) limit has become the method of choice for computing accurate interaction energies of noncovalently bound complexes. Here, interaction energies are computed for several biologically relevant hydrogen-bonded and dispersion-bound complexes that contain divalent sulfur. Eight-point estimated CCSD(T)/CBS dissociation curves along the noncovalent interaction vector are computed for each complex. As a comparison of high-accuracy ab initio methods, interaction energies are also calculated for each complex using the correlation-consistent Composite Approach (ccCA). We find that, on average, the two methods yield energies within 0.1 kcal mol(-1) of each other. The interaction energies provided here should be useful for developing and assessing the accuracy of more approximate ab initio, density functional theory, semiempirical, and classical force field approaches.

  20. PEGylated N-Heterocyclic Carbene Anchors Designed To Stabilize Gold Nanoparticles in Biologically Relevant Media.

    PubMed

    MacLeod, Michelle J; Johnson, Jeremiah A

    2015-07-01

    N-Heterocyclic carbenes (NHCs) have emerged as versatile ligands for surface functionalization. Their ease of synthesis and ability to form strong bonds with a range of substrates provide a unique complement to traditional surface modification methods. Gold nanoparticles (NPs) are a particularly useful class of materials whose applications intimately depend on surface functionalization. Here we report the development of PEGylated-NHC ligands for Au-NP surfaces and the first example of NHC-functionalized NPs that are compatible with biologically relevant conditions. Our PEGylated-NHC-Au-NPs are stable toward aggregation in aqueous solutions in the pH range of 3-14, in <250 mM electrolyte solutions, at high and low temperatures (95 and -78 °C), in cell culture media, and in aqueous H2O2 solutions. This work demonstrates for the first time that NHCs can serve as anchors for water-soluble Au-NPs and opens the door to potential biomedical applications of NHC surface anchors. PMID:26081724

  1. Laser spectroscopy and mass spectrometry of biologically relevant systems: chiral discrimination

    NASA Astrophysics Data System (ADS)

    Piccirillo, Susanna; Satta, Mauro; Coreno, Marcello; Catone, Daniele; Rondino, Flaminia; Scuderi, Debora; Paladini, Alessandra; Speranza, Maurizio; Giardini, Anna

    2005-06-01

    Radical ions are open-shell elusive species of paramount importance in many organic reactions and in biological processes. Oxidative bond breaking and forming involving radical ions are common process taking place in asymmetric enzyme cavities. Side-chain Cα-CΒ bond fragmentation in the radical cations of aromatic alcohols is a common process in solution [1-3], whose efficiency is enhanced in polar solvents such as water. Hydrogen-bonding between the ion and the solvent in the relevant transition structure is thought as responsible of the rate acceleration [4]. Effects of achiral and chiral microsolvation on the radical cation of R-(+)-l-phenyl-l-propanol, have been investigated. The energy thresholds of the homolytic Cα-Cβ bond breaking of R-(+)-1-phenyl-1-propanol radical cation, its mono-hydrated cluster, and its clusters with (2R,3R)-(-)-2,3-butanediol and (2S,3S)-(+)-2,3-butanediol have been studied through two color Resonant Two Photon Ionization, Photodissociation and Mass Spectrometry. The barrier of the Cα-Cβ fragmentation is appreciably higher for the unsolvated molecular ion than for its adducts with solvent molecules. Moreover, marked differences in the ethyl loss fragmentation energy are observed for the clusters with water and with the two diols. In particular the homochiral cluster with (2R, 3R)-(-)-2,3-butanediol exhibits a fragmentation barrier higher than that of the corresponding heterochiral adduct with (25, 35)-(+)-2,3-butanediol.

  2. Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

    PubMed

    Pattaro, Cristian; Teumer, Alexander; Gorski, Mathias; Chu, Audrey Y; Li, Man; Mijatovic, Vladan; Garnaas, Maija; Tin, Adrienne; Sorice, Rossella; Li, Yong; Taliun, Daniel; Olden, Matthias; Foster, Meredith; Yang, Qiong; Chen, Ming-Huei; Pers, Tune H; Johnson, Andrew D; Ko, Yi-An; Fuchsberger, Christian; Tayo, Bamidele; Nalls, Michael; Feitosa, Mary F; Isaacs, Aaron; Dehghan, Abbas; d'Adamo, Pio; Adeyemo, Adebowale; Dieffenbach, Aida Karina; Zonderman, Alan B; Nolte, Ilja M; van der Most, Peter J; Wright, Alan F; Shuldiner, Alan R; Morrison, Alanna C; Hofman, Albert; Smith, Albert V; Dreisbach, Albert W; Franke, Andre; Uitterlinden, Andre G; Metspalu, Andres; Tonjes, Anke; Lupo, Antonio; Robino, Antonietta; Johansson, Åsa; Demirkan, Ayse; Kollerits, Barbara; Freedman, Barry I; Ponte, Belen; Oostra, Ben A; Paulweber, Bernhard; Krämer, Bernhard K; Mitchell, Braxton D; Buckley, Brendan M; Peralta, Carmen A; Hayward, Caroline; Helmer, Catherine; Rotimi, Charles N; Shaffer, Christian M; Müller, Christian; Sala, Cinzia; van Duijn, Cornelia M; Saint-Pierre, Aude; Ackermann, Daniel; Shriner, Daniel; Ruggiero, Daniela; Toniolo, Daniela; Lu, Yingchang; Cusi, Daniele; Czamara, Darina; Ellinghaus, David; Siscovick, David S; Ruderfer, Douglas; Gieger, Christian; Grallert, Harald; Rochtchina, Elena; Atkinson, Elizabeth J; Holliday, Elizabeth G; Boerwinkle, Eric; Salvi, Erika; Bottinger, Erwin P; Murgia, Federico; Rivadeneira, Fernando; Ernst, Florian; Kronenberg, Florian; Hu, Frank B; Navis, Gerjan J; Curhan, Gary C; Ehret, George B; Homuth, Georg; Coassin, Stefan; Thun, Gian-Andri; Pistis, Giorgio; Gambaro, Giovanni; Malerba, Giovanni; Montgomery, Grant W; Eiriksdottir, Gudny; Jacobs, Gunnar; Li, Guo; Wichmann, H-Erich; Campbell, Harry; Schmidt, Helena; Wallaschofski, Henri; Völzke, Henry; Brenner, Hermann; Kroemer, Heyo K; Kramer, Holly; Lin, Honghuang; Leach, I Mateo; Ford, Ian; Guessous, Idris; Rudan, Igor; Prokopenko, Inga; Borecki, Ingrid; Heid, Iris M; Kolcic, Ivana; Persico, Ivana; Jukema, J Wouter; Wilson, James F; Felix, Janine F; Divers, Jasmin; Lambert, Jean-Charles; Stafford, Jeanette M; Gaspoz, Jean-Michel; Smith, Jennifer A; Faul, Jessica D; Wang, Jie Jin; Ding, Jingzhong; Hirschhorn, Joel N; Attia, John; Whitfield, John B; Chalmers, John; Viikari, Jorma; Coresh, Josef; Denny, Joshua C; Karjalainen, Juha; Fernandes, Jyotika K; Endlich, Karlhans; Butterbach, Katja; Keene, Keith L; Lohman, Kurt; Portas, Laura; Launer, Lenore J; Lyytikäinen, Leo-Pekka; Yengo, Loic; Franke, Lude; Ferrucci, Luigi; Rose, Lynda M; Kedenko, Lyudmyla; Rao, Madhumathi; Struchalin, Maksim; Kleber, Marcus E; Cavalieri, Margherita; Haun, Margot; Cornelis, Marilyn C; Ciullo, Marina; Pirastu, Mario; de Andrade, Mariza; McEvoy, Mark A; Woodward, Mark; Adam, Martin; Cocca, Massimiliano; Nauck, Matthias; Imboden, Medea; Waldenberger, Melanie; Pruijm, Menno; Metzger, Marie; Stumvoll, Michael; Evans, Michele K; Sale, Michele M; Kähönen, Mika; Boban, Mladen; Bochud, Murielle; Rheinberger, Myriam; Verweij, Niek; Bouatia-Naji, Nabila; Martin, Nicholas G; Hastie, Nick; Probst-Hensch, Nicole; Soranzo, Nicole; Devuyst, Olivier; Raitakari, Olli; Gottesman, Omri; Franco, Oscar H; Polasek, Ozren; Gasparini, Paolo; Munroe, Patricia B; Ridker, Paul M; Mitchell, Paul; Muntner, Paul; Meisinger, Christa; Smit, Johannes H; Kovacs, Peter; Wild, Philipp S; Froguel, Philippe; Rettig, Rainer; Mägi, Reedik; Biffar, Reiner; Schmidt, Reinhold; Middelberg, Rita P S; Carroll, Robert J; Penninx, Brenda W; Scott, Rodney J; Katz, Ronit; Sedaghat, Sanaz; Wild, Sarah H; Kardia, Sharon L R; Ulivi, Sheila; Hwang, Shih-Jen; Enroth, Stefan; Kloiber, Stefan; Trompet, Stella; Stengel, Benedicte; Hancock, Stephen J; Turner, Stephen T; Rosas, Sylvia E; Stracke, Sylvia; Harris, Tamara B; Zeller, Tanja; Zemunik, Tatijana; Lehtimäki, Terho; Illig, Thomas; Aspelund, Thor; Nikopensius, Tiit; Esko, Tonu; Tanaka, Toshiko; Gyllensten, Ulf; Völker, Uwe; Emilsson, Valur; Vitart, Veronique; Aalto, Ville; Gudnason, Vilmundur; Chouraki, Vincent; Chen, Wei-Min; Igl, Wilmar; März, Winfried; Koenig, Wolfgang; Lieb, Wolfgang; Loos, Ruth J F; Liu, Yongmei; Snieder, Harold; Pramstaller, Peter P; Parsa, Afshin; O'Connell, Jeffrey R; Susztak, Katalin; Hamet, Pavel; Tremblay, Johanne; de Boer, Ian H; Böger, Carsten A; Goessling, Wolfram; Chasman, Daniel I; Köttgen, Anna; Kao, W H Linda; Fox, Caroline S

    2016-01-01

    Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways. PMID:26831199

  3. Action video game players' visual search advantage extends to biologically relevant stimuli.

    PubMed

    Chisholm, Joseph D; Kingstone, Alan

    2015-07-01

    Research investigating the effects of action video game experience on cognition has demonstrated a host of performance improvements on a variety of basic tasks. Given the prevailing evidence that these benefits result from efficient control of attentional processes, there has been growing interest in using action video games as a general tool to enhance everyday attentional control. However, to date, there is little evidence indicating that the benefits of action video game playing scale up to complex settings with socially meaningful stimuli - one of the fundamental components of our natural environment. The present experiment compared action video game player (AVGP) and non-video game player (NVGP) performance on an oculomotor capture task that presented participants with face stimuli. In addition, the expression of a distractor face was manipulated to assess if action video game experience modulated the effect of emotion. Results indicate that AVGPs experience less oculomotor capture than NVGPs; an effect that was not influenced by the emotional content depicted by distractor faces. It is noteworthy that this AVGP advantage emerged despite participants being unaware that the investigation had to do with video game playing, and participants being equivalent in their motivation and treatment of the task as a game. The results align with the notion that action video game experience is associated with superior attentional and oculomotor control, and provides evidence that these benefits can generalize to more complex and biologically relevant stimuli. PMID:26071923

  4. Discrimination between biologically relevant calcium phosphate phases by surface-analytical techniques

    NASA Astrophysics Data System (ADS)

    Kleine-Boymann, Matthias; Rohnke, Marcus; Henss, Anja; Peppler, Klaus; Sann, Joachim; Janek, Juergen

    2014-08-01

    The spatially resolved phase identification of biologically relevant calcium phosphate phases (CPPs) in bone tissue is essential for the elucidation of bone remodeling mechanisms and for the diagnosis of bone diseases. Analytical methods with high spatial resolution for the discrimination between chemically quite close phases are rare. Therefore the applicability of state-of-the-art ToF-SIMS, XPS and EDX as chemically specific techniques was investigated. The eight CPPs hydroxyapatite (HAP), β-tricalcium phosphate (β-TCP), α-tricalcium phosphate (α-TCP), octacalcium phosphate (OCP), dicalcium phosphate dihydrate (DCPD), dicalcium phosphate (DCP), monocalcium phosphate (MCP) and amorphous calcium phosphate (ACP) were either commercial materials in high purity or synthesized by ourselves. The phase purity was proven by XRD analysis. All of the eight CPPs show different mass spectra and the phases can be discriminated by applying the principal component analysis method to the mass spectrometric data. The Ca/P ratios of all phosphates were determined by XPS and EDX. With both methods some CPPs can be distinguished, but the obtained Ca/P ratios deviate systematically from their theoretical values. It is necessary in any case to determine a calibration curve, respectively the ZAF values, from appropriate standards. In XPS also the O(1s)-satellite signals are correlated to the CPPs composition. Angle resolved and long-term XPS measurements of HAP clearly prove that there is no phosphate excess at the surface. Decomposition due to X-ray irradiation has not been observed.

  5. Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function

    PubMed Central

    Pattaro, Cristian; Teumer, Alexander; Gorski, Mathias; Chu, Audrey Y.; Li, Man; Mijatovic, Vladan; Garnaas, Maija; Tin, Adrienne; Sorice, Rossella; Li, Yong; Taliun, Daniel; Olden, Matthias; Foster, Meredith; Yang, Qiong; Chen, Ming-Huei; Pers, Tune H.; Johnson, Andrew D.; Ko, Yi-An; Fuchsberger, Christian; Tayo, Bamidele; Nalls, Michael; Feitosa, Mary F.; Isaacs, Aaron; Dehghan, Abbas; d'Adamo, Pio; Adeyemo, Adebowale; Dieffenbach, Aida Karina; Zonderman, Alan B.; Nolte, Ilja M.; van der Most, Peter J.; Wright, Alan F.; Shuldiner, Alan R.; Morrison, Alanna C.; Hofman, Albert; Smith, Albert V.; Dreisbach, Albert W.; Franke, Andre; Uitterlinden, Andre G.; Metspalu, Andres; Tonjes, Anke; Lupo, Antonio; Robino, Antonietta; Johansson, Åsa; Demirkan, Ayse; Kollerits, Barbara; Freedman, Barry I.; Ponte, Belen; Oostra, Ben A.; Paulweber, Bernhard; Krämer, Bernhard K.; Mitchell, Braxton D.; Buckley, Brendan M.; Peralta, Carmen A.; Hayward, Caroline; Helmer, Catherine; Rotimi, Charles N.; Shaffer, Christian M.; Müller, Christian; Sala, Cinzia; van Duijn, Cornelia M.; Saint-Pierre, Aude; Ackermann, Daniel; Shriner, Daniel; Ruggiero, Daniela; Toniolo, Daniela; Lu, Yingchang; Cusi, Daniele; Czamara, Darina; Ellinghaus, David; Siscovick, David S.; Ruderfer, Douglas; Gieger, Christian; Grallert, Harald; Rochtchina, Elena; Atkinson, Elizabeth J.; Holliday, Elizabeth G.; Boerwinkle, Eric; Salvi, Erika; Bottinger, Erwin P.; Murgia, Federico; Rivadeneira, Fernando; Ernst, Florian; Kronenberg, Florian; Hu, Frank B.; Navis, Gerjan J.; Curhan, Gary C.; Ehret, George B.; Homuth, Georg; Coassin, Stefan; Thun, Gian-Andri; Pistis, Giorgio; Gambaro, Giovanni; Malerba, Giovanni; Montgomery, Grant W.; Eiriksdottir, Gudny; Jacobs, Gunnar; Li, Guo; Wichmann, H-Erich; Campbell, Harry; Schmidt, Helena; Wallaschofski, Henri; Völzke, Henry; Brenner, Hermann; Kroemer, Heyo K.; Kramer, Holly; Lin, Honghuang; Leach, I. Mateo; Ford, Ian; Guessous, Idris; Rudan, Igor; Prokopenko, Inga; Borecki, Ingrid; Heid, Iris M.; Kolcic, Ivana; Persico, Ivana; Jukema, J. Wouter; Wilson, James F.; Felix, Janine F.; Divers, Jasmin; Lambert, Jean-Charles; Stafford, Jeanette M.; Gaspoz, Jean-Michel; Smith, Jennifer A.; Faul, Jessica D.; Wang, Jie Jin; Ding, Jingzhong; Hirschhorn, Joel N.; Attia, John; Whitfield, John B.; Chalmers, John; Viikari, Jorma; Coresh, Josef; Denny, Joshua C.; Karjalainen, Juha; Fernandes, Jyotika K.; Endlich, Karlhans; Butterbach, Katja; Keene, Keith L.; Lohman, Kurt; Portas, Laura; Launer, Lenore J.; Lyytikäinen, Leo-Pekka; Yengo, Loic; Franke, Lude; Ferrucci, Luigi; Rose, Lynda M.; Kedenko, Lyudmyla; Rao, Madhumathi; Struchalin, Maksim; Kleber, Marcus E.; Cavalieri, Margherita; Haun, Margot; Cornelis, Marilyn C.; Ciullo, Marina; Pirastu, Mario; de Andrade, Mariza; McEvoy, Mark A.; Woodward, Mark; Adam, Martin; Cocca, Massimiliano; Nauck, Matthias; Imboden, Medea; Waldenberger, Melanie; Pruijm, Menno; Metzger, Marie; Stumvoll, Michael; Evans, Michele K.; Sale, Michele M.; Kähönen, Mika; Boban, Mladen; Bochud, Murielle; Rheinberger, Myriam; Verweij, Niek; Bouatia-Naji, Nabila; Martin, Nicholas G.; Hastie, Nick; Probst-Hensch, Nicole; Soranzo, Nicole; Devuyst, Olivier; Raitakari, Olli; Gottesman, Omri; Franco, Oscar H.; Polasek, Ozren; Gasparini, Paolo; Munroe, Patricia B.; Ridker, Paul M.; Mitchell, Paul; Muntner, Paul; Meisinger, Christa; Smit, Johannes H.; Abecasis, Goncalo R.; Adair, Linda S.; Alexander, Myriam; Altshuler, David; Amin, Najaf; Arking, Dan E.; Arora, Pankaj; Aulchenko, Yurii; Bakker, Stephan J. L.; Bandinelli, Stefania; Barroso, Ines; Beckmann, Jacques S.; Beilby, John P.; Bergman, Richard N.; Bergmann, Sven; Bis, Joshua C.; Boehnke, Michael; Bonnycastle, Lori L.; Bornstein, Stefan R.; Bots, Michiel L.; Bragg-Gresham, Jennifer L.; Brand, Stefan-Martin; Brand, Eva; Braund, Peter S.; Brown, Morris J.; Burton, Paul R.; Casas, Juan P.; Caulfield, Mark J.; Chakravarti, Aravinda; Chambers, John C.; Chandak, Giriraj R.; Chang, Yen-Pei C.; Charchar, Fadi J.; Chaturvedi, Nish; Shin Cho, Yoon; Clarke, Robert; Collins, Francis S.; Collins, Rory; Connell, John M.; Cooper, Jackie A.; Cooper, Matthew N.; Cooper, Richard S.; Corsi, Anna Maria; Dörr, Marcus; Dahgam, Santosh; Danesh, John; Smith, George Davey; Day, Ian N. M.; Deloukas, Panos; Denniff, Matthew; Dominiczak, Anna F.; Dong, Yanbin; Doumatey, Ayo; Elliott, Paul; Elosua, Roberto; Erdmann, Jeanette; Eyheramendy, Susana; Farrall, Martin; Fava, Cristiano; Forrester, Terrence; Fowkes, F. Gerald R.; Fox, Ervin R.; Frayling, Timothy M.; Galan, Pilar; Ganesh, Santhi K.; Garcia, Melissa; Gaunt, Tom R.; Glazer, Nicole L.; Go, Min Jin; Goel, Anuj; Grässler, Jürgen; Grobbee, Diederick E.; Groop, Leif; Guarrera, Simonetta; Guo, Xiuqing; Hadley, David; Hamsten, Anders; Han, Bok-Ghee; Hardy, Rebecca; Hartikainen, Anna-Liisa; Heath, Simon; Heckbert, Susan R.; Hedblad, Bo; Hercberg, Serge; Hernandez, Dena; Hicks, Andrew A.; Hilton, Gina; Hingorani, Aroon D.; Bolton, Judith A Hoffman; Hopewell, Jemma C.; Howard, Philip; Humphries, Steve E.; Hunt, Steven C.; Hveem, Kristian; Ikram, M. Arfan; Islam, Muhammad; Iwai, Naoharu; Jarvelin, Marjo-Riitta; Jackson, Anne U.; Jafar, Tazeen H.; Janipalli, Charles S.; Johnson, Toby; Kathiresan, Sekar; Khaw, Kay-Tee; Kim, Hyung-Lae; Kinra, Sanjay; Kita, Yoshikuni; Kivimaki, Mika; Kooner, Jaspal S.; Kumar, M. J. Kranthi; Kuh, Diana; Kulkarni, Smita R.; Kumari, Meena; Kuusisto, Johanna; Kuznetsova, Tatiana; Laakso, Markku; Laan, Maris; Laitinen, Jaana; Lakatta, Edward G.; Langefeld, Carl D.; Larson, Martin G.; Lathrop, Mark; Lawlor, Debbie A.; Lawrence, Robert W.; Lee, Jong-Young; Lee, Nanette R.; Levy, Daniel; Li, Yali; Longstreth, Will T.; Luan, Jian'an; Lucas, Gavin; Ludwig, Barbara; Mangino, Massimo; Mani, K. Radha; Marmot, Michael G.; Mattace-Raso, Francesco U. S.; Matullo, Giuseppe; McArdle, Wendy L.; McKenzie, Colin A.; Meitinger, Thomas; Melander, Olle; Meneton, Pierre; Meschia, James F.; Miki, Tetsuro; Milaneschi, Yuri; Mohlke, Karen L.; Mooser, Vincent; Morken, Mario A.; Morris, Richard W.; Mosley, Thomas H.; Najjar, Samer; Narisu, Narisu; Newton-Cheh, Christopher; Nguyen, Khanh-Dung Hoang; Nilsson, Peter; Nyberg, Fredrik; O'Donnell, Christopher J.; Ogihara, Toshio; Ohkubo, Takayoshi; Okamura, Tomonori; Ong, RickTwee-Hee; Ongen, Halit; Onland-Moret, N. Charlotte; O'Reilly, Paul F.; Org, Elin; Orru, Marco; Palmas, Walter; Palmen, Jutta; Palmer, Lyle J.; Palmer, Nicholette D.; Parker, Alex N.; Peden, John F.; Peltonen, Leena; Perola, Markus; Pihur, Vasyl; Platou, Carl G. P.; Plump, Andrew; Prabhakaran, Dorairajan; Psaty, Bruce M.; Raffel, Leslie J.; Rao, Dabeeru C.; Rasheed, Asif; Ricceri, Fulvio; Rice, Kenneth M.; Rosengren, Annika; Rotter, Jerome I.; Rudock, Megan E.; Sõber, Siim; Salako, Tunde; Saleheen, Danish; Salomaa, Veikko; Samani, Nilesh J.; Schwartz, Steven M.; Schwarz, Peter E. H.; Scott, Laura J.; Scott, James; Scuteri, Angelo; Sehmi, Joban S.; Seielstad, Mark; Seshadri, Sudha; Sharma, Pankaj; Shaw-Hawkins, Sue; Shi, Gang; Shrine, Nick R. G.; Sijbrands, Eric J. G.; Sim, Xueling; Singleton, Andrew; Sjögren, Marketa; Smith, Nicholas L.; Artigas, Maria Soler; Spector, Tim D.; Staessen, Jan A.; Stancakova, Alena; Steinle, Nanette I.; Strachan, David P.; Stringham, Heather M.; Sun, Yan V.; Swift, Amy J.; Tabara, Yasuharu; Tai, E-Shyong; Talmud, Philippa J.; Taylor, Andrew; Terzic, Janos; Thelle, Dag S.; Tobin, Martin D.; Tomaszewski, Maciej; Tripathy, Vikal; Tuomilehto, Jaakko; Tzoulaki, Ioanna; Uda, Manuela; Ueshima, Hirotsugu; Uiterwaal, Cuno S. P. M.; Umemura, Satoshi; van der Harst, Pim; van der Schouw, Yvonne T.; van Gilst, Wiek H.; Vartiainen, Erkki; Vasan, Ramachandran S.; Veldre, Gudrun; Verwoert, Germaine C.; Viigimaa, Margus; Vinay, D. G.; Vineis, Paolo; Voight, Benjamin F.; Vollenweider, Peter; Wagenknecht, Lynne E.; Wain, Louise V.; Wang, Xiaoling; Wang, Thomas J.; Wareham, Nicholas J.; Watkins, Hugh; Weder, Alan B.; Whincup, Peter H.; Wiggins, Kerri L.; Witteman, Jacqueline C. M.; Wong, Andrew; Wu, Ying; Yajnik, Chittaranjan S.; Yao, Jie; Young, J. H.; Zelenika, Diana; Zhai, Guangju; Zhang, Weihua; Zhang, Feng; Zhao, Jing Hua; Zhu, Haidong; Zhu, Xiaofeng; Zitting, Paavo; Zukowska-Szczechowska, Ewa; Okada, Yukinori; Wu, Jer-Yuarn; Gu, Dongfeng; Takeuchi, Fumihiko; Takahashi, Atsushi; Maeda, Shiro; Tsunoda, Tatsuhiko; Chen, Peng; Lim, Su-Chi; Wong, Tien-Yin; Liu, Jianjun; Young, Terri L.; Aung, Tin; Teo, Yik-Ying; Kim, Young Jin; Kang, Daehee; Chen, Chien-Hsiun; Tsai, Fuu-Jen; Chang, Li-Ching; Fann, S. -J. Cathy; Mei, Hao; Hixson, James E.; Chen, Shufeng; Katsuya, Tomohiro; Isono, Masato; Albrecht, Eva; Yamamoto, Kazuhiko; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki; Kato, Norihiro; He, Jiang; Chen, Yuan-Tsong; Tanaka, Toshihiro; Reilly, Muredach P; Schunkert, Heribert; Assimes, Themistocles L.; Hall, Alistair; Hengstenberg, Christian; König, Inke R.; Laaksonen, Reijo; McPherson, Ruth; Thompson, John R.; Thorsteinsdottir, Unnur; Ziegler, Andreas; Absher, Devin; Chen, Li; Cupples13, L. Adrienne; Halperin, Eran; Li, Mingyao; Musunuru, Kiran; Preuss, Michael; Schillert, Arne; Thorleifsson, Gudmar; Wells, George A.; Holm, Hilma; Roberts, Robert; Stewart, Alexandre F. R.; Fortmann, Stephen; Go, Alan; Hlatky, Mark; Iribarren, Carlos; Knowles, Joshua; Myers, Richard; Quertermous, Thomas; Sidney, Steven; Risch, Neil; Tang, Hua; Blankenberg, Stefan; Schnabel, Renate; Sinning, Christoph; Lackner, Karl J.; Tiret, Laurence; Nicaud, Viviane; Cambien, Francois; Bickel, Christoph; Rupprecht, Hans J.; Perret, Claire; Proust, Carole; Münzel, Thomas F.; Barbalic, Maja; Chen, Ida Yii-Der; Demissie-Banjaw, Serkalem; Folsom, Aaron; Lumley, Thomas; Marciante, Kristin; Taylor, Kent D.; Volcik, Kelly; Gretarsdottir, Solveig; Gulcher, Jeffrey R.; Kong, Augustine; Stefansson, Kari; Thorgeirsson, Gudmundur; Andersen, Karl; Fischer, Marcus; Grosshennig, Anika; Linsel-Nitschke, Patrick; Stark, Klaus; Schreiber, Stefan; Aherrahrou, Zouhair; Bruse, Petra; Doering, Angela; Klopp, Norman; Diemert, Patrick; Loley, Christina; Medack, Anja; Nahrstedt, Janja; Peters, Annette; Wagner, Arnika K.; Willenborg, Christina; Böhm, Bernhard O.; Dobnig, Harald; Grammer, Tanja B.; Hoffmann, Michael M.; Meinitzer, Andreas; Winkelmann, Bernhard R.; Pilz, Stefan; Renner, Wilfried; Scharnagl, Hubert; Stojakovic, Tatjana; Tomaschitz, Andreas; Winkler, Karl; Guiducci, Candace; Burtt, Noel; Gabriel, Stacey B.; Dandona, Sonny; Jarinova, Olga; Qu, Liming; Wilensky, Robert; Matthai, William; Hakonarson, Hakon H.; Devaney, Joe; Burnett, Mary Susan; Pichard, Augusto D.; Kent, Kenneth M.; Satler, Lowell; Lindsay, Joseph M.; Waksman, Ron; Knouff, Christopher W.; Waterworth, Dawn M.; Walker, Max C.; Epstein, Stephen E.; Rader, Daniel J.; Nelson, Christopher P.; Wright, Benjamin J.; Balmforth, Anthony J.; Ball, Stephen G.; Loehr, Laura R.; Rosamond, Wayne D.; Benjamin, Emelia; Haritunians, Talin; Couper, David; Murabito, Joanne; Wang, Ying A.; Stricker, Bruno H.; Chang, Patricia P.; Willerson, James T.; Felix, Stephan B.; Watzinger, Norbert; Aragam, Jayashri; Zweiker, Robert; Lind, Lars; Rodeheffer, Richard J.; Greiser, Karin Halina; Deckers, Jaap W.; Stritzke, Jan; Ingelsson, Erik; Kullo, Iftikhar; Haerting, Johannes; Reffelmann, Thorsten; Redfield, Margaret M.; Werdan, Karl; Mitchell, Gary F.; Arnett, Donna K.; Gottdiener, John S.; Blettner, Maria; Friedrich, Nele; Kovacs, Peter; Wild, Philipp S.; Froguel, Philippe; Rettig, Rainer; Mägi, Reedik; Biffar, Reiner; Schmidt, Reinhold; Middelberg, Rita P. S.; Carroll, Robert J.; Penninx, Brenda W.; Scott, Rodney J.; Katz, Ronit; Sedaghat, Sanaz; Wild, Sarah H.; Kardia, Sharon L. R.; Ulivi, Sheila; Hwang, Shih-Jen; Enroth, Stefan; Kloiber, Stefan; Trompet, Stella; Stengel, Benedicte; Hancock, Stephen J.; Turner, Stephen T.; Rosas, Sylvia E.; Stracke, Sylvia; Harris, Tamara B.; Zeller, Tanja; Zemunik, Tatijana; Lehtimäki, Terho; Illig, Thomas; Aspelund, Thor; Nikopensius, Tiit; Esko, Tonu; Tanaka, Toshiko; Gyllensten, Ulf; Völker, Uwe; Emilsson, Valur; Vitart, Veronique; Aalto, Ville; Gudnason, Vilmundur; Chouraki, Vincent; Chen, Wei-Min; Igl, Wilmar; März, Winfried; Koenig, Wolfgang; Lieb, Wolfgang; Loos, Ruth J. F.; Liu, Yongmei; Snieder, Harold; Pramstaller, Peter P.; Parsa, Afshin; O'Connell, Jeffrey R.; Susztak, Katalin; Hamet, Pavel; Tremblay, Johanne; de Boer, Ian H.; Böger, Carsten A.; Goessling, Wolfram; Chasman, Daniel I.; Köttgen, Anna; Kao, W. H. Linda; Fox, Caroline S.

    2016-01-01

    Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways. PMID:26831199

  6. Action video game players' visual search advantage extends to biologically relevant stimuli.

    PubMed

    Chisholm, Joseph D; Kingstone, Alan

    2015-07-01

    Research investigating the effects of action video game experience on cognition has demonstrated a host of performance improvements on a variety of basic tasks. Given the prevailing evidence that these benefits result from efficient control of attentional processes, there has been growing interest in using action video games as a general tool to enhance everyday attentional control. However, to date, there is little evidence indicating that the benefits of action video game playing scale up to complex settings with socially meaningful stimuli - one of the fundamental components of our natural environment. The present experiment compared action video game player (AVGP) and non-video game player (NVGP) performance on an oculomotor capture task that presented participants with face stimuli. In addition, the expression of a distractor face was manipulated to assess if action video game experience modulated the effect of emotion. Results indicate that AVGPs experience less oculomotor capture than NVGPs; an effect that was not influenced by the emotional content depicted by distractor faces. It is noteworthy that this AVGP advantage emerged despite participants being unaware that the investigation had to do with video game playing, and participants being equivalent in their motivation and treatment of the task as a game. The results align with the notion that action video game experience is associated with superior attentional and oculomotor control, and provides evidence that these benefits can generalize to more complex and biologically relevant stimuli.

  7. Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

    PubMed

    Pattaro, Cristian; Teumer, Alexander; Gorski, Mathias; Chu, Audrey Y; Li, Man; Mijatovic, Vladan; Garnaas, Maija; Tin, Adrienne; Sorice, Rossella; Li, Yong; Taliun, Daniel; Olden, Matthias; Foster, Meredith; Yang, Qiong; Chen, Ming-Huei; Pers, Tune H; Johnson, Andrew D; Ko, Yi-An; Fuchsberger, Christian; Tayo, Bamidele; Nalls, Michael; Feitosa, Mary F; Isaacs, Aaron; Dehghan, Abbas; d'Adamo, Pio; Adeyemo, Adebowale; Dieffenbach, Aida Karina; Zonderman, Alan B; Nolte, Ilja M; van der Most, Peter J; Wright, Alan F; Shuldiner, Alan R; Morrison, Alanna C; Hofman, Albert; Smith, Albert V; Dreisbach, Albert W; Franke, Andre; Uitterlinden, Andre G; Metspalu, Andres; Tonjes, Anke; Lupo, Antonio; Robino, Antonietta; Johansson, Åsa; Demirkan, Ayse; Kollerits, Barbara; Freedman, Barry I; Ponte, Belen; Oostra, Ben A; Paulweber, Bernhard; Krämer, Bernhard K; Mitchell, Braxton D; Buckley, Brendan M; Peralta, Carmen A; Hayward, Caroline; Helmer, Catherine; Rotimi, Charles N; Shaffer, Christian M; Müller, Christian; Sala, Cinzia; van Duijn, Cornelia M; Saint-Pierre, Aude; Ackermann, Daniel; Shriner, Daniel; Ruggiero, Daniela; Toniolo, Daniela; Lu, Yingchang; Cusi, Daniele; Czamara, Darina; Ellinghaus, David; Siscovick, David S; Ruderfer, Douglas; Gieger, Christian; Grallert, Harald; Rochtchina, Elena; Atkinson, Elizabeth J; Holliday, Elizabeth G; Boerwinkle, Eric; Salvi, Erika; Bottinger, Erwin P; Murgia, Federico; Rivadeneira, Fernando; Ernst, Florian; Kronenberg, Florian; Hu, Frank B; Navis, Gerjan J; Curhan, Gary C; Ehret, George B; Homuth, Georg; Coassin, Stefan; Thun, Gian-Andri; Pistis, Giorgio; Gambaro, Giovanni; Malerba, Giovanni; Montgomery, Grant W; Eiriksdottir, Gudny; Jacobs, Gunnar; Li, Guo; Wichmann, H-Erich; Campbell, Harry; Schmidt, Helena; Wallaschofski, Henri; Völzke, Henry; Brenner, Hermann; Kroemer, Heyo K; Kramer, Holly; Lin, Honghuang; Leach, I Mateo; Ford, Ian; Guessous, Idris; Rudan, Igor; Prokopenko, Inga; Borecki, Ingrid; Heid, Iris M; Kolcic, Ivana; Persico, Ivana; Jukema, J Wouter; Wilson, James F; Felix, Janine F; Divers, Jasmin; Lambert, Jean-Charles; Stafford, Jeanette M; Gaspoz, Jean-Michel; Smith, Jennifer A; Faul, Jessica D; Wang, Jie Jin; Ding, Jingzhong; Hirschhorn, Joel N; Attia, John; Whitfield, John B; Chalmers, John; Viikari, Jorma; Coresh, Josef; Denny, Joshua C; Karjalainen, Juha; Fernandes, Jyotika K; Endlich, Karlhans; Butterbach, Katja; Keene, Keith L; Lohman, Kurt; Portas, Laura; Launer, Lenore J; Lyytikäinen, Leo-Pekka; Yengo, Loic; Franke, Lude; Ferrucci, Luigi; Rose, Lynda M; Kedenko, Lyudmyla; Rao, Madhumathi; Struchalin, Maksim; Kleber, Marcus E; Cavalieri, Margherita; Haun, Margot; Cornelis, Marilyn C; Ciullo, Marina; Pirastu, Mario; de Andrade, Mariza; McEvoy, Mark A; Woodward, Mark; Adam, Martin; Cocca, Massimiliano; Nauck, Matthias; Imboden, Medea; Waldenberger, Melanie; Pruijm, Menno; Metzger, Marie; Stumvoll, Michael; Evans, Michele K; Sale, Michele M; Kähönen, Mika; Boban, Mladen; Bochud, Murielle; Rheinberger, Myriam; Verweij, Niek; Bouatia-Naji, Nabila; Martin, Nicholas G; Hastie, Nick; Probst-Hensch, Nicole; Soranzo, Nicole; Devuyst, Olivier; Raitakari, Olli; Gottesman, Omri; Franco, Oscar H; Polasek, Ozren; Gasparini, Paolo; Munroe, Patricia B; Ridker, Paul M; Mitchell, Paul; Muntner, Paul; Meisinger, Christa; Smit, Johannes H; Kovacs, Peter; Wild, Philipp S; Froguel, Philippe; Rettig, Rainer; Mägi, Reedik; Biffar, Reiner; Schmidt, Reinhold; Middelberg, Rita P S; Carroll, Robert J; Penninx, Brenda W; Scott, Rodney J; Katz, Ronit; Sedaghat, Sanaz; Wild, Sarah H; Kardia, Sharon L R; Ulivi, Sheila; Hwang, Shih-Jen; Enroth, Stefan; Kloiber, Stefan; Trompet, Stella; Stengel, Benedicte; Hancock, Stephen J; Turner, Stephen T; Rosas, Sylvia E; Stracke, Sylvia; Harris, Tamara B; Zeller, Tanja; Zemunik, Tatijana; Lehtimäki, Terho; Illig, Thomas; Aspelund, Thor; Nikopensius, Tiit; Esko, Tonu; Tanaka, Toshiko; Gyllensten, Ulf; Völker, Uwe; Emilsson, Valur; Vitart, Veronique; Aalto, Ville; Gudnason, Vilmundur; Chouraki, Vincent; Chen, Wei-Min; Igl, Wilmar; März, Winfried; Koenig, Wolfgang; Lieb, Wolfgang; Loos, Ruth J F; Liu, Yongmei; Snieder, Harold; Pramstaller, Peter P; Parsa, Afshin; O'Connell, Jeffrey R; Susztak, Katalin; Hamet, Pavel; Tremblay, Johanne; de Boer, Ian H; Böger, Carsten A; Goessling, Wolfram; Chasman, Daniel I; Köttgen, Anna; Kao, W H Linda; Fox, Caroline S

    2016-01-21

    Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.

  8. Reactivity pathways for nitric oxide and nitrosonium with iron complexes in biologically relevant sulfur coordination spheres.

    PubMed

    Harrop, Todd C; Song, Datong; Lippard, Stephen J

    2007-11-01

    The interaction of nitric oxide (NO) with iron-sulfur cluster proteins results in the formation of dinitrosyl iron complexes (DNICs) coordinated by cysteine residues from the peptide backbone or with low molecular weight sulfur-containing molecules like glutathione. Such DNICs are among the modes available in biology to store, transport, and deliver NO to its relevant targets. In order to elucidate the fundamental chemistry underlying the formation of DNICs and to characterize possible intermediates in the process, we have investigated the interaction of NO (g) and NO(+) with iron-sulfur complexes having the formula [Fe(SR)(4)](2-), where R=(t)Bu, Ph, or benzyl, chosen to mimic sulfur-rich iron sites in biology. The reaction of NO (g) with [Fe(S(t)Bu)(4)](2-) or [Fe(SBz)(4)](2-) cleanly affords the mononitrosyl complexes (MNICs), [Fe(S(t)Bu)(3)(NO)](-) (1) and [Fe(SBz)(3)(NO)](-) (3), respectively, by ligand displacement. Mononitrosyl species of this kind were previously unknown. These complexes further react with NO (g) to generate the corresponding DNICs, [Fe(SPh)(2)(NO)(2)](-) (4) and [Fe(SBz)(2)(NO)(2)](-) (5), with concomitant reductive elimination of the coordinated thiolate donors. Reaction of [Fe(SR)(4)](2-) complexes with NO(+) proceeds by a different pathway to yield the corresponding dinitrosyl S-bridged Roussin red ester complexes, [Fe(2)(mu-S(t)Bu)(2)(NO)(4)] (2), [Fe(2)(mu-SPh)(2)(NO)(4)] (7) and [Fe(2)(mu-SBz)(2)(NO)(4)] (8). The NO/NO(+) reactivity of an Fe(II) complex with a mixed nitrogen/sulfur coordination sphere was also investigated. The DNIC and red ester species, [Fe(S-o-NH(2)C(6)H(4))(2)(NO)(2)](-) (6) and [Fe(2)(mu-S-o-NH(2)C(6)H(4))(2)(NO)(4)] (9), were generated. The structures of 8 and 9 were verified by X-ray crystallography. The MNIC complex 1 can efficiently deliver NO to iron-porphyrin complexes like [Fe(TPP)Cl], a reaction that is aided by light. Removal of the coordinated NO ligand of 1 by photolysis and addition of elemental

  9. Identifying genes relevant to specific biological conditions in time course microarray experiments.

    PubMed

    Singh, Nitesh Kumar; Repsilber, Dirk; Liebscher, Volkmar; Taher, Leila; Fuellen, Georg

    2013-01-01

    Microarrays have been useful in understanding various biological processes by allowing the simultaneous study of the expression of thousands of genes. However, the analysis of microarray data is a challenging task. One of the key problems in microarray analysis is the classification of unknown expression profiles. Specifically, the often large number of non-informative genes on the microarray adversely affects the performance and efficiency of classification algorithms. Furthermore, the skewed ratio of sample to variable poses a risk of overfitting. Thus, in this context, feature selection methods become crucial to select relevant genes and, hence, improve classification accuracy. In this study, we investigated feature selection methods based on gene expression profiles and protein interactions. We found that in our setup, the addition of protein interaction information did not contribute to any significant improvement of the classification results. Furthermore, we developed a novel feature selection method that relies exclusively on observed gene expression changes in microarray experiments, which we call "relative Signal-to-Noise ratio" (rSNR). More precisely, the rSNR ranks genes based on their specificity to an experimental condition, by comparing intrinsic variation, i.e. variation in gene expression within an experimental condition, with extrinsic variation, i.e. variation in gene expression across experimental conditions. Genes with low variation within an experimental condition of interest and high variation across experimental conditions are ranked higher, and help in improving classification accuracy. We compared different feature selection methods on two time-series microarray datasets and one static microarray dataset. We found that the rSNR performed generally better than the other methods.

  10. An investigation of hemopexin redox properties by spectroelectrochemistry: biological relevance for heme uptake.

    PubMed

    Flaherty, Meghan M; Rish, Kimberley R; Smith, Ann; Crumbliss, Alvin L

    2008-06-01

    Hemopexin (HPX) has two principal roles: it sequesters free heme in vivo for the purpose of preventing the toxic effects of this moiety, which is largely due to heme's ability to catalyze free radical formation, and it transports heme intracellularly thus limiting its availability as an iron source for pathogens. Spectroelectrochemistry was used to determine the redox potential for heme and meso-heme (mH) when bound by HPX. At pH 7.2, the heme-HPX assembly exhibits E (1/2) values in the range 45-90 mV and the mH-HPX assembly in the range 5-55 mV, depending on environmental electrolyte identity. The E (1/2) value exhibits a 100 mV positive shift with a change in pH from 7.2 to 5.5 for mH-HPX, suggesting a single proton dependent equilibrium. The E (1/2) values for heme-HPX are more positive in the presence of NaCl than KCl indicating that Na(+), as well as low pH (5.5) stabilizes ferro-heme-HPX. Furthermore, comparing KCl with K(2)HPO(4), the chloride salt containing system has a lower potential, indicating that heme-HPX is easier to oxidize. These physical properties related to ferri-/ferro-heme reduction are both structurally and biologically relevant for heme release from HPX for transport and regulation of heme oxygenase expression. Consistent with this, when the acidification of endosomes is prevented by bafilomycin then heme oxygenase-1 induction by heme-HPX no longer occurs. PMID:17712531

  11. Epigenetic regulation of EFEMP1 in prostate cancer: biological relevance and clinical potential

    PubMed Central

    Almeida, Mafalda; Costa, Vera L; Costa, Natália R; Ramalho-Carvalho, João; Baptista, Tiago; Ribeiro, Franclim R; Paulo, Paula; Teixeira, Manuel R; Oliveira, Jorge; Lothe, Ragnhild A; Lind, Guro E; Henrique, Rui; Jerónimo, Carmen

    2014-01-01

    Epigenetic alterations are common in prostate cancer (PCa) and seem to contribute decisively to its initiation and progression. Moreover, aberrant promoter methylation is a promising biomarker for non-invasive screening. Herein, we sought to characterize EFEMP1 as biomarker for PCa, unveiling its biological relevance in prostate carcinogenesis. Microarray analyses of treated PCa cell lines and primary tissues enabled the selection of differentially methylated genes, among which EFEMP1 was further validated by MSP and bisulfite sequencing. Assessment of biomarker performance was accomplished by qMSP. Expression analysis of EFEMP1 and characterization of histone marks were performed in tissue samples and cancer cell lines to determine the impact of epigenetic mechanisms on EFEMP1 transcriptional regulation. Phenotypic assays, using transfected cell lines, permitted the evaluation of EFEMP1’s role in PCa development. EFEMP1 methylation assay discriminated PCa from normal prostate tissue (NPT; P < 0.001, Kruskall–Wallis test) and renal and bladder cancers (96% sensitivity and 98% specificity). EFEMP1 transcription levels inversely correlated with promoter methylation and histone deacetylation, suggesting that both epigenetic mechanisms are involved in gene regulation. Phenotypic assays showed that EFEMP1 de novo expression reduces malignant phenotype of PCa cells. EFEMP1 promoter methylation is prevalent in PCa and accurately discriminates PCa from non-cancerous prostate tissues and other urological neoplasms. This epigenetic alteration occurs early in prostate carcinogenesis and, in association with histone deacetylation, progressively leads to gene down-regulation, fostering cell proliferation, invasion and evasion of apoptosis. PMID:25211630

  12. The interaction of aluminum with silicic acid in dilute solution and its biological relevance

    SciTech Connect

    Chappell, J.S.; Birchall, J.D. )

    1988-09-01

    The affinity of silicic acid, Si(OH){sub 4}, for aluminum is a unique one in chemistry, owing to ionic size, charge, and coordination geometry of the species involved. The chemistry of aluminosilicates generally has been concerned with the solid state (minerals such as clays, feldspars and zeolites), and relatively little attention has been given to the species which exist in solution since aluminosilicates are highly insoluble near neutral pH. However, under dilute conditions the kinetics of colloid formation can be quite slow and the soluble precursors to a solid phase may be reasonably metastable. When equilibrium is approached, the solubility levels are typically 0.05-0.28 {mu}mol/L Al and 18-210 {mu}mol/L Si. These soluble species are usually regarded as simple hydroxyaluminum ions and silicic acid, although it remains arguable as to whether these species may be associated with each other. The formation of a stable soluble specie would allow for molecular aluminosilicates to exist at below saturation levels. So at concentrations above saturation stable aluminosilicates do form (as a part of an insoluble phase), and they may possibly exist at below saturation (as a stable soluble specie). This interaction is then relevant to biology, where human plasma levels (0.06-0.54 {mu}mol/L Al, 14-39 {mu}mol/L Si) (6,7) fall among saturation values. There is a growing concern over the toxic effects of aluminum, but its chemistry with silicic acid has not been addressed. This chemistry is the topic of this study.

  13. Solid-supported cross-metathesis and a formal alkane metathesis for the generation of biologically relevant molecules.

    PubMed

    Méndez, Luciana; Mata, Ernesto G

    2015-02-01

    Solid-phase synthetic strategies toward the generation of libraries of biologically relevant molecules were developed using olefin cross-metathesis as a key step. It is remarkably the formal alkane metathesis based on a one-pot, microwave-assisted, ruthenium-catalyzed cross-metathesis and reduction to obtain Csp3-Csp3 linkages.

  14. Exploring the other side of biologically relevant chemical space: insights into carboxylic, sulfonic and phosphonic acid bioisosteric relationships.

    PubMed

    Macchiarulo, Antonio; Pellicciari, Roberto

    2007-11-01

    Bioisosteric replacements have been widely and successfully applied to develop bioisosteric series of biologically active compounds in medicinal chemistry. In this work, the concept of bioisosterism is revisited using a novel approach based on charting the "other side" of biologically relevant chemical space. This space is composed by the ensemble of binding sites of protein structures. Explorations into the "other side" of biologically relevant chemical space are exploited to gain insight into the principles that rules molecular recognition and bioisosteric relationships of molecular fragments. We focused, in particular, on the construction of the "other side" of chemical space covered by binding sites of small molecules containing carboxylic, sulfonic, and phosphonic acidic groups. The analysis of differences in the occupation of that space by distinct types of binding sites unveils how evolution has worked in assessing principles that rule the selectivity of molecular recognition, and improves our knowledge on the molecular basis of bioisosteric relationships among carboxylic, sulfonic, and phosphonic acidic groups.

  15. Enhanced stability and local structure in biologically relevant amorphous materials containing pyrophosphate

    SciTech Connect

    Slater, Colin; Laurencin, Danielle; Burnell, Victoria; Smith, Mark E.; Grover, Liam M.; Hriljac, Joseph A.; Wright, Adrian J.

    2012-10-25

    There is increasing evidence that amorphous inorganic materials play a key role in biomineralisation in many organisms, however the inherent instability of synthetic analogues in the absence of the complex in vivo matrix limits their study and clinical exploitation. To address this, we report here an approach that enhances long-term stability to >1 year of biologically relevant amorphous metal phosphates, in the absence of any complex stabilizers, by utilizing pyrophosphates (P{sub 2}O{sub 7}{sup 4-}); species themselves ubiquitous in vivo. Ambient temperature precipitation reactions were employed to synthesise amorphous Ca{sub 2}P{sub 2}O{sub 7}.nH{sub 2}O and Sr{sub 2}P{sub 2}O{sub 7}.nH{sub 2}O (3.8 < n < 4.2) and their stability and structure were investigated. Pair distribution functions (PDF) derived from synchrotron X-ray data indicated a lack of structural order beyond 8 {angstrom} in both phases, with this local order found to resemble crystalline analogues. Further studies, including {sup 1}H and {sup 31}P solid state NMR, suggest the unusually high stability of these purely inorganic amorphous phases is partly due to disorder in the P-O-P bond angles within the P{sub 2}O{sub 7} units, which impede crystallization, and to water molecules, which are involved in H-bonds of various strengths within the structures and hamper the formation of an ordered network. In situ high temperature powder X-ray diffraction data indicated that the amorphous nature of both phases surprisingly persisted to 450 C. Further NMR and TGA studies found that above ambient temperature some water molecules reacted with P{sub 2}O{sub 7} anions, leading to the hydrolysis of some P-O-P linkages and the formation of HPO{sub 4}{sup 2-} anions within the amorphous matrix. The latter anions then recombined into P{sub 2}O{sub 7} ions at higher temperatures prior to crystallization. Together, these findings provide important new materials with unexplored potential for enzyme

  16. "Evo in the News:" Understanding Evolution and Students' Attitudes toward the Relevance of Evolutionary Biology

    ERIC Educational Resources Information Center

    Infanti, Lynn M.; Wiles, Jason R.

    2014-01-01

    This investigation evaluated the effects of exposure to the "Evo in the News" section of the "Understanding Evolution" website on students' attitudes toward biological evolution in undergraduates in a mixed-majors introductory biology course at Syracuse University. Students' attitudes toward evolution and changes therein were…

  17. CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

    PubMed Central

    Bleda, Marta; Tarraga, Joaquin; de Maria, Alejandro; Salavert, Francisco; Garcia-Alonso, Luz; Celma, Matilde; Martin, Ainoha; Dopazo, Joaquin; Medina, Ignacio

    2012-01-01

    During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase. PMID:22693220

  18. Enhanced surface functionality via plasma modification and plasma deposition techniques to create more biologically relevant materials

    NASA Astrophysics Data System (ADS)

    Shearer, Jeffrey C.

    Functionalizing nanoparticles and other unusually shaped substrates to create more biologically relevant materials has become central to a wide range of research programs. One of the primary challenges in this field is creating highly functionalized surfaces without modifying the underlying bulk material. Traditional wet chemistry techniques utilize thin film depositions to functionalize nanomaterials with oxygen and nitrogen containing functional groups, such as --OH and --NHx. These functional groups can serve to create surfaces that are amenable to cell adhesion or can act as reactive groups for further attachment of larger structures, such as macromolecules or antiviral agents. Additional layers, such as SiO2, are often added between the nanomaterial and the functionalized coating to act as a barrier films, adhesion layers, and to increase overall hydrophilicity. However, some wet chemistry techniques can damage the bulk material during processing. This dissertation examines the use of plasma processing as an alternative method for producing these highly functionalized surfaces on nanoparticles and polymeric scaffolds through the use of plasma modification and plasma enhanced chemical vapor deposition techniques. Specifically, this dissertation will focus on (1) plasma deposition of SiO2 barrier films on nanoparticle substrates; (2) surface functionalization of amine and alcohol groups through (a) plasma co-polymerization and (b) plasma modification; and (3) the design and construction of plasma hardware to facilitate plasma processing of nanoparticles and polymeric scaffolds. The body of work presented herein first examines the fabrication of composite nanoparticles by plasma processing. SiOxC y and hexylamine films were coated onto TiO2 nanoparticles to demonstrate enhanced water dispersion properties. Continuous wave and pulsed allyl alcohol plasmas were used to produce highly functionalized Fe2 O3 supported nanoparticles. Specifically, film composition was

  19. Biologically effective dose distribution based on the linear quadratic model and its clinical relevance

    SciTech Connect

    Lee, S.P.; Smathers, J.B.; Withers, H.R.

    1995-09-30

    Radiotherapy plans based on physical dose distributions do not necessarily entirely reflect the biological effects under various fractionation schemes. Over the past decade, the linear-quadratic (LQ) model has emerged as a convenient tool to quantify biological effects for radiotherapy. In this work, we set out to construct a mechanism to display biologically oriented dose distribution based on the LQ model. A computer program that converts a physical dose distribution calculated by a commercially available treatment planning system to a biologically effective dose (BED) distribution has been developed and verified against theoretical calculations. This software accepts a user`s input of biological parameters for each structure of interest (linear and quadratic dose-response and repopulation kinetic parameters), as well as treatment scheme factors (number of fractions, fractional dose, and treatment time). It then presents a two-dimensional BED display in conjunction with anatomical structures. Furthermore, to facilitate clinicians` intuitive comparison with conventional fractionation regimen, a conversion of BED to normalized isoeffective dose (NID) is also allowed. We have demonstrated the feasibility of constructing a biologically oriented dose distribution for clinical practice of radiotherapy. The discordance between physical dose distributions and the biological counterparts based on the given treatment schemes was quantified. The computerized display of BED at nonprescription points greatly enhanced the versatility of this tool. Although the routine use of this implementation in clinical radiotherapy should be cautiously done, depending largely on the accuracy of the published biological parameters, it may, nevertheless, help the clinicians derive an optimal treatment plan with a particular fractionation scheme or use it as a quantitative tool for outcome analysis in clinical research. 45 refs., 3 figs., 5 tabs.

  20. Metal-based nanotoxicity and detoxification pathways in higher plants.

    PubMed

    Ma, Chuanxin; White, Jason C; Dhankher, Om Parkash; Xing, Baoshan

    2015-06-16

    The potential risks from metal-based nanoparticles (NPs) in the environment have increased with the rapidly rising demand for and use of nanoenabled consumer products. Plant's central roles in ecosystem function and food chain integrity ensure intimate contact with water and soil systems, both of which are considered sinks for NPs accumulation. In this review, we document phytotoxicity caused by metal-based NPs exposure at physiological, biochemical, and molecular levels. Although the exact mechanisms of plant defense against nanotoxicity are unclear, several relevant studies have been recently published. Possible detoxification pathways that might enable plant resistance to oxidative stress and facilitate NPs detoxification are reviewed herein. Given the importance of understanding the effects and implications of metal-based NPs on plants, future research should focus on the following: (1) addressing key knowledge gaps in understanding molecular and biochemical responses of plants to NPs stress through global transcriptome, proteome, and metablome assays; (2) designing long-term experiments under field conditions at realistic exposure concentrations to investigate the impact of metal-based NPs on edible crops and the resulting implications to the food chain and to human health; and (3) establishing an impact assessment to evaluate the effects of metal-based NPs on plants with regard to ecosystem structure and function.

  1. Teleology then and now: the question of Kant's relevance for contemporary controversies over function in biology.

    PubMed

    Zammito, John

    2006-12-01

    'Naturalism' is the aspiration of contemporary philosophy of biology, and Kant simply cannot be refashioned into a naturalist. Instead, epistemological 'deflation' was the decisive feature of Kant's treatment of the 'biomedical' science in his day, so it is not surprising that this might attract some philosophers of science to him today. A certain sense of impasse in the contemporary 'function talk' seems to motivate renewed interest in Kant. Kant--drawing on his eighteenth-century predecessors-provided a discerning and powerful characterization of what biologists had to explain in organic form. His difference from the rest is that he opined that it was impossible to explain it. Its 'inscrutability' was intrinsic. The third Critique essentially proposed the reduction of biology to a kind of pre-scientific descriptivism, doomed never to attain authentic scientificity, to have its 'Newton of the blade of grass'. By contrast, for Locke, and a fortiori for Buffon and his followers, 'intrinsic purposiveness' was a fact of the matter about concrete biological phenomena; the features of internal self-regulation were hypotheses arising out of actual research practice. The difference comes most vividly to light once we recognize Kant's distinction of the concept of organism from the concept of life. If biology must conceptualize self-organization as actual in the world, Kant's regulative/constitutive distinction is pointless in practice and the (naturalist) philosophy of biology has urgent work to undertake for which Kant turns out not to be very helpful. PMID:17157770

  2. Teleology then and now: the question of Kant's relevance for contemporary controversies over function in biology.

    PubMed

    Zammito, John

    2006-12-01

    'Naturalism' is the aspiration of contemporary philosophy of biology, and Kant simply cannot be refashioned into a naturalist. Instead, epistemological 'deflation' was the decisive feature of Kant's treatment of the 'biomedical' science in his day, so it is not surprising that this might attract some philosophers of science to him today. A certain sense of impasse in the contemporary 'function talk' seems to motivate renewed interest in Kant. Kant--drawing on his eighteenth-century predecessors-provided a discerning and powerful characterization of what biologists had to explain in organic form. His difference from the rest is that he opined that it was impossible to explain it. Its 'inscrutability' was intrinsic. The third Critique essentially proposed the reduction of biology to a kind of pre-scientific descriptivism, doomed never to attain authentic scientificity, to have its 'Newton of the blade of grass'. By contrast, for Locke, and a fortiori for Buffon and his followers, 'intrinsic purposiveness' was a fact of the matter about concrete biological phenomena; the features of internal self-regulation were hypotheses arising out of actual research practice. The difference comes most vividly to light once we recognize Kant's distinction of the concept of organism from the concept of life. If biology must conceptualize self-organization as actual in the world, Kant's regulative/constitutive distinction is pointless in practice and the (naturalist) philosophy of biology has urgent work to undertake for which Kant turns out not to be very helpful.

  3. The Molecular Biology Database Collection: an online compilation of relevant database resources

    PubMed Central

    Baxevanis, Andreas D.

    2000-01-01

    The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists. This online resource, available at http://www.oup.co.uk/nar/Volume_28/Issue_01/html/gkd115_gml.html, is intended to serve as a searchable, up-to-date, centralized jumping-off point to individual Web sites. An emphasis has also been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections, or other innovative approaches. PMID:10592167

  4. The Specific Relationship between Disgust and Interest: Relevance during Biology Class Dissections and Gender Differences

    ERIC Educational Resources Information Center

    Holstermann, Nina; Ainley, Mary; Grube, Dietmar; Roick, Thorsten; Bogeholz, Susanne

    2012-01-01

    This investigation examined trajectories of interest and disgust related to a biology dissection class. Three hundred and two secondary students completed ratings of disgust sensitivity and individual interest in the topic of the heart approximately one week before a dissection class. States of disgust and interest were recorded before, during,…

  5. An overview of computational life science databases & exchange formats of relevance to chemical biology research.

    PubMed

    Smalter Hall, Aaron; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

    2013-03-01

    Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities.

  6. Soluble Epidermal Growth Factor Receptors (sEGFRs) in Cancer: Biological Aspects and Clinical Relevance

    PubMed Central

    Maramotti, Sally; Paci, Massimiliano; Manzotti, Gloria; Rapicetta, Cristian; Gugnoni, Mila; Galeone, Carla; Cesario, Alfredo; Lococo, Filippo

    2016-01-01

    The identification of molecules that can reliably detect the presence of a tumor or predict its behavior is one of the biggest challenges of research in cancer biology. Biological fluids are intriguing mediums, containing many molecules that express the individual health status and, accordingly, may be useful in establishing the potential risk of cancer, defining differential diagnosis and prognosis, predicting the response to treatment, and monitoring the disease progression. The existence of circulating soluble growth factor receptors (sGFRs) deriving from their membrane counterparts has stimulated the interest of researchers to investigate the use of such molecules as potential cancer biomarkers. But what are the origins of circulating sGFRs? Are they naturally occurring molecules or tumor-derived products? Among these, the epidermal growth factor receptor (EGFR) is a cell-surface molecule significantly involved in cancer development and progression; it can be processed into biological active soluble isoforms (sEGFR). We have carried out an extensive review of the currently available literature on the sEGFRs and their mechanisms of regulation and biological function, with the intent to clarify the role of these molecules in cancer (and other pathological conditions) and, on the basis of the retrieved evidences, speculate about their potential use in the clinical setting. PMID:27104520

  7. Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments (Final Report)

    EPA Science Inventory

    This technical paper provides defensible approximations for what the depth of the biologically active zone, or “biotic zone” is within certain environments. The methods used in this study differ somewhat between Part 1 (Terrestrial Biotic Zone) and Part 2 (Aquatic Biotic Zone). ...

  8. AN OVERVIEW OF COMPUTATIONAL LIFE SCIENCE DATABASES & EXCHANGE FORMATS OF RELEVANCE TO CHEMICAL BIOLOGY RESEARCH

    PubMed Central

    Hall, Aaron Smalter; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

    2016-01-01

    Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities. PMID:22934944

  9. Biologically relevant mechanism for catalytic superoxide removal by simple manganese compounds

    PubMed Central

    Barnese, Kevin; Gralla, Edith Butler; Valentine, Joan Selverstone; Cabelli, Diane E.

    2012-01-01

    Nonenzymatic manganese was first shown to provide protection against superoxide toxicity in vivo in 1981, but the chemical mechanism responsible for this protection subsequently became controversial due to conflicting reports concerning the ability of Mn to catalyze superoxide disproportionation in vitro. In a recent communication, we reported that low concentrations of a simple Mn phosphate salt under physiologically relevant conditions will indeed catalyze superoxide disproportionation in vitro. We report now that two of the four Mn complexes that are expected to be most abundant in vivo, Mn phosphate and Mn carbonate, can catalyze superoxide disproportionation at physiologically relevant concentrations and pH, whereas Mn pyrophosphate and citrate complexes cannot. Additionally, the chemical mechanisms of these reactions have been studied in detail, and the rates of reactions of the catalytic removal of superoxide by Mn phosphate and carbonate have been modeled. Physiologically relevant concentrations of these compounds were found to be sufficient to mimic an effective concentration of enzymatic superoxide dismutase found in vivo. This mechanism provides a likely explanation as to how Mn combats superoxide stress in cellular systems. PMID:22505740

  10. Biologically Relevant Mechanism For Catalytic Removal of Superoxide by Simple Manganese Compounds

    SciTech Connect

    Barnese K.; Cabelli D.; Gralla, E.B.; Valentine, J.S.

    2012-05-01

    Nonenzymatic manganese was first shown to provide protection against superoxide toxicity in vivo in 1981, but the chemical mechanism responsible for this protection subsequently became controversial due to conflicting reports concerning the ability of Mn to catalyze superoxide disproportionation in vitro. In a recent communication, we reported that low concentrations of a simple Mn phosphate salt under physiologically relevant conditions will indeed catalyze superoxide disproportionation in vitro. We report now that two of the four Mn complexes that are expected to be most abundant in vivo, Mn phosphate and Mn carbonate, can catalyze superoxide disproportionation at physiologically relevant concentrations and pH, whereas Mn pyrophosphate and citrate complexes cannot. Additionally, the chemical mechanisms of these reactions have been studied in detail, and the rates of reactions of the catalytic removal of superoxide by Mn phosphate and carbonate have been modeled. Physiologically relevant concentrations of these compounds were found to be sufficient to mimic an effective concentration of enzymatic superoxide dismutase found in vivo. This mechanism provides a likely explanation as to how Mn combats superoxide stress in cellular systems.

  11. Relevance of Crop Biology for Environmental Risk Assessment of Genetically Modified Crops in Africa.

    PubMed

    Akinbo, Olalekan; Hancock, James F; Makinde, Diran

    2015-01-01

    Knowledge about the crop biology of economic crops in Africa is needed for regulators to accurately review dossiers and conduct comprehensive environmental risk assessments (ERAs). This information allows regulators to decide whether biotech crops present a risk to biodiversity, since crossing between domesticated crops and their wild relatives could affect the adaptations of the wild species. The criteria that should be used in the evaluation of African crops for ERA include growth habit, center of origin, center of genetic diversity, proximity of wild relatives, inter-fertility, mode of pollen dispersal, length of pollen viability, mating system, invasiveness, weediness, mode of propagation, mode of seed dispersal, and length of seed dormancy. In this paper, we discuss the crops being genetic engineered in Africa and describe the crop biology of those with native relatives.

  12. Relevance of Crop Biology for Environmental Risk Assessment of Genetically Modified Crops in Africa

    PubMed Central

    Akinbo, Olalekan; Hancock, James F.; Makinde, Diran

    2015-01-01

    Knowledge about the crop biology of economic crops in Africa is needed for regulators to accurately review dossiers and conduct comprehensive environmental risk assessments (ERAs). This information allows regulators to decide whether biotech crops present a risk to biodiversity, since crossing between domesticated crops and their wild relatives could affect the adaptations of the wild species. The criteria that should be used in the evaluation of African crops for ERA include growth habit, center of origin, center of genetic diversity, proximity of wild relatives, inter-fertility, mode of pollen dispersal, length of pollen viability, mating system, invasiveness, weediness, mode of propagation, mode of seed dispersal, and length of seed dormancy. In this paper, we discuss the crops being genetic engineered in Africa and describe the crop biology of those with native relatives. PMID:26501055

  13. Inorganic concepts relevant to metal binding, activity, and toxicity in a biological system

    SciTech Connect

    Hoeschele, J.D. . Parke-Davis Pharmaceutical Research Div.); Turner, J.E.; England, M.W. )

    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.

  14. Plasma Jet (V)UV-Radiation Impact on Biologically Relevant Liquids and Cell Suspension

    NASA Astrophysics Data System (ADS)

    Tresp, H.; Bussiahn, R.; Bundscherer, L.; Monden, A.; Hammer, M. U.; Masur, K.; Weltmann, K.-D.; Woedtke, Th. V.; Reuter, S.

    2014-10-01

    In this study the generation of radicals in plasma treated liquids has been investigated. To quantify the contribution of plasma vacuum ultraviolet (VUV) and ultraviolet (UV) radiation on the species investigated, three cases have been studied: UV of plasma jet only, UV and VUV of plasma jet combined, and the plasma effluent including all reactive components. The emitted VUV has been observed by optical emission spectroscopy and its effect on radical formation in liquids has been analyzed by electron spin resonance spectroscopy. Radicals have been determined in ultrapure water (dH2O), as well as in more complex, biorelevant solutions like phosphate buffered saline (PBS) solution, and two different cell culture media. Various compositions lead to different reactive species formation, e.g. in PBS superoxide anion and hydroxyl radicals have been detected, in cell suspension also glutathione thiyl radicals have been found. This study highlights that UV has no impact on radical generation, whereas VUV is relevant for producing radicals. VUV treatment of dH2O generates one third of the radical concentration produced by plasma-effluent treatment. It is relevant for plasma medicine because although plasma sources are operated in open air atmosphere, still VUV can lead to formation of biorelevant radicals. This work is funded by German Federal Ministry of Education a Research (BMBF) (Grant # 03Z2DN12+11).

  15. The relevance and potential roles of microphysiological systems in biology and medicine

    PubMed Central

    Wikswo, John P.

    2014-01-01

    Microphysiological systems (MPS), consisting of interacting organs-on-chips or tissue-engineered, 3D organ constructs that use human cells, present an opportunity to bring new tools to biology, medicine, pharmacology, physiology, and toxicology. This issue of Experimental Biology and Medicine describes the ongoing development of MPS that can serve as in vitro models for bone and cartilage, brain, gastrointestinal tract, lung, liver, microvasculature, reproductive tract, skeletal muscle, and skin. Related topics addressed here are the interconnection of organs-on-chips to support physiologically based pharmacokinetics and drug discovery and screening, and the microscale technologies that regulate stem cell differentiation. The initial motivation for creating MPS was to increase the speed, efficiency, and safety of pharmaceutical development and testing, paying particular regard to the fact that neither monolayer monocultures of immortal or primary cell lines nor animal studies can adequately recapitulate the dynamics of drug-organ, drug-drug, and drug-organ-organ interactions in humans. Other applications include studies of the effect of environmental toxins on humans, identification, characterization, and neutralization of chemical and biological weapons, controlled studies of the microbiome and infectious disease that cannot be conducted in humans, controlled differentiation of induced pluripotent stem cells into specific adult cellular phenotypes, and studies of the dynamics of metabolism and signaling within and between human organs. The technical challenges are being addressed by many investigators, and in the process, it seems highly likely that significant progress will be made toward providing more physiologically realistic alternatives to monolayer monocultures or whole animal studies. The effectiveness of this effort will be determined in part by how easy the constructs are to use, how well they function, how accurately they recapitulate and report human

  16. Biologically relevant 3D tumor arrays: treatment response and the importance of stromal partners

    NASA Astrophysics Data System (ADS)

    Rizvi, Imran; Celli, Jonathan P.; Xu, Feng; Evans, Conor L.; Abu-Yousif, Adnan O.; Muzikansky, Alona; Elrington, Stefan A.; Pogue, Brian W.; Finkelstein, Dianne M.; Demirci, Utkan; Hasan, Tayyaba

    2011-02-01

    The development and translational potential of therapeutic strategies for cancer is limited, in part, by a lack of biological models that capture important aspects of tumor growth and treatment response. It is also becoming increasingly evident that no single treatment will be curative for this complex disease. Rationally-designed combination regimens that impact multiple targets provide the best hope of significantly improving clinical outcomes for cancer patients. Rapidly identifying treatments that cooperatively enhance treatment efficacy from the vast library of candidate interventions is not feasible, however, with current systems. There is a vital, unmet need to create cell-based research platforms that more accurately mimic the complex biology of human tumors than monolayer cultures, while providing the ability to screen therapeutic combinations more rapidly than animal models. We have developed a highly reproducible in vitro three-dimensional (3D) tumor model for micrometastatic ovarian cancer (OvCa), which in conjunction with quantitative image analysis routines to batch-process large datasets, serves as a high throughput reporter to screen rationally-designed combination regimens. We use this system to assess mechanism-based combination regimens with photodynamic therapy (PDT), which sensitizes OvCa to chemo and biologic agents, and has shown promise in clinic trials. We show that PDT synergistically enhances carboplatin efficacy in a sequence dependent manner. In printed heterocellular cultures we demonstrate that proximity of fibroblasts enhances 3D tumor growth and investigate co-cultures with endothelial cells. The principles described here could inform the design and evaluation of mechanism-based therapeutic options for a broad spectrum of metastatic solid tumors.

  17. Concise Review: Quiescence in Adult Stem Cells: Biological Significance and Relevance to Tissue Regeneration.

    PubMed

    Rumman, Mohammad; Dhawan, Jyotsna; Kassem, Moustapha

    2015-10-01

    Adult stem cells (ASCs) are tissue resident stem cells responsible for tissue homeostasis and regeneration following injury. In uninjured tissues, ASCs exist in a nonproliferating, reversibly cell cycle-arrested state known as quiescence or G0. A key function of the quiescent state is to preserve stemness in ASCs by preventing precocious differentiation, and thus maintaining a pool of undifferentiated ASCs. Recent evidences suggest that quiescence is an actively maintained state and that excessive or defective quiescence may lead to compromised tissue regeneration or tumorigenesis. The aim of this review is to provide an update regarding the biological mechanisms of ASC quiescence and their role in tissue regeneration.

  18. Ion-selective interactions of biologically relevant inorganic ions with alanine zwitterion: a 3D-RISM study.

    PubMed

    Fedotova, Marina V; Dmitrieva, Olga A

    2015-05-01

    The ion-molecular association between inorganic ions and the charged groups of alanine zwitterion in biologically relevant aqueous salt solutions, namely NaCl(aq), KCl(aq), MgCl2(aq), and CaCl2(aq), has been investigated over a wide range of electrolyte concentration. The influence of salt concentration on the stability of the formed ion-molecular associates is analyzed. The structure of the formed aggregates and its dependence on salt concentration and chemical nature of the inorganic ion are discussed.

  19. Solid State Structures of Alkali Metal Ion Complexes Formed by Low-Molecular-Weight Ligands of Biological Relevance.

    PubMed

    Aoki, Katsuyuki; Murayama, Kazutaka; Hu, Ning-Hai

    2016-01-01

    This chapter provides structural data, mainly metal binding sites/modes, observed in crystal structures of alkali metal ion complexes containing low-molecular-weight ligands of biological relevance, mostly obtained from the Cambridge Structural Database (the CSD version 5.35 updated to February 2014). These ligands include (i) amino acids and small peptides, (ii) nucleic acid constituents (excluding quadruplexes and other oligonucleotides), (iii) simple carbohydrates, and (iv) naturally occurring antibiotic ionophores. For some representative complexes of these ligands, some details on the environment of the metal coordination and structural characteristics are described. PMID:26860299

  20. The relevance of nanoscale biological fragments for ice nucleation in clouds

    NASA Astrophysics Data System (ADS)

    O‧Sullivan, D.; Murray, B. J.; Ross, J. F.; Whale, T. F.; Price, H. C.; Atkinson, J. D.; Umo, N. S.; Webb, M. E.

    2015-01-01

    Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles.

  1. The relevance of nanoscale biological fragments for ice nucleation in clouds

    PubMed Central

    O′Sullivan, D.; Murray, B. J.; Ross, J. F.; Whale, T. F.; Price, H. C.; Atkinson, J. D.; Umo, N. S.; Webb, M. E.

    2015-01-01

    Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles. PMID:25626414

  2. Recent advances in superhydrophobic surfaces and their relevance to biology and medicine.

    PubMed

    Ciasca, G; Papi, M; Businaro, L; Campi, G; Ortolani, M; Palmieri, V; Cedola, A; De Ninno, A; Gerardino, A; Maulucci, G; De Spirito, M

    2016-02-01

    By mimicking naturally occurring superhydrophobic surfaces, scientists can now realize artificial surfaces on which droplets of a few microliters of water are forced to assume an almost spherical shape and an extremely high contact angle. In recent decades, these surfaces have attracted much attention due to their technological applications for anti-wetting and self-cleaning materials. Very recently, researchers have shifted their interest to investigate whether superhydrophobic surfaces can be exploited to study biological systems. This research effort has stimulated the design and realization of new devices that allow us to actively organize, visualize and manipulate matter at both the microscale and nanoscale levels. Such precise control opens up wide applications in biomedicine, as it allows us to directly manipulate objects at the typical length scale of cells and macromolecules. This progress report focuses on recent biological and medical applications of superhydrophobicity. Particular regard is paid to those applications that involve the detection, manipulation and study of extremely small quantities of molecules, and to those that allow high throughput cell and biomaterial screening. PMID:26844980

  3. The relevance of nanoscale biological fragments for ice nucleation in clouds.

    PubMed

    O'Sullivan, D; Murray, B J; Ross, J F; Whale, T F; Price, H C; Atkinson, J D; Umo, N S; Webb, M E

    2015-01-28

    Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles.

  4. Advances in clarifying the phylogenetic relationships of acacias: Relevance for biological control

    NASA Astrophysics Data System (ADS)

    Kleinjan, C. A.; Hoffmann, J. H.

    2013-04-01

    Biological control of invasive Australian acacias will benefit from recent advances in resolving the phylogenetic relationships of Acacia s.l. and Acacia s.s. ("Australian acacias") within the subfamily Mimosoideae. Some of the phytophage taxa associated with Acacia s.s. display fidelity to a derived clade within the genus. This derived clade contains most of the Acacia s.s. species that have become problematic around the world. Phytophages that are demonstrably restricted to species within the derived clade pose essentially no risk to species outside Acacia s.s.. In contrast, prospective agents able to develop on species in the basal lineages of Acacia s.s. would require more-expansive testing because Acacia s.s. is closely related to the Ingeae, and then sequentially to the genera Acaciella, Mariosousa and Senegalia. Importantly, Vachellia is distantly related to Acacia s.s., being nested in basal Mimoseae lineages, and is thus less likely to be at risk than previously envisaged. Elucidation of these trends shows the benefits of having a comprehensive knowledge of the phylogeny of plants and phytophages under consideration for biological control.

  5. Collisions between low-energy electrons and small polyatomic targets of biological relevance

    NASA Astrophysics Data System (ADS)

    Hargreaves, Leigh

    2016-05-01

    Over the last decade, cross section measurements and calculations for DNA prototype molecules have received significant attention from the collisions community, due to the potential applications of this data in modelling electron transport through biological matter with a view to improving radiation dosimetry. Such data are additionally interesting from a fundamental aspect, as small carbon-based molecules are ideal targets for considering effects including target conformation, long-range dynamical interactions and coupling effects between the various degrees of freedom on the scattering properties of the target. At the California State University Fullerton, we have made a series of measurements of the elastic, vibrationally inelastic and electronically inelastic cross sections for a variety of small polyatomic targets, including water and the basic alcohols, ethylene, toluene and several fluorinated alkanes. These processes are important in a range of applications, primarily for modelling electron transport and thermalization, and energy deposition to a biological media. The data were obtained using a high resolution electron energy-loss spectrometer, operating in a crossed beam configuration with a moveable aperture gas source. The gas source design facilitates both an expedient and highly accurate method of removing background signal, and removes uncertainties from the data due to uncertainties in the beam profile. We have also performed scattering calculations employing the Schwinger Multichannel method, in collaboration with the California institute of technology, to compare with our measurements. In this talk, I will present an overview of our recent data and future research plans.

  6. A rapid Q-PCR titration protocol for adenovirus and helper-dependent adenovirus vectors that produces biologically relevant results.

    PubMed

    Gallaher, Sean D; Berk, Arnold J

    2013-09-01

    Adenoviruses are employed in the study of cellular processes and as expression vectors used in gene therapy. The success and reproducibility of these studies is dependent in part on having accurate and meaningful titers of replication competent and helper-dependent adenovirus stocks, which is problematic due to the use of varied and divergent titration protocols. Physical titration methods, which quantify the total number of viral particles, are used by many, but are poor at estimating activity. Biological titration methods, such as plaque assays, are more biologically relevant, but are time consuming and not applicable to helper-dependent gene therapy vectors. To address this, a protocol was developed called "infectious genome titration" in which viral DNA is isolated from the nuclei of cells ~3 h post-infection, and then quantified by Q-PCR. This approach ensures that only biologically active virions are counted as part of the titer determination. This approach is rapid, robust, sensitive, reproducible, and applicable to all forms of adenovirus. Unlike other Q-PCR-based methods, titers determined by this protocol are well correlated with biological activity.

  7. Attitudes towards the relevance of biological, behavioural and social sciences in nursing education.

    PubMed

    Thornton, T

    1997-07-01

    This paper explores the perceptions of staff and students regarding the supporting sciences within nursing education and how they feel such content relates to the 'real world' of nursing. A qualitative study examining the perceptions of students and teaching staff, particularly the concept of relevance, was conducted to explore factors which impact upon the integration of theory and practice. The teaching approaches used, assessment items selected, and the perceptions held about what nurses actually do all impinge upon what, and how, students learn in subjects which are essentially non-nursing in their orientation. Through an awareness of factors affecting how students and teaching staff actually approach supporting sciences content, better informed curriculum decisions can be made. PMID:9231293

  8. Paul Ehrlich's mastzellen: a historical perspective of relevant developments in mast cell biology.

    PubMed

    Ghably, Jack; Saleh, Hana; Vyas, Harsha; Peiris, Emma; Misra, Niva; Krishnaswamy, Guha

    2015-01-01

    Following the discovery of mast cells (or mastzellen) by the prolific physician researcher, Paul Ehrlich, many advances have improved our understanding of these cells and their fascinating biology. The discovery of immunoglobulin E and receptors for IgE and IgG on mast cells heralded further in vivo and in vitro studies, using molecular technologies and gene knockout models. Mast cells express an array of inflammatory mediators including tryptase, histamine, cytokines, chemokines, and growth factors. They play a role in many varying disease states, from atopic diseases, parasitic infections, hematological malignancies, and arthritis to osteoporosis. This review will attempt to summarize salient evolving areas in mast cell research over the last few centuries that have led to our current understanding of this pivotal multifunctional cell.

  9. Solid state structures of cadmium complexes with relevance for biological systems.

    PubMed

    Carballo, Rosa; Castiñeiras, Alfonso; Domínguez-Martín, Alicia; García-Santos, Isabel; Niclós-Gutiérrez, Juan

    2013-01-01

    This chapter provides a review of the literature on structural information from crystal structures determined by X-ray diffractometry of cadmium(II) complexes containing ligands of potential biological interest. These ligands fall into three broad classes, (i) those containing N-donors such as purine or pyrimidine bases and derivatives of adenine, guanine or cytosine, (ii) those containing carboxylate groups such as α-amino acids, in particular the twenty essential ones, the water soluble vitamins (B-complex) or the polycarboxylates of EDTA type ligands, and (iii) S-donors such as thiols/thiolates or dithiocarbamates. A crystal and molecular structural analysis has been carried out for some representative complexes of these ligands, specifically addressing the coordination mode of ligands, the coordination environment of cadmium and, in some significant cases, the intermolecular interactions. PMID:23430774

  10. Biomechanical forces in the skeleton and their relevance to bone metastasis: biology and engineering considerations

    PubMed Central

    Lynch, Maureen; Fischbach, Claudia

    2014-01-01

    Bone metastasis represents the leading cause of breast cancer related-deaths. However, the effect of skeleton-associated biomechanical signals on the initiation, progression, and therapy response of breast cancer bone metastasis is largely unknown. This review seeks to highlight possible functional connections between skeletal mechanical signals and breast cancer bone metastasis and their contribution to clinical outcome. It provides an introduction to the physical and biological signals underlying bone functional adaptation and discusses the modulatory roles of mechanical loading and breast cancer metastasis in this process. Following a definition of biophysical design criteria, in vitro and in vivo approaches from the fields of bone biomechanics and tissue engineering will be reviewed that may be suitable to investigate breast cancer bone metastasis as a function of varied mechano-signaling. Finally, an outlook of future opportunities and challenges associated with this newly emerging field will be provided. PMID:25174311

  11. Biological relevance of oxidative debris present in as-prepared graphene oxide

    PubMed Central

    Pattammattel, Ajith; Williams, Christina L.; Pande, Paritosh; Tsui, William G.; Basu, Ashis K.

    2015-01-01

    The influence of oxidative debris (OD) present in as-prepared graphene oxide (GO) suspensions on proteins and its toxicity to human embryonic kidney cells (HEK-293T) are reported here. The OD was removed by repeated washing with aqueous ammonia to produce the corresponding base-washed GO (bwGO). The loading (w/w) of bovine serum albumin (BSA) was increased by 85% after base washing, whereas the loading of hemoglobin (Hb) and lysozyme (Lyz), respectively, was decreased by 160% and 100%. The secondary structures of 13 different proteins bound to bwGO were compared with the corresponding proteins bound to GO using the UV circular dichroism spectroscopy. There was a consistent loss of protein secondary structure with bwGO when compared with proteins bound to GO, but no correlation between either the isoelectric point or hydrophobicity of the protein and the extent of structure loss was observed. All enzymes bound to bwGO and GO indicated significant activities, and a strong correlation between the enzymatic activity and the extent of structure retention was noted, regardless of the presence or absence of OD. At low loadings (<100 μg/mL) both GO and bwGO showed excellent cell viability but substantial cytotoxicity (~40% cell death) was observed at high loadings (>100 μg/mL). In control studies, OD by itself did not alter the growth rate even after a 48-h incubation. Thus, the presence of OD in GO played a very important role in controlling the chemical and biological nature of the protein-GO interface and the presence of OD in GO improved its biological compatibility when compared to bwGO. PMID:26257893

  12. Biological Production of a Hydrocarbon Fuel Intermediate Polyhydroxybutyrate (Phb) from a Process Relevant Lignocellulosic Derived Sugar

    SciTech Connect

    Wang, Wei; Mohagheghi, Ali; Mittal, Ashutosh; Pilath, Heidi; Johnson, David K.

    2015-03-22

    PHAs are synthesized by many microorganisms to serve as intracellular carbon storage molecules. In some bacterial strains, PHB can account for up to 80% of cell mass. In addition to its application in the packaging sector, PHB also has great potential as an intermediate in the production of hydrocarbon fuels. PHB can be thermally depolymerized and decarboxylated to propene which can be upgraded to hydrocarbon fuels via commercial oligomerization technologies. In recent years a great effort has been made in bacterial production of PHB, yet the production cost of the polymer is still much higher than conventional petrochemical plastics. The high cost of PHB is because the cost of the substrates can account for as much as half of the total product cost in large scale fermentation. Thus searching for cheaper and better substrates is very necessary for PHB production. In this study, we demonstrate production of PHB by Cupriavidus necator from a process relevant lignocellulosic derived sugar stream, i.e., saccharified hydrolysate slurry from pretreated corn stover. Good cell growth was observed on slurry saccharified with advanced enzymes and 40~60% of PHB was accumulated in the cells. The mechanism of inhibition in the toxic hydrolysate generated by pretreatment and saccharification of biomass, will be discussed.

  13. Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens.

    PubMed Central

    Moxon, R; Tang, C

    2000-01-01

    Recent innovations have increased enormously the opportunities for investigating the molecular basis of bacterial pathogenicity, including the availability of whole-genome sequences, techniques for identifying key virulence genes, and the use of microarrays and proteomics. These methods should provide powerful tools for analysing the patterns of gene expression and function required for investigating host-microbe interactions in vivo. But, the challenge is exacting. Pathogenicity is a complex phenotype and the reductionist approach does not adequately address the eclectic and variable outcomes of host-microbe interactions, including evolutionary dynamics and ecological factors. There are difficulties in distinguishing bacterial 'virulence' factors from the many determinants that are permissive for pathogenicity, for example those promoting general fitness. A further practical problem for some of the major bacterial pathogens is that there are no satisfactory animal models or experimental assays that adequately reflect the infection under investigation. In this review, we give a personal perspective on the challenge of characterizing how bacterial pathogens behave in vivo and discuss some of the methods that might be most relevant for understanding the molecular basis of the diseases for which they are responsible. Despite the powerful genomic, molecular, cellular and structural technologies available to us, we are still struggling to come to grips with the question of 'What is a pathogen?' PMID:10874737

  14. A functional [NiFe]-hydrogenase model compound that undergoes biologically relevant reversible thiolate protonation.

    PubMed

    Weber, Katharina; Krämer, Tobias; Shafaat, Hannah S; Weyhermüller, Thomas; Bill, Eckhard; van Gastel, Maurice; Neese, Frank; Lubitz, Wolfgang

    2012-12-26

    Two model compounds of the active site of [NiFe]-hydrogenases with an unusual {S(2)Ni(μ-S)(μ-CO)Fe(CO)(2)S}-coordination environment around the metals are reported. The neutral compound [Ni(xbsms)(μ-CO)(μ-S)Fe(CO)(2)('S')], (1) (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) is converted to [1H][BF(4)] by reversible protonation using HBF(4)·Et(2)O. The protonation takes place at the terminal thiolate sulfur atom that is coordinated to nickel. Catalytic intermediates with a protonated terminal cysteinate were suggested for the native protein but have not yet been confirmed experimentally. [1H][BF(4)] is the first dinuclear [NiFe] model compound for such a species. Both complexes have been synthesized and characterized by X-ray crystallography, NMR-, FTIR-, and (57)Fe-Mössbauer spectroscopy as well as by electronic absorption and resonance Raman spectroscopy. The experimental results clearly show that the protonation has a significant impact on the electronic structure of the iron center, although it takes place at the nickel site. DFT calculations support the interpretation of the spectroscopic data and indicate the presence of a bonding interaction between the metal ions, which is relevant for the enzyme as well. Electrochemical experiments show that both 1 and [1H][BF(4)] are active for electrocatalytic proton reduction in aprotic solvents.

  15. A functional [NiFe]-hydrogenase model compound that undergoes biologically relevant reversible thiolate protonation.

    PubMed

    Weber, Katharina; Krämer, Tobias; Shafaat, Hannah S; Weyhermüller, Thomas; Bill, Eckhard; van Gastel, Maurice; Neese, Frank; Lubitz, Wolfgang

    2012-12-26

    Two model compounds of the active site of [NiFe]-hydrogenases with an unusual {S(2)Ni(μ-S)(μ-CO)Fe(CO)(2)S}-coordination environment around the metals are reported. The neutral compound [Ni(xbsms)(μ-CO)(μ-S)Fe(CO)(2)('S')], (1) (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) is converted to [1H][BF(4)] by reversible protonation using HBF(4)·Et(2)O. The protonation takes place at the terminal thiolate sulfur atom that is coordinated to nickel. Catalytic intermediates with a protonated terminal cysteinate were suggested for the native protein but have not yet been confirmed experimentally. [1H][BF(4)] is the first dinuclear [NiFe] model compound for such a species. Both complexes have been synthesized and characterized by X-ray crystallography, NMR-, FTIR-, and (57)Fe-Mössbauer spectroscopy as well as by electronic absorption and resonance Raman spectroscopy. The experimental results clearly show that the protonation has a significant impact on the electronic structure of the iron center, although it takes place at the nickel site. DFT calculations support the interpretation of the spectroscopic data and indicate the presence of a bonding interaction between the metal ions, which is relevant for the enzyme as well. Electrochemical experiments show that both 1 and [1H][BF(4)] are active for electrocatalytic proton reduction in aprotic solvents. PMID:23194246

  16. Standardizing Analysis of Circulating MicroRNA: Clinical and Biological Relevance

    PubMed Central

    Farina, Nicholas H.; Wood, Marie E.; Perrapato, Scott D.; Francklyn, Christopher S.; Stein, Gary S.; Stein, Janet L.; Lian, Jane B.

    2014-01-01

    Circulating microRNAs (c-miRNAs) provide a new dimension as clinical biomarkers for disease diagnosis, progression, and response to treatment. However, the discovery of individual miRNAs from biofluids that reliably reflect disease states is in its infancy. The highly variable nature of published studies exemplifies a need to standardize the analysis of miRNA in circulation. Here, we show that differential sample handling of serum leads to inconsistent and incomparable results. We present a standardized method of RNA isolation from serum that eliminates multiple freeze/thaw cycles, provides at least 3 normalization mechanisms, and can be utilized in studies that compare both archived and prospectively collected samples. It is anticipated that serum processed as described here can be profiled, either globally or on a gene by gene basis, for c-miRNAs and other non-coding RNA in the circulation to reveal novel, clinically relevant epigenetic signatures for a wide range of diseases. PMID:24357537

  17. The androgen receptor: a biologically relevant vaccine target for the treatment of prostate cancer

    PubMed Central

    Olson, Brian M.; Johnson, Laura E.

    2012-01-01

    The androgen receptor (AR) plays an essential role in the development and progression of prostate cancer. However, while it has long been the primary molecular target of metastatic prostate cancer therapies, it has not been explored as an immunotherapeutic target. In particular, the AR ligand-binding domain (LBD) is a potentially attractive target, as it has an identical sequence among humans as well as among multiple species, providing a logical candidate for preclinical evaluation. In this report, we evaluated the immune and anti-tumor efficacy of a DNA vaccine targeting the AR LBD (pTVG-AR) in relevant rodent preclinical models. We found immunization of HHDII-DR1 mice, which express human HLA-A2 and HLA-DR1, with pTVG-AR augmented AR LBD HLA-A2-restricted peptide-specific, cytotoxic immune responses in vivo that could lyse human prostate cancer cells. Using an HLA-A2-expressing autochthonous model of prostate cancer, immunization with pTVG-AR augmented HLA-A2-restricted immune responses that could lyse syngeneic prostate tumor cells and led to a decrease in tumor burden and an increase in overall survival of tumor-bearing animals. Finally, immunization decreased prostate tumor growth in Copenhagen rats that was associated with a Th1-type immune response. These data show that the AR is as a prostate cancer immunological target antigen and that a DNA vaccine targeting the AR LBD is an attractive candidate for clinical evaluation. PMID:23108626

  18. O2 reduction reaction by biologically relevant anionic ligand bound iron porphyrin complexes.

    PubMed

    Samanta, Subhra; Das, Pradip Kumar; Chatterjee, Sudipta; Sengupta, Kushal; Mondal, Biswajit; Dey, Abhishek

    2013-11-18

    Iron porphyrin complex with a covalently attached thiolate ligand and another with a covalently attached phenolate ligand has been synthesized. The thiolate bound complex shows spectroscopic features characteristic of P450, including the hallmark absorption spectrum of the CO adduct. Electrocatalytic O2 reduction by this complex, which bears a terminal alkyne group, is investigated by both physiabsorbing on graphite surfaces (fast electron transfer rates) and covalent attachment to azide terminated self-assembled monolayer (physiologically relevant electron transfer rates) using the terminal alkyne group. Analysis of the steady state electrochemical kinetics reveals that this catalyst can selectively reduce O2 to H2O with a second-order k(cat.) ~10(7) M(-1 )s(-1) at pH 7. The analogous phenolate bound iron porphyrin complex reduces O2 with a second-order rate constant of 10(5) M(-1) s(-1) under the same conditions. The anionic ligand bound iron porphyrin complexes catalyze oxygen reduction reactions faster than any known synthetic heme porphyrin analogues. The kinetic parameters of O2 reduction of the synthetic thiolate bound complex, which is devoid of any second sphere effects present in protein active sites, provide fundamental insight into the role of the protein environment in tuning the reactivity of thiolate bound iron porphyrin containing metalloenzymes. PMID:24171513

  19. Diverse, Biologically Relevant, and Targetable Gene Rearrangements in Triple-Negative Breast Cancer and Other Malignancies.

    PubMed

    Shaver, Timothy M; Lehmann, Brian D; Beeler, J Scott; Li, Chung-I; Li, Zhu; Jin, Hailing; Stricker, Thomas P; Shyr, Yu; Pietenpol, Jennifer A

    2016-08-15

    Triple-negative breast cancer (TNBC) and other molecularly heterogeneous malignancies present a significant clinical challenge due to a lack of high-frequency "driver" alterations amenable to therapeutic intervention. These cancers often exhibit genomic instability, resulting in chromosomal rearrangements that affect the structure and expression of protein-coding genes. However, identification of these rearrangements remains technically challenging. Using a newly developed approach that quantitatively predicts gene rearrangements in tumor-derived genetic material, we identified and characterized a novel oncogenic fusion involving the MER proto-oncogene tyrosine kinase (MERTK) and discovered a clinical occurrence and cell line model of the targetable FGFR3-TACC3 fusion in TNBC. Expanding our analysis to other malignancies, we identified a diverse array of novel and known hybrid transcripts, including rearrangements between noncoding regions and clinically relevant genes such as ALK, CSF1R, and CD274/PD-L1 The over 1,000 genetic alterations we identified highlight the importance of considering noncoding gene rearrangement partners, and the targetable gene fusions identified in TNBC demonstrate the need to advance gene fusion detection for molecularly heterogeneous cancers. Cancer Res; 76(16); 4850-60. ©2016 AACR. PMID:27231203

  20. Altitude training causes haematological fluctuations with relevance for the Athlete Biological Passport.

    PubMed

    Bonne, Thomas Christian; Lundby, Carsten; Lundby, Anne Kristine; Sander, Mikael; Bejder, Jacob; Nordsborg, Nikolai Baastrup

    2015-08-01

    The impact of altitude training on haematological parameters and the Athlete Biological Passport (ABP) was evaluated in international-level elite athletes. One group of swimmers lived high and trained high (LHTH, n = 10) for three to four weeks at 2130 m or higher whereas a control group (n = 10) completed a three-week training camp at sea-level. Haematological parameters were determined weekly three times before and four times after the training camps. ABP thresholds for haemoglobin concentration ([Hb]), reticulocyte percentage (RET%), OFF score and the abnormal blood profile score (ABPS) were calculated using the Bayesian model. After altitude training, six swimmers exceeded the 99% ABP thresholds: two swimmers exceeded the OFF score thresholds at day +7; one swimmer exceeded the OFF score threshold at day +28; one swimmer exceeded the threshold for RET% at day +14; and one swimmer surpassed the ABPS threshold at day +14. In the control group, no values exceeded the individual ABP reference range. In conclusion, LHTH induces haematological changes in Olympic-level elite athletes which can exceed the individually generated references in the ABP. Training at altitude should be considered a confounding factor for ABP interpretation for up to four weeks after altitude exposure but does not consistently cause abnormal values in the ABP.

  1. Biological, clinical and population relevance of 95 loci for blood lipids.

    PubMed

    Teslovich, Tanya M; Musunuru, Kiran; Smith, Albert V; Edmondson, Andrew C; Stylianou, Ioannis M; Koseki, Masahiro; Pirruccello, James P; Ripatti, Samuli; Chasman, Daniel I; Willer, Cristen J; Johansen, Christopher T; Fouchier, Sigrid W; Isaacs, Aaron; Peloso, Gina M; Barbalic, Maja; Ricketts, Sally L; Bis, Joshua C; Aulchenko, Yurii S; Thorleifsson, Gudmar; Feitosa, Mary F; Chambers, John; Orho-Melander, Marju; Melander, Olle; Johnson, Toby; Li, Xiaohui; Guo, Xiuqing; Li, Mingyao; Shin Cho, Yoon; Jin Go, Min; Jin Kim, Young; Lee, Jong-Young; Park, Taesung; Kim, Kyunga; Sim, Xueling; Twee-Hee Ong, Rick; Croteau-Chonka, Damien C; Lange, Leslie A; Smith, Joshua D; Song, Kijoung; Hua Zhao, Jing; Yuan, Xin; Luan, Jian'an; Lamina, Claudia; Ziegler, Andreas; Zhang, Weihua; Zee, Robert Y L; Wright, Alan F; Witteman, Jacqueline C M; Wilson, James F; Willemsen, Gonneke; Wichmann, H-Erich; Whitfield, John B; Waterworth, Dawn M; Wareham, Nicholas J; Waeber, Gérard; Vollenweider, Peter; Voight, Benjamin F; Vitart, Veronique; Uitterlinden, Andre G; Uda, Manuela; Tuomilehto, Jaakko; Thompson, John R; Tanaka, Toshiko; Surakka, Ida; Stringham, Heather M; Spector, Tim D; Soranzo, Nicole; Smit, Johannes H; Sinisalo, Juha; Silander, Kaisa; Sijbrands, Eric J G; Scuteri, Angelo; Scott, James; Schlessinger, David; Sanna, Serena; Salomaa, Veikko; Saharinen, Juha; Sabatti, Chiara; Ruokonen, Aimo; Rudan, Igor; Rose, Lynda M; Roberts, Robert; Rieder, Mark; Psaty, Bruce M; Pramstaller, Peter P; Pichler, Irene; Perola, Markus; Penninx, Brenda W J H; Pedersen, Nancy L; Pattaro, Cristian; Parker, Alex N; Pare, Guillaume; Oostra, Ben A; O'Donnell, Christopher J; Nieminen, Markku S; Nickerson, Deborah A; Montgomery, Grant W; Meitinger, Thomas; McPherson, Ruth; McCarthy, Mark I; McArdle, Wendy; Masson, David; Martin, Nicholas G; Marroni, Fabio; Mangino, Massimo; Magnusson, Patrik K E; Lucas, Gavin; Luben, Robert; Loos, Ruth J F; Lokki, Marja-Liisa; Lettre, Guillaume; Langenberg, Claudia; Launer, Lenore J; Lakatta, Edward G; Laaksonen, Reijo; Kyvik, Kirsten O; Kronenberg, Florian; König, Inke R; Khaw, Kay-Tee; Kaprio, Jaakko; Kaplan, Lee M; Johansson, Asa; Jarvelin, Marjo-Riitta; Janssens, A Cecile J W; Ingelsson, Erik; Igl, Wilmar; Kees Hovingh, G; Hottenga, Jouke-Jan; Hofman, Albert; Hicks, Andrew A; Hengstenberg, Christian; Heid, Iris M; Hayward, Caroline; Havulinna, Aki S; Hastie, Nicholas D; Harris, Tamara B; Haritunians, Talin; Hall, Alistair S; Gyllensten, Ulf; Guiducci, Candace; Groop, Leif C; Gonzalez, Elena; Gieger, Christian; Freimer, Nelson B; Ferrucci, Luigi; Erdmann, Jeanette; Elliott, Paul; Ejebe, Kenechi G; Döring, Angela; Dominiczak, Anna F; Demissie, Serkalem; Deloukas, Panagiotis; de Geus, Eco J C; de Faire, Ulf; Crawford, Gabriel; Collins, Francis S; Chen, Yii-der I; Caulfield, Mark J; Campbell, Harry; Burtt, Noel P; Bonnycastle, Lori L; Boomsma, Dorret I; Boekholdt, S Matthijs; Bergman, Richard N; Barroso, Inês; Bandinelli, Stefania; Ballantyne, Christie M; Assimes, Themistocles L; Quertermous, Thomas; Altshuler, David; Seielstad, Mark; Wong, Tien Y; Tai, E-Shyong; Feranil, Alan B; Kuzawa, Christopher W; Adair, Linda S; Taylor, Herman A; Borecki, Ingrid B; Gabriel, Stacey B; Wilson, James G; Holm, Hilma; Thorsteinsdottir, Unnur; Gudnason, Vilmundur; Krauss, Ronald M; Mohlke, Karen L; Ordovas, Jose M; Munroe, Patricia B; Kooner, Jaspal S; Tall, Alan R; Hegele, Robert A; Kastelein, John J P; Schadt, Eric E; Rotter, Jerome I; Boerwinkle, Eric; Strachan, David P; Mooser, Vincent; Stefansson, Kari; Reilly, Muredach P; Samani, Nilesh J; Schunkert, Heribert; Cupples, L Adrienne; Sandhu, Manjinder S; Ridker, Paul M; Rader, Daniel J; van Duijn, Cornelia M; Peltonen, Leena; Abecasis, Gonçalo R; Boehnke, Michael; Kathiresan, Sekar

    2010-08-01

    Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.

  2. Biological, Clinical, and Population Relevance of 95 Loci for Blood Lipids

    PubMed Central

    Teslovich, Tanya M.; Musunuru, Kiran; Smith, Albert V.; Edmondson, Andrew C.; Stylianou, Ioannis M.; Koseki, Masahiro; Pirruccello, James P.; Ripatti, Samuli; Chasman, Daniel I.; Willer, Cristen J.; Johansen, Christopher T.; Fouchier, Sigrid W.; Isaacs, Aaron; Peloso, Gina M.; Barbalic, Maja; Ricketts, Sally L.; Bis, Joshua C.; Aulchenko, Yurii S.; Thorleifsson, Gudmar; Feitosa, Mary F.; Chambers, John; Orho-Melander, Marju; Melander, Olle; Johnson, Toby; Li, Xiaohui; Guo, Xiuqing; Li, Mingyao; Cho, Yoon Shin; Go, Min Jin; Kim, Young Jin; Lee, Jong-Young; Park, Taesung; Kim, Kyunga; Sim, Xueling; Ong, Rick Twee-Hee; Croteau-Chonka, Damien C.; Lange, Leslie A.; Smith, Joshua D.; Song, Kijoung; Zhao, Jing Hua; Yuan, Xin; Luan, Jian'an; Lamina, Claudia; Ziegler, Andreas; Zhang, Weihua; Zee, Robert Y.L.; Wright, Alan F.; Witteman, Jacqueline C.M.; Wilson, James F.; Willemsen, Gonneke; Wichmann, H-Erich; Whitfield, John B.; Waterworth, Dawn M.; Wareham, Nicholas J.; Waeber, Gérard; Vollenweider, Peter; Voight, Benjamin F.; Vitart, Veronique; Uitterlinden, Andre G.; Uda, Manuela; Tuomilehto, Jaakko; Thompson, John R.; Tanaka, Toshiko; Surakka, Ida; Stringham, Heather M.; Spector, Tim D.; Soranzo, Nicole; Smit, Johannes H.; Sinisalo, Juha; Silander, Kaisa; Sijbrands, Eric J.G.; Scuteri, Angelo; Scott, James; Schlessinger, David; Sanna, Serena; Salomaa, Veikko; Saharinen, Juha; Sabatti, Chiara; Ruokonen, Aimo; Rudan, Igor; Rose, Lynda M.; Roberts, Robert; Rieder, Mark; Psaty, Bruce M.; Pramstaller, Peter P.; Pichler, Irene; Perola, Markus; Penninx, Brenda W.J.H.; Pedersen, Nancy L.; Pattaro, Cristian; Parker, Alex N.; Pare, Guillaume; Oostra, Ben A.; O'Donnell, Christopher J.; Nieminen, Markku S.; Nickerson, Deborah A.; Montgomery, Grant W.; Meitinger, Thomas; McPherson, Ruth; McCarthy, Mark I.; McArdle, Wendy; Masson, David; Martin, Nicholas G.; Marroni, Fabio; Mangino, Massimo; Magnusson, Patrik K.E.; Lucas, Gavin; Luben, Robert; Loos, Ruth J. F.; Lokki, Maisa; Lettre, Guillaume; Langenberg, Claudia; Launer, Lenore J.; Lakatta, Edward G.; Laaksonen, Reijo; Kyvik, Kirsten O.; Kronenberg, Florian; König, Inke R.; Khaw, Kay-Tee; Kaprio, Jaakko; Kaplan, Lee M.; Johansson, Åsa; Jarvelin, Marjo-Riitta; Janssens, A. Cecile J.W.; Ingelsson, Erik; Igl, Wilmar; Hovingh, G. Kees; Hottenga, Jouke-Jan; Hofman, Albert; Hicks, Andrew A.; Hengstenberg, Christian; Heid, Iris M.; Hayward, Caroline; Havulinna, Aki S.; Hastie, Nicholas D.; Harris, Tamara B.; Haritunians, Talin; Hall, Alistair S.; Gyllensten, Ulf; Guiducci, Candace; Groop, Leif C.; Gonzalez, Elena; Gieger, Christian; Freimer, Nelson B.; Ferrucci, Luigi; Erdmann, Jeanette; Elliott, Paul; Ejebe, Kenechi G.; Döring, Angela; Dominiczak, Anna F.; Demissie, Serkalem; Deloukas, Panagiotis; de Geus, Eco J.C.; de Faire, Ulf; Crawford, Gabriel; Collins, Francis S.; Chen, Yii-der I.; Caulfield, Mark J.; Campbell, Harry; Burtt, Noel P.; Bonnycastle, Lori L.; Boomsma, Dorret I.; Boekholdt, S. Matthijs; Bergman, Richard N.; Barroso, Inês; Bandinelli, Stefania; Ballantyne, Christie M.; Assimes, Themistocles L.; Quertermous, Thomas; Altshuler, David; Seielstad, Mark; Wong, Tien Y.; Tai, E-Shyong; Feranil, Alan B.; Kuzawa, Christopher W.; Adair, Linda S.; Taylor, Herman A.; Borecki, Ingrid B.; Gabriel, Stacey B.; Wilson, James G.; Stefansson, Kari; Thorsteinsdottir, Unnur; Gudnason, Vilmundur; Krauss, Ronald M.; Mohlke, Karen L.; Ordovas, Jose M.; Munroe, Patricia B.; Kooner, Jaspal S.; Tall, Alan R.; Hegele, Robert A.; Kastelein, John J.P.; Schadt, Eric E.; Rotter, Jerome I.; Boerwinkle, Eric; Strachan, David P.; Mooser, Vincent; Holm, Hilma; Reilly, Muredach P.; Samani, Nilesh J; Schunkert, Heribert; Cupples, L. Adrienne; Sandhu, Manjinder S.; Ridker, Paul M; Rader, Daniel J.; van Duijn, Cornelia M.; Peltonen, Leena; Abecasis, Gonçalo R.; Boehnke, Michael; Kathiresan, Sekar

    2010-01-01

    Serum concentrations of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with serum lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 × 10-8), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (e.g., CYP7A1, NPC1L1, and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and impact lipid traits in three non-European populations (East Asians, South Asians, and African Americans). Our results identify several novel loci associated with serum lipids that are also associated with CAD. Finally, we validated three of the novel genes—GALNT2, PPP1R3B, and TTC39B—with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD. PMID:20686565

  3. Altitude training causes haematological fluctuations with relevance for the Athlete Biological Passport.

    PubMed

    Bonne, Thomas Christian; Lundby, Carsten; Lundby, Anne Kristine; Sander, Mikael; Bejder, Jacob; Nordsborg, Nikolai Baastrup

    2015-08-01

    The impact of altitude training on haematological parameters and the Athlete Biological Passport (ABP) was evaluated in international-level elite athletes. One group of swimmers lived high and trained high (LHTH, n = 10) for three to four weeks at 2130 m or higher whereas a control group (n = 10) completed a three-week training camp at sea-level. Haematological parameters were determined weekly three times before and four times after the training camps. ABP thresholds for haemoglobin concentration ([Hb]), reticulocyte percentage (RET%), OFF score and the abnormal blood profile score (ABPS) were calculated using the Bayesian model. After altitude training, six swimmers exceeded the 99% ABP thresholds: two swimmers exceeded the OFF score thresholds at day +7; one swimmer exceeded the OFF score threshold at day +28; one swimmer exceeded the threshold for RET% at day +14; and one swimmer surpassed the ABPS threshold at day +14. In the control group, no values exceeded the individual ABP reference range. In conclusion, LHTH induces haematological changes in Olympic-level elite athletes which can exceed the individually generated references in the ABP. Training at altitude should be considered a confounding factor for ABP interpretation for up to four weeks after altitude exposure but does not consistently cause abnormal values in the ABP. PMID:25545030

  4. Next generation techniques in the high resolution spectroscopy of biologically relevant molecules.

    PubMed

    Neill, Justin L; Douglass, Kevin O; Pate, Brooks H; Pratt, David W

    2011-04-28

    Recent advances in the technology of test and measurement equipment driven by the computer and telecommunications industries have made possible the development of a new broadband, Fourier-transform microwave spectrometer that operates on principles similar to FTNMR. This technique uses a high sample-rate arbitrary waveform generator to construct a phase-locked chirped microwave pulse that gives a linear frequency sweep over a wide frequency range in 1 μs. The chirped pulse efficiently polarizes the molecular sample at all frequencies lying within this band. The subsequent free induction decay of this polarization is measured with a high-speed digitizer and then fast Fourier-transformed to yield a broadband, frequency-resolved rotational spectrum, spanning up to 11.5 GHz and containing lines that are as narrow as 100 kHz. This new technique is called chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy. The technique offers the potential to determine the structural and dynamical properties of very large molecules solely from fully resolved pure rotational spectra. FTMW double resonance techniques employing a low-resolution UV laser facilitate an easy assignment of overlapping spectra produced by different conformers in the sample. Of particular interest are the energy landscapes of conformationally flexible molecules of biological importance, including studies of their interaction with solvent and/or other weakly bound molecules. An example is provided from the authors' work on p-methoxyphenethylamine, a neurotransmitter, and its complexes with water. PMID:21394332

  5. Photochemical reactions of metal nitrosyl complexes. Mechanisms of NO reactions with biologically relevant metal centers

    DOE PAGESBeta

    Ford, Peter C.

    2001-01-01

    Tmore » he discoveries that nitric oxide (a.k.a. nitrogen monoxide) serves important roles in mammalian bioregulation and immunology have stimulated intense interest in the chemistry and biochemistry of NO and derivatives such as metal nitrosyl complexes. Also of interest are strategies to deliver NO to biological targets on demand. One such strategy would be to employ a precursor which displays relatively low thermal reactivity but is photochemically active to release NO.his proposition led us to investigate laser flash and continuous photolysis kinetics of nitrosyl complexes such as the Roussin's iron-sulfur-nitrosyl cluster anions Fe 2 S 2 ( NO ) 4 2 − and Fe 4 S 3 ( NO ) 7 − and several ruthenium salen and porphyrin nitrosyls.hese include studies using metal-nitrosyl photochemistry as a vehicle for delivering NO to hypoxic cell cultures in order to sensitize γ -radiation damage. Also studied were the rates and mechanisms of NO “on” reactions with model water soluble heme compounds, the ferriheme protein met-myoglobin and various ruthenium complexes using ns laser flash photolysis techniques. An overview of these studies is presented.« less

  6. Food Polyphenols Fail to Cause a Biologically Relevant Reduction of COX-2 Activity

    PubMed Central

    Willenberg, Ina; Meschede, Anna K.; Gueler, Faikah; Jang, Mi-Sun; Shushakova, Nelli; Schebb, Nils Helge

    2015-01-01

    Epidemiologic studies show a correlation between the dietary intake of food polyphenols and beneficial health effects. Several in vitro studies indicate that the anti-inflammatory potential of polyphenols is, at least in part, mediated by a modulation of the enzymes of the arachidonic acid cascade, such as the prostaglandin forming cyclooxygenases (COXs). Evidence that this mode of action can be transferred to the situation in vivo is scarce. This study characterized effects of a subset of polyphenols on COX–2 expression and activity in vitro and compared the potency with known drugs. Next, the in vivo relevance of the observed in vitro effects was tested. Enzyme assays and incubations of polyphenols with the cancer cell line HCA–7 and lipopolysaccharide (LPS) stimulated primary monocytes support the hypothesis that polyphenols can effect COX–2 expression and activity in vitro. The effects were most pronounced in the monocyte assay for wogonin, apigenin, resveratrol and genistein with IC50 values of 1.5 μM, 2.6 μM, 2.8 μM and 7.4 μM. However, these values are 100- to 1000-fold higher in comparison to those of the known pharmaceuticals celecoxib, indomethacin and dexamethasone. In an animal model of LPS induced sepsis, pretreatment with polyphenols (i. p. 100 mg/kg bw) did not result in decreased plasma or tissue prostaglandin levels, whereas the positive control celecoxib effectively attenuated LPS induced prostaglandin formation. These data suggest that despite the moderate potency in vitro, an effect of polyphenols on COX–2 during acute inflammation is unlikely, even if a high dose of polyphenols is ingested. PMID:26440517

  7. A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

    PubMed Central

    2015-01-01

    Background Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A key component of typical machine learning pipelines for omics data is feature selection, which is used to reduce the raw high-dimensional data into a tractable number of features. Feature selection needs to balance the objective of using as few features as possible, while maintaining high predictive power. This balance is crucial when the goal of data analysis is the identification of highly accurate but small panels of biomarkers with potential clinical utility. In this paper we propose a heuristic for the selection of very small feature subsets, via an iterative feature elimination process that is guided by rule-based machine learning, called RGIFE (Rule-guided Iterative Feature Elimination). We use this heuristic to identify putative biomarkers of osteoarthritis (OA), articular cartilage degradation and synovial inflammation, using both proteomic and transcriptomic datasets. Results and discussion Our RGIFE heuristic increased the classification accuracies achieved for all datasets when no feature selection is used, and performed well in a comparison with other feature selection methods. Using this method the datasets were reduced to a smaller number of genes or proteins, including those known to be relevant to OA, cartilage degradation and joint inflammation. The results have shown the RGIFE feature reduction method to be suitable for analysing both proteomic and transcriptomics data. Methods that generate large ‘omics’ datasets are increasingly being used in the area of rheumatology. Conclusions Feature reduction methods are advantageous for the analysis of omics data in the field of rheumatology, as the applications of such techniques are likely to result in improvements in diagnosis, treatment and drug discovery. PMID:25923811

  8. Copper isotope fractionation between aqueous compounds relevant to low temperature geochemistry and biology

    NASA Astrophysics Data System (ADS)

    Fujii, Toshiyuki; Moynier, Frédéric; Abe, Minori; Nemoto, Keisuke; Albarède, Francis

    2013-06-01

    Isotope fractionation between the common Cu species present in solution (Cu+, Cu2+, hydroxide, chloride, sulfide, carbonate, oxalate, and ascorbate) has been investigated using both ab initio methods and experimental solvent extraction techniques. In order to establish unambiguously the existence of equilibrium isotope fractionation (as opposed to kinetic isotope fractionation), we first performed laboratory-scale liquid-liquid distribution experiments. Upon exchange between HCl medium and a macrocyclic complex, the 65Cu/63Cu ratio fractionated by -1.06‰ to -0.39‰. The acidity dependence of the fractionation was appropriately explained by ligand exchange reactions between hydrated H2O and Cl- via intramolecular vibrations. The magnitude of the Cu isotope fractionation among important Cu ligands was also estimated by ab initio methods. The magnitude of the nuclear field shift effect to the Cu isotope fractionation represents only ˜3% of the mass-dependent fractionation. The theoretical estimation was expanded to chlorides, hydroxides, sulfides, sulfates, and carbonates under different conditions of pH. Copper isotope fractionation of up to 2‰ is expected for different forms of Cu present in seawater and for different sediments (carbonates, hydroxides, and sulfides). We found that Cu in dissolved carbonates and sulfates is isotopically much heavier (+0.6‰) than free Cu. Isotope fractionation of Cu in hydroxide is minimal. The relevance of these new results to the understanding of metabolic processes was also discussed. Copper is an essential element used by a large number of proteins for electron transfer. Further theoretical estimates of δ65Cu in hydrated Cu(I) and Cu(II) ions, Cu(II) ascorbates, and Cu(II) oxalate predict Cu isotope fractionation during the breakdown of ascorbate into oxalate and account for the isotopically heavy Cu found in animal kidneys.

  9. Relevance of the neuropeptide Y system in the biology of cancer progression.

    PubMed

    Ruscica, M; Dozio, E; Motta, M; Magni, P

    2007-01-01

    The peptides pancreatic polypeptide (PP), peptide YY (PYY), and neuropeptide Y (NPY) share a similar structure, known as PP-fold. Within this family of peptides, NPY, a highly conserved 36-aminoacid residue peptide, is involved in the regulation of a wide range of physiological functions, such as food intake and energy metabolism, as well as in the promotion of some remarkable aspects of tumor progression, including cell proliferation, matrix invasion, metastatization, and angiogenesis. NPY exerts its biological effects through five G-protein coupled receptors, named Y1-, Y2-, Y4-, Y5-, and y6-R, which appear associated with different aspects of oncogenesis. Y1-R seems involved in the modulation of cancer cell proliferation, whereas Y2-R activation appears to promote angiogenesis. The development of NPY receptor subtype selective analogs has helped to elucidate the physiological and pathophysiological role and localization of each receptor and may contribute to a better understanding of the receptor-ligand interaction. The NPY system appears to be variously associated with specific tumors, including neural crest-derived tumors, breast and prostate cancers. In addition to NPY, PYY is also able to affect cancer cell growth in a dose-dependent manner and through Y-Rs. In conclusion, peptides of the NPY family and the related receptors play an important role in the progression of different cancer types, with some molecular specificity according to each step of this process. On this basis, future studies may be directed to the implementation of novel diagnostic and therapeutic approaches targeting this system.

  10. Relevance of Biologically Equivalent Dose Values in Outcome Evaluation of Stereotactic Radiotherapy for Lung Nodules

    SciTech Connect

    Casamassima, Franco Masi, Laura; Bonucci, Ivano; Polli, Caterina; Menichelli, Claudia; Gulisano, Massimo; Pacini, Stefania; Aterini, Stefano; Cavedon, Carlo

    2008-05-01

    Purpose: Different biologically equivalent dose (BED) values associated with stereotactic radiotherapy (SRT) of patients with primary and metastatic pulmonary nodules were studied. The BED values were calculated for tumoral tissue and low {alpha}/{beta} ratio, assuming that better local response could be obtained by using stereotactic high-BED treatment. Methods and Materials: Fifty-eight patients with T1-T3 N0 non-small-cell lung cancer and 46 patients with metastatic lung nodules were treated with SRT. The BED was calculated for {alpha}/{beta} ratios of 3 and 10. Overall survival (OS) was assessed according to Kaplan-Meier and appraised as a function of three BED levels: low (30-50 Gy), medium (50-70 Gy), and high (70-98 Gy; {alpha}/{beta} = 10). Results: The OS rates for all 104 patients at 12, 24, and 36 months were 73%, 48.3%, and 35.8%, respectively. Local response greater than 50% for low, medium, and high BED values was observed in 54%, 47%, and 73%, respectively. In the high-BED treated group, OS rates at 12, 24, and 36 months (80.9%, 70%, and 53.6%, respectively) were significantly improved compared with low- (69%, 46.1%, and 30.7%, respectively) and medium-BED (67%, 28%, and 21%, respectively) treated patients. Results are also discussed in terms of BED calculated on {alpha}/{beta} 3 Gy characteristic of the microcapillary bed. No acute toxicity higher than Grade 1 was observed. Conclusions: Radioablation of pulmonary neoplastic nodules may be achieved with SRT delivered by using a high-dose fraction with high BED value.

  11. Transcriptional profiling of formalin fixed paraffin embedded tissue: pitfalls and recommendations for identifying biologically relevant changes.

    PubMed

    Rentoft, Matilda; Coates, Philip John; Laurell, Göran; Nylander, Karin

    2012-01-01

    Expression profiling techniques have been used to study the biology of many types of cancer but have been limited to some extent by the requirement for collection of fresh tissue. In contrast, formalin fixed paraffin embedded (FFPE) samples are widely available and represent a vast resource of potential material. The techniques used to handle the degraded and modified RNA from these samples are relatively new and all the pitfalls and limitations of this material for whole genome expression profiling are not yet clarified. Here, we analyzed 70 FFPE tongue carcinoma samples and 17 controls using the whole genome DASL array covering nearly 21000 genes. We identified that sample age is related to quality of extracted RNA and that sample quality influences apparent expression levels in a non-random manner related to gene probe sequence, leading to spurious results. However, by removing sub-standard samples and analysing only those 28 cancers and 15 controls that had similar quality we were able to generate a list of 934 genes significantly altered in tongue cancer compared to control samples of tongue. This list contained previously identified changes and was enriched for genes involved in many cancer-related processes such as tissue remodelling, inflammation, differentiation and apoptosis. Four novel genes of potential importance in tongue cancer development and maintenance, SH3BGL2, SLC2A6, SLC16A3 and CXCL10, were independently confirmed, validating our data. Hence, gene expression profiling can be performed usefully on archival material if appropriate quality assurance steps are taken to ensure sample consistency and we present some recommendations for the use of FFPE material based on our findings.

  12. Biological processes and optical measurements near the sea surface: Some issues relevant to remote sensing

    NASA Technical Reports Server (NTRS)

    Cullen, John J.; Lewis, Marlon R.

    1995-01-01

    The advent of remote sensing, the develpmemt of new optical instrumentation, and the associated advances in hydrological optics have transformed oceanography; it is now feasible to describe ocean-scale biogeochemical dynamcis from satellite observations, verified and complemented by measurements from optical sensors on profilers, moorings, and drifters. Only near-surface observations are common to both remote sensing and in situ observation, so it is critical to understand processes in the upper euphotic zone. Unfortunately, the biological principles that must be used to interpret optical variability near the sea surface are weaker than we would like, because relatively few experiments and analyses have examined bio-optical relationships under high irradiance characteristic of the upper optical depth. Special consideration of this stratum is justified, because there is good evidence that bio-optical relationships are altered near the surface; (1) the fluorescence yield from chlorophyll declines, leading to bias in the estimation of pigment from fluorometry; (2) the modeled relationship between solar-stimulated fluorecence and photosynthesis seems to deviate significantly from that presented for the lower euphotic zone; and (3) carbon-specific and cellular attenuation cross sections of phytoplankton change substantially during exposures to bright light. Even the measurement of primary productivity is problematic near the sea surface, because vertical mixing is not simulated and artifactual inhibition of photosynthesis can result. These problems can be addressed by focusing more sampling effort, experimental simulation, and analytical consideration on the upper optical depth, and by shortening timescales for the measurement of marine photosynthesis. Special efforts to study near-surface processes are justified, because new bio-optical algorithms will require quantitaitve descriptions of the responses of phytoplankton to bright light.

  13. Developing mononuclear copper-active-oxygen complexes relevant to reactive intermediates of biological oxidation reactions.

    PubMed

    Itoh, Shinobu

    2015-07-21

    Active-oxygen species generated on a copper complex play vital roles in several biological and chemical oxidation reactions. Recent attention has been focused on the reactive intermediates generated at the mononuclear copper active sites of copper monooxygenases such as dopamine β-monooxygenase (DβM), tyramine β-monooxygenase (TβM), peptidylglycine-α-hydroxylating monooxygenase (PHM), and polysaccharide monooxygenases (PMO). In a simple model system, reaction of O2 and a reduced copper(I) complex affords a mononuclear copper(II)-superoxide complex or a copper(III)-peroxide complex, and subsequent H(•) or e(-)/H(+) transfer, which gives a copper(II)-hydroperoxide complex. A more reactive species such as a copper(II)-oxyl radical type species could be generated via O-O bond cleavage of the peroxide complex. However, little had been explored about the chemical properties and reactivity of the mononuclear copper-active-oxygen complexes due to the lack of appropriate model compounds. Thus, a great deal of effort has recently been made to develop efficient ligands that can stabilize such reactive active-oxygen complexes in synthetic modeling studies. In this Account, I describe our recent achievements of the development of a mononuclear copper(II)-(end-on)superoxide complex using a simple tridentate ligand consisting of an eight-membered cyclic diamine with a pyridylethyl donor group. The superoxide complex exhibits a similar structure (four-coordinate tetrahedral geometry) and reactivity (aliphatic hydroxylation) to those of a proposed reactive intermediate of copper monooxygenases. Systematic studies based on the crystal structures of copper(I) and copper(II) complexes of the related tridentate supporting ligands have indicated that the rigid eight-membered cyclic diamine framework is crucial for controlling the geometry and the redox potential, which are prerequisites for the generation of such a unique mononuclear copper(II)-(end-on)superoxide complex

  14. Mapping biological soil crusts for understanding their functional relevance in dryland ecosystems

    NASA Astrophysics Data System (ADS)

    Rodriguez-Caballero, E.; Escribano, P.; Chamizo, S.; Canton, Y.

    2012-04-01

    Biological soil crusts (BSCs) are considered a key element in the functioning of arid and semiarid ecosystems as they modify numerous soil surface properties involved in primary ecosystem processes such as hydrological and erosion processes, and nutrient cycling.. It is known that arid and semiarid ecosystems are conformed by a complex matrix of vegetated and open ground patches usually covered by BSCs. Geomorphic evolution of drylands depends on the individual response of patches and also on the interactions and feedback-processes among patches. These interactions are controlled by patch spatial distribution. On this account, to understand the role of BSCs in the system, it is necessary to introduce their effect at coarser scales, and to have accurate and spatially continuous information of BSC distribution. The inherent complexity and the spatial heterogeneity of drylands make field survey methods very limited for BSC mapping. Images reported by remote sensors are presented as a powerful tool for mapping BSC spatial distribution. Remote sensors provide synoptic and spatially continuous information of the territory. Different indices for mapping BSCs have been published. These indices are based on distinctive spectral characteristic of BSCs and differ in nature and objectives. The aim of this work was to analyze the feasibility of some of these indices in a semiarid area characterized by sparse vegetation cover usually mixed at subpixel level with elements characterized by very similar spectral response (bare soil, BSCs and dry vegetation). These indices were: i) CRCIA, index applied for mapping BSCs from hyperspectral images. ii) CI, index developed for mapping of cyanobacteria-dominated BSCs and iii) BSCI, index for mapping of lichen-dominated BSCs. The multispectral indices (CI and BSCI) classified as BSCs 50% of the pixels dominated by BSCs. The CRCIA hyperspectral index, showed better results than those obtained with multispectral indices. This index

  15. The scaling law of climate change and its relevance to assessing (palaeo)biological responses

    NASA Astrophysics Data System (ADS)

    Kiessling, Wolfgang; Eichenseer, Kilian

    2014-05-01

    interglacials, are not monotonic, but punctuated by short-term cooling intervals. The fossil record tells us that biodiversity responded dramatically to ancient intervals of climate warming. We can now see that the apparently slower rates of change in some mass extinctions (Permian-Triassic, Triassic-Jurassic) were greater than today when the scaling law is considered. This reassures us that studying deep time patterns of organismic response to climate change is a worthwhile endeavor that is relevant for predicting the future. References Burrows, M. T., Schoeman, D. S., Buckley, L. B., Moore, P., Poloczanska, E. S., Brander, K. M., Brown, C., Bruno, J. F., Duarte, C. M., Halpern, B. S., Holding, J., Kappel, C. V., Kiessling, W., O'Connor, M. I., Pandolfi, J. M., Parmesan, C., Schwing, F. B., Sydeman, W. J., and Richardson, A. J.: The pace of shifting climate in marine and terrestrial ecosystems, Science, 334, 652-655, 2011. Gingerich, P. D.: Quantification and comparison of evolutionary rates, American Journal of Science, 293A, 453-478, 1993. Sadler, P. M.: Sediment accumulation rates and the completeness of stratigraphic sections, Journal of Geology, 89, 569-584, 1981. Sun, Y., Joachimski, M. M., Wignall, P. B., Yan, C., Chen, Y., Jiang, H., Wang, L., and Lai, X.: Lethally hot temperatures during the Early Triassic greenhouse, Science, 338, 366-370, 2012.

  16. Organocatalytic enantioselective Pictet-Spengler approach to biologically relevant 1-benzyl-1,2,3,4-tetrahydroisoquinoline alkaloids.

    PubMed

    Ruiz-Olalla, Andrea; Würdemann, Martien A; Wanner, Martin J; Ingemann, Steen; van Maarseveen, Jan H; Hiemstra, Henk

    2015-05-15

    A general procedure for the synthesis of 1-benzyl-1,2,3,4-tetrahydroisoquinolines was developed, based on organocatalytic, regio- and enantioselective Pictet-Spengler reactions (86-92% ee) of N-(o-nitrophenylsulfenyl)-2-arylethylamines with arylacetaldehydes. The presence of the o-nitrophenylsulfenyl group, together with the MOM-protection in the catechol part of the tetrahydroisoquinoline ring system, appeared to be a productive combination. To demonstrate the versatility of this approach, 10 biologically and pharmaceutically relevant alkaloids were prepared using (R)-TRIP as the chiral catalyst: (R)-norcoclaurine, (R)-coclaurine, (R)-norreticuline, (R)-reticuline, (R)-trimemetoquinol, (R)-armepavine, (R)-norprotosinomenine, (R)-protosinomenine, (R)-laudanosine, and (R)-5-methoxylaudanosine. PMID:25909585

  17. Sex differences in panic-relevant responding to a 10% carbon dioxide-enriched air biological challenge.

    PubMed

    Nillni, Yael I; Berenz, Erin C; Rohan, Kelly J; Zvolensky, Michael J

    2012-01-01

    The current study examined sex differences in psychological (i.e., self-reported anxiety, panic symptoms, and avoidance) and physiological (i.e., heart rate and skin conductance level) response to, and recovery from, a laboratory biological challenge. Participants were a community-recruited sample of 128 adults (63.3% women; M(age)=23.2 years, SD=8.9) who underwent a 4-min 10% CO(2)-enriched air biological challenge. As predicted, women reported more severe physical panic symptoms and avoidance (i.e., less willingness to participate in another challenge) and demonstrated increased heart rate as compared to men above and beyond the variance accounted for by other theoretically relevant variables (recent panic attack history, neuroticism, and anxiety sensitivity). Additionally, women demonstrated a faster rate of recovery with respect to heart rate compared to men. These results are in line with literature documenting sex-specific differences in panic psychopathology, and results are discussed in the context of possible mechanisms underlying sex differences in panic vulnerability.

  18. Quantum Dots: An Insight and Perspective of Their Biological Interaction and How This Relates to Their Relevance for Clinical Use

    PubMed Central

    Clift, Martin J. D.; Stone, Vicki

    2012-01-01

    Due to their novel physico-chemical characteristics, semi-conductor nanocrystal quantum dots (QDs) provide an advantageous perspective towards numerous different consumer and medical applications. The most notable potential application of QDs is their use as therapeutic and diagnostic tools in nanomedicine. Despite the many benefits posed by QDs, the proposed, intentional exposure to humans has raised concerns towards their potential impact upon human health. These concerns are predominantly based upon the heterogeneous composition of QDs, which most commonly comprises of a cadmium-based core and zinc sulphide shell. Whilst other nanoparticle (NP) types possess a similar structure to QDs (i.e. core-shell technology (e.g. Fe2O3, Au and superparamagnetic iron oxide NPs)), the importance of the concerns surrounding human exposure to QDs is amplified further since, due to the sophisticated chemical and light-emitting properties of QDs, the use of these NPs within any (nano)medical setting/application could be suggested as realistic, rather than simply an advantageous possibility. It is therefore imperative that a thorough understanding of how QDs interact with various biological systems, predominantly those relative to humans and what the consequences of such interactions are is gained with extreme alacrity. It is the aim of this review to highlight the current knowledge base of QD-biological system interactions, where the knowledge gaps (still) remain and how the understanding of this interaction relates to the most notable of applications for QDs; their clinical relevance. PMID:22896769

  19. Culturally relevant inquiry-based laboratory module implementations in upper-division genetics and cell biology teaching laboratories.

    PubMed

    Siritunga, Dimuth; Montero-Rojas, María; Carrero, Katherine; Toro, Gladys; Vélez, Ana; Carrero-Martínez, Franklin A

    2011-01-01

    Today, more minority students are entering undergraduate programs than ever before, but they earn only 6% of all science or engineering PhDs awarded in the United States. Many studies suggest that hands-on research activities enhance students' interest in pursuing a research career. In this paper, we present a model for the implementation of laboratory research in the undergraduate teaching laboratory using a culturally relevant approach to engage students. Laboratory modules were implemented in upper-division genetics and cell biology courses using cassava as the central theme. Students were asked to bring cassava samples from their respective towns, which allowed them to compare their field-collected samples against known lineages from agricultural stations at the end of the implementation. Assessment of content and learning perceptions revealed that our novel approach allowed students to learn while engaged in characterizing Puerto Rican cassava. In two semesters, based on the percentage of students who answered correctly in the premodule assessment for content knowledge, there was an overall improvement of 66% and 55% at the end in the genetics course and 24% and 15% in the cell biology course. Our proposed pedagogical model enhances students' professional competitiveness by providing students with valuable research skills as they work on a problem to which they can relate.

  20. Spatial release from masking improves sound pattern discrimination along a biologically relevant pulse-rate continuum in gray treefrogs

    PubMed Central

    Ward, Jessica L.; Buerkle, Nathan P.; Bee, Mark A.

    2013-01-01

    Frogs form large choruses during the mating season in which males produce loud advertisement calls to attract females and repel rival males. High background noise levels in these social aggregations can impair vocal perception. In humans, spatial release from masking contributes to our ability to understand speech in noisy social groups. Here, we tested the hypothesis that spatial separation between target signals and ‘chorus-shaped noise’ improves the ability of female gray treefrogs (Hyla chrysoscelis) to perform a behavioral discrimination task based on perceiving differences in the pulsatile structure of advertisement calls. We used two-stimulus choice tests to measure phonotaxis (approach toward sound) in response to calls differing in pulse rate along a biologically relevant continuum between conspecific (50 pulses s−1) and heterospecific (20 pulses s−1) calls. Signals were presented in quiet, in colocated noise, and in spatially separated noise. In quiet conditions, females exhibited robust preferences for calls with relatively faster pulse rates more typical of conspecific calls. Behavioral discrimination between calls differing in pulse rate was impaired in the presence of colocated noise but similar between quiet and spatially separated noise conditions. Our results indicate that spatial release from energetic masking facilitates a biologically important temporal discrimination task in frogs. We discuss these results in light of previous work on spatial release from masking in frogs and other animals. PMID:24055623

  1. Biologically relevant 3D tumor arrays: imaging-based methods for quantification of reproducible growth and analysis of treatment response

    NASA Astrophysics Data System (ADS)

    Celli, Jonathan P.; Rizvi, Imran; Blanden, Adam R.; Abu-Yousif, Adnan O.; Spring, Bryan Q.; Hasan, Tayyaba

    2011-02-01

    Three-dimensional in vitro tumor models have emerged as powerful research tools in cancer biology, though the vast potential of these systems as high-throughput, biologically relevant reporters of treatment response has yet to be adequately explored. Here, building on previous studies, we demonstrate the utility of using 3D models for ovarian and pancreatic cancers in conjunction with quantitative image processing to reveal aspects of growth behavior and treatment response that would not be evident without either modeling or quantitative analysis component. In this report we specifically focus on recent improvements in the imaging component of this integrative research platform and emphasize analysis to establish reproducible growth properties in 3D tumor arrays, a key consideration in establishing the utility of this platform as a reliable reporter of therapeutic response. Building on previous studies using automated segmentation of low magnification image fields containing large numbers of nodules to study size dependent treatment effects, we introduce an improvement to this method using multiresolution decomposition to remove gradient background from transmitted light images for more reliable feature identification. This approach facilitates the development of a new treatment response metric, disruption fraction (Dfrac), which quantifies dose dependent distribution shifts from nodular fragmentation induced by cytotoxic therapies. Using this approach we show that PDT treatment is associated with significant dose-dependent increases in Dfrac, while this is not observed with carboplatin treatment. The ability to quantify this response to therapy could play a key role in design of combination regimens involving these two modalities.

  2. The development of Army relevant peptide-based surface enhanced Raman scattering (SERS) sensors for biological threat detection

    NASA Astrophysics Data System (ADS)

    Farrell, Mikella E.; Strobbia, Pietro; Sarkes, Deborah A.; Stratis-Cullum, Dimitra N.; Cullum, Brian M.; Pellegrino, Paul M.

    2016-05-01

    The utility of peptide-based molecular sensing for the development of novel biosensors has resulted in a significant increase in their development and usage for sensing targets like chemical, biological, energetic and toxic materials. Using peptides as a molecular recognition element is particularly advantageous because there are several mature peptide synthesis protocols that already exist, peptide structures can be tailored, selected and manipulated to be highly discerning towards desired targets, peptides can be modified to be very stable in a host of environments and stable under many different conditions, and through the development of bifunctionalized peptides can be synthesized to also bind onto desired sensing platforms (various metal materials, glass, etc.). Two examples of the several Army relevant biological targets for peptide-based sensing platforms include Ricin and Abrin. Ricin and Abrin are alarming threats because both can be weaponized and there is no antidote for exposure. Combining the sensitivity of SERS with the selectivity of a bifunctional peptide allows for the emergence of dynamic hazard sensor for Army application.

  3. Metallomics insights for in vivo studies of metal based nanomaterials.

    PubMed

    Wang, Bing; Feng, Weiyue; Zhao, Yuliang; Chai, Zhifang

    2013-06-01

    With the rapid development of engineered nanomaterials (NMs) and wide biomedical applications for new types of multifunctional NMs, an understanding of the behavior patterns of NMs in vivo and clarification of their potential health impact as a result of their novel physicochemical properties is essential for ensuring safety in biomedical applications of nanotechnology. NMs have heterogeneous characteristics in that they combine the bulk properties of solids with the mobility of molecules, and present phase transformation, dissolution, oxidation/reduction as well as nano-bio interface reactions in biological milieu, which affect their in vivo behaviors and biological effects. The accurate study of identification, quantification, transformation state of NMs and their biological effects in vivo remains a challenge. This review aims to provide a "metallomics" (an integrated metal-assisted function bioscience) insight into the in vivo behavior and biological effects of NMs, particularly for metal-based nanomaterials (MNMs) and is based mainly on our own research and other previous works.

  4. Metal-Based Nanoparticles and the Immune System: Activation, Inflammation, and Potential Applications

    PubMed Central

    Luo, Yueh-Hsia; Chang, Louis W.; Lin, Pinpin

    2015-01-01

    Nanomaterials, including metal-based nanoparticles, are used for various biological and medical applications. However, metals affect immune functions in many animal species including humans. Different physical and chemical properties induce different cellular responses, such as cellular uptake and intracellular biodistribution, leading to the different immune responses. The goals of this review are to summarize and discuss the innate and adaptive immune responses triggered by metal-based nanoparticles in a variety of immune system models. PMID:26125021

  5. Functionally relevant microorganisms to enhanced biological phosphorus removal performance at full-scale wastewater treatment plants in the United States.

    PubMed

    Gu, April Z; Saunders, A; Neethling, J B; Stensel, H D; Blackall, L L

    2008-08-01

    The abundance and relevance ofAccumulibacter phosphatis (presumed to be polyphosphate-accumulating organisms [PAOs]), Competibacter phosphatis (presumed to be glycogen-accumulating organisms [GAOs]), and tetrad-forming organisms (TFOs) to phosphorus removal performance at six full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plants were investigated. Coexistence of various levels of candidate PAOs and GAOs were found at these facilities. Accumulibacter were found to be 5 to 20% of the total bacterial population, and Competibacter were 0 to 20% of the total bacteria population. The TFO abundance varied from nondetectable to dominant. Anaerobic phosphorus (P) release to acetate uptake ratios (P(rel)/HAc(up)) obtained from bench tests were correlated positively with the abundance ratio of Accumulibacter/(Competibacter +TFOs) and negatively with the abundance of (Competibacter +TFOs) for all plants except one, suggesting the relevance of these candidate organisms to EBPR processes. However, effluent phosphorus concentration, amount of phosphorus removed, and process stability in an EBPR system were not directly related to high PAO abundance or mutually exclusive with a high GAO fraction. The plant that had the lowest average effluent phosphorus and highest stability rating had the lowest P(rel)/HAc(up) and the most TFOs. Evaluation of full-scale EBPR performance data indicated that low effluent phosphorus concentration and high process stability are positively correlated with the influent readily biodegradable chemical oxygen demand-to-phosphorus ratio. A system-level carbon-distribution-based conceptual model is proposed for capturing the dynamic competition between PAOs and GAOs and their effect on an EBPR process, and the results from this study seem to support the model hypothesis. PMID:18751532

  6. Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

    NASA Astrophysics Data System (ADS)

    Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

    2006-07-01

    Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

  7. p-type metal-base transistor

    NASA Astrophysics Data System (ADS)

    Delatorre, R. G.; Munford, M. L.; Zandonay, R.; Zoldan, V. C.; Pasa, A. A.; Schwarzacher, W.; Meruvia, M. S.; Hümmelgen, I. A.

    2006-06-01

    In this work we present data from a novel p-type metal-base transistor with common-base gain α ˜1, fabricated at ambient temperature and pressure by electrodepositing sequentially on a p-type Si collector, a Co base and a Cu2O emitter. The high gain and the dependence of potential between emitter and base (VEB) on the potential between collector and base (VCB) when the emitter current (IE) is held constant both suggest that the device functions as a natural permeable base transistor for very thin metal bases.

  8. Transcriptional responses to biologically relevant doses of UV-B radiation in the model archaeon, Halobacterium sp. NRC-1

    PubMed Central

    Boubriak, Ivan; Ng, Wooi Loon; DasSarma, Priya; DasSarma, Shiladitya; Crowley, David J; McCready, Shirley J

    2008-01-01

    Background Most studies of the transcriptional response to UV radiation in living cells have used UV doses that are much higher than those encountered in the natural environment, and most focus on short-wave UV (UV-C) at 254 nm, a wavelength that never reaches the Earth's surface. We have studied the transcriptional response of the sunlight-tolerant model archaeon, Halobacterium sp. NRC-1, to low doses of mid-wave UV (UV-B) to assess its response to UV radiation that is likely to be more biologically relevant. Results Halobacterium NRC-1 cells were irradiated with UV-B at doses equivalent to 30 J/m2 and 5 J/m2 of UV-C. Transcriptional profiling showed that only 11 genes were up-regulated 1.5-fold or more by both UV-B doses. The most strongly up-regulated gene was radA1 (vng2473), the archaeal homologue of RAD51/recA recombinase. The others included arj1 (vng779) (recJ-like exonuclease), top6A (vng884) and top6B (vng885) (coding for Topoisomerase VI subunits), and nrdJ (vng1644) (which encodes a subunit of ribonucleotide reductase). We have found that four of the consistently UV-B up-regulated genes, radA1 (vng2473), vng17, top6B (vng885) and vng280, share a common 11-base pair motif in their promoter region, TTTCACTTTCA. Similar sequences were found in radA promoters in other halophilic archaea, as well as in the radA promoter of Methanospirillum hungatei. We analysed the transcriptional response of a repair-deficient ΔuvrA (vng2636) ΔuvrC (vng2381) double-deletion mutant and found common themes between it and the response in repair proficient cells. Conclusion Our results show a core set of genes is consistently up-regulated after exposure to UV-B light at low, biologically relevant doses. Eleven genes were up-regulated, in wild-type cells, after two UV-B doses (comparable to UV-C doses of 30 J/m2 and 5 J/m2), and only four genes were up-regulated by all doses of UV-B and UV-C that we have used in this work and previously. These results suggest that high doses

  9. V-type nerve agents phosphonylate ubiquitin at biologically relevant lysine residues and induce intramolecular cyclization by an isopeptide bond.

    PubMed

    Schmidt, Christian; Breyer, Felicitas; Blum, Marc-Michael; Thiermann, Horst; Worek, Franz; John, Harald

    2014-08-01

    Toxic organophosphorus compounds (e.g., pesticides and nerve agents) are known to react with nucleophilic side chains of different amino acids (phosphylation), thus forming adducts with endogenous proteins. Most often binding to serine, tyrosine, or threonine residues is described as being of relevance for toxicological effects (e.g., acetylcholinesterase and neuropathy target esterase) or as biomarkers for post-exposure analysis (verification, e.g., albumin and butyrylcholinesterase). Accordingly, identification of novel protein targets might be beneficial for a better understanding of the toxicology of these compounds, revealing new bioanalytical verification tools, and improving knowledge on chemical reactivity. In the present study, we investigated the reaction of ubiquitin (Ub) with the V-type nerve agents Chinese VX, Russian VX, and VX in vitro. Ub is a ubiquitous protein with a mass of 8564.8 Da present in the extra- and intracellular space that plays an important physiological role in several essential processes (e.g., proteasomal degradation, DNA repair, protein turnover, and endocytosis). Reaction products were analyzed by matrix-assisted laser desorption/ionization-time-of-flight- mass spectrometry (MALDI-TOF MS) and μ-high-performance liquid chromatography online coupled to UV-detection and electrospray ionization MS (μHPLC-UV/ESI MS). Our results originally document that a complex mixture of at least mono-, di, and triphosphonylated Ub adducts was produced. Surprisingly, peptide mass fingerprint analysis in combination with MALDI and ESI MS/MS revealed that phosphonylation occurred with high selectivity in at least 6 of 7 surface-exposed lysine residues that are essential for the biological function of Ub. These reaction products were found not to age. In addition, we herein report for the first time that phosphonylation induced intramolecular cyclization by formation of an isopeptide bond between the ε-amino group of a formerly phosphonylated

  10. Tyrosyl radicals in dehaloperoxidase: how nature deals with evolving an oxygen-binding globin to a biologically relevant peroxidase.

    PubMed

    Dumarieh, Rania; D'Antonio, Jennifer; Deliz-Liang, Alexandria; Smirnova, Tatyana; Svistunenko, Dimitri A; Ghiladi, Reza A

    2013-11-15

    Dehaloperoxidase (DHP) from Amphitrite ornata, having been shown to catalyze the hydrogen peroxide-dependent oxidation of trihalophenols to dihaloquinones, is the first oxygen binding globin that possesses a biologically relevant peroxidase activity. The catalytically competent species in DHP appears to be Compound ES, a reactive intermediate that contains both a ferryl heme and a tyrosyl radical. By simulating the EPR spectra of DHP activated by H2O2, Thompson et al. (Thompson, M. K., Franzen, S., Ghiladi, R. A., Reeder, B. J., and Svistunenko, D. A. (2010) J. Am. Chem. Soc. 132, 17501-17510) proposed that two different radicals, depending on the pH, are formed, one located on either Tyr-34 or Tyr-28 and the other on Tyr-38. To provide additional support for these simulation-based assignments and to deduce the role(s) that tyrosyl radicals play in DHP, stopped-flow UV-visible and rapid-freeze-quench EPR spectroscopic methods were employed to study radical formation in DHP when three tyrosine residues, Tyr-28, Tyr-34, and Tyr-38, were replaced either individually or in combination with phenylalanines. The results indicate that radicals form on all three tyrosines in DHP. Evidence for the formation of DHP Compound I in several tyrosine mutants was obtained. Variants that formed Compound I showed an increase in the catalytic rate for substrate oxidation but also an increase in heme bleaching, suggesting that the tyrosines are necessary for protecting the enzyme from oxidizing itself. This protective role of tyrosines is likely an evolutionary adaptation allowing DHP to avoid self-inflicted damage in the oxidative environment.

  11. V-type nerve agents phosphonylate ubiquitin at biologically relevant lysine residues and induce intramolecular cyclization by an isopeptide bond.

    PubMed

    Schmidt, Christian; Breyer, Felicitas; Blum, Marc-Michael; Thiermann, Horst; Worek, Franz; John, Harald

    2014-08-01

    Toxic organophosphorus compounds (e.g., pesticides and nerve agents) are known to react with nucleophilic side chains of different amino acids (phosphylation), thus forming adducts with endogenous proteins. Most often binding to serine, tyrosine, or threonine residues is described as being of relevance for toxicological effects (e.g., acetylcholinesterase and neuropathy target esterase) or as biomarkers for post-exposure analysis (verification, e.g., albumin and butyrylcholinesterase). Accordingly, identification of novel protein targets might be beneficial for a better understanding of the toxicology of these compounds, revealing new bioanalytical verification tools, and improving knowledge on chemical reactivity. In the present study, we investigated the reaction of ubiquitin (Ub) with the V-type nerve agents Chinese VX, Russian VX, and VX in vitro. Ub is a ubiquitous protein with a mass of 8564.8 Da present in the extra- and intracellular space that plays an important physiological role in several essential processes (e.g., proteasomal degradation, DNA repair, protein turnover, and endocytosis). Reaction products were analyzed by matrix-assisted laser desorption/ionization-time-of-flight- mass spectrometry (MALDI-TOF MS) and μ-high-performance liquid chromatography online coupled to UV-detection and electrospray ionization MS (μHPLC-UV/ESI MS). Our results originally document that a complex mixture of at least mono-, di, and triphosphonylated Ub adducts was produced. Surprisingly, peptide mass fingerprint analysis in combination with MALDI and ESI MS/MS revealed that phosphonylation occurred with high selectivity in at least 6 of 7 surface-exposed lysine residues that are essential for the biological function of Ub. These reaction products were found not to age. In addition, we herein report for the first time that phosphonylation induced intramolecular cyclization by formation of an isopeptide bond between the ε-amino group of a formerly phosphonylated

  12. UV and skin cancer: specific p53 gene mutation in normal skin as a biologically relevant exposure measurement.

    PubMed Central

    Nakazawa, H; English, D; Randell, P L; Nakazawa, K; Martel, N; Armstrong, B K; Yamasaki, H

    1994-01-01

    Many human skin tumors contain mutated p53 genes that probably result from UV exposure. To investigate the link between UV exposure and p53 gene mutation, we developed two methods to detect presumptive UV-specific p53 gene mutations in UV-exposed normal skin. The methods are based on mutant allele-specific PCRs and ligase chain reactions and designed to detect CC to TT mutations at codons 245 and 247/248, using 10 micrograms of DNA samples. These specific mutations in the p53 gene have been reported in skin tumors. CC to TT mutations in the p53 gene were detected in cultured human skin cells only after UV irradiation, and the mutation frequency increased with increasing UV dose. Seventeen of 23 samples of normal skin from sun-exposed sites (74%) on Australian skin cancer patients contained CC to TT mutations in one or both of codons 245 and 247/248 of the p53 gene, and only 1 of 20 samples from non-sun-exposed sites (5%) harbored the mutation. None of 15 biopsies of normal skin from non-sun-exposed or intermittently exposed sites on volunteers living in France carried such mutations. Our results suggest that specific p53 gene mutations associated with human skin cancer are induced in normal skin by solar UV radiation. Measurement of these mutations may be useful as a biologically relevant measure of UV exposure in humans and as a possible predictor of risk for skin cancer. Images Fig. 2 Fig. 3 Fig. 4 PMID:8278394

  13. Dose addition models based on biologically-relevant reductions in fetal testosterone accurately predict postnatal reproductive tract alterations by a phthalate mixture in rats

    EPA Science Inventory

    Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the curren...

  14. Design, Development, and Psychometric Analysis of a General, Organic, and Biological Chemistry Topic Inventory Based on the Identified Main Chemistry Topics Relevant to Nursing Clinical Practice

    ERIC Educational Resources Information Center

    Brown, Corina E.

    2013-01-01

    This two-stage study focused on the undergraduate nursing course that covers topics in general, organic, and biological (GOB) chemistry. In the first stage, the central objective was to identify the main concepts of GOB chemistry relevant to the clinical practice of nursing. The collection of data was based on open-ended interviews of both nursing…

  15. Establishing the "Biological Relevance" of Dipentyl Phthalate Reductions in Fetal Rat Testosterone Production and Plasma and Testis Testosterone Levels.

    PubMed

    Gray, Leon Earl; Furr, Johnathan; Tatum-Gibbs, Katoria R; Lambright, Christy; Sampson, Hunter; Hannas, Bethany R; Wilson, Vickie S; Hotchkiss, Andrew; Foster, Paul M D

    2016-01-01

    Phthalate esters (PEs) constitute a large class of compounds that are used for many consumer product applications. Many of the C2-C7 di-ortho PEs reduce fetal testicular hormone and gene expression levels in rats resulting in adverse effects seen later in life but it appears that relatively large reductions in fetal testosterone (T) levels and testis gene expression may be required to adversely affect reproductive development (Hannas, B. R., Lambright, C. S., Furr, J., Evans, N., Foster, P. M., Gray, E. L., and Wilson, V. S. (2012). Genomic biomarkers of phthalate-induced male reproductive developmental toxicity: a targeted RT-PCR array approach for defining relative potency. Toxicol. Sci. 125, 544-557). The objectives of this study were (1) to model the relationships between changes in fetal male rat plasma testosterone (PT), T levels in the testis (TT), T production (PROD), and testis gene expression with the reproductive malformation rates, and (2) to quantify the "biologically relevant reductions" (BRRs) in fetal T necessary to induce adverse effects in the offspring. In the fetal experiment, Harlan Sprague-Dawley rats were dosed with dipentyl phthalate (DPeP) at 0, 11, 33, 100, and 300 mg/kg/day from gestational days (GD) 14-18 and fetal testicular T, PT levels, and T Prod and gene expression were assessed on GD 18. In the postnatal experiment, rats were dosed with DPeP from GD 8-18 and reproductive development was monitored through adulthood. The dose-response curves for TT levels (ED(50) = 53 mg/kg) and T PROD (ED(50) = 45 mg/kg) were similar, whereas PT was reduced at ED50 = 19 mg/kg. When the reductions in TPROD and Insl3 mRNA were compared with the postnatal effects of in utero DPeP, dose-related reproductive alterations were noted when T PROD and Insl3 mRNA were reduced by >45% and 42%, respectively. The determination of BRR levels may enable risk assessors to utilize fetal endocrine data to help establish points of departure for

  16. "Evo in the News": A Pedagogical Tool to Enhance Students' Perceptions of the Relevance of Evolutionary Biology

    ERIC Educational Resources Information Center

    Infanti, Lynn M.

    2012-01-01

    This investigation evaluated the effects of the use of the pedagogical tool "Evo in the News" on the attitudes toward and knowledge of biological evolution in a sample of undergraduate non-major biology students at a large, private research university. In addition, this study looked at the initial attitudes of the students and their…

  17. Hydration Structures and Thermodynamic Properties of Cationized Biologically Relevant Molecules, M+(Indole)(H2O)n (M = Na, K; n = 3-6)

    NASA Astrophysics Data System (ADS)

    Ke, Haochen; Lisy, James

    2015-03-01

    The balance between various noncovalent interactions plays a key role in determining the hydration structures and thermodynamic properties of biologically relevant molecules in biological mediums. Such properties of biologically relevant molecules are closely related to their often unique biological functionalities. The indole moiety is a basic functional group of many important neurotransmitters and hormones and has been used as tractable model for more complex biomolecules. The cationized indole water cluster is a perfect system for the quantitative and systematic study of the competition and cooperation of noncovalent interactions, as electrostatic interactions can be adjusted by introducing different monovalent cations and hydrogen bonding interactions can be adjusted by varying the level of hydration. IRPD spectra with isotopic (H/D) analysis helped unravel the overlapping N-H and O-H stretching modes, a major challenge of earlier studies. Thermodynamic analysis using relative Gibbs free energies, for energy ordering, together with spectral analysis provided unambiguous assignment of spectral features and structural configurations. A systematic hydration model with an in-depth account of noncovalent interactions is presented.

  18. The role of the spectral sensitivity curve in the selection of relevant biological dosimeters for solar UV monitoring.

    PubMed

    Modos, K; Gaspar, S; Kerekgyarto, T; Vink, A A; Roza, L; Fekete, A

    1999-01-01

    To estimate the risk of enhanced UV-B radiation due to stratospheric ozone depletion, phage T7 and uracil thin-layer biological dosimeters have been developed, which weight the UV irradiance according to induced DNA damage. To study the molecular basis of the biological effects observed after UV irradiation, the spectral sensitivity curves of the two dosimeters and induction of the two major DNA photoproducts, cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts ((6-4)PDs), in phage T7 have been determined for polychromatic UV sources. CPDs and (6-4)PDs are determined by lesion-specific monoclonal antibodies in an immunodotblot assay. Phage T7 and uracil biological dosimeters together with a Robertson-Berger (RB) meter have been used for monitoring environmental radiation from the polar region to the equator. The biologically effective dose (BED) established with the three different dosimeters increases according to the changes in the solar angle and ozone column, but the degree of the change differs significantly. The results can be explained based on the different spectral sensitivities of the dosimeters. A possible method for determining the trend of the increase in the biological risk due to ozone depletion is suggested.

  19. Modeling pCO{sub 2} in the upper ocean: A review of relevant physical, chemical, and biological processes

    SciTech Connect

    1990-12-01

    The pCO{sub 2} of the surface ocean is controlled by a combination of physical, chemical, and biological processes. Modeling surface ocean pCO{sub 2} is analogous to modeling sea surface temperature (SST), in that sea surface pCO{sub 2} is affected by fluxes across the air-sea interface and by exchange with deeper water. However, pCO{sub 2} is also affected by chemical and biological processes which have no analog in SST. Seawater pCO{sub 2} is buffered by pH equilibrium reactions between the species CO{sub 2}, HCO{sub 3}-, and CO{sub 3}{sup =}. This effect provides an effective reservoir for CO{sub 2} in seawater that is 10 times larger than it would be for an unbuffered gas. The equilibrium between dissolved and atmospheric CO{sub 2} is sensitive to temperature, tending to higher pCO{sub 2} in warmer water. Biological export of carbon as sinking particles maintains a gradient of pCO{sub 2}, with lower values near the surface (this processes is called the {open_quotes}biological pump{close_quotes}). In most of the ocean, biological activity removes all of the available nutrients from the surface water; that is, the rate of carbon export in these locations is limited by the rate of nutrient supply to the euphotic zone. However, in much of the high-latitude oceans, primary production does not deplete the euphotic zone of nutrients, a fact to which the atmospheric pCO{sub 2} is extraordinarily sensitive. Understanding the limits to phytoplankton growth in the high latitudes, and how these limits might change under different climatic regimes, is essential to prediction of future ocean uptake of fossil fuel CO{sub 2}.

  20. A Heteroepitaxial Perovskite Metal-Base Transistor

    SciTech Connect

    Yajima, T.; Hikita, Y.; Hwang, H.Y.; /Tokyo U. /JST, PRESTO /SLAC

    2011-08-11

    'More than Moore' captures a concept for overcoming limitations in silicon electronics by incorporating new functionalities in the constituent materials. Perovskite oxides are candidates because of their vast array of physical properties in a common structure. They also enable new electronic devices based on strongly-correlated electrons. The field effect transistor and its derivatives have been the principal oxide devices investigated thus far, but another option is available in a different geometry: if the current is perpendicular to the interface, the strong internal electric fields generated at back-to-back heterojunctions can be used for oxide electronics, analogous to bipolar transistors. Here we demonstrate a perovskite heteroepitaxial metal-base transistor operating at room temperature, enabled by interface dipole engineering. Analysis of many devices quantifies the evolution from hot-electron to permeable-base behaviour. This device provides a platform for incorporating the exotic ground states of perovskite oxides, as well as novel electronic phases at their interfaces.

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

    PubMed Central

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

    2013-01-01

    SysBioCube is an integrated data warehouse and analysis platform for experimental data relating to diseases of military relevance developed for the US Army Medical Research and Materiel Command Systems Biology Enterprise (SBE). It brings together, under a single database environment, pathophysio-, psychological, molecular and biochemical data from mouse models of post-traumatic stress disorder and (pre-) clinical data from human PTSD patients.. SysBioCube will organize, centralize and normalize this data and provide an access portal for subsequent analysis to the SBE. It provides new or expanded browsing, querying and visualization to provide better understanding of the systems biology of PTSD, all brought about through the integrated environment. We employ Oracle database technology to store the data using an integrated hierarchical database schema design. The web interface provides researchers with systematic information and option to interrogate the profiles of pan-omics component across different data types, experimental designs and other covariates. PMID:24303294

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

    PubMed

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

    2013-01-01

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

  3. Improving biological relevancy of transcriptional biomarkers experiments by applying the MIQE guidelines to pre-clinical and clinical trials.

    PubMed

    Dooms, M; Chango, A; Barbour, E; Pouillart, P; Abdel Nour, A M

    2013-01-01

    The "Minimum Information for the Publication of qPCR Experiments" (MIQE [3]) guidelines are very much targeted at basic research experiments and have to our knowledge not been applied to qPCR assays carried out in the context of clinical trials. This report details the use of the MIQE qPCR app for iPhone (App Store, Apple) to assess the MIQE compliance of one clinical and five pre-clinical trials. This resulted in the need to include 14 modifications that make the guidelines more relevant for the assessment of this special type of application. We also discuss the need for flexibility, since while some parameters increase experimental quality, they also require more reagents and more time, which is not always feasible in a clinical setting. PMID:22910527

  4. Emotional interference-based forgetting in short-term memory. Cognitive inhibition of pleasant but not unpleasant biologically relevant distractors

    PubMed Central

    García-Pacios, Javier; Del Río, David; Villalobos, Dolores; Ruiz-Vargas, José M.; Maestú, Fernando

    2015-01-01

    Emotional stimuli automatically recruit attentional resources. Although this usually brings more adaptive responses, it may suppose a disadvantage when emotional information is task-irrelevant and should be ignored. Previous studies have shown how emotional stimuli with a negative content exert a greater interference than neutral stimuli during a concurrent working memory (WM) task. However, the impact of positively valenced stimuli as interference has not been addressed to date. In three experiments and one re-analysis we explore the impact of pleasant and unpleasant emotional distractors during WM maintenance. The results suggest that our cognitive control can cope with the interference posed by pleasant distractors as well as with the interference posed by neutral stimuli. However, unpleasant distractors are harder to control in the context of WM maintenance. As unpleasant stimuli usually convey relevant information that we should not to ignore, our executive control seems to be less able to reallocate cognitive resources after unpleasant distraction. PMID:25999894

  5. Emotional interference-based forgetting in short-term memory. Cognitive inhibition of pleasant but not unpleasant biologically relevant distractors.

    PubMed

    García-Pacios, Javier; Del Río, David; Villalobos, Dolores; Ruiz-Vargas, José M; Maestú, Fernando

    2015-01-01

    Emotional stimuli automatically recruit attentional resources. Although this usually brings more adaptive responses, it may suppose a disadvantage when emotional information is task-irrelevant and should be ignored. Previous studies have shown how emotional stimuli with a negative content exert a greater interference than neutral stimuli during a concurrent working memory (WM) task. However, the impact of positively valenced stimuli as interference has not been addressed to date. In three experiments and one re-analysis we explore the impact of pleasant and unpleasant emotional distractors during WM maintenance. The results suggest that our cognitive control can cope with the interference posed by pleasant distractors as well as with the interference posed by neutral stimuli. However, unpleasant distractors are harder to control in the context of WM maintenance. As unpleasant stimuli usually convey relevant information that we should not to ignore, our executive control seems to be less able to reallocate cognitive resources after unpleasant distraction. PMID:25999894

  6. Dicarba-closo-dodecarborane-containing half-sandwich complexes of ruthenium, osmium, rhodium and iridium: biological relevance and synthetic strategies.

    PubMed

    Barry, Nicolas P E; Sadler, Peter J

    2012-04-21

    This review describes how the incorporation of dicarba-closo-dodecarboranes into half-sandwich complexes of ruthenium, osmium, rhodium and iridium might lead to the development of a new class of compounds with applications in medicine. Such a combination not only has unexplored potential in traditional areas such as Boron Neutron Capture Therapy agents, but also as pharmacophores for the targeting of biologically important proteins and the development of targeted drugs. The synthetic pathways used for the syntheses of dicarba-closo-dodecarboranes-containing half-sandwich complexes of ruthenium, osmium, rhodium and iridium are also reviewed. Complexes with a wide variety of geometries and characteristics can be prepared. Examples of addition reactions on the metal centre, B-H activation, transmetalation reactions and/or direct formation of metal-metal bonds are discussed (103 references).

  7. Biological Production of a Hydrocarbon Fuel Intermediate Polyhydroxybutyrate (PHB) from a Process Relevant Lignocellulosic Derived Sugar (Poster)

    SciTech Connect

    Wang, W.; Mittal, A.; Mohagheghi, A.; Johnson, D. K.

    2014-04-01

    PHAs are synthesized by many microorganisms to serve as intracellular carbon storage molecules. In some bacterial strains, PHB can account for up to 80% of cell mass. In addition to its application in the packaging sector, PHB also has great potential as an intermediate in the production of hydrocarbon fuels. PHB can be thermally depolymerized and decarboxylated to propene which can be upgraded to hydrocarbon fuels via commercial oligomerization technologies. Cupriavidus necator is the microorganism that has been most extensively studied and used for PHB production on an industrial scale; However the substrates used for producing PHB are mainly fructose, glucose, sucrose, fatty acids, glycerol, etc., which are expensive. In this study, we demonstrate production of PHB from a process relevant lignocellulosic derived sugar stream, i.e., saccharified slurry from pretreated corn stover. The strain was first investigated in shake flasks for its ability to utilize glucose, xylose and acetate. In addition, the strain was also grown on pretreated lignocellulose hydrolyzate slurry and evaluated in terms of cell growth, sugar utilization, PHB accumulation, etc. The mechanism of inhibition in the toxic hydrolysate generated by the pretreatment and saccharification process of biomass, was also studied.

  8. Identification of Genes Relevant to Pesticides and Biology from Global Transcriptome Data of Monochamus alternatus Hope (Coleoptera: Cerambycidae) Larvae

    PubMed Central

    Shao, Ensi; Rebeca, Carballar-Lejarazú; Guo, Yajie; Xiong, Yueting; Mou, Yani; Xu, Runxue; Hu, Xia; Liang, Guanghong; Zou, Shuangquan; Guan, Xiong; Zhang, Feiping

    2016-01-01

    Monochamus alternatus Hope is the main vector in China of the Pine Wilt Disease caused by the pine wood nematode Bursaphelenchus xylophilus. Although chemical control is traditionally used to prevent pine wilt disease, new strategies based in biological control are promising ways for the management of the disease. However, there is no deep sequence analysis of Monochamus alternatus Hope that describes the transcriptome and no information is available about gene function of this insect vector. We used next generation sequencing technology to sequence the whole fourth instar larva transcriptome of Monochamus alternatus Hope and successfully built a Monochamus alternatus Hope transcriptome database. In total, 105,612 unigenes were assigned for Gene Ontology (GO) terms, information for 16,730 classified unigenes was obtained in the Clusters of Orthologous Groups (COGs) database, and 13,024 unigenes matched with 224 predicted pathways in the Kyoto Encyclopedia of Genes and Genome (KEGG). In addition, genes related to putative insecticide resistance-related genes, RNAi, the Bt receptor, intestinal digestive enzymes, possible future insect control targets and immune-related molecules are described. This study provides valuable basic information that can be used as a gateway to develop new molecular tools for Monochamus alternatus Hope control strategies. PMID:26815657

  9. The nonconservative property of dissolved molybdenum in the western Taiwan Strait: Relevance of submarine groundwater discharges and biological utilization

    NASA Astrophysics Data System (ADS)

    Wang, Deli; Xia, Weiwei; Lu, Shuimiao; Wang, Guizhi; Liu, Qian; Moore, Willard S.; Arthur Chen, Chen-Tung

    2016-01-01

    This study examined dissolved Mo and sedimentary Mo along with hydrochemical parameters in the western Taiwan Strait (WTS) in May and August 2012. The results demonstrate that dissolved Mo could be depleted of as high as 10-20 nM during our May sampling period when the nutrient-enriched Min-Zhe coastal current ceased and spring blooms developed. The negative correlation between Chl-a and dissolved Mo suggests the possible involvement of high algal productivity in removing dissolved Mo out of the water column. Specific oceanographic settings (little currents) permitted a high sedimentary enrichment of Mo (>6 µg/g Mo) within the highly productive waters outside the Jiulong River mouth. Possibly, the high algal productivities and consequent organic matter sinks provide a pathway of Mo burial from water columns into sediments. Dissolved Mo was relatively high in groundwater samples, but we observed that submarine groundwater discharges (SGDs) only contributed to a relatively small percentage of the total dissolved Mo pool in WTS. It is probably attributable to the immediate removal of SGD-released Mo ions via adsorption onto newly formed Mn oxides once exposed to oxygenated seawater, followed by an elevated sedimentary Mo accumulation near the SGDs (˜5 µg/g). In addition to metal oxide particle scavenging and sulfide precipitation, we estimated that biological uptake along with Mo adsorption onto organic matter carriers could finally provide more than 10% of the annual sedimentary Mo accumulation in WTS.

  10. Genomic profiling of mitochondrion-rich breast carcinoma: chromosomal changes may be relevant for mitochondria accumulation and tumour biology.

    PubMed

    Geyer, Felipe C; de Biase, Dario; Lambros, Maryou B K; Ragazzi, Moira; Lopez-Garcia, Maria A; Natrajan, Rachael; Mackay, Alan; Kurelac, Ivana; Gasparre, Giuseppe; Ashworth, Alan; Eusebi, Vincenzo; Reis-Filho, Jorge S; Tallini, Giovanni

    2012-02-01

    , at least a subset of mitochondrion-rich breast carcinomas may be underpinned by a distinct pattern of chromosomal changes potentially relevant for mitochondria accumulation and constitute a discrete molecular entity.

  11. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State 17O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds

    PubMed Central

    Rorick, Amber; Michael, Matthew A.; Yang, Liu; Zhang, Yong

    2015-01-01

    Oxygen is an important element in most biologically significant molecules and experimental solid-state 17O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state 17O NMR chemical shift tensor properties are still challenging in many cases and in particular each of the prior computational work is basically limited to one type of oxygen-containing systems. This work provides the first systematic study of the effects of geometry refinement, method and basis sets for metal and non-metal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups, X= H, C, N, P, and metal. The experimental range studied is of 1455 ppm, a major part of the reported 17O NMR chemical shifts in organic and organometallic compounds. A number of computational factors towards relatively general and accurate predictions of 17O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied various kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient R2 of 0.9880 and mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and R2 of 0.9926 for all shift tensor properties. These results shall facilitate future computational studies of 17O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help refinement and determination of active-site structures of some oxygen-containing substrate bound proteins. PMID:26274812

  12. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

    PubMed

    Rorick, Amber; Michael, Matthew A; Yang, Liu; Zhang, Yong

    2015-09-01

    Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

  13. Spontaneous encapsulation and concentration of biological macromolecules in liposomes: an intriguing phenomenon and its relevance in origins of life.

    PubMed

    de Souza, Tereza Pereira; Fahr, Alfred; Luisi, Pier Luigi; Stano, Pasquale

    2014-12-01

    One of the main open questions in origin of life research focuses on the formation, by self-organization, of primitive cells composed by macromolecular compounds enclosed within a semi-permeable membrane. A successful experimental strategy for studying the emergence and the properties of primitive cells relies on a synthetic biology approach, consisting in the laboratory assembly of cell models of minimal complexity (semi-synthetic minimal cells). Despite the recent advancements in the construction and characterization of synthetic cells, an important physical aspect related to their formation is still not well known, namely, the mechanism of solute entrapment inside liposomes (in particular, the entrapment of macromolecules). In the past years, we have investigated this phenomenon and here we shortly review our experimental results. We show how the detailed cryo-transmission electron microscopy analyses of liposome populations created in the presence of ferritin (taken as model protein) or ribosomes have revealed that a small fraction of liposomes contains a high number of solutes, against statistical expectations. The local (intra-liposomal) macromolecule concentration in these liposomes largely exceeds the bulk concentration. A similar behaviour is observed when multi-molecular reaction mixtures are used, whereby the reactions occur effectively only inside those liposomes that have entrapped high number of molecules. If similar mechanisms operated in early times, these intriguing results support a scenario whereby the formation of lipid compartments plays an important role in concentrating the components of proto-metabolic systems-in addition to their well-known functions of confinement and protection.

  14. A multicomponent bioactive tissue-engineered blood vessel: Fabrication, mechanical evaluation and biological evaluation with physiological-relevant conditions

    NASA Astrophysics Data System (ADS)

    Bonani, Walter

    The high long-term failure rate of synthetic vascular grafts in the replacement of small vessels is known to be associated with the lack of physiological signals to vascular cells causing adverse hemodynamic, inflammatory or coagulatory events. Current studies focus on developing engineered vascular devices with ability of directing cell activity in vitro and in vivo for tissue regeneration. It is also known that controlled molecule release from scaffolds can dramatically increase the scaffold ability of directing cell activities in vitro and in vivo for tissue regeneration. To address the mechanical and biological problems associated with graft materials, we demonstrated a degradable polyester-fibroin composite tubular scaffolds which shows well-integrated nanofibrous structure, endothelial-conducive surface and anisotropic mechanical property, suitable as engineered vascular constructs. Tissue regeneration needs not only functional biomolecules providing signaling cues to cells and guide tissue remodeling, but also an adequate modality of molecule delivery. In fact, healthy tissue formation requires specific signals at well-defined place and time. To develop scaffolds with multi-modal presentation of biomolecules, we patterned electrospun nanofibers over the thickness of the 3-dimensional scaffolds by programming the deposition of interpenetrating networks of degradable polymers poly(a-caprolactone) and poly(lactide-co-glycolide) acid in tailored proportion. Fluorescent model molecules, drug and growth factors were embedded in the polymeric fibers with different techniques and release profiles were obtained and discussed. Fabrication process resulted in precise gradient patterns of materials and functional biomolecules throughout the thickness of the scaffold. These graded materials showed programmable spatio-temporal control over the release. Molecule release profiles on each side of the scaffolds were used to determine the separation efficiency of molecule

  15. Synthesis of fluorophore encapsulated silica nanoparticles for the evaluation of the biological fate and toxicity of food relevant nanoparticles

    NASA Astrophysics Data System (ADS)

    Zane, Andrew Paul

    fluorophores, rhodamine 6G and rhodamine 800, into silica shells for direct monitoring in intestinal epithelial cells and tissues of exposed mice. We show that, for small nanoparticles, a typical Stober-type ammonia driven synthesis does not yield stable fluorescence. This has been observed in literature and is attributed to incompletely hydrolyzed silica precursor causing partial dissolution of the silica shell. We remedy this by applying an arginine driven silica shell synthesis, which is known to produce a denser and more stable product at smaller particle sizes. We show that all three fluorophores can be coated in a simple generalized procedure, and the resulting particles all show stable fluorescence with no evidence of dye leakage. Using these particles, we demonstrate that silica nanoparticles can be observed internalizing into C2BBe1 intestinal epithelial cells, and in the tissues of mice that were fed the particles by gavage. We find direct evidence that the particles are absorbed into circulation and subsequently localize in organs throughout the body. Future efforts will attempt to better quantify this accumulation, as well as generalize the procedure to other food relevant nanoparticles such as TiO2.

  16. Insight into the Local Solvent Environment of Biologically Relevant Iron-nitroysl Systems through Two-Dimensional Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Brookes, Jennifer Faith

    Iron-nitrosyl systems, particularly in the form of heme proteins, with their iron metal active sites play an important role in biological systems. Heme proteins act as storage, transporters, and receptors for nitric oxide (NO), a signaling molecule that is important in immune, nervous, and cardiovascular systems of mammals. By better understanding the local environment of the active site of NO binding heme proteins we can gain insight into disease in which the NO pathways have been implicated. This is an important step to being able to develop pharmaceuticals targeting NO pathways in humans. Sodium nitroprusside ((SNP, Na2[Fe(CN)5is NO]·2H 2O) investigated as a model system for the active site of nitric oxide binding heme proteins. Using two-dimensional infrared spectroscopy (2D IR) to obtain dephasing dynamics of the nitrosyl stretch (nuNO) in a series of solvents we are able to better understand the local environment of the more complicated metalloproteins. Rigorous line shape analysis is performed by using nonlinear response theory to simulate 2D IR spectra which are then fit to experimental data in an iterative process to extract frequency-frequency correlation functions (FFCFs). The time scales obtained are then correlated to empirical solvent polarity parameters. The analysis of the 2D IR lineshapes reveal that the spectral diffusion timescale of the nuNO in SNP varies from 0.8 -- 4 ps and is negatively correlated with the empirical solvent polarity scales. We continue to investigate NO binding of metalloproteins through 2D IR experiments on nitrophorin 4 (NP4). NP4 is a pH-sensitive NO transporter protein present in the salivary gland of the blood sucking insect Rhodius prolixus which undergoes a pH sensitive structural change between a closed and open conformation allowing for the storage and delivery of NO. The two structures are observed spectroscopically as two distinct pH-dependent nu NO frequencies at ~1904 and ~1917 cm-1. We obtain FFCFs by globally

  17. Simultaneous determination of C2-C22 non-esterified fatty acids and other metabolically relevant carboxylic acids in biological material by gas chromatography of their benzyl esters.

    PubMed

    Schatowitz, B; Gercken, G

    1988-03-18

    A method for the simultaneous determination of non-esterified short-, medium- and long-chain fatty acids and other types of metabolically relevant carboxylic acids such as hydroxy, keto, aromatic and dicarboxylic acids in biological material by capillary gas chromatography of benzyl ester derivatives is described. Sample preparation avoiding incomplete isolation of carboxylic acids consisted of deproteinization and extraction with ethanol, fixation of carboxylic acids as carboxylates, removal of interfering compounds such as neutral lipids by hexane extraction and amino acids, acyl carnitines and other cations by cation-exchange chromatography, derivatization of keto groups of ketocarboxylic acids into O-methyl oximes and benzyl ester formation by reaction of the potassium carboxylates with benzyl bromide via crown ether catalysis. The sample preparation conditions were investigated, showing the usefulness of this method for quantitative determinations. Chromatograms obtained from human serum, human urine and rat heart ventricle and concentrations of carboxylic acids in these specimens are presented. PMID:3372640

  18. Imino [4+4] cycloaddition products as exclusive and biologically relevant acrolein-amine conjugates are intermediates of 3-formyl-3,4-dehydropiperidine (FDP), an acrolein biomarker.

    PubMed

    Takamatsu, Masayuki; Fukase, Koichi; Kurbangalieva, Almira; Tanaka, Katsunori

    2014-11-15

    We demonstrated synthetically that the eight-membered heterocycles 2,6,9-triazabicyclo[3.3.1]nonanes and 1,5-diazacyclooctanes are the initial and exclusive products of the reaction, through an imino [4+4] cycloaddition, of biologically relevant amines with acrolein. The stabilities of the aminoacetals within the eight-membered heterocycles determined whether the product was subsequently transformed gradually into the 3-formyl-3,4-dehydropiperidine (FDP), which is widely used as an oxidative stress marker. The reactivity profiles discovered in this study suggested that some of the imino [4+4] cycloaddition products are reactive intermediates of FDP and contribute to the mechanisms underlying the oxidative stress response to acrolein.

  19. Dose Addition Models Based on Biologically Relevant Reductions in Fetal Testosterone Accurately Predict Postnatal Reproductive Tract Alterations by a Phthalate Mixture in Rats.

    PubMed

    Howdeshell, Kembra L; Rider, Cynthia V; Wilson, Vickie S; Furr, Johnathan R; Lambright, Christy R; Gray, L Earl

    2015-12-01

    Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the current study were 2-fold: (1) to test whether a mixture model of dose addition based on the fetal T production data of individual phthalates would predict the effects of a 5 phthalate mixture on androgen-sensitive postnatal male reproductive tract development, and (2) to determine the biological relevance of the reductions in fetal T to induce abnormal postnatal reproductive tract development using data from the mixture study. We administered a dose range of the mixture (60, 40, 20, 10, and 5% of the top dose used in the previous fetal T production study consisting of 300 mg/kg per chemical of benzyl butyl (BBP), di(n)butyl (DBP), diethyl hexyl phthalate (DEHP), di-isobutyl phthalate (DiBP), and 100 mg dipentyl (DPP) phthalate/kg; the individual phthalates were present in equipotent doses based on their ability to reduce fetal T production) via gavage to Sprague Dawley rat dams on GD8-postnatal day 3. We compared observed mixture responses to predictions of dose addition based on the previously published potencies of the individual phthalates to reduce fetal T production relative to a reference chemical and published postnatal data for the reference chemical (called DAref). In addition, we predicted DA (called DAall) and response addition (RA) based on logistic regression analysis of all 5 individual phthalates when complete data were available. DA ref and DA all accurately predicted the observed mixture effect for 11 of 14 endpoints. Furthermore, reproductive tract malformations were seen in 17-100% of F1 males when fetal T production was reduced by about 25-72%, respectively. PMID:26350170

  20. Centenarians as super-controls to assess the biological relevance of genetic risk factors for common age-related diseases: a proof of principle on type 2 diabetes.

    PubMed

    Garagnani, Paolo; Giuliani, Cristina; Pirazzini, Chiara; Olivieri, Fabiola; Bacalini, Maria Giulia; Ostan, Rita; Mari, Daniela; Passarino, Giuseppe; Monti, Daniela; Bonfigli, Anna Rita; Boemi, Massimo; Ceriello, Antonio; Genovese, Stefano; Sevini, Federica; Luiselli, Donata; Tieri, Paolo; Capri, Miriam; Salvioli, Stefano; Vijg, Jan; Suh, Yousin; Delledonne, Massimo; Testa, Roberto; Franceschi, Claudio

    2013-05-01

    Genetic association studies of age-related, chronic human diseases often suffer from a lack of power to detect modest effects. Here we propose an alternative approach of including healthy centenarians as a more homogeneous and extreme control group. As a proof of principle we focused on type 2 diabetes (T2D) and assessed /genotypic associations of 31 SNPs associated with T2D, diabetes complications and metabolic diseases and SNPs of genes relevant for telomere stability and age-related diseases. We hypothesized that the frequencies of risk variants are inversely correlated with decreasing health and longevity. We performed association analyses comparing diabetic patients and non-diabetic controls followed by association analyses with extreme phenotypic groups (T2D patients with complications and centenarians). Results drew attention to rs7903146 (TCF7L2 gene) that showed a constant increase in the frequencies of risk genotype (TT) from centenarians to diabetic patients who developed macro-complications and the strongest genotypic association was detected when diabetic patients were compared to centenarians (p_value = 9.066*10⁻⁷). We conclude that robust and biologically relevant associations can be obtained when extreme phenotypes, even with a small sample size, are compared.

  1. Chemometric analysis of correlations between electronic absorption characteristics and structural and/or physicochemical parameters for ampholytic substances of biological and pharmaceutical relevance.

    PubMed

    Judycka-Proma, U; Bober, L; Gajewicz, A; Puzyn, T; Błażejowski, J

    2015-03-01

    Forty ampholytic compounds of biological and pharmaceutical relevance were subjected to chemometric analysis based on unsupervised and supervised learning algorithms. This enabled relations to be found between empirical spectral characteristics derived from electronic absorption data and structural and physicochemical parameters predicted by quantum chemistry methods or phenomenological relationships based on additivity rules. It was found that the energies of long wavelength absorption bands are correlated through multiparametric linear relationships with parameters reflecting the bulkiness features of the absorbing molecules as well as their nucleophilicity and electrophilicity. These dependences enable the quantitative analysis of spectral features of the compounds, as well as a comparison of their similarities and certain pharmaceutical and biological features. Three QSPR models to predict the energies of long-wavelength absorption in buffers with pH=2.5 and pH=7.0, as well as in methanol, were developed and validated in this study. These models can be further used to predict the long-wavelength absorption energies of untested substances (if they are structurally similar to the training compounds). PMID:25544186

  2. Chemometric analysis of correlations between electronic absorption characteristics and structural and/or physicochemical parameters for ampholytic substances of biological and pharmaceutical relevance

    NASA Astrophysics Data System (ADS)

    Judycka-Proma, U.; Bober, L.; Gajewicz, A.; Puzyn, T.; Błażejowski, J.

    2015-03-01

    Forty ampholytic compounds of biological and pharmaceutical relevance were subjected to chemometric analysis based on unsupervised and supervised learning algorithms. This enabled relations to be found between empirical spectral characteristics derived from electronic absorption data and structural and physicochemical parameters predicted by quantum chemistry methods or phenomenological relationships based on additivity rules. It was found that the energies of long wavelength absorption bands are correlated through multiparametric linear relationships with parameters reflecting the bulkiness features of the absorbing molecules as well as their nucleophilicity and electrophilicity. These dependences enable the quantitative analysis of spectral features of the compounds, as well as a comparison of their similarities and certain pharmaceutical and biological features. Three QSPR models to predict the energies of long-wavelength absorption in buffers with pH = 2.5 and pH = 7.0, as well as in methanol, were developed and validated in this study. These models can be further used to predict the long-wavelength absorption energies of untested substances (if they are structurally similar to the training compounds).

  3. Development of metal based thermal barrier coatings

    NASA Astrophysics Data System (ADS)

    Shin, Dong-Il

    In this work, metal-based thermal barrier coatings (MBTBCs) have been produced, using high frequency induction plasma spraying (IPS) of iron-based nanostructured alloy powders. Important advances have been made over recent years to the development of ceramic-based thermal barrier coatings (TBCs) for internal combustion engines application, but they are not yet applied in mass production situations. Besides the important economic considerations, the reliability of ceramic: TBCs is also an issue, being associated with the difficulty of predicting their "in-service" lifetime. Through engineering of the nano/amorphous structure of MBTBCs, their thermal conductivity can be made as low as those of ceramic-based TBCs, with reduced mean free paths of the electrons/phonons scattering. In this work, nano/amorphous structured coatings were deposited by IPS using the following spray parameters: spraying distance (210 ˜ 270 mm), plasma gas composition (Ar/N2), IPS torch power (24kW), and powder feed-rate (16g/min.). The structure and properties of the deposited layers were characterized through SEM (Scanning Electron Microscopy) observations. The thermal diffusivity (alpha) properties of the MBTBCs were measured using a laser flash method. Density (rho) and specific heat (Cp) of the MBTBCs were also measured, and their thermal conductivity (k) calculated (k =alpharhoCp). The thermal conductivity of MBTBCs was found to be as low as 1.99 W/m/K. The heat treatment study showed that crystal structure changes, and grain size growth from a few nanometers to tenth of nanometers occurred at 550°C under static exposure conditions. Thermal expansion coefficient (TEC) of MBTBCs was 13E-6/K, which is close to the TEC of cast iron and thus, closer to the TEC values of aluminium alloys than are conventional TBCs. Fracture toughness of MBTBCs has also been assessed by use of Vickers hardness tests, with a 500 g load for 15 s, and the results show that there are no measurable crack

  4. Making Biology Relevant to Undergraduates

    ERIC Educational Resources Information Center

    Musante, Susan

    2012-01-01

    This article features Science Education for New Civic Engagements and Responsibilities (SENCER; www.sencer.net) Summer Institute. The SENCER program, which began formally in 2001, was the vision of David Burns; Karen Oates, currently Peterson Family Dean of Arts and Sciences at Worcester Polytechnic Institute; and Ric Wiebl, currently director of…

  5. The biological relevance of virus neutralisation sites for virulence and vaccine protection in the guinea pig model of foot-and-mouth disease.

    PubMed

    Dunn, C S; Samuel, A R; Pullen, L A; Anderson, J

    1998-07-20

    Five neutralisation epitopes have been defined for the O1 Kaufbeuren strain of foot-and-mouth disease virus (FMDV) by neutralising murine monoclonal antibodies (Mabs). A mutant virus which is resistant to all these Mabs also resists neutralisation by bovine polyclonal sera, and this characteristic was exploited in the current study to investigate the biological relevance of neutralisation sites in FMDV virulence and vaccine protection. The five site neutralisation-resistant mutant was shown to be as pathogenic as wild-type virus in the guinea pig model of FMD. Guinea pigs were protected in cross-challenge studies from virulent wild-type and mutant viruses using either wild-type or mutant 146S antigen as inactivated whole virus vaccine. Furthermore, hyperimmune sera raised to either wild-type or mutant antigen offered passive protection against wild-type challenge, in spite of the serum raised against the mutant antigen having minimal neutralising activity in vitro. These results imply that virus neutralisation, at least as defined by the in vitro assay, may not play an essential role in the mechanism of immunity induced by whole inactivated FMDV vaccines. PMID:9683571

  6. Identification of functionally relevant populations in enhanced biological phosphorus removal processes based on intracellular polymers profiles and insights into the metabolic diversity and heterogeneity.

    PubMed

    Majed, Nehreen; Chernenko, Tatyana; Diem, Max; Gu, April Z

    2012-05-01

    This study proposed and demonstrated the application of a new Raman microscopy-based method for metabolic state-based identification and quantification of functionally relevant populations, namely polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), in enhanced biological phosphorus removal (EBPR) system via simultaneous detection of multiple intracellular polymers including polyphosphate (polyP), glycogen, and polyhydroxybutyrate (PHB). The unique Raman spectrum of different combinations of intracellular polymers within a cell at a given stage of the EBPR cycle allowed for its identification as PAO, GAO, or neither. The abundance of total PAOs and GAOs determined by Raman method were consistent with those obtained with polyP staining and fluorescence in situ hybridization (FISH). Different combinations and quantities of intracellular polymer inclusions observed in single cells revealed the distribution of different sub-PAOs groups among the total PAO populations, which exhibit phenotypic and metabolic heterogeneity and diversity. These results also provided evidence for the hypothesis that different PAOs may employ different extents of combination of glycolysis and TCA cycle pathways for anaerobic reducing power and energy generation and it is possible that some PAOs may rely on TCA cycle solely without glycolysis. Sum of cellular level quantification of the internal polymers associated with different population groups showed differentiated and distributed trends of glycogen and PHB level between PAOs and GAOs, which could not be elucidated before with conventional bulk measurements of EBPR mixed cultures.

  7. Identification of functionally relevant populations in enhanced biological phosphorus removal processes based on intracellular polymers profiles and insights into the metabolic diversity and heterogeneity.

    PubMed

    Majed, Nehreen; Chernenko, Tatyana; Diem, Max; Gu, April Z

    2012-05-01

    This study proposed and demonstrated the application of a new Raman microscopy-based method for metabolic state-based identification and quantification of functionally relevant populations, namely polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), in enhanced biological phosphorus removal (EBPR) system via simultaneous detection of multiple intracellular polymers including polyphosphate (polyP), glycogen, and polyhydroxybutyrate (PHB). The unique Raman spectrum of different combinations of intracellular polymers within a cell at a given stage of the EBPR cycle allowed for its identification as PAO, GAO, or neither. The abundance of total PAOs and GAOs determined by Raman method were consistent with those obtained with polyP staining and fluorescence in situ hybridization (FISH). Different combinations and quantities of intracellular polymer inclusions observed in single cells revealed the distribution of different sub-PAOs groups among the total PAO populations, which exhibit phenotypic and metabolic heterogeneity and diversity. These results also provided evidence for the hypothesis that different PAOs may employ different extents of combination of glycolysis and TCA cycle pathways for anaerobic reducing power and energy generation and it is possible that some PAOs may rely on TCA cycle solely without glycolysis. Sum of cellular level quantification of the internal polymers associated with different population groups showed differentiated and distributed trends of glycogen and PHB level between PAOs and GAOs, which could not be elucidated before with conventional bulk measurements of EBPR mixed cultures. PMID:22471394

  8. A handy liquid metal based electroosmotic flow pump.

    PubMed

    Gao, Meng; Gui, Lin

    2014-06-01

    A room temperature liquid metal based electroosmotic flow (EOF) pump has been proposed in this work. This low-cost EOF pump is convenient for both fabrication and integration. It utilizes polydimethylsiloxane (PDMS) microchannels filled with the liquid-metal as non-contact pump electrodes. The electrode channels are fabricated symmetrically to both sides of the pumping channel, having no contact with the pumping channel. To test the pumping performance of the EOF pump, the mean flow velocities of the fluid (DI water) in the EOF pumps were experimentally measured by tracing the fluorescent microparticles in the flow. To provide guidance for designing a low voltage EOF pump, parametric studies on dimensions of the electrode and pumping channels were performed in this work. According to the experimental results, the pumping speed can reach 5.93 μm s(-1) at a driving voltage of only 1.6 V, when the gap between the electrode and the pumping channel is 20 μm. Injecting a room temperature liquid metal into microchannels can provide a simple, rapid, low-cost but accurately self-aligned way to fabricate microelectrodes for EOF pumps, which is a promising method to achieve the miniaturization and integration of the EOF pump in microfluidic systems. The non-contact liquid electrodes have no influence on the fluid in the pumping channel when pumping, reducing Joule heat generation and preventing gas bubble formation at the surface of electrodes. The pump has great potential to drive a wide range of fluids, such as drug reagents, cell suspensions and biological macromolecule solutions.

  9. A handy liquid metal based electroosmotic flow pump.

    PubMed

    Gao, Meng; Gui, Lin

    2014-06-01

    A room temperature liquid metal based electroosmotic flow (EOF) pump has been proposed in this work. This low-cost EOF pump is convenient for both fabrication and integration. It utilizes polydimethylsiloxane (PDMS) microchannels filled with the liquid-metal as non-contact pump electrodes. The electrode channels are fabricated symmetrically to both sides of the pumping channel, having no contact with the pumping channel. To test the pumping performance of the EOF pump, the mean flow velocities of the fluid (DI water) in the EOF pumps were experimentally measured by tracing the fluorescent microparticles in the flow. To provide guidance for designing a low voltage EOF pump, parametric studies on dimensions of the electrode and pumping channels were performed in this work. According to the experimental results, the pumping speed can reach 5.93 μm s(-1) at a driving voltage of only 1.6 V, when the gap between the electrode and the pumping channel is 20 μm. Injecting a room temperature liquid metal into microchannels can provide a simple, rapid, low-cost but accurately self-aligned way to fabricate microelectrodes for EOF pumps, which is a promising method to achieve the miniaturization and integration of the EOF pump in microfluidic systems. The non-contact liquid electrodes have no influence on the fluid in the pumping channel when pumping, reducing Joule heat generation and preventing gas bubble formation at the surface of electrodes. The pump has great potential to drive a wide range of fluids, such as drug reagents, cell suspensions and biological macromolecule solutions. PMID:24706096

  10. Discovery of Anti-inflammatory Ingredients in Chinese Herbal Formula Kouyanqing Granule based on Relevance Analysis between Chemical Characters and Biological Effects

    PubMed Central

    Liu, Hong; Zheng, Yan-fang; Li, Chu-yuan; Zheng, Yu-ying; Wang, De-qin; Wu, Zhong; Huang, Lin; Wang, Yong-gang; Li, Pei-bo; Peng, Wei; Su, Wei-wei

    2015-01-01

    Kouyanqing Granule (KYQG) is a traditional Chinese herbal formula composed of Flos lonicerae (FL), Radix scrophulariae (RS), Radix ophiopogonis (RO), Radix asparagi (RA), and Radix et rhizoma glycyrrhizae (RG). In contrast with the typical method of separating and then biologicalily testing the components individually, this study was designed to establish an approach in order to define the core bioactive ingredients of the anti-inflammatory effects of KYQG based on the relevance analysis between chemical characters and biological effects. Eleven KYQG samples with different ingredients were prepared by changing the ratios of the 5 herbs. Thirty-eight ingredients in KYQG were identified using Ultra-fast liquid chromatography-Diode array detector-Quadrupole-Time-of-flight-Tandem mass spectrometry (UFLC-DAD-Q-TOF-MS/MS) technology. Human oral keratinocytes (HOK) were cultured for 24 hours with 5% of Cigarette smoke extract (CSE) to induce inflammation stress. Interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), and tumour necrosis factor-α (TNF-α) were evaluated after treatment with the eleven KYQG samples. Grey relational analysis(GRA), Pearson’s correlations (PCC), and partial least-squares (PLS) were utilized to evaluate the contribution of each ingredient. The results indicated that KYQG significantly reduced interleukin-1β, interleukin-6, interleukin-8, and tumour necrosis factor-α levels, in which lysine, γ-aminobutyric acid, chelidonic acid, tyrosine, harpagide, neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, isoquercitrin, luteolin-7-o-glucoside, 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid, angoroside C, harpagoside, cinnamic acid, and ruscogenin play a vital role. PMID:26657159

  11. Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization.

    PubMed

    Ambrus, Attila; Chen, Ding; Dai, Jixun; Jones, Roger A; Yang, Danzhou

    2005-02-15

    The nuclease hypersensitivity element III(1) (NHE III(1)) of the c-MYC promoter strongly controls the transcriptional activity of the c-MYC oncogene. The purine-rich strand of the NHE III(1) element has been shown to be a silencer element for c-MYC transcription upon formation of a G-quadruplex structure. We have determined the predominant G-quadruplex structure of this silencer element in potassium solution by NMR. The G-quadruplex structure adopts an intramolecular parallel-stranded quadruplex conformation with three guanine tetrads and three side loops, including two single-nucleotide side loops and one double-nucleotide side loop, that connect the four guanine strands. The three side loops are very stable and well-defined. The 3'-flanking sequence forms a stable fold-back stacking conformation capping the top end of the G-quadruplex structure. The 5'-flanking A and G bases cap the bottom end of the G-quadruplex, with the adenine stacking very well with the bottom tetrad. This paper reports the first solution structure of a G-quadruplex found to form in the promoter region of an oncogene (c-MYC). This G-quadruplex structure is extremely stable, with a similar melting temperature (>85 degrees C) to that of the wild-type 27-mer purine-rich NHE III(1) sequence of the c-MYC promoter. This predominant quadruplex structure has been shown to be biologically relevant, and the structural information revealed in this research provides an important basis for the design of new drug candidates that specifically target the c-MYC G-quadruplex structure and modulate gene expression. PMID:15697230

  12. AroER Tri-Screen Is a Biologically Relevant Assay for Endocrine Disrupting Chemicals Modulating the Activity of Aromatase and/or the Estrogen Receptor

    PubMed Central

    Chen, Shiuan; Zhou, Dujin; Hsin, Li-Yu; Kanaya, Noriko; Wong, Cynthie; Yip, Richard; Sakamuru, Srilatha; Xia, Menghang; Yuan, Yate-Ching; Witt, Kristine; Teng, Christina

    2014-01-01

    Endocrine disrupting chemicals (EDCs) interfere with the biosynthesis, metabolism, and functions of steroid hormones, including estrogens and androgens. Aromatase enzyme converts androgen to estrogen. Thus, EDCs against aromatase significantly impact estrogen- and/or androgen-dependent functions, including the development of breast cancer. The current study aimed to develop a biologically relevant cell-based high-throughput screening assay to identify EDCs that act as aromatase inhibitors (AIs), estrogen receptor (ER) agonists, and/or ER antagonists. The AroER tri-screen assay was developed by stable transfection of ER-positive, aromatase-expressing MCF-7 breast cancer cells with an estrogen responsive element (ERE) driven luciferase reporter plasmid. The AroER tri-screen can identify: estrogenic EDCs, which increase luciferase signal without 17β-estradiol (E2); anti-estrogenic EDCs, which inhibit the E2-induced luciferase signal; and AI-like EDCs, which suppress a testosterone-induced luciferase signal. The assay was first optimized in a 96-well plate format and then miniaturized into a 1536-well plate format. The AroER tri-screen was demonstrated to be suitable for high-throughput screening in the 1536-well plate format, with a 6.9-fold signal-to-background ratio, a 5.4% coefficient of variation, and a screening window coefficient (Z-factor) of 0.78. The assay suggested that bisphenol A (BPA) functions mainly as an ER agonist. Results from screening the 446 drugs in the National Institutes of Health Clinical Collection revealed 106 compounds that modulated ER and/or aromatase activities. Among these, two AIs (bifonazole and oxiconazole) and one ER agonist (paroxetine) were confirmed through alternative aromatase and ER activity assays. These findings indicate that AroER tri-screen is a useful high-throughput screening system for identifying ER ligands and aromatase-inhibiting chemicals. PMID:24496634

  13. Relevancy 101

    NASA Technical Reports Server (NTRS)

    Lynnes, Chris; Newman, Doug

    2016-01-01

    Where we present an overview on why relevancy is a problem, how important it is and how we can improve it. The topic of relevancy is becoming increasingly important in earth data discovery as our audience is tuned to the accuracy of standard search engines like Google.

  14. Bioinspired nanoreactors for the biomineralisation of metallic-based nanoparticles for nanomedicine.

    PubMed

    Bain, Jennifer; Staniland, Sarah S

    2015-06-28

    This review explores the synthesis of inorganic metallic-based nanoparticles (MBNPs) (metals, alloys, metal oxides) using biological and biologically inspired nanoreactors for precipitation/crystallisation. Such nanoparticles exhibit a range of nanoscale properties such as surface plasmon resonance (nobel metals e.g. Au), fluorescence (semiconductor quantum dots e.g. CdSe) and nanomagnetism (magnetic alloys e.g. CoPt and iron oxides e.g. magnetite), which are currently the subject of intensive research for their applicability in diagnostic and therapeutic nanomedicine. For such applications, MBNPs are required to be biocompatible, of a precise size and shape for a consistent signal or output and be easily modified with biomolecules for applications. Ideally the MBNPs would be obtained via an environmentally-friendly synthetic route. A biological or biologically inspired nanoreactor synthesis of MBNPs is shown to address these issues. Biological nanoreactors for crystallizing MBNPs within cells (magnetosomes), protein cages (ferritin) and virus capsids (cowpea chlorotic mottle, cowpea mosaic and tobacco mosaic viruses), are discussed along with how these have been modified for applications and for the next generation of new materials. Biomimetic liposome, polymersome and even designed self-assembled proteinosome nanoreactors are also reviewed for MBNP crystallisation and further modification for applications. With the advent of synthetic biology, the research and understanding in this field is growing, with the goal of realising nanoreactor synthesis of MBNPs for biomedical applications within our grasp in the near future.

  15. Role of quantity of additional food to predators as a control in predator-prey systems with relevance to pest management and biological conservation.

    PubMed

    Srinivasu, P D N; Prasad, B S R V

    2011-10-01

    Necessity to understand the role of additional food as a tool in biological control programs is being increasingly felt, particularly due to its eco-friendly nature. A thorough mathematical analysis in this direction revealed the vital role of quality and quantity of the additional food in the controllability of the predator-prey systems. In this article controllability of the additional food--provided predator-prey system is studied from perspectives of pest eradication and biological conservation. Time optimal paths have been constructed to drive the state of the system to a desired terminal state by choosing quantity of the additional food as control variable. The theory developed in this article has been illustrated by solving problems related to pest eradication and biological conservation.

  16. Redox activation of metal-based prodrugs as a strategy for drug delivery

    PubMed Central

    Graf, Nora

    2012-01-01

    This review provides an overview of metal-based anticancer drugs and drug candidates. In particular, we focus on metal complexes that can be activated in the reducing environment of cancer cells, thus serving as prodrugs. There are many reports of Pt and Ru complexes as redox-activatable drug candidates, but other d-block elements with variable oxidation states have a similar potential to serve as prodrugs in this manner. In this context are compounds based on Fe, Co, or Cu chemistry, which are also covered. A trend in the field of medicinal inorganic chemistry has been toward molecularly targeted, metal-based drugs obtained by functionalizing complexes with biologically active ligands. Another recent activity is the use of nanomaterials for drug delivery, exploiting passive targeting of tumors with nanosized constructs made from Au, Fe, carbon, or organic polymers. Although complexes of all of the above mentioned metals will be described, this review focuses primarily on Pt compounds, including constructs containing nanomaterials. PMID:22289471

  17. X-ray diffraction studies of lipid phase transitions in hydrated mixtures of cholesterol and diacylphosphatidylcholines and their relevance to the structure of biological membranes.

    PubMed

    Finean, J B

    1989-03-01

    Previous X-ray diffraction data on the effects of temperature on hydrated cholesterol/dimyristoylphosphatidylcholine mixtures have been confirmed and equivalent new data on cholesterol/stearolyoleoylphosphatidylcholine obtained. Molecular interpretations are discussed and related to previous studies of cholesterol/dioleoylphosphatidylcholine and of cholesterol-rich biological membranes.

  18. Interaction of nitric oxide with tetrathiolato iron(II) complexes: relevance to the reaction pathways of iron nitrosyls in sulfur-rich biological coordination environments.

    PubMed

    Harrop, Todd C; Song, Datong; Lippard, Stephen J

    2006-03-22

    The mechanism of formation of dinitrosyl iron complexes (DNICs) coordinated by cysteine residues at iron-sulfur protein sites has received little attention in the chemical literature. As a logical first step toward elucidating this mechanism and characterizing new iron-nitrosyl intermediates, we investigated the interaction of NO (g) and NO+ with iron-sulfur complexes chosen to mimic sulfur-rich iron sites in biology. The reaction of NO (g) with [Fe(StBu)4]2- cleanly affords the mononitrosyl complex, [Fe(StBu)3(NO)]- (1), a previously unknown species evoked in this chemistry. Reaction of [Fe(StBu)4]2- with NO derivatives, such as NO+, yields the corresponding dinitrosyl S-bridged Roussin red ester [Fe2(mu-StBu)2(NO)4] (2). The nitrosyl complexes 1 and 2 can chemically convert to the DNIC, [Fe(StBu)2(NO)2]- (3). The results should aid in the spectroscopic identification and elucidation of reaction pathways for the nitrosylation of iron in biologically related sulfur-rich coordination environments.

  19. Density functional theory estimation of isotope fractionation of Fe, Ni, Cu, and Zn among species relevant to geochemical and biological environments

    NASA Astrophysics Data System (ADS)

    Fujii, Toshiyuki; Moynier, Frédéric; Blichert-Toft, Janne; Albarède, Francis

    2014-09-01

    This paper reports the values of reduced partition function ratios (as 1000 ln β) for Fe, Ni, Cu, and Zn bound to a number of inorganic and organic ligands. We used Density Functional Techniques to update the existing data and calculate ln β for new ligands. This work allows for the mass-dependent isotope fractionation to be predicted for various inorganic (hydrated cation, hydroxide, chloride, sulfate, sulfide, phosphate) and organic (citrate, amino acid) complexes of Fe, Ni, Cu, and Zn. Isotope fractionation among coexisting complexes of these metals was evaluated from the ln β values in a variety of geochemical and biological environments. The results provide a framework for interpretation of isotope fractionation observed in seawater and chemical sediments, in the roots and aerial parts of plants, and among the organs and body fluids of mammals.

  20. Hierarchical and cybernetic nature of biologic systems and their relevance to homeostatic adaptation to low-level exposures to oxidative stress-inducing agents.

    PubMed Central

    Trosko, J E

    1998-01-01

    During evolution in an aerobic environment, multicellular organisms survived by adaptive responses to both the endogenous oxidative metabolism in the cells of the organism and the chemicals and low-level radiation to which they had been exposed. The defense repertoire exists at all levels of the biological hierarchy--from the molecular and biochemical level to the cellular and tissue level to the organ and organ system level. Cells contain preventive antioxidants to suppress oxidative damage to membranes. Cells also contain proteins and DNA; built-in redundancies for damaged molecules and organelles; tightly coupled redox systems; pools of reductants; antioxidants; DNA repair mechanisms and sensitive sensor molecules such as nuclear factor kappa beta; and signal transduction mechanisms affecting both transcription and post-translational modification of proteins needed to cope with oxidative stress. The biologic consequences of the low-level radiation that exceeds the background level of oxidative damage could be necrosis or apoptosis, cell proliferation, or cell differentiation. These effects are triggered by oxidative stress-induced signal transduction mechanisms--an epigenetic, not genotoxic, process. If the end points of cell proliferation, differentiation, or cell death are not seen at frequencies above background levels in an organism, it is unlikely that low-level radiation would play a role in the multistep processes of chronic diseases such as cancer. The mechanism linked to homeostatic regulation of proliferation and adaptive functions in a multicellular organism could provide protection of any one cell receiving deposited energy by the radiation tract through the sharing of reductants and by triggering apoptosis of target stem cells. Examples of the role of gap junctional intercellular communication in the adaptive response of cells and the bystander effect illustrate how the interaction of cells can modulate the effect of radiation on the single cell

  1. The Fluid-Mosaic Model of Membrane Structure: still relevant to understanding the structure, function and dynamics of biological membranes after more than 40 years.

    PubMed

    Nicolson, Garth L

    2014-06-01

    In 1972 the Fluid-Mosaic Membrane Model of membrane structure was proposed based on thermodynamic principals of organization of membrane lipids and proteins and available evidence of asymmetry and lateral mobility within the membrane matrix [S. J. Singer and G. L. Nicolson, Science 175 (1972) 720-731]. After over 40years, this basic model of the cell membrane remains relevant for describing the basic nano-structures of a variety of intracellular and cellular membranes of plant and animal cells and lower forms of life. In the intervening years, however, new information has documented the importance and roles of specialized membrane domains, such as lipid rafts and protein/glycoprotein complexes, in describing the macrostructure, dynamics and functions of cellular membranes as well as the roles of membrane-associated cytoskeletal fences and extracellular matrix structures in limiting the lateral diffusion and range of motion of membrane components. These newer data build on the foundation of the original model and add new layers of complexity and hierarchy, but the concepts described in the original model are still applicable today. In updated versions of the model more emphasis has been placed on the mosaic nature of the macrostructure of cellular membranes where many protein and lipid components are limited in their rotational and lateral motilities in the membrane plane, especially in their natural states where lipid-lipid, protein-protein and lipid-protein interactions as well as cell-matrix, cell-cell and intracellular membrane-associated protein and cytoskeletal interactions are important in restraining the lateral motility and range of motion of particular membrane components. The formation of specialized membrane domains and the presence of tightly packed integral membrane protein complexes due to membrane-associated fences, fenceposts and other structures are considered very important in describing membrane dynamics and architecture. These structures along

  2. Using Vitek MALDI-TOF mass spectrometry to identify species belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex: a relevant alternative to molecular biology?

    PubMed

    Pailhoriès, Hélène; Daure, Sophie; Eveillard, Matthieu; Joly-Guillou, Marie-Laure; Kempf, Marie

    2015-10-01

    Acinetobacter baumannii belongs to the Acinetobacter calcoaceticus-baumannii complex (Acb) containing 2 other pathogenic species: Acinetobacter pittii and Acinetobacter nosocomialis. Identification of these bacteria remains problematic despite the use of matrix-assisted laser ionization time-of-flight mass spectrometry (MALDI-TOF MS). Here, we enriched the SARAMIS™ database of the Vitek MS® plus mass spectrometer to improve the identification of species of the Acb complex. For each species, we incremented reference spectra. Then, a SuperSpectrum was created based on the selection of 40 specific masses. In a second step, we validated reference spectra and SuperSpectra with 100 isolates identified by rpoB gene sequencing. All the isolates were correctly identified by MALDI-TOF MS with the database we created as compared to the identifications obtained by rpoB sequencing. Our database enabled rapid and reliable identification of the pathogen species belonging to the Acb complex. Identification by MALDI-TOF MS with our database is a good alternative to molecular biology.

  3. Studies to assess the biological relevance of anti-Tamm-Horsfall protein antibodies detected by direct-binding enzyme-linked immunosorbent assay.

    PubMed

    Hunt, J S; Groufsky, A; Lynn, K L

    1987-11-01

    1. A role has been suggested for anti-Tamm-Horsfall protein (THP) antibodies in renal disease based on the results of immunoassays of pathological sera. The putative autoantibodies have not been isolated from such sera nor have definitive inhibition studies of their binding been carried out. We have carried out such studies using rabbit anti-THP antibodies as control reagents. 2. Urinary THP prepared by salt precipitation was used to prepare four immunoabsorbent columns by covalent coupling to CNBr-activated Sepharose 4B. After washing with a variety of dissociating agents to remove any non-covalently bound subunit THP, each column was incubated with normal and immune rabbit serum. Fractions washed and eluted from columns were tested for anti-THP antibodies by enzyme-linked immunosorbent assay (ELISA) and THP antigen by radioimmunoassay, and showed NH4SCN (3 mol/l) and guanidine hydrochloride (GuHCl) (6 mol/l) equivalent and sodium dodecyl sulphate (20 g/l) to be inferior in their capacity to produce immunoabsorbent THP capable of isolating specific antibodies from immune rabbit serum. 3. The column treated with GuHCl (6 mol/l) was used further in attempts to isolate putative anti-THP antibodies from five patients, who had a history of urinary tract infections and whose sera showed strong binding by ELISA. 4. Results from direct and inhibition ELISA experiments on fractions collected after washing and elution with all sera suggested that the putative human anti-THP antibodies were of very low affinity and/or directed against non-subunit THP. 5. The pathological relevance of human anti-THP antibodies measured by ELISA remains to be established.

  4. Effect of manganese treatment on the accumulation on biologically relevant metals in rat cochlea and brain by inductively coupled plasma mass spectrometry.

    PubMed

    Mullin, Elizabeth J; Wegst-Uhrich, Stacia R; Ding, Dalian; Manohar, Senthilvelan; Krishnan Muthaiah, Vijaya Prakash; Salvi, Richard; Aga, Diana S; Roth, Jerome A

    2015-12-01

    Manganese (Mn), iron (Fe), zinc (Zn), and copper (Cu) are essential transitions metals that are required in trace amounts, however chronic exposure to high concentrations can cause severe and irreversible neurotoxicity. Since prolonged exposure to Mn leads to manganism, a disorder exhibiting a diverse array of neurological impairments progressing to a debilitating and irreversible extrapyramidal condition symptomatically similar to Parkinson's disease, we measured the concentration of Mn as well as Fe, Zn and Cu in three region of the brain (globus pallidus, striatum and inferior colliculus) and three regions in the cochlea (stria vascularis, basilar membrane and modiolus) under normal conditions or after 30 or 60 days of oral administration of Mn (10 mg/ml ad libitum). Under normal conditions, Mn, Zn and Fe were typically higher in the cochlea than in the three brain regions whereas Cu was equal to or lower. Oral treatment with Mn for 30 or 60 days resulted in 20-75 % increases in Mn concentrations in both cochlea and brain samples, but had little effect on Cu and Fe levels. In contrast, Zn levels decreased (20-80 %) with Mn exposure. Our results show for the first time how prolonged oral Mn-ingestion affects the concentration of Mn, Cu, Zn and Fe, in the three regions of the cochlea, the inferior colliculus in auditory midbrain and the striatum and globus pallidus, two regions implicated in Parkinson's disorder. The Mn-induced changes in the concentration of Mn, Cu, Zn and Fe may provide new insights relevant to the neurotoxicity of Mn and the transport and accumulation of these metals in cochlea and brain. PMID:26433897

  5. Effect of biologically relevant ions on the corrosion products formed on alloy AZ31B: an improved understanding of magnesium corrosion.

    PubMed

    Jang, Yongseok; Collins, Boyce; Sankar, Jagannathan; Yun, Yeoheung

    2013-11-01

    Simulated physiological solutions mimicking human plasma have been utilized to study the in vitro corrosion of biodegradable metals. However, corrosion and corrosion product formation are different for different solutions with varied responses and, hence, the prediction of in vivo degradation behavior is not feasible based on these studies alone. This paper reports the role of physiologically relevant salts and their concentrations on the corrosion behavior of a magnesium alloy (AZ31B) and subsequent corrosion production formation. Immersion tests were performed for three different concentrations of Ca(2+), HPO4(2-), HCO3(-) to identify the effect of each ion on the corrosion of AZ31B assessed at 1, 3 and 10 days. Time-lapse morphological characterization of the samples was performed using X-ray computed tomography and scanning electron microscopy. The chemical composition of the surface corrosion products was determined by electron dispersive X-ray spectroscopy and X-ray diffraction. The results show that: (1) calcium is not present in the corrosion product layer when only Cl(-) and OH(-) anions are available; (2) the presence of phosphate induces formation of a densely packed amorphous magnesium phosphate corrosion product layer when HPO4(2-) and Cl(-) are present in solution; (3) octacalcium phosphate and hydroxyapatite (HAp) are deposited on the surface of the magnesium alloy when HPO4(2-) and Ca(2+) are present together in NaCl solution (this coating limits localized corrosion and increases general corrosion resistance); (4) addition of HCO3(-) accelerates the overall corrosion rate, which increases with increasing bicarbonate concentration; (5) the corrosion rate decreases due to the formation of insoluble HAp on the surface when HCO3(-), Ca(2+), and HPO4(2-) are present together.

  6. Heme versus non-heme iron-nitroxyl {FeN(H)O}⁸ complexes: electronic structure and biologically relevant reactivity.

    PubMed

    Speelman, Amy L; Lehnert, Nicolai

    2014-04-15

    Researchers have completed extensive studies on heme and non-heme iron-nitrosyl complexes, which are labeled {FeNO}(7) in the Enemark-Feltham notation, but they have had very limited success in producing corresponding, one-electron reduced, {FeNO}(8) complexes where a nitroxyl anion (NO(-)) is formally bound to an iron(II) center. These complexes, and their protonated iron(II)-NHO analogues, are proposed key intermediates in nitrite (NO2(-)) and nitric oxide (NO) reducing enzymes in bacteria and fungi. In addition, HNO is known to have a variety of physiological effects, most notably in the cardiovascular system. HNO may also serve as a signaling molecule in mammals. For these functions, iron-containing proteins may mediate the production of HNO and serve as receptors for HNO in vivo. In this Account, we highlight recent key advances in the preparation, spectroscopic characterization, and reactivity of ferrous heme and non-heme nitroxyl (NO(-)/HNO) complexes that have greatly enhanced our understanding of the potential biological roles of these species. Low-spin (ls) heme {FeNO}(7) complexes (S = 1/2) can be reversibly reduced to the corresponding {FeNO}(8) species, which are stable, diamagnetic compounds. Because the reduction is ligand (NO) centered in these cases, it occurs at extremely negative redox potentials that are at the edge of the biologically feasible range. Interestingly, the electronic structures of ls-{FeNO}(7) and ls-{FeNO}(8) species are strongly correlated with very similar frontier molecular orbitals (FMOs) and thermodynamically strong Fe-NO bonds. In contrast, high-spin (hs) non-heme {FeNO}(7) complexes (S = 3/2) can be reduced at relatively mild redox potentials. Here, the reduction is metal-centered and leads to a paramagnetic (S = 1) {FeNO}(8) complex. The increased electron density at the iron center in these species significantly decreases the covalency of the Fe-NO bond, making the reduced complexes highly reactive. In the absence of

  7. An anatomical, histopathological, and molecular biological function study of the fascias posterior to the interperitoneal colon and its associated mesocolon: their relevance to colonic surgery.

    PubMed

    Gao, Zhidong; Ye, Yingjiang; Zhang, Weiguang; Shen, Danhua; Zhong, Yanfeng; Jiang, Kewei; Yang, Xiaodong; Yin, Mujun; Liang, Bin; Tian, Long; Wang, Shan

    2013-08-01

    The study aim was to explore the anatomy, histopathology, and molecular biological function of the fascias posterior to the interperitoneal colon and its mesocolon to provide information for improving complete mesocolic excision. To accomplish this aim, we performed intraoperative observations in 60 interperitoneal colon-cancer patients accepted for complete mesocolic excision and conducted local anatomy observations for five embalmed cadavers. An additional two embalmed child cadaver specimens were studied with large slices and paraffin sections. Ten of the 60 patients were examined with a lymph node tracer technique in vivo, while fresh specimens from these patients were assessed by histopathological examination and transwell cell migration assays in vitro. The anatomical and histopathological findings showed that the fascias posterior to the interperitoneal colon and its associated mesocolon were composed of two independent layers: the visceral and parietal fascias. These two fascias were primarily composed of collagen fibers, with the parietal fascia containing a small amount of muscle fiber. The in vivo test showed that the visceral fascia surrounded the colon and its associated mesocolon, including vessels and lymphatics, and that it had no lymphatic flow through it into the rear tissues. Moreover, the in vitro assays showed the visceral fascia was able to block tumor cell migration. Although many surgical scholars have known of the existence of fascia tissue posterior to the intraperitoneal colon, the detailed structure has been ignored and been unclear. As shown by our findings, the visceral and parietal fascias are truly formed structures that have not been previously reported. A thorough understanding of fascial structures and the function of the visceral fascia barrier in blocking tumor cells will facilitate surgeons when performing high-quality complete mesocolic excision procedures.

  8. The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations.

    PubMed

    Scavenius, Carsten; Nikolajsen, Camilla Lund; Stenvang, Marcel; Thøgersen, Ida B; Wyrożemski, Łukasz; Wisniewski, Hans-Georg; Otzen, Daniel E; Sanggaard, Kristian W; Enghild, Jan J

    2016-02-26

    Inter-α-inhibitor is a proteoglycan of unique structure. The protein consists of three subunits, heavy chain 1, heavy chain 2, and bikunin covalently joined by a chondroitin sulfate chain originating at Ser-10 of bikunin. Inter-α-inhibitor interacts with an inflammation-associated protein, tumor necrosis factor-inducible gene 6 protein, in the extracellular matrix. This interaction leads to transfer of the heavy chains from the chondroitin sulfate of inter-α-inhibitor to hyaluronan and consequently to matrix stabilization. Divalent cations and heavy chain 2 are essential co-factors in this transfer reaction. In the present study, we have investigated how divalent cations in concert with the chondroitin sulfate chain influence the structure and stability of inter-α-inhibitor. The results showed that Mg(2+) or Mn(2+), but not Ca(2+), induced a conformational change in inter-α-inhibitor as evidenced by a decrease in the Stokes radius and a bikunin chondroitin sulfate-dependent increase of the thermodynamic stability. This structure was shown to be essential for the ability of inter-α-inhibitor to participate in extracellular matrix stabilization. In addition, the data revealed that bikunin was positioned adjacent to both heavy chains and that the two heavy chains also were in close proximity. The chondroitin sulfate chain interacted with all protein components and inter-α-inhibitor dissociated when it was degraded. Conventional purification protocols result in the removal of the Mg(2+) found in plasma and because divalent cations influence the conformation and affect function it is important to consider this when characterizing the biological activity of inter-α-inhibitor.

  9. Gene expression profile in the muscles of patients with inflammatory myopathies: effect of therapy with IVIg and biological validation of clinically relevant genes.

    PubMed

    Raju, Raghavan; Dalakas, Marinos C

    2005-08-01

    To explore the biological significance of gene expression in the pathogenesis of inflammatory myopathies, we performed microarray experiments followed by real-time PCR and immunohistochemistry on muscle biopsies obtained before and after therapy from patients with dermatomyositis (DM) who improved and patients with inclusion body myositis (sIBM) who did not improve after controlled trials with three monthly intravenous immunoglobulin (IVIg) infusions. The pretreatment biopsies showed high expression of immunoglobulin, adhesion molecules, chemokines and cytokine genes in both sIBM and DM (sIBM > DM). In the repeated biopsies of DM patients who clinically improved, 2206 genes were downregulated more than 1.5-fold; in contrast, 1700 of the same genes remained unchanged in sIBM patients who did not improve. Genes markedly downregulated in DM, but not sIBM, were interleukin 22, Kallmann syndrome 1 (KAL-1), an adhesion molecule shown for the first time in muscle, ICAM-1, complement C1q, and several structural protein genes. Because mRNA for KAL-1 was selectively upregulated in vitro by transforming growth factor (TGF) beta1, a fibrogenic cytokine immunolocalized in the endomysial connective tissue of pretreatment DM muscles, the downregulation of both TGF-beta and KAL-1 after IVIg only in DM suggests that these molecules have a functional role in connective tissue proliferation and fibrosis. The improved muscles of DM, but not sIBM, showed upregulation of chemokines CXCL9 (Mig) and CXCL11, and several immunoglobulin-related genes, suggesting an effect on muscle remodelling and regeneration. The results suggest that IVIg modulates several immunoregulatory or structural muscle genes, but only a subset of them associated with inflammatory mediators, fibrosis and muscle remodelling are connected with the clinical response. Gene arrays, when combined with clinical assessments, may provide important information in the pathogenesis of inflammatory myopathies.

  10. Diverging DOS strategy using an allene-containing tryptophan scaffold and a library design that maximizes biologically relevant chemical space while minimizing the number of compounds.

    PubMed

    Painter, Thomas O; Wang, Lirong; Majumder, Supriyo; Xie, Xiang-Qun; Brummond, Kay M

    2011-03-14

    A diverging diversity-oriented synthesis (DOS) strategy using an allene-containing tryptophan as a key starting material was investigated. An allene-yne substituted derivative of tryptophan 12 gave indolylmethylazabicyclooctadiene 17 when subjected to a microwave-assisted allenic [2 + 2] cycloaddition reaction. This same tryptophan-derived precursor afforded an indolylmethyldihydrocyclopentapyridinone 14 when subjected to a rhodium(I)-catalyzed cyclocarbonylation reaction and an indolylmethylpyrrolidinocyclopentenones 16 when reacted with molybdenum hexacarbonyl. Construction of allenic tetrahydro-β-carboline scaffolds via a Pictet-Spengler reaction and subsequent silver(I)-catalyzed cycloisomerization afforded tetrahydroindolizinoindoles (21). Attachment of allene and alkyne groups to the tetrahydro-β-carboline, followed by a microwave-assisted allenic [2 + 2] cycloaddition reaction, provided tetrahydrocyclobutaindoloquinolizinones 24 and the tetrahydrocyclopentenone indolizinoindolone 26 when reacted with molybdenum hexacarbonyl. These six scaffolds were used as templates for the construction of a virtual library of 11 748 compounds employing 44 indoles, 12 aldehydes, and 51 alkynes. Diversity analyses using a combination of cell-based chemistry space computations using BCUT (Burden (B) CAS (C) Pearlman at the University of Texas (UT)) metrics and Tanimoto coefficient (Tc) similarity calculations using two-dimensional (2D) fingerprints showed that the compounds in the virtual library occupied new chemical space when compared to the 327,000 compounds in the molecular libraries small molecule repository (MLSMR). A subset of fifty-three compounds was identified from the virtual library using the DVS package of Sybyl 8.0; this subset represents the most diverse compounds within the chemical space defined by these compounds and will be synthesized and screened for biological activity.

  11. How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically relevant set of molecules.

    PubMed

    Matta, Chérif F

    2010-04-30

    This article compares molecular properties and atomic properties defined by the quantum theory of atoms in molecules (QTAIM) obtained from three underlying levels of theory: MP2(full), density functional theory (DFT) (B3LYP), and Hartree-Fock (H-F). The same basis set (6-311++G(d,p)) has been used throughout the study. The calculations and comparisons were applied to a set of 30 small molecules representing common fragments of biological molecules. The molecular properties investigated are the energies and the electrostatic moments (up to and including the quadrupoles), and the atomic properties include electron populations (and atomic charge), atomic dipolar and quadrupolar polarizations, atomic volumes, and corrected and raw atomic energies. The Cartesian distance between dipole vectors and the Frobenius distance between the quadrupole tensors calculated at the three levels of theory provide a measure of their correlation (or lack thereof). With the exception of energies (atomic and molecular), it is found that both DFT and H-F are in excellent agreement with MP2, especially with regards to the electrostatic mutipoles up to the quadrupoles, but DFT and MP2 agree better in almost all studied properties (with the exception of molecular geometries). QTAIM properties whether obtained from H-F, DFT(B3LYP), or MP2 calculations when used in the construction of empirical correlations with experiment such as quantitative structure-activity-(or property)-relationships (QSAR/QSPR) are equivalent (because the properties calculated at the three levels are very highly correlated among themselves with r(2) typically >0.95, and therefore preserving trends). These results suggest that the massive volume of results that were published in the older literature at the H-F level is valid especially when used to study trends or in QSAR or QSPR studies, and, as long as our test set of molecules is representative, there is no pressing need to re-evaluate them at other levels of theory

  12. Iron-Clad Fibers: A Metal-Based Biological Strategy for Hard Flexible Coatings

    PubMed Central

    Harrington, Matthew J.; Masic, Admir; Holten-Andersen, Niels; Waite, J. Herbert; Fratzl, Peter

    2011-01-01

    The extensible byssal threads of marine mussels are shielded from abrasion in wave-swept habitats by an outer cuticle that is largely proteinaceous and approximately fivefold harder than the thread core. Threads from several species exhibit granular cuticles containing a protein that is rich in the catecholic amino acid 3,4-dihydroxyphenylalanine (dopa) as well as inorganic ions, notably Fe3+. Granular cuticles exhibit a remarkable combination of high hardness and high extensibility. We explored byssus cuticle chemistry by means of in situ resonance Raman spectroscopy and demonstrated that the cuticle is a polymeric scaffold stabilized by catecholato-iron chelate complexes having an unusual clustered distribution. Consistent with byssal cuticle chemistry and mechanics, we present a model in which dense cross-linking in the granules provides hardness, whereas the less cross-linked matrix provides extensibility. PMID:20203014

  13. Exploring the DNA binding mode of transition metal based biologically active compounds

    NASA Astrophysics Data System (ADS)

    Raman, N.; Sobha, S.

    2012-01-01

    Few novel 4-aminoantipyrine derived Schiff bases and their metal complexes were synthesized and characterized. Their structural features and other properties were deduced from the elemental analysis, magnetic susceptibility and molar conductivity as well as from mass, IR, UV-vis, 1H NMR and EPR spectral studies. The binding of the complexes with CT-DNA was analyzed by electronic absorption spectroscopy, viscosity measurement, and cyclic voltammetry. The interaction of the metal complexes with DNA was also studied by molecular modeling with special reference to docking. The experimental and docking results revealed that the complexes have the ability of interaction with DNA of minor groove binding mode. The intrinsic binding constants ( Kb) of the complexes with CT-DNA were found out which show that they are minor groove binders. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pUC19 DNA in the presence of AH 2 (ascorbic acid). Moreover, the oxidative cleavage studies using distamycin revealed the minor groove binding for the newly synthesized 4-aminoantipyrine derived Schiff bases and their metal complexes. Evaluation of antibacterial activity of the complexes against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, and Klebsiella pneumoniae exhibited that the complexes have potent biocidal activity than the free ligands.

  14. Metal-based biologically active azoles and β-lactams derived from sulfa drugs.

    PubMed

    Ebrahimi, Hossein Pasha; Hadi, Jabbar S; Almayah, Abdulelah A; Bolandnazar, Zeinab; Swadi, Ali G; Ebrahimi, Amirpasha

    2016-03-01

    Metal complexes of Schiff bases derived from sulfamethoxazole (SMZ) and sulfathiazole (STZ), converted to their β-lactam derivatives have been synthesized and experimentally characterized by elemental analysis, spectral (IR, (1)H NMR, (13)C NMR, and EI-mass), molar conductance measurements and thermal analysis techniques. The structural and electronic properties of the studied molecules were investigated theoretically by performing density functional theory (DFT) to access reliable results to the experimental values. The spectral and thermal analysis reveals that the Schiff bases act as bidentate ligands via the coordination of azomethine nitrogen to metal ions as well as the proton displacement from the phenolic group through the metal ions; therefore, Cu complexes can attain the square planner arrangement and Zn complexes have a distorted tetrahedral structure. The thermogravimetric (TG/DTG) analyses confirm high stability for all complexes followed by thermal decomposition in different steps. In addition, the antibacterial activities of synthesized compounds have been screened in vitro against various pathogenic bacterial species. Inspection of the results revealed that all newly synthesized complexes individually exhibit varying degrees of inhibitory effects on the growth of the tested bacterial species, therefore, they may be considered as drug candidates for bacterial pathogens. The free Schiff base ligands (1-2) exhibited a broad spectrum antibacterial activity against Gram negative Escherichia coli, Pseudomonas aeruginosa, and Proteus spp., and Gram positive Staphylococcus aureus bacterial strains. The results also indicated that the β-lactam derivatives (3-4) have high antibacterial activities on Gram positive bacteria as well as the metal complexes (5-8), particularly Zn complexes, have a significant activity against all Gram negative bacterial strains. It has been shown that the metal complexes have significantly higher activity than corresponding ligands due to chelation process which reduces the polarity of metal ion by coordinating with ligands.

  15. Metal based isatin-derived sulfonamides: their synthesis, characterization, coordination behavior and biological activity.

    PubMed

    Chohan, Zahid H; Supuran, Claudiu T; Ben Hadda, Taibi; Nasim, Faiz-Ul-Hassan; Khan, Khalid M

    2009-06-01

    Some isatin derived sulfonamides and their transition metal [Co(II), Cu(II), Ni(II), Zn(II)] complexes have been synthesized and characterized. The structure of synthesized compounds and their nature of bonding have been inferred on the basis of their physical (magnetic susceptibility and conductivity measurements), analytical (elemental analyses) and spectral (IR, (1)H NMR and (13)C NMR) properties. An octahedral geometry has been suggested for Co(II), Ni(II) and Zn(II) and square-planar for Cu(II) complexes. In order to assess the antibacterial and antifungal behavior, the ligands and their metal(II) complexes were screened for their in vitro antibacterial activity against four Gram-negative species, Escherichia coli, Shigella flexneri, Pseudomonas aeruginosa and Salmonella typhi and two Gram-positive species, Staphylococcus aureus and Bacillus subtilis and, for in vitro antifungal activity against Trichophyton longifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glaberata. In vitro cytotoxic properties of all the compounds were also studied against Artemia salina by brine shrimp bioassay. The results of average antibacterial/antifungal activity showed that zinc(II) complexes were found to be the most active against one or more bacterial/fungal strains as compared to the other metal complexes. PMID:18825557

  16. CRISPR-Cas: biology, mechanisms and relevance

    PubMed Central

    Hille, Frank

    2016-01-01

    Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent. This article is part of the themed issue ‘The new bacteriology’. PMID:27672148

  17. Mammalian Sirtuins: Biological Insights and Disease Relevance

    PubMed Central

    Haigis, Marcia C.; Sinclair, David A.

    2010-01-01

    Aging is accompanied by a decline in the healthy function of multiple organ systems, leading to increased incidence and mortality from diseases such as type II diabetes mellitus, neurodegenerative diseases, cancer, and cardiovascular disease. Historically, researchers have focused on investigating individual pathways in isolated organs as a strategy to identify the root cause of a disease, with hopes of designing better drugs. Studies of aging in yeast led to the discovery of a family of conserved enzymes known as the sirtuins, which affect multiple pathways that increase the life span and the overall health of organisms. Since the discovery of the first known mammalian sirtuin, SIRT1, 10 years ago, there have been major advances in our understanding of the enzymology of sirtuins, their regulation, and their ability to broadly improve mammalian physiology and health span. This review summarizes and discusses the advances of the past decade and the challenges that will confront the field in the coming years. PMID:20078221

  18. CRISPR-Cas: biology, mechanisms and relevance.

    PubMed

    Hille, Frank; Charpentier, Emmanuelle

    2016-11-01

    Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes-termed spacers-into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent.This article is part of the themed issue 'The new bacteriology'.

  19. Prion biology relevant to bovine spongiform encephalopathy.

    PubMed

    Novakofski, J; Brewer, M S; Mateus-Pinilla, N; Killefer, J; McCusker, R H

    2005-06-01

    Bovine spongiform encephalopathy (BSE) and chronic wasting disease (CWD) of deer and elk are a threat to agriculture and natural resources, as well as a human health concern. Both diseases are transmissible spongiform encephalopathies (TSE), or prion diseases, caused by autocatalytic conversion of endogenously encoded prion protein (PrP) to an abnormal, neurotoxic conformation designated PrPsc. Most mammalian species are susceptible to TSE, which, despite a range of species-linked names, is caused by a single highly conserved protein, with no apparent normal function. In the simplest sense, TSE transmission can occur because PrPsc is resistant to both endogenous and environmental proteinases, although many details remain unclear. Questions about the transmission of TSE are central to practical issues such as livestock testing, access to international livestock markets, and wildlife management strategies, as well as intangible issues such as consumer confidence in the safety of the meat supply. The majority of BSE cases seem to have been transmitted by feed containing meat and bone meal from infected animals. In the United Kingdom, there was a dramatic decrease in BSE cases after neural tissue and, later, all ruminant tissues were banned from ruminant feed. However, probably because of heightened awareness and widespread testing, there is growing evidence that new variants of BSE are arising "spontaneously," suggesting ongoing surveillance will continue to find infected animals. Interspecies transmission is inefficient and depends on exposure, sequence homology, TSE donor strain, genetic polymorphism of the host, and architecture of the visceral nerves if exposure is by an oral route. Considering the low probability of interspecies transmission, the low efficiency of oral transmission, and the low prion levels in nonnervous tissues, consumption of conventional animal products represents minimal risk. However, detection of rare events is challenging, and TSE literature is characterized by subsequently unsupported claims of species barriers or absolute tissue safety. This review presents an overview of TSE and summarizes recent research on pathogenesis and transmission.

  20. Chlorosulfolipids: Structure, synthesis, and biological relevance

    PubMed Central

    Bedke, D. Karl; Vanderwal, Christopher D.

    2011-01-01

    Chlorosulfolipids have been isolated from freshwater algae and from toxic mussels. They appear to have a structural role in algal membranes and have been implicated in Diarrhetic Shellfish Poisoning. Further fascinating aspects of these compounds include their stereochemically complex polychlorinated structures and the resulting strong conformational biases, and their poorly understood (yet surely compelling) biosynthesis. Discussions of each of these topics and of efforts in structural and stereochemical elucidation and synthesis are the subject of this Highlight. PMID:21125121

  1. CRISPR-Cas: biology, mechanisms and relevance.

    PubMed

    Hille, Frank; Charpentier, Emmanuelle

    2016-11-01

    Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes-termed spacers-into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent.This article is part of the themed issue 'The new bacteriology'. PMID:27672148

  2. Formability Evaluation of Sheet Metals Based on Global Strain Distribution

    NASA Astrophysics Data System (ADS)

    Zhang, Ling; Lin, Jianping; Min, Junying; Ye, You; Kang, Liugen

    2016-06-01

    According to the conventional methods for formability evaluation, e.g., forming limit curve (FLC), limit dome height, and total elongation, inconsistent results are observed when comparing the formability of four advanced high-strength steels (AHSS) with an ultimate tensile strength grade of 1000 MPa. The strain distribution analysis with the aid of digital image correlation technique shows that different uniform deformation capabilities of sheet metals under the same loading conditions are responsible for this inconsistency. In addition, metallurgical analysis suggests that inhomogeneous microstructure distribution and phase transformation during deformation in some materials play important roles in the uniform deformation capability of sheet metal. Limit strains on the commonly used FLC only relate to the major and minor strains of local deforming elements associated with the onset of necking. However, the formability of a sheet metal component is determined by the strain magnitudes of all deforming elements involved during the forming process. Hence, the formability evaluation of sheet metals from a global aspect is more applicable for practical engineering. A new method based on two indices (i.e., which represent global formability and uniform deformation capability, respectively) is proposed to evaluate the formability of sheet metals based on global strain distribution. The formability and evolution of deformation uniformity of the investigated AHSS at different stress states are studied with this new method. Compared with other formability evaluation methods, the new method is demonstrated to be more appropriate for practical engineering, and it is applicable to both in-plane and out-of-plane deformation. Additionally, the global formability of sheet metals can be more comprehensively understood with this new method.

  3. Genetic characterization of interleukins (IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18) with relevant biological roles in lagomorphs

    PubMed Central

    Neves, Fabiana; Abrantes, Joana; Almeida, Tereza; de Matos, Ana Lemos; Costa, Paulo P

    2015-01-01

    ILs, as essential innate immune modulators, are involved in an array of biological processes. In the European rabbit (Oryctolagus cuniculus) IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18 have been implicated in inflammatory processes and in the immune response against rabbit hemorrhagic disease virus and myxoma virus infections. In this study we characterized these ILs in six Lagomorpha species (European rabbit, pygmy rabbit, two cottontail rabbit species, European brown hare and American pika). Overall, these ILs are conserved between lagomorphs, including in their exon/intron structure. Most differences were observed between leporids and American pika. Indeed, when comparing both, some relevant differences were observed in American pika, such as the location of the stop codon in IL-1α and IL-2, the existence of a different transcript in IL8 and the number of cysteine residues in IL-1β. Changes at N-glycosylation motifs were also detected in IL-1, IL-10, IL-12B and IL-15. IL-1α is the protein that presents the highest evolutionary distances, which is in contrast to IL-12A where the distances between lagomorphs are the lowest. For all these ILs, sequences of human and European rabbit are more closely related than between human and mouse or European rabbit and mouse. PMID:26395994

  4. Genetic characterization of interleukins (IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18) with relevant biological roles in lagomorphs.

    PubMed

    Neves, Fabiana; Abrantes, Joana; Almeida, Tereza; de Matos, Ana Lemos; Costa, Paulo P; Esteves, Pedro J

    2015-11-01

    ILs, as essential innate immune modulators, are involved in an array of biological processes. In the European rabbit (Oryctolagus cuniculus) IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18 have been implicated in inflammatory processes and in the immune response against rabbit hemorrhagic disease virus and myxoma virus infections. In this study we characterized these ILs in six Lagomorpha species (European rabbit, pygmy rabbit, two cottontail rabbit species, European brown hare and American pika). Overall, these ILs are conserved between lagomorphs, including in their exon/intron structure. Most differences were observed between leporids and American pika. Indeed, when comparing both, some relevant differences were observed in American pika, such as the location of the stop codon in IL-1α and IL-2, the existence of a different transcript in IL8 and the number of cysteine residues in IL-1β. Changes at N-glycosylation motifs were also detected in IL-1, IL-10, IL-12B and IL-15. IL-1α is the protein that presents the highest evolutionary distances, which is in contrast to IL-12A where the distances between lagomorphs are the lowest. For all these ILs, sequences of human and European rabbit are more closely related than between human and mouse or European rabbit and mouse. PMID:26395994

  5. Proteomic Approaches in Understanding Action Mechanisms of Metal-Based Anticancer Drugs

    PubMed Central

    Wang, Ying; Chiu, Jen-Fu

    2008-01-01

    Medicinal inorganic chemistry has been stimulating largely by the success of the anticancer drug, cisplatin. Various metal complexes are currently used as therapeutic agents (e.g., Pt, Au, and Ru) in the treatment of malignant diseases, including several types of cancers. Understanding the mechanism of action of these metal-based drugs is for the design of more effective drugs. Proteomic approaches combined with other biochemical methods can provide comprehensive understanding of responses that are involved in metal-based anticancer drugs-induced cell death, including insights into cytotoxic effects of metal-based anticancer drugs, correlation of protein alterations to drug targets, and prediction of drug resistance and toxicity. This information, when coupled with clinical data, can provide rational basses for the future design and modification of present used metal-based anticancer drugs. PMID:18670610

  6. Antibacterial and antifungal metal based triazole Schiff bases.

    PubMed

    Chohan, Zahid H; Hanif, Muhammad

    2013-10-01

    A new series of four biologically active triazole derived Schiff base ligands (L(1)-L(4)) and their cobalt(II), nickel(II), copper(II) and zinc(II) complexes (1-16) have been synthesized and characterized. The ligands were prepared by the condensation reaction of 3-amino-5-methylthio-1H-1,2,4-triazole with chloro-, bromo- and nitro-substituted 2-hydroxybenzaldehyde in an equimolar ratio. The antibacterial and antifungal bioactivity data showed the metal(II) complexes to be more potent antibacterial and antifungal than the parent Schiff bases against one or more bacterial and fungal species.

  7. Endothelial cell activation, oxidative stress and inflammation induced by a panel of metal-based nanomaterials.

    PubMed

    Danielsen, Pernille Høgh; Cao, Yi; Roursgaard, Martin; Møller, Peter; Loft, Steffen

    2015-01-01

    The importance of composition, size, crystal structure, charge and coating of metal-based nanomaterials (NMs) were evaluated in human umbilical vein endothelial cells (HUVECs) and/or THP-1 monocytic cells. Biomarkers of oxidative stress and inflammation were assessed because they are important in the development of cardiovascular diseases. The NMs used were five TiO(2) NMs with different charge, size and crystal structure, coated and uncoated ZnO NMs and Ag which were tested in a wide concentration range. There were major differences between the types of NMs; exposure to ZnO and Ag resulted in cytotoxicity and increased gene expression levels of HMOX1 and IL8. The intracellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1(VCAM-1) expression were highest in TiO(2) NM-exposed cells. There was increased adhesion of THP-1 monocytic cells onto HUVECs with Ag exposure. None of the NMs increased the intracellular ROS production. There were no major effects of the coating of ZnO NMs. The TiO(2) NMs data on ICAM-1 and VCAM-1 expression suggested that the anatase form was more potent than the rutile form. In addition, the larger TiO(2) NM was more potent than the smaller for gene expression and ICAM-1 and VCAM-1 expression. The toxicological profile of cardiovascular disease-relevant biomarkers depended on composition, size and crystal structure of TiO(2) NMs, whereas the charge on TiO(2) NMs and the coating of ZnO NMs were not associated with differences in toxicological profile.

  8. Photodynamic Therapy and the Development of Metal-Based Photosensitisers

    PubMed Central

    Josefsen, Leanne B.; Boyle, Ross W.

    2008-01-01

    Photodynamic therapy (PDT) is a treatment modality that has been used in the successful treatment of a number of diseases and disorders, including age-related macular degeneration (AMD), psoriasis, and certain cancers. PDT uses a combination of a selectively localised light-sensitive drug (known as a photosensitiser) and light of an appropriate wavelength. The light-activated form of the drug reacts with molecular oxygen to produce reactive oxygen species (ROS) and radicals; in a biological environment these toxic species can interact with cellular constituents causing biochemical disruption to the cell. If the homeostasis of the cell is altered significantly then the cell enters the process of cell death. The first photosensitiser to gain regulatory approval for clinical PDT was Photofrin. Unfortunately, Photofrin has a number of associated disadvantages, particularly pro-longed patient photosensitivity. To try and overcome these disadvantages second and third generation photosensitisers have been developed and investigated. This Review highlights the key photosensitisers investigated, with particular attention paid to the metallated and non-metallated cyclic tetrapyrrolic derivatives that have been studied in vitro and in vivo; those which have entered clinical trials; and those that are currently in use in the clinic for PDT. PMID:18815617

  9. Earthdata Search: The Relevance of Relevance

    NASA Technical Reports Server (NTRS)

    Quinn, Patrick

    2016-01-01

    Through recent usability studies, the issue of relevance became increasingly clear in the Earthdata Search Client. After all, if a user can't find the data they are looking for, nothing else we do matters. This presentation walks through usability testing findings and recent relevance improvements made to the Earthdata Search Client.

  10. Selective cancer-killing ability of metal-based nanoparticles: implications for cancer therapy.

    PubMed

    Akhtar, Mohd Javed; Alhadlaq, Hisham A; Kumar, Sudhir; Alrokayan, Salman A; Ahamed, Maqusood

    2015-11-01

    There has been little focus on the promising ability of metal-based nanoparticles (NPs) to kill cancer cells while sparing normal cells. Many in vitro and in vivo reports suggest that certain metal-based NPs are able to induce apoptosis and autophagy in cancer cells at specific concentrations that are not significantly toxic to non-cancerous cells. Those NPs are thought to exploit the oxidative stress conditions that prevail in cancer cells, which are largely exhausted of antioxidant ability. This review considers the induction of reactive oxygen species (ROS) by metal-based NPs as a mechanism for the specific killing of cancer cells. The article concomitantly provides a comprehensive description of the important pathways and molecules leading to programmed cell death (PCD), which occurs mainly via apoptosis, autophagy, and necroptosis. The PCD pathways are followed as ROS-burdened cancer cells succumb to ROS-generating metal-based NPs. Exploration of nanotechnology interventions in anticancer therapy demands further research into the mechanism of intracellular induction of ROS by metal-based NPs. Furthermore, the induction of ROS by NPs should be strictly controlled if ROS-based therapy is to become a paradigm in cancer therapy.

  11. Bivalent metal-based MIL-53 analogues: Synthesis, properties and application

    SciTech Connect

    Liu, Yongxin; Liu, Dan; Wang, Cheng

    2015-03-15

    Trivalent metal-based MIL-53 (Al{sup 3+}, Cr{sup 3+}, Fe{sup 3+}, In{sup 3+}) compounds are interesting metal–organic frameworks (MOFs) with breathing effect and are promising gas sorption materials. Replacing bridging μ{sub 2}-OH group by neutral ligands such as pyridine N-oxide and its derivatives (PNOs), the trivalent metal-based MIL-53 analogous structures could be extended to bivalent metal systems. The introduction of PNOs and bivalent metal elements endows the frameworks with new structural features and physical and chemical properties. This minireview summarizes the recent development of bivalent metal-based MIL-53 analogues (Mn{sup 2+}, Co{sup 2+}, Ni{sup 2+}), typically, focusing on the synthetic strategies and potential applications based on our own works and literatures. We present the synthetic strategy to achieve structures evolution from single-ligand-walled to double-ligand-walled channel. Properties and application of these new materials in a wide range of potential areas are discussed including thermal stability, gas adsorption, magnetism and liquid-phase separation. Promising directions of this research field are also highlighted. - Graphical abstract: The recent development of bivalent metal-based MIL-53 analogues (Mn{sup 2+}, Co{sup 2+}, Ni{sup 2+}) on their synthetic strategies, properties and potential applications was reviewed. - Highlights: • Structure features of bivalent metal-based MIL-53 analogues are illustrated. • Important properties and application are presented. • Host–guest interactions are main impetus for liquid-phase separation. • Promising directions of bivalent metal-based MIL-53 analogues are highlighted.

  12. Engineered metal based nanomaterials in aqueous environments: Interactions, transformations and implications

    NASA Astrophysics Data System (ADS)

    Mudunkotuwa, Imali Ama

    Nanoscience and nanotechnology offer potential routes towards addressing critical issues such as clean and sustainable energy, environmental protection and human health. Specifically, metal and metal oxide nanomaterials are found in a wide range of applications and therefore hold a greater potential of possible release into the environment or for the human to be exposed. Understanding the aqueous phase behavior of metal and metal oxide nanomaterials is a key factor in the safe design of these materials because their interactions with living systems are always mediated through the aqueous phase. Broadly the transformations in the aqueous phase can be classified as dissolution, aggregation and adsorption which are dependent and linked processes to one another. The complexity of these processes at the liquid-solid interface has therefore been one of the grand challenges that has persisted since the beginning of nanotechnology. Although classical models provide guidance for understanding dissolution and aggregation of nanoparticles in water, there are many uncertainties associated with the recent findings. This is often due to a lack of fundamental knowledge of the surface structure and surface energetics for very small particles. Therefore currently the environmental health and safety studies related to nanomaterials are more focused on understanding the surface chemistry that governs the overall processes in the liquid-solid interfacial region at the molecular level. The metal based nanomaterials focused on in this dissertation include TiO2, ZnO, Cu and CuO. These are among the most heavily used in a number of applications ranging from uses in the construction industry to cosmetic formulation. Therefore they are produced in large scale and have been detected in the environment. There is debate within the scientific community related to their safety as a result of the lack of understanding on the surface interactions that arise from the detailed nature of the surfaces

  13. Synthesis and property investigation of metal-based nanomaterials for biotechnological applications

    NASA Astrophysics Data System (ADS)

    Darsanasiri, Nalin Dammika

    Luminescent lanthanide-based materials have drawn recent interest due to their applications in in vitro cellular imaging. Sensitive biological analysis requires optical labels with high water dispersibility & stability and excellent luminescent properties. Most literature reported lanthanide complexes with high luminescence intensity are hydrophobic and unstable, limiting their biological applications. This project was designed to incorporate a highly luminescent lanthanide beta-diketonate complex in a silica nanoparticle. Eu(btfa)3dmph complex was synthesized, which exhibits red luminescence at 614 nm with a narrow (15 nm) full with half-maximum (btfa=4,4,4-trifluoro-1-phenyl-1,3-butanedione, dmph=4,7-dimethyl,1,10-phenanthroline). A synthetic procedure was optimized to incorporate the Eu-complex in a silica-based nanoparticle with an average particle diameter of 36 nm. Eu-complex based silica nanoparticles exhibit high stability and water-dispersibility with a luminescence quantum yield of 10 %. The nanoparticles showed antimicrobial activity against clinically important E.coli, S.aureus and S.epidermidis. Synthesis, materials characterization, and antimicrobial studies of the complex and the nanoparticles was discussed in the first part of this thesis. Nanotechnology is emerging as a new interdisciplinary field combining biology, chemistry, physics, and material science. Recent advances promise developments in the synthesis, modification and practical applications of polymer-coated manganese (Mn)-based zinc oxide (ZnO) nanoparticles (NPs). The size distribution, shape, and surface modification of metal-based ZnO nanoparticles are the key factors determining their specific physical properties. Due to the strong antibacterial properties and low toxicity towards mammalian cells, ZnO NPs have been successfully used in a wide range of applications including wound dressing, protective clothing, antibacterial surfaces, food preservation, and cosmetics as biocidal and

  14. SINGLE-PARTICLE ICPMS FOR CHARACTERIZING METAL-BASED NANOPARTICLES IN THE ENVIRONMENT - ADVANCES AND CHALLENGES

    EPA Science Inventory

    As engineered metal-based nanomaterials become widely used in consumer and industrial products, the amount of these materials introduced into the environment by a variety of paths will increase. The concentration of metal associated with these engineered nanoparticles will be s...

  15. Characterizing Metal-Based Nanoparticles in Surface Water by Single-Particle ICPMS

    EPA Science Inventory

    Engineered metal-based nanomaterials are being used in increasing quantities in consumer and industrial products. These materials may be introduced into surface waters by a variety of paths depending on usage, and will be superimposed on concentrations of other particles containi...

  16. Single Particle ICPMS for Characterizing Metal-based Nanoparticles and Monitoring Transformation Processes in Surface Water

    EPA Science Inventory

    Engineered metal-based nanomaterials will likely be used in increasing quantities in consumer and industrial products. These may be introduced into surface waters by a variety of paths depending on usage. Other naturally occurring and anthropogenic particles containing these met...

  17. Removal of inorganic mercury and methylmercury from surface waters following coagulation of dissolved organic matter with metal-based salts

    USGS Publications Warehouse

    Henneberry, Y.K.; Kraus, T.E.C.; Fleck, J.A.; Krabbenhoft, D.P.; Bachand, P.M.; Horwath, W.R.

    2011-01-01

    The presence of inorganic mercury (IHg) and methylmercury (MeHg) in surface waters is a health concern worldwide. This study assessed the removal potential use of metal-based coagulants as a means to remove both dissolved IHg and MeHg from natural waters and provides information regarding the importance of Hg associations with the dissolved organic matter (DOM) fraction and metal hydroxides. Previous research indicated coagulants were not effective at removing Hg from solution; however these studies used high concentrations of Hg and did not reflect naturally occurring concentrations of Hg. In this study, water collected from an agricultural drain in the Sacramento-San Joaquin Delta was filtered to isolate the dissolved organic matter (DOM) fraction. The DOM was then treated with a range of coagulant doses to determine the efficacy of removing all forms of Hg from solution. Three industrial-grade coagulants were tested: ferric chloride, ferric sulfate, and polyaluminum chloride. Coagulation removed up to 85% of DOM from solution. In the absence of DOM, all three coagulants released IHg into solution, however in the presence of DOM the coagulants removed up to 97% of IHg and 80% of MeHg. Results suggest that the removal of Hg is mediated by DOM-coagulant interactions. There was a preferential association of IHg with the more aromatic, higher molecular weight fraction of DOM but no such relationship was found for MeHg. This study offers new fundamental insights regarding large-scale removal of Hg at environmentally relevant regarding large-scale removal of Hg at environmentally relevant concentrations.

  18. Culturally Relevant Pedagogy

    ERIC Educational Resources Information Center

    Irvine, Jacqueline Jordan

    2010-01-01

    Many teachers have only a cursory understanding of culturally relevant pedagogy, and their efforts to bridge the cultural gap often fall short. Culturally relevant pedagogy is a term that describes effective teaching in culturally diverse classrooms. It can be a daunting idea to understand and implement. Yet people tend to appreciate culturally…

  19. Making Science Relevant

    ERIC Educational Resources Information Center

    Eick, Charles; Deutsch, Bill; Fuller, Jennifer; Scott, Fletcher

    2008-01-01

    Science teachers are always looking for ways to demonstrate the relevance of science to students. By connecting science learning to important societal issues, teachers can motivate students to both enjoy and engage in relevant science (Bennet, Lubben, and Hogarth 2007). To develop that connection, teachers can help students take an active role in…

  20. The Relevant Counselor.

    ERIC Educational Resources Information Center

    Herr, Edwin L.

    1986-01-01

    Addresses the questions of school counselors' obsolescence and relevance. Cites examples of national indicators of support for school counselors. Suggests the need for sharpening the counselor's role and reducing the unevenness in guidance services' availability. (ABB)

  1. Sverdrup's Biology

    NASA Astrophysics Data System (ADS)

    McGowan, J.

    2002-12-01

    Sverdrup's contribution to Biological Oceanography were more than merely substantial, they were of fundamental importance. His plan for the training of graduate students at Scripps did not recognize the traditional division of the basic disciplines into separate categories of physics, chemistry, biology and geology. He insisted that Oceanography was a multi-disciplinary subject and that all entering students should study all four subjects. Today this is not very unusual but it was in the early 50s when I took those courses. We biologists carried away from those courses an appreciation of the importance of both spatial and temporal scale. It was of clear relevance to problems of oceanic population and community biology. But there was still more to his biology. He is responsible for a very simple, but very elegant model of the regulation of oceanic primary productivity. The elements of this model are found today in the ten or so highly derivative models. He also published a map predicting global ocean productivity based on the ideas in the model plus some wonderfully intuitive thinking. This map does not differ strongly from those glorious false color ones being published today.

  2. Bioinformatics and School Biology

    ERIC Educational Resources Information Center

    Dalpech, Roger

    2006-01-01

    The rapidly changing field of bioinformatics is fuelling the need for suitably trained personnel with skills in relevant biological "sub-disciplines" such as proteomics, transcriptomics and metabolomics, etc. But because of the complexity--and sheer weight of data--associated with these new areas of biology, many school teachers feel…

  3. Ceramics reinforced metal base composite coatings produced by CO II laser cladding

    NASA Astrophysics Data System (ADS)

    Yang, Xichen; Wang, Yu; Yang, Nan

    2008-03-01

    Due to the excellent performance in high strength, anti-temperature and anti-wear, ceramics reinforced metal base composite material was used in some important fields of aircraft, aerospace, automobile and defense. The traditional bulk metal base composite materials are the expensive cost, which is limited in its industrial application. Development of laser coating of ceramics reinforced metal base composite is very interesting in economy. This paper is focused on three laser cladding ceramics coatings of SiC particle /Al matrix , Al IIO 3 powder/ Al matrix and WC + Co/mild steel matrix. Powder particle sizes are of 10-60μm. Chemical contents of aluminum matrix are of 3.8-4.0% Cu, 1.2-1.8% Mg, 0.3-0.99% Mn and balance Al. 5KW CO II laser, 5 axes CNC table, JKF-6 type powder feeder and co-axis feeder nozzle are used in laser cladding. Microstructure and performance of laser composite coatings have been respectively examined with OM,SEM and X-ray diffraction. Its results are as follows : Microstructures of 3C-,6H- and 5H- SiC particles + Al + Al 4SiC 4 + Si in SiC/Al composite, hexagonal α-Al IIO 3 + cubic γ-Al IIO 3 + f.c.c Al in Al IIO 3 powder/ Al composite and original WC particles + separated WC particles + eutectic WC + γ-Co solid solution + W IIC particles in WC + Co/steel coatings are respectively recognized. New microstructures of 5H-SiC in SiC/Al composite, cubic γ-Al IIO 3 in Al IIO 3 composite and W IIC in WC + Co/ steel composite by laser cladding have been respectively observed.

  4. Relevance, Derogation and Permission

    NASA Astrophysics Data System (ADS)

    Stolpe, Audun

    We show that a recently developed theory of positive permission based on the notion of derogation is hampered by a triviality result that indicates a problem with the underlying full-meet contraction operation. We suggest a solution that presupposes a particular normal form for codes of norms, adapted from the theory of relevance through propositional letter sharing. We then establish a correspondence between contractions on sets of norms in input/output logic (derogations), and AGM-style contractions on sets of formulae, and use it as a bridge to migrate results on propositional relevance from the latter to the former idiom. Changing the concept accordingly we show that positive permission now incorporates a relevance requirement that wards off triviality.

  5. Integrated Design and Rapid Development of Refractory Metal Based Alloys for Fossil Energy Applications

    SciTech Connect

    Dogan, O.N.; King, P.E.; Gao, M.C.

    2008-07-01

    One common barrier in the development of new technologies for future energy generating systems is insufficiency of existing materials at high temperatures (>1150oC) and aggressive atmospheres (e.g., steam, oxygen, CO2). To overcome this barrier, integrated design methodology will be applied to the development of refractory metal based alloys. The integrated design utilizes the multi-scale computational methods to design materials for requirements of processing and performance. This report summarizes the integrated design approach to the alloy development and project accomplishments in FY 2008.

  6. Recent advances in noble metal based composite nanocatalysts: colloidal synthesis, properties, and catalytic applications.

    PubMed

    Xu, Yong; Chen, Lei; Wang, Xuchun; Yao, Weitang; Zhang, Qiao

    2015-06-28

    This Review article provides a report on progress in the synthesis, properties and catalytic applications of noble metal based composite nanomaterials. We begin with a brief discussion on the categories of various composite materials. We then present some important colloidal synthetic approaches to the composite nanostructures; here, major attention has been paid to bimetallic nanoparticles. We also introduce some important physiochemical properties that are beneficial from composite nanomaterials. Finally, we highlight the catalytic applications of such composite nanoparticles and conclude with remarks on prospective future directions. PMID:26036784

  7. Recent advances in noble metal based composite nanocatalysts: colloidal synthesis, properties, and catalytic applications

    NASA Astrophysics Data System (ADS)

    Xu, Yong; Chen, Lei; Wang, Xuchun; Yao, Weitang; Zhang, Qiao

    2015-06-01

    This Review article provides a report on progress in the synthesis, properties and catalytic applications of noble metal based composite nanomaterials. We begin with a brief discussion on the categories of various composite materials. We then present some important colloidal synthetic approaches to the composite nanostructures; here, major attention has been paid to bimetallic nanoparticles. We also introduce some important physiochemical properties that are beneficial from composite nanomaterials. Finally, we highlight the catalytic applications of such composite nanoparticles and conclude with remarks on prospective future directions.

  8. The Limits to Relevance

    NASA Astrophysics Data System (ADS)

    Averill, M.; Briggle, A.

    2006-12-01

    Science policy and knowledge production lately have taken a pragmatic turn. Funding agencies increasingly are requiring scientists to explain the relevance of their work to society. This stems in part from mounting critiques of the "linear model" of knowledge production in which scientists operating according to their own interests or disciplinary standards are presumed to automatically produce knowledge that is of relevance outside of their narrow communities. Many contend that funded scientific research should be linked more directly to societal goals, which implies a shift in the kind of research that will be funded. While both authors support the concept of useful science, we question the exact meaning of "relevance" and the wisdom of allowing it to control research agendas. We hope to contribute to the conversation by thinking more critically about the meaning and limits of the term "relevance" and the trade-offs implicit in a narrow utilitarian approach. The paper will consider which interests tend to be privileged by an emphasis on relevance and address issues such as whose goals ought to be pursued and why, and who gets to decide. We will consider how relevance, narrowly construed, may actually limit the ultimate utility of scientific research. The paper also will reflect on the worthiness of research goals themselves and their relationship to a broader view of what it means to be human and to live in society. Just as there is more to being human than the pragmatic demands of daily life, there is more at issue with knowledge production than finding the most efficient ways to satisfy consumer preferences or fix near-term policy problems. We will conclude by calling for a balanced approach to funding research that addresses society's most pressing needs but also supports innovative research with less immediately apparent application.

  9. High-energy in-beam neutron measurements of metal-based shielding for accelerator-driven spallation neutron sources

    NASA Astrophysics Data System (ADS)

    DiJulio, D. D.; Cooper-Jensen, C. P.; Björgvinsdóttir, H.; Kokai, Z.; Bentley, P. M.

    2016-05-01

    Metal-based shielding plays an important role in the attenuation of harmful and unwanted radiation at an accelerator-driven spallation neutron source. At the European Spallation Source, currently under construction in Lund, Sweden, metal-based materials are planned to be used extensively as neutron guide substrates in addition to other shielding structures around neutron guides. The usage of metal-based materials in the vicinity of neutron guides however requires careful consideration in order to minimize potential background effects in a neutron instrument at the facility. Therefore, we have carried out a combined study involving high-energy neutron measurements and Monte Carlo simulations of metal-based shielding, both to validate the simulation methodology and also to investigate the benefits and drawbacks of different metal-based solutions. The measurements were carried out at The Svedberg Laboratory in Uppsala, Sweden, using a 174.1 MeV neutron beam and various thicknesses of aluminum-, iron-, and copper-based shielding blocks. The results were compared to geant4 simulations and revealed excellent agreement. Our combined study highlights the particular situations where one type of metal-based solution may be preferred over another.

  10. Is Information Still Relevant?

    ERIC Educational Resources Information Center

    Ma, Lia

    2013-01-01

    Introduction: The term "information" in information science does not share the characteristics of those of a nomenclature: it does not bear a generally accepted definition and it does not serve as the bases and assumptions for research studies. As the data deluge has arrived, is the concept of information still relevant for information…

  11. The Relevance of Literature.

    ERIC Educational Resources Information Center

    Dunham, L. L.

    1971-01-01

    The "legacy" of the humanities is discussed in terms of relevance, involvement, and other philosophical considerations. Reasons for studying foreign literature in language classes are developed in the article. Comment is also made on attitudes and ideas culled from the writings of Clifton Fadiman, Jean Paul Sartre, and James Baldwin. (RL)

  12. Relevance and Definition.

    ERIC Educational Resources Information Center

    Watson, Rita

    1995-01-01

    Examined whether the use of superordinate terms in 206 children's definitions is predictable by relevance theory. Children (ages 5-10) gave definitions for 16 basic-level words and 4 superordinate words from natural kind and artifact semantic domains. Superordinate terms were used more frequently when they supported more inferences. Findings…

  13. Reading, Writing and Relevance.

    ERIC Educational Resources Information Center

    Hoffman, Mary

    This monograph presents classroom activities that were designed to encourage children to read and write in a self-reliant and responsible manner. The activities were chosen for their relevance to the children involved and because the vocabulary involved was interesting, familiar, and worth remembering and using again. The topics are arranged in…

  14. Metal-based nanoparticles in soil: fate, behavior, and effects on soil invertebrates.

    PubMed

    Tourinho, Paula S; van Gestel, Cornelis A M; Lofts, Stephen; Svendsen, Claus; Soares, Amadeu M V M; Loureiro, Susana

    2012-08-01

    Metal-based nanoparticles (NPs) (e.g., silver, zinc oxide, titanium dioxide, iron oxide) are being widely used in the nanotechnology industry. Because of the release of particles from NP-containing products, it is likely that NPs will enter the soil compartment, especially through land application of sewage sludge derived from wastewater treatment. This review presents an overview of the literature dealing with the fate and effects of metal-based NPs in soil. In the environment, the characteristics of NPs (e.g., size, shape, surface charge) and soil (e.g., pH, ionic strength, organic matter, and clay content) will affect physical and chemical processes, resulting in NP dissolution, agglomeration, and aggregation. The behavior of NPs in soil will control their mobility and their bioavailability to soil organisms. Consequently, exposure characterization in ecotoxicological studies should obtain as much information as possible about dissolution, agglomeration, and aggregation processes. Comparing existing studies is a challenging task, because no standards exist for toxicity tests with NPs. In many cases, the reporting of associated characterization data is sparse, or missing, making it impossible to interpret and explain observed differences in results among studies.

  15. Theoretical investigation of all-metal-based mushroom plasmonic metamaterial absorbers at infrared wavelengths

    NASA Astrophysics Data System (ADS)

    Ogawa, Shinpei; Fujisawa, Daisuke; Kimata, Masafumi

    2015-12-01

    High-performance wavelength-selective infrared (IR) sensors require small pixel structures, a low-thermal mass, and operation in the middle-wavelength infrared (MWIR) and long-wavelength infrared (LWIR) regions for multicolor IR imaging. All-metal-based mushroom plasmonic metamaterial absorbers (MPMAs) were investigated theoretically and were designed to enhance the performance of wavelength-selective uncooled IR sensors. All components of the MPMAs are based on thin layers of metals such as Au without oxide insulators for increased absorption. The absorption properties of the MPMAs were investigated by rigorous coupled-wave analysis. Strong wavelength-selective absorption is realized over a wide range of MWIR and LWIR wavelengths by the plasmonic resonance of the micropatch and the narrow-gap resonance, without disturbance from the intrinsic absorption of oxide insulators. The absorption wavelength is defined mainly by the micropatch size and is longer than its period. The metal post width has less impact on the absorption properties and can maintain single-mode operation. Through-holes can be formed on the plate area to reduce the thermal mass. A small pixel size with reduced thermal mass and wideband single-mode operation can be realized using all-metal-based MPMAs.

  16. Metallomics insights into the programmed cell death induced by metal-based anticancer compounds.

    PubMed

    Tan, Cai-Ping; Lu, Yi-Ying; Ji, Liang-Nian; Mao, Zong-Wan

    2014-05-01

    Since the discovery of cisplatin more than 40 years ago, enormous research efforts have been dedicated to developing metal-based anticancer agents and to elucidating the mechanisms involved in the action of these compounds. Abnormal metabolism and the evasion of apoptosis are important hallmarks of malignant transformation, and the induction of apoptotic cell death has been considered to be a main pathway by which cytotoxic metal complexes combat cancer. However, many cancers have cellular defects involving the apoptotic machinery, which results in an acquired resistance to apoptotic cell death and therefore reduced chemotherapeutic effectiveness. Over the past decade, it has been revealed that a growing number of cell death pathways induced by metal complexes are not dependent on apoptosis. Metal complexes specifically triggering these alternative cell death pathways have been identified and explored as novel cancer treatment options. In this review, we discuss recent examples of metallomics studies on the different types of cell death induced by metal-based anticancer drugs, especially on the three major forms of programmed cell death (PCD) in mammalian cells: apoptosis, autophagy and regulated necrosis, also called necroptosis.

  17. Investigating extent of dissolved organic carbon stabilization by metal based coagulant in a wetland environment

    NASA Astrophysics Data System (ADS)

    Henneberry, Y.; Mourad, D.; Kraus, T.; Bachand, P.; Fujii, R.; Horwath, W.

    2008-12-01

    This study is part of a larger project designed to investigate the feasibility of using metal-based coagulants to remove dissolved organic carbon (DOC) from island drainage water in the San Joaquin Delta and subsequently retaining the metal-DOC precipitate (floc) in wetlands constructed at the foot of levees to promote levee stability. Dissolved organic carbon is a constituent of concern as some forms of DOC can be converted to carcinogenic compounds during drinking water treatment. The focus of this work is to assess floc stability over time and to determine whether floc can be permanently sequestered as part of wetland sediment. Drainage water collected seasonally from Twitchell Island was coagulated with ferric sulfate and polyaluminum chloride at optimal and 50%-optimal dosage levels. Floc was incubated in the laboratory under anaerobic conditions for six weeks under various conditions including different DOC concentrations, microbial inoculants, and addition of nutrients. Preliminary results indicate the floc is a stable system; little to no DOC was released from the floc into the water column under incubations with native microbial inoculate. In addition, floc incubated with previously coagulated water appeared to remove additional DOC from the water column. Future work will involve field and laboratory studies using 13C labeled plant material to examine the effects of fresh plant matter and the effects of peat soil DOC on floc stability, in order to elucidate mechanisms behind carbon stabilization by metal-based floc.

  18. Core Bioactive Components Promoting Blood Circulation in the Traditional Chinese Medicine Compound Xueshuantong Capsule (CXC) Based on the Relevance Analysis between Chemical HPLC Fingerprint and In Vivo Biological Effects

    PubMed Central

    Liu, Hong; Liang, Jie-ping; Li, Pei-bo; Peng, Wei; Peng, Yao-yao; Zhang, Gao-min; Xie, Cheng-shi; Long, Chao-feng; Su, Wei-wei

    2014-01-01

    Compound xueshuantong capsule (CXC) is an oral traditional Chinese herbal formula (CHF) comprised of Panax notoginseng (PN), Radix astragali (RA), Salvia miltiorrhizae (SM), and Radix scrophulariaceae (RS). The present investigation was designed to explore the core bioactive components promoting blood circulation in CXC using high-performance liquid chromatography (HPLC) and animal studies. CXC samples were prepared with different proportions of the 4 herbs according to a four-factor, nine-level uniform design. CXC samples were assessed with HPLC, which identified 21 components. For the animal experiments, rats were soaked in ice water during the time interval between two adrenaline hydrochloride injections to reduce blood circulation. We assessed whole-blood viscosity (WBV), erythrocyte aggregation and red corpuscle electrophoresis indices (EAI and RCEI, respectively), plasma viscosity (PV), maximum platelet aggregation rate (MPAR), activated partial thromboplastin time (APTT), and prothrombin time (PT). Based on the hypothesis that CXC sample effects varied with differences in components, we performed grey relational analysis (GRA), principal component analysis (PCA), ridge regression (RR), and radial basis function (RBF) to evaluate the contribution of each identified component. Our results indicate that panaxytriol, ginsenoside Rb1, angoroside C, protocatechualdehyde, ginsenoside Rd, and calycosin-7-O-β-D-glucoside are the core bioactive components, and that they might play different roles in the alleviation of circulation dysfunction. Panaxytriol and ginsenoside Rb1 had close relevance to red blood cell (RBC) aggregation, angoroside C was related to platelet aggregation, protocatechualdehyde was involved in intrinsic clotting activity, ginsenoside Rd affected RBC deformability and plasma proteins, and calycosin-7-O-β-D-glucoside influenced extrinsic clotting activity. This study indicates that angoroside C, calycosin-7-O-β-D-glucoside, panaxytriol, and

  19. Core bioactive components promoting blood circulation in the traditional Chinese medicine compound xueshuantong capsule (CXC) based on the relevance analysis between chemical HPLC fingerprint and in vivo biological effects.

    PubMed

    Liu, Hong; Liang, Jie-ping; Li, Pei-bo; Peng, Wei; Peng, Yao-yao; Zhang, Gao-min; Xie, Cheng-shi; Long, Chao-feng; Su, Wei-wei

    2014-01-01

    Compound xueshuantong capsule (CXC) is an oral traditional Chinese herbal formula (CHF) comprised of Panax notoginseng (PN), Radix astragali (RA), Salvia miltiorrhizae (SM), and Radix scrophulariaceae (RS). The present investigation was designed to explore the core bioactive components promoting blood circulation in CXC using high-performance liquid chromatography (HPLC) and animal studies. CXC samples were prepared with different proportions of the 4 herbs according to a four-factor, nine-level uniform design. CXC samples were assessed with HPLC, which identified 21 components. For the animal experiments, rats were soaked in ice water during the time interval between two adrenaline hydrochloride injections to reduce blood circulation. We assessed whole-blood viscosity (WBV), erythrocyte aggregation and red corpuscle electrophoresis indices (EAI and RCEI, respectively), plasma viscosity (PV), maximum platelet aggregation rate (MPAR), activated partial thromboplastin time (APTT), and prothrombin time (PT). Based on the hypothesis that CXC sample effects varied with differences in components, we performed grey relational analysis (GRA), principal component analysis (PCA), ridge regression (RR), and radial basis function (RBF) to evaluate the contribution of each identified component. Our results indicate that panaxytriol, ginsenoside Rb1, angoroside C, protocatechualdehyde, ginsenoside Rd, and calycosin-7-O-β-D-glucoside are the core bioactive components, and that they might play different roles in the alleviation of circulation dysfunction. Panaxytriol and ginsenoside Rb1 had close relevance to red blood cell (RBC) aggregation, angoroside C was related to platelet aggregation, protocatechualdehyde was involved in intrinsic clotting activity, ginsenoside Rd affected RBC deformability and plasma proteins, and calycosin-7-O-β-D-glucoside influenced extrinsic clotting activity. This study indicates that angoroside C, calycosin-7-O-β-D-glucoside, panaxytriol, and

  20. Core bioactive components promoting blood circulation in the traditional Chinese medicine compound xueshuantong capsule (CXC) based on the relevance analysis between chemical HPLC fingerprint and in vivo biological effects.

    PubMed

    Liu, Hong; Liang, Jie-ping; Li, Pei-bo; Peng, Wei; Peng, Yao-yao; Zhang, Gao-min; Xie, Cheng-shi; Long, Chao-feng; Su, Wei-wei

    2014-01-01

    Compound xueshuantong capsule (CXC) is an oral traditional Chinese herbal formula (CHF) comprised of Panax notoginseng (PN), Radix astragali (RA), Salvia miltiorrhizae (SM), and Radix scrophulariaceae (RS). The present investigation was designed to explore the core bioactive components promoting blood circulation in CXC using high-performance liquid chromatography (HPLC) and animal studies. CXC samples were prepared with different proportions of the 4 herbs according to a four-factor, nine-level uniform design. CXC samples were assessed with HPLC, which identified 21 components. For the animal experiments, rats were soaked in ice water during the time interval between two adrenaline hydrochloride injections to reduce blood circulation. We assessed whole-blood viscosity (WBV), erythrocyte aggregation and red corpuscle electrophoresis indices (EAI and RCEI, respectively), plasma viscosity (PV), maximum platelet aggregation rate (MPAR), activated partial thromboplastin time (APTT), and prothrombin time (PT). Based on the hypothesis that CXC sample effects varied with differences in components, we performed grey relational analysis (GRA), principal component analysis (PCA), ridge regression (RR), and radial basis function (RBF) to evaluate the contribution of each identified component. Our results indicate that panaxytriol, ginsenoside Rb1, angoroside C, protocatechualdehyde, ginsenoside Rd, and calycosin-7-O-β-D-glucoside are the core bioactive components, and that they might play different roles in the alleviation of circulation dysfunction. Panaxytriol and ginsenoside Rb1 had close relevance to red blood cell (RBC) aggregation, angoroside C was related to platelet aggregation, protocatechualdehyde was involved in intrinsic clotting activity, ginsenoside Rd affected RBC deformability and plasma proteins, and calycosin-7-O-β-D-glucoside influenced extrinsic clotting activity. This study indicates that angoroside C, calycosin-7-O-β-D-glucoside, panaxytriol, and

  1. Noble metal based plasmonic nanomaterials and their application for bio-imaging and photothermal therapy

    NASA Astrophysics Data System (ADS)

    Zhu, Dewei

    During the past two decades, researchers have gained more and more insight into the manipulation of nanomaterials to create useful technologies. Numerous classes of nanomaterials have been produced and studied based upon their intriguing chemical and physical properties and their potential applications in diverse fields, ranging from electronics to renewable energy and biomedicine. In this dissertation, we describe the synthesis and potential biomedical applications of several types of noble metal-based nanomaterials in which we control size, shape, and coupling to other materials to tune their localized surface plasmon resonance (LSPR) interaction with light. We demonstrate the application of these novel nanostructures as contrast agents for photoacoustic imaging and as photosensitizers for photothermal therapy. Chapter one first presents protocols for producing monodisperse spherical nanoparticles of gold and silver. The diameter of the nanospheres can be adjusted from less than 2 nm to greater than 10 nm by controlling the reaction conditions, including ligands that cap the nanosphere surfaces, reaction time, and reaction temperature. Next, we describe the synthesis of multi-branched Au nanocrystals with predominantly tripodal, tetrapodal and star-shaped morphologies. We demonstrate tuning of the LSPR energy in these materials by changing the branch length. In the third part of this chapter, we present a novel method for coupling heavily-doped p-type copper selenide (Cu2-xSe) NPs with Au NPs by seeded nanocrystal growth to form a new type of semiconductor-metal heterogeneous nanostructure. This new class of plasmonic nanomaterials can simultaneously exhibit two types of LSPR in a single system, producing a broad optical absorbance that is nearly flat across the near infrared (NIR) spectral region (750-1150nm), along with a small shoulder at 566 nm that originates from the Au NP. We conclude this first chapter by demonstrating the use of self-doped copper sulfide

  2. Noble metal based plasmonic nanomaterials and their application for bio-imaging and photothermal therapy

    NASA Astrophysics Data System (ADS)

    Zhu, Dewei

    During the past two decades, researchers have gained more and more insight into the manipulation of nanomaterials to create useful technologies. Numerous classes of nanomaterials have been produced and studied based upon their intriguing chemical and physical properties and their potential applications in diverse fields, ranging from electronics to renewable energy and biomedicine. In this dissertation, we describe the synthesis and potential biomedical applications of several types of noble metal-based nanomaterials in which we control size, shape, and coupling to other materials to tune their localized surface plasmon resonance (LSPR) interaction with light. We demonstrate the application of these novel nanostructures as contrast agents for photoacoustic imaging and as photosensitizers for photothermal therapy. Chapter one first presents protocols for producing monodisperse spherical nanoparticles of gold and silver. The diameter of the nanospheres can be adjusted from less than 2 nm to greater than 10 nm by controlling the reaction conditions, including ligands that cap the nanosphere surfaces, reaction time, and reaction temperature. Next, we describe the synthesis of multi-branched Au nanocrystals with predominantly tripodal, tetrapodal and star-shaped morphologies. We demonstrate tuning of the LSPR energy in these materials by changing the branch length. In the third part of this chapter, we present a novel method for coupling heavily-doped p-type copper selenide (Cu2-xSe) NPs with Au NPs by seeded nanocrystal growth to form a new type of semiconductor-metal heterogeneous nanostructure. This new class of plasmonic nanomaterials can simultaneously exhibit two types of LSPR in a single system, producing a broad optical absorbance that is nearly flat across the near infrared (NIR) spectral region (750-1150nm), along with a small shoulder at 566 nm that originates from the Au NP. We conclude this first chapter by demonstrating the use of self-doped copper sulfide

  3. Chemical space and biology.

    PubMed

    Dobson, Christopher M

    2004-12-16

    Chemical space--which encompasses all possible small organic molecules, including those present in biological systems--is vast. So vast, in fact, that so far only a tiny fraction of it has been explored. Nevertheless, these explorations have greatly enhanced our understanding of biology, and have led to the development of many of today's drugs. The discovery of new bioactive molecules, facilitated by a deeper understanding of the nature of the regions of chemical space that are relevant to biology, will advance our knowledge of biological processes and lead to new strategies to treat disease.

  4. Enhancing Skin Permeation of Biphenylacetic Acid (BPA) Using Salt Formation with Organic and Alkali Metal Bases.

    PubMed

    Pawar, Vijay; Naik, Prashant; Giridhar, Rajani; Yadav, Mange Ram

    2015-01-01

    In the present study, a series of organic and alkali metal salts of biphenylacetic acid (BPA) have been prepared and evaluated in vitro for percutaneous drug delivery. The physicochemical properties of BPA salts were determined using solubility measurements, DSC, and IR. The DSC thermogram and FTIR spectra confirmed the salt formation with organic and alkali metal bases. Among the series, salts with organic amines (ethanolamine, diethanolamine, triethanolamine, and diethylamine) had lowered melting points while the alkali metal salt (sodium) had a higher melting point than BPA. The in vitro study showed that salt formation improves the physicochemical properties of BPA, leading to improved permeability through the skin. Amongst all the prepared salts, ethanolamine salt (1b) showed 7.2- and 5.4-fold higher skin permeation than the parent drug at pH 7.4 and 5.0, respectively, using rat skin.

  5. Metal-based drugs for malaria, trypanosomiasis and leishmaniasis: recent achievements and perspectives.

    PubMed

    Navarro, Maribel; Gabbiani, Chiara; Messori, Luigi; Gambino, Dinorah

    2010-12-01

    Tropical diseases today constitute a major health problem and a big challenge for drug discovery. Because of the limited arsenal of effective antiparasitic agents and the frequent appearance of chemoresistance, there is an urgent and continuous need to develop new drugs against these ailments. Metal compounds still offer excellent opportunities to find new 'leads' against the major protozoan diseases such as malaria, leishmaniasis and trypanosomiasis. A few metal-based drugs are already available in this therapeutic area, and others are currently being developed. Recent progress in parasite genomics and the identification of a few biomolecular targets hold great promise for the discovery of new 'mechanism-based' antiparasitic metallodrugs. The trends and perspectives for this exciting research field are outlined here.

  6. Quasiparticle band structure of the almost-gapless transition-metal-based Heusler semiconductors

    NASA Astrophysics Data System (ADS)

    Tas, M.; Şaşıoǧlu, E.; Galanakis, I.; Friedrich, C.; Blügel, S.

    2016-05-01

    Transition-metal-based Heusler semiconductors are promising materials for a variety of applications ranging from spintronics to thermoelectricity. Employing the G W approximation within the framework of the FLAPW method, we study the quasiparticle band structure of a number of such compounds being almost gapless semiconductors. We find that in contrast to the s p -electron based semiconductors such as Si and GaAs, in these systems, the many-body corrections have a minimal effect on the electronic band structure and the energy band gap increases by less than 0.2 eV, which makes the starting point density functional theory (DFT) a good approximation for the description of electronic and optical properties of these materials. Furthermore, the band gap can be tuned either by the variation of the lattice parameter or by the substitution of the s p -chemical element.

  7. [Eco-toxicological effect of metal-based nanoparticles on plants: Research progress].

    PubMed

    Zhang, Hai; Peng, Cheng; Yang, Jian-Jun; Shi, Ji-yan

    2013-03-01

    The rapid development of nanotechnology and the potential environmental risk of wide application of artificial nanoparticles (NPs) have raised considerable concerns. Metal-based nanoparticles (MB NPs) have dual-toxicity of metal and NPs, and thus, their bio-toxicity and ecological risk are the hotspots in the studies of nanotoxicology. Plant, as a main component of ecosystem, is a potential pathway for NPs bioaccumulation and entering into food chain. This paper discussed the MB NPs absorption, translocation, and accumulation by plants, and summarized the eco-toxicological effect of MB NPs on plants and related mechanisms. The factors affecting the phytotoxicity of MB NPs were approached, and the research progress on the eco-toxicological effect of MB NPs on plants, especially on food crops, was reviewed. Also, the existing problems in present MB NPs phytotoxicity studies were analyzed, and the future research directions were proposed.

  8. Metal-dielectric-metal based narrow band absorber for sensing applications.

    PubMed

    Lu, Xiaoyuan; Wan, Rengang; Zhang, Tongyi

    2015-11-16

    We have investigated numerically the narrowband absorption property of a metal-dielectric-metal based structure which includes a top metallic nanoring arrays, a metal backed plate, and a middle dielectric spacer. Its absorption is up to 90% with linewidth narrower than 10 nm. This can be explained in terms of surface lattice resonance of the periodic structure. The spectrum with the sharp absorption dip, i.e. the lattice resonance, strongly depends on the refractive index of media surrounding the nanorings. This feature can be explored to devise a refractive index sensor, of which the bulk sensitivity factor is one order larger than that based on gap resonance mode, while the surface sensitivity factor can be two times larger. The proposed narrowband absorber has potential in applications of plasmonic biosensors. PMID:26698467

  9. Insights on Metal Based Dental Implants and their Interaction with the Surrounding Tissues.

    PubMed

    Popa, Marcela; Hussien, Mohamed D; Cirstea, Alexandra; Grigore, Raluca; Lazar, Veronica; Bezirtzoglou, Eugenia; Chifiriuc, Mariana Carmen; Sakizlian, Monica; Stavropoulou, Elisavet; Bertesteanu, Serban

    2015-01-01

    At present, the use of dental implants is a very common practice as tooth loss is a frequent problem and can occur as a result of disease or trauma. An implant is usually made of biocompatible materials that do not cause rejection reactions and allow the implant union with the respective bone. To achieve this goal, the implant surface may have different structures and coatings, generally used to increase the adherence of the implant to the bone and to decrease the risk of the periimplantar inflammatory reactions. This review gives some insights of the metal based materials used for dental implants, their limits, improvement strategies as well as the pathophysiology, diagnosis, treatment and prevention of periimplantary diseases.

  10. An innovative metal base denture design for a 55-year-old menopausal woman

    PubMed Central

    Bhatia, Vishwas; Bhatia, Garima; Jain, Nitul; Jadon, Ashwani Kumar

    2013-01-01

    Menopause is a normal developmental stage in a woman's life, marking the permanent cessation of menstruation resulting from irreversible changes in the hormonal and reproductive functions of the ovaries and is associated with a large number of symptoms ranging from physical to psychological. Some of the common oral manifestations are oral burning sensation with associated mucosal infections, pain, altered taste perception, and alveolar bone loss. These symptoms may unfavorably affect oral health and treatment needs requiring dentists to devise newer methods that would add along to the treatment modalities advised by gynecologists in relieving menopausal women from above symptoms. The present case report describes an innovative method of fabricating a metal base denture in an edentulous female that would help perimenopausal/menopausal/post-menopausal edentulous women feel hot/cold sensations of food/liquids, thereby giving them relief from pain, better taste perception, and relief from associated allergic and candidal infections that are common with conventional acrylic base dentures. PMID:24082754

  11. Biological Threats

    MedlinePlus

    ... Thunderstorms & Lightning Tornadoes Tsunamis Volcanoes Wildfires Main Content Biological Threats Biological agents are organisms or toxins that ... Centers for Disease Control and Prevention . Before a Biological Threat Unlike an explosion, a biological attack may ...

  12. Computational systems chemical biology.

    PubMed

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

    2011-01-01

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

  13. Vygotsky's Crisis: Argument, context, relevance.

    PubMed

    Hyman, Ludmila

    2012-06-01

    Vygotsky's The Historical Significance of the Crisis in Psychology (1926-1927) is an important text in the history and philosophy of psychology that has only become available to scholars in 1982 in Russian, and in 1997 in English. The goal of this paper is to introduce Vygotsky's conception of psychology to a wider audience. I argue that Vygotsky's argument about the "crisis" in psychology and its resolution can be fully understood only in the context of his social and political thinking. Vygotsky shared the enthusiasm, widespread among Russian leftist intelligentsia in the 1920s, that Soviet society had launched an unprecedented social experiment: The socialist revolution opened the way for establishing social conditions that would let the individual flourish. For Vygotsky, this meant that "a new man" of the future would become "the first and only species in biology that would create itself." He envisioned psychology as a science that would serve this humanist teleology. I propose that The Crisis is relevant today insofar as it helps us define a fundamental problem: How can we systematically account for the development of knowledge in psychology? I evaluate how Vygotsky addresses this problem as a historian of the crisis. PMID:22520196

  14. Vygotsky's Crisis: Argument, context, relevance.

    PubMed

    Hyman, Ludmila

    2012-06-01

    Vygotsky's The Historical Significance of the Crisis in Psychology (1926-1927) is an important text in the history and philosophy of psychology that has only become available to scholars in 1982 in Russian, and in 1997 in English. The goal of this paper is to introduce Vygotsky's conception of psychology to a wider audience. I argue that Vygotsky's argument about the "crisis" in psychology and its resolution can be fully understood only in the context of his social and political thinking. Vygotsky shared the enthusiasm, widespread among Russian leftist intelligentsia in the 1920s, that Soviet society had launched an unprecedented social experiment: The socialist revolution opened the way for establishing social conditions that would let the individual flourish. For Vygotsky, this meant that "a new man" of the future would become "the first and only species in biology that would create itself." He envisioned psychology as a science that would serve this humanist teleology. I propose that The Crisis is relevant today insofar as it helps us define a fundamental problem: How can we systematically account for the development of knowledge in psychology? I evaluate how Vygotsky addresses this problem as a historian of the crisis.

  15. Information Theory in Biology after 18 Years

    ERIC Educational Resources Information Center

    Johnson, Horton A.

    1970-01-01

    Reviews applications of information theory to biology, concluding that they have not proved very useful. Suggests modifications and extensions to increase the biological relevance of the theory, and speculates about applications in quantifying cell proliferation, chemical homeostasis and aging. (EB)

  16. Evaluation of Colloidal Stability and Ecotoxicity of Metal-based Nanoparticles in the Aquatic and Terrestrial Systems

    NASA Astrophysics Data System (ADS)

    Pokhrel, Lok Raj

    NPs, ZnONPs, or their ions. Overall, various metal-based nanoparticles revealed lower toxicity than their ions against multiple organisms. This study showed that particle size, surface properties, and ion release kinetics of AgNPs modify following release into aquatic environment, suggesting potential implications to ecosystem health and functions, and that caution be applied when extending one species toxicity results to another because obvious differences in organism biology---supporting species sensitivity paradigm---can significantly alter nanoparticle or ionic toxicity.

  17. Towards a barrier height benchmark set for biologically relevant systems

    PubMed Central

    Kromann, Jimmy C.; Christensen, Anders S.; Cui, Qiang

    2016-01-01

    We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10–15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4–5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems, geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model, the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process. PMID:27168993

  18. Relevant Features of Science: Values in Conservation Biology

    ERIC Educational Resources Information Center

    van Dijk, Esther M.

    2013-01-01

    The development of an understanding of the nature of science is generally assumed to be an important aspect of science communication with respect to the enhancement of scientific literacy. At present, a general characterization of the nature of science is still lacking and probably such a characterization will not be achievable. The overall aim of…

  19. Towards a barrier height benchmark set for biologically relevant systems.

    PubMed

    Kromann, Jimmy C; Christensen, Anders S; Cui, Qiang; Jensen, Jan H

    2016-01-01

    We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10-15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4-5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems, geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model, the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process. PMID:27168993

  20. Developments in ghrelin biology and potential clinical relevance.

    PubMed

    Smith, Roy G; Jiang, Hong; Sun, Yuxiang

    2005-11-01

    The spiropiperidine, MK0677, has been exploited to characterize and expression clone the growth hormone secretagogue receptor (GHS-R). Cloning of this receptor led to identification of its natural ligands, ghrelin and adenosine. Targeted disruption of the Ghsr gene demonstrated unambiguously that the GH-releasing and orexigenic properties of ghrelin are dependent on Ghsr expression and that the orexigenic signal is mediated through neuropeptide Y and agouti-related peptide neurons. This review summarizes new developments in our understanding of the physiological roles of ghrelin and its receptor (GHS-R). Recent discoveries of the effects of ghrelin on the thymus and proinflammatory and chemotactic cytokine pathways stimulate renewed interest in potential clinical applications, which include age-associated disorders, such as metabolic disease, sarcopenia, congestive heart failure, atherosclerosis and anorexia. PMID:16213742

  1. Biologically Relevant Exposure Science for 21st Century Toxicity Testing

    EPA Science Inventory

    High visibility efforts in toxicity testing and computational toxicology including the recent NRC report, Toxicity Testing in the 21st Century: a Vision and Strategy (NRC, 2007), raise important research questions and opportunities for the field of exposure science. The authors ...

  2. Impact Ignition and Combustion Behavior of Amorphous Metal-Based Reactive Composites

    NASA Astrophysics Data System (ADS)

    Mason, Benjamin; Groven, Lori; Son, Steven

    2013-06-01

    Recently published molecular dynamic simulations have shown that metal-based reactive powder composites consisting of at least one amorphous component could lead to improved reaction performance due to amorphous materials having a zero heat of fusion, in addition to having high energy densities and potential uses such as structural energetic materials and enhanced blast materials. In order to investigate the feasibility of these systems, thermochemical equilibrium calculations were performed on various amorphous metal/metalloid based reactive systems with an emphasis on commercially available or easily manufactured amorphous metals, such as Zr and Ti based amorphous alloys in combination with carbon, boron, and aluminum. Based on the calculations and material availability material combinations were chosen. Initial materials were either mixed via a Resodyn mixer or mechanically activated using high energy ball milling where the microstructure of the milled material was characterized using x-ray diffraction, optical microscopy and scanning electron microscopy. The mechanical impact response and combustion behavior of select reactive systems was characterized using the Asay shear impact experiment where impact ignition thresholds, ignition delays, combustion velocities, and temperatures were quantified, and reported. Funding from the Defense Threat Reduction Agency (DTRA), Grant Number HDTRA1-10-1-0119. Counter-WMD basic research program, Dr. Suhithi M. Peiris, program director is gratefully acknowledged.

  3. An oxidized liquid metal-based microfluidic platform for tunable electronic device applications.

    PubMed

    Li, Guangyong; Parmar, Mitesh; Lee, Dong-Weon

    2015-02-01

    Easy movement of oxidized Galinstan in microfluidic channels is a promising way for the wide application of the non-toxic liquid metal. In this paper, two different surface modification techniques (physical and chemical) are reported, which dramatically improve the non-wetting characteristics of oxidized Galinstan in the microfluidic channel. In the physical technique, normal paper textures are transferred to the inner wall of polydimethylsiloxane (PDMS) channels and four types of nanoparticles are then coated on the surface of the wall for further improvement of the non-wetting characteristics. Highest advancing angle of 167° and receding angle of 151° are achieved on the paper-textured PDMS with titanium oxide (TiO2) nanoparticles. In the chemical technique, three types of inorganic acids are employed to generate dual-scale structures on the PDMS surface. The inner wall surface treated with sulfuric acid (H2SO4) shows the highest contact angle of 167° and a low hysteresis of ~14° in the dynamic measurement. Creating, transporting, separating and merging of oxidized Galinstan droplets are successfully demonstrated in the fabricated PDMS microfluidic channels. After optimization of these modification techniques, the potential application of tunable capacitors and electronic filters is realized by using liquid metal-based microfluidic devices.

  4. Simulation of the emission properties of patterned metal-based nanostructures

    NASA Astrophysics Data System (ADS)

    Li, Weijun; Luo, Jun; Peng, Sha; Zhu, Yaping; Lei, Yu; Tong, Qing; Zhang, Xinyu; Sang, Hongshi; Xie, Changsheng

    2015-12-01

    Enormous pressures have been puts on current optical storage technologies as the rapid development of information technologies. Recently, it has been found that the surface plasmon-polaritons'modes (SPPMs) in metallic nanostructures may lead to the high localization of guided light beams with nanometer size and only limited by several factors such as atomic structure, dissipation, and light dispersion, and thus far beyond the common diffraction limit of electromagnetic waves in dielectric media. This discovery provides a way to produce nanoscale light signal and thus makes a significant breakthrough in optical storage technologies. In this paper, our work focuses on the modeling and simulation of particular kinds of patterned metal-based nanostructure fabricated over silicon dioxide (SiO2) wafer. The nanostructures designed are expected to concentrate, deliver incident light energy into nanoscale regions and generate nanoscale light signal. In our research, the duty cycle of patterned nanostructures is taken as a key parameter, and then the factors including the patterned nanostructures, the frequency of the incident electromagnetic wave, the size of patterned nanostructure and the distance arrangement between adjacent single patterns, are taken as variables. The common CST microwave studio is used to simulate beam transportation and transformation behaviors. By comparing electric-field intensity distribution in nano-areas and the reflectance of the nanostructure array, the nano-light-emission effects are analyzed.

  5. Association constants of Pb2+ with binding sites of fungal biomass using metal-based titrations.

    PubMed

    Naja, G; Mustin, C; Volesky, B; Berthelin, J

    2006-01-01

    Biosorption is perceived as an alternative method for toxic heavy metal removal/recovery from aqueous effluents. This work focused on derivation of some key quantitative physico-chemical characteristics of a representative biosorbent material required for its further effective exploitation. The newly developed acid-base and metal-based titrator allowed the characterization of the chemisorption active sites of Rhizopus arrhizus biomass and the study of their metal affinity. This experimental approach, combined with an analytical method consisting of transforming the initial data enabled the calculation of the number and capacity of the reactive sites (Qads) and the metal affinity constants (Km) for lead sorption by R. arrhizus biomass. The pKm values for Rhizopus biomass varied between -3 and -6 for sites releasing no protons, -1 and 1 for sites releasing one proton, and > 8 for sites releasing two protons - combined with the Pb precipitation phenomenon. At low temperatures, the active binding site number was lower at lower lead concentrations whereas the precipitation was promoted at higher lead concentration values. Lead adsorption contributed modestly (11%) to its overall uptake and occurred at low lead concentrations onto strong and medium affinity binding sites. Micro-precipitation quickly commenced around active binding sites distinguished by their weak affinity whenever the solution lead concentrations reached 10(-6) or 10(-5) M and represented more than 85% of the total sorbed metal quantity. The work also demonstrated the usefulnes of the methodology reported here for characterizing complex biosorbent materials.

  6. Characterizing and modeling electrical response to light for metal-based EUV photoresists

    NASA Astrophysics Data System (ADS)

    Pret, Alessandro V.; Kocsis, Mike; De Simone, Danilo; Vandenberghe, Geert; Stowers, Jason; Giglia, Angelo; de Schepper, Peter; Mani, Antonio; Biafore, John J.

    2016-03-01

    Metal-based photoresists are appealing for use in EUV lithography due to their improved etch resistance and absorption compared with organic resists, and due to their resolving power demonstrated with 13.53 nm exposures using synchrotron light. Recently imec has started a new project to study novel photoresists for EUV lithography, with particular attention to metal containing materials, in order to explore alternative approaches that may offer superior characteristics in photoresist imaging and etching performance compared with more mature chemically amplified resists. In order to model these novel resists it is mandatory to understand both the optical properties and the electronic response to photon absorption. As in previous experiments on organic materials, some of the optical properties can be determined by merging analysis from high-energy electron scattering models (e.g. CXRO website), X-ray absorption spectroscopy, and DUV spectroscopic ellipsometry. Dispersion curves can be used to calculate the electronic inelastic and elastic mean-free paths; convolved with the expected spectrum at wafer level it is possible to estimate the electron yield and the secondary electron blur of the photoresist. These material properties can be used to modify the physical models currently used to simulate organic photoresist performance in computational lithography software.

  7. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  8. Reproducible direct exposure environmental testing of metal-based magnetic media

    NASA Technical Reports Server (NTRS)

    Sides, Paul J.

    1994-01-01

    A flow geometry and flow rate for mixed flowing gas testing is proposed. Use of an impinging jet of humid polluted air can provide a uniform and reproducible exposure of coupons of metal-based magnetic media. Numerical analysis of the fluid flow and mass transfer in such as system has shown that samples confined within a distance equal to the nozzle radius on the surface of impingement are uniformly accessible to pollutants in the impinging gas phase. The critical factor is the nozzle height above the surface of impingement. In particular, the uniformity of exposure is less than plus/minus 2% for a volumetric flow rate of 1600 cm(exp 3)/minute total flow with the following specifications: For a one inch nozzle, the height of the nozzle opening above the stage should be 0.177 inches; for a 2 inch nozzle - 0.390 inches. Not only is the distribution uniform, but one can calculate the maximum delivery rate of pollutants to the samples for comparison with the observed deterioration.

  9. Psychological Relevance and Information Science.

    ERIC Educational Resources Information Center

    Harter, Stephen P.

    1992-01-01

    Explores the theory of psychological relevance and its relationship to information retrieval, and provides an extended example. Topics discussed include information need, the search process, the nature of information, topical relevance, relevance judgments and retrieval testing, information retrieval and bibliometrics, and suggestions for further…

  10. A brief survey of sensing for metal-based powder bed fusion additive manufacturing

    NASA Astrophysics Data System (ADS)

    Foster, Bryant K.; Reutzel, Edward W.; Nassar, Abdalla R.; Dickman, Corey J.; Hall, Benjamin T.

    2015-05-01

    Purpose - Powder bed fusion additive manufacturing (PBFAM) of metal components has attracted much attention, but the inability to quickly and easily ensure quality has limited its industrial use. Since the technology is currently being investigated for critical engineered components and is largely considered unsuitable for high volume production, traditional statistical quality control methods cannot be readily applied. An alternative strategy for quality control is to monitor the build in real time with a variety of sensing methods and, when possible, to correct any defects as they occur. This article reviews the cause of common defects in powder bed additive manufacturing, briefly surveys process monitoring strategies in the literature, and summarizes recently-developed strategies to monitor part quality during the build process. Design/methodology/approach - Factors that affect part quality in powder bed additive manufacturing are categorized as those influenced by machine variables and those affected by other build attributes. Within each category, multiple process monitoring methods are presented. Findings - A multitude of factors contribute to the overall quality of a part built using PBFAM. Rather than limiting processing to a pre-defined build recipe and assuming complete repeatability, part quality will be ensured by monitoring the process as it occurs and, when possible, altering the process conditions or build plan in real-time. Recent work shows promise in this area and brings us closer to the goal of wide-spread adoption of additive manufacturing technology. Originality/value - This work serves to introduce and define the possible sources of defects and errors in metal-based PBFAM, and surveys sensing and control methods which have recently been investigated to increase overall part quality. Emphasis has been placed on novel developments in the field and their contribution to the understanding of the additive manufacturing process.

  11. Bacteriophage lambda: early pioneer and still relevant

    PubMed Central

    Casjens, Sherwood R.; Hendrix, Roger W.

    2015-01-01

    Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid 1950's to mid 1980's was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives have continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle. PMID:25742714

  12. Chromosomal data relevant for Q values

    NASA Astrophysics Data System (ADS)

    Edwards, A. A.

    1992-07-01

    It has been known for many years that relationships between absorbed dose and biological effect vary with the type of radiation. In particular, neutrons and alpha particles are more damaging than x or γ radiations. This applies to a range of biological effects such as cell killing, chromosome aberrations, cell mutation, cell transformation as well as life shortening and cancer induction in animals. The application of this knowledge to devise a scheme for specifying the quality factor (Q) in radiological protection has been the subject of much debate. There are no tumour data in humans from which the quality factor may be derived. The problems of using animal and cell transformation data which are probably the next best choice are discussed. The extensive data base on chromosomal aberrations in human lymphocytes is described and discussed in terms of relevance to deducing quality factors. Particular emphasis is placed on data obtained at low doses and low dose rates.

  13. Biological Technicians

    MedlinePlus

    ... Biological technicians typically need a bachelor’s degree in biology or a closely related field. It is important ... Biological technicians typically need a bachelor’s degree in biology or a closely related field. It is important ...

  14. Relevance in the science classroom: A multidimensional analysis

    NASA Astrophysics Data System (ADS)

    Hartwell, Matthew F.

    While perceived relevance is considered a fundamental component of adaptive learning, the experience of relevance and its conceptual definition have not been well described. The mixed-methods research presented in this dissertation aimed to clarify the conceptual meaning of relevance by focusing on its phenomenological experience from the students' perspective. Following a critical literature review, I propose an identity-based model of perceived relevance that includes three components: a contextual target, an identity target, and a connection type, or lens. An empirical investigation of this model that consisted of two general phases was implemented in four 9th grade-biology classrooms. Participants in Phase 1 (N = 118) completed a series of four open-ended writing activities focused on eliciting perceived personal connections to academic content. Exploratory qualitative content analysis of a 25% random sample of the student responses was used to identify the main meaning-units of the proposed model as well as different dimensions of student relevance perceptions. These meaning-units and dimensions provided the basis for the construction of a conceptual mapping sentence capturing students' perceived relevance, which was then applied in a confirmatory analysis to all other student responses. Participants in Phase 2 (N = 139) completed a closed survey designed based on the mapping sentence to assess their perceived relevance of a biology unit. The survey also included scales assessing other domain-level motivational processes. Exploratory factor analysis and non-metric multidimensional scaling indicated a coherent conceptual structure, which included a primary interpretive relevance dimension. Comparison of the conceptual structure across various groups (randomly-split sample, gender, academic level, domain-general motivational profiles) provided support for its ubiquity and insight into variation in the experience of perceived relevance among students of different

  15. Vibrations, quanta and biology

    NASA Astrophysics Data System (ADS)

    Huelga, S. F.; Plenio, M. B.

    2013-07-01

    Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental assumptions and questions in the field, identify basic design principles and develop a key underlying theme - the dynamics of quantum dynamical networks in the presence of an environment and the fruitful interplay that the two may enter. At the hand of three biological phenomena whose understanding is held to require quantum mechanical processes, namely excitation and charge transfer in photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for quantum biology.

  16. Acrylic and metal based Y-branch plastic optical fiber splitter with optical NOA63 polymer waveguide taper region

    NASA Astrophysics Data System (ADS)

    Ehsan, Abang Annuar; Shaari, Sahbudin; Rahman, Mohd Kamil Abd.

    2011-01-01

    We proposed a simple low-cost acrylic and metal-based Y-branch plastic optical fiber (POF) splitter which utilizes a low cost optical polymer glue NOA63 as the main waveguiding medium at the waveguide taper region. The device is composed of three sections: an input POF waveguide, a middle waveguide taper region and output POF waveguides. A desktop high speed CNC engraver is utilized to produce the mold inserts used for the optical devices. Short POF fibers are inserted into the engraved slots at the input and output ports. UV curable optical polymer glue NOA63 is injected into the waveguide taper region and cured. The assembling is completed when the top plate is positioned to enclose the device structure and connecting screws are secured. Both POF splitters have an average insertion loss of 7.8 dB, coupling ratio of 55: 45 and 57: 43 for the acrylic and metal-based splitters respectively. The devices have excess loss of 4.82 and 4.73 dB for the acrylic and metal-based splitters respectively.

  17. On the Existence of Our Metals-Based Civilization: I. Phase Space Analysis

    SciTech Connect

    D.D. Macdonald

    2005-06-22

    than are equilibrium thermodynamic diagrams. Thus, KSDs more accurately account for the limits of passivity in highly acidic systems, where acid depassivation occurs, and at high potentials, where transition to the transpassive state may occur in some systems. In any event, phase space analysis of the PDM permits specification of the conditions over which reactive metals will remain passive in contact with aqueous systems and hence of the conditions that must be met for the existence of our metals-based civilization.

  18. Is shared governance still relevant?

    PubMed

    Porter-O'Grady, T

    2001-10-01

    Is shared governance still relevant in this era of significant changes in healthcare? Requisites to support nurses and others are more important now than ever before. Shared decision-making is not only relevant, it is essential. The road to empowerment is not easy. Many patterns of organization and relationship must be changed forever through commitment and leadership today.

  19. Biological and Chemical Security

    SciTech Connect

    Fitch, P J

    2002-12-19

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

  20. Biological Filters.

    ERIC Educational Resources Information Center

    Klemetson, S. L.

    1978-01-01

    Presents the 1978 literature review of wastewater treatment. The review is concerned with biological filters, and it covers: (1) trickling filters; (2) rotating biological contractors; and (3) miscellaneous reactors. A list of 14 references is also presented. (HM)

  1. Biological Agents

    MedlinePlus

    ... to Z Index Contact Us FAQs What's New Biological Agents This page requires that javascript be enabled ... and Health Topics A-Z Index What's New Biological agents include bacteria, viruses, fungi, other microorganisms and ...

  2. [Biological markers of alcoholism].

    PubMed

    Marcos Martín, M; Pastor Encinas, I; Laso Guzmán, F J

    2005-09-01

    Diagnosis of alcoholism is very important, given its high prevalence and possibility of influencing the disease course. For this reason, the so-called biological markers of alcoholism are useful. These are analytic parameters that alter in the presence of excessive alcohol consumption. The two most relevant markers are the gamma-glutamyltranspeptidase and carbohydrate deficient transferrin. With this clinical comment, we aim to contribute to the knowledge of these tests and promote its use in the clinical practice. PMID:16194480

  3. A relevance theory of induction.

    PubMed

    Medin, Douglas L; Coley, John D; Storms, Gert; Hayes, Brett K

    2003-09-01

    A framework theory, organized around the principle of relevance, is proposed for category-based reasoning. According to the relevance principle, people assume that premises are informative with respect to conclusions. This idea leads to the prediction that people will use causal scenarios and property reinforcement strategies in inductive reasoning. These predictions are contrasted with both existing models and normative logic. Judgments of argument strength were gathered in three different countries, and the results showed the importance of both causal scenarios and property reinforcement in category-based inferences. The relation between the relevance framework and existing models of category-based inductive reasoning is discussed in the light of these findings.

  4. Trends in Ground-State Entropies for Transition Metal Based Hydrogen Atom Transfer Reactions

    SciTech Connect

    Mader, Elizabeth A.; Manner, Virginia W.; Markle, Todd F.; Wu, Adam; Franz, James A.; Mayer, James M.

    2009-03-10

    Reported herein are thermochemical studies of hydrogen atom transfer (HAT) reactions involving transition metal H-atom donors MIILH and oxyl radicals. [FeII(H2bip)3]2+, [FeII(H2bim)3]2+, [CoII(H2bim)3]2+ and RuII(acac)2(py-imH) [H2bip = 2,2’-bi-1,4,5,6-tetrahydro¬pyrimidine, H2bim = 2,2’-bi-imidazoline, acac = 2,4-pentandionato, py-imH = 2-(2’-pyridyl)¬imidazole)] each react with TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) or tBu3PhO• (2,4,6-tri-tert-butylphenoxyl) to give the deprotonated, oxidized metal complex MIIIL, and TEMPOH or tBu3PhOH. Solution equilibrium measurements for the reactions of Co and Fe complexes with TEMPO show a large, negative ground-state entropy for hydrogen atom transfer: ΔSºHAT = -30 ± 2 cal mol-1 K-1 for the two iron complexes and -41 ± 2 cal mol-1 K-1 for [CoII(H2bim)3]2+. The ΔSºHAT for TEMPO + RuII(acac)2(py-imH) is much closer to zero, 4.9 ± 1.1 cal mol-1 K-1. Calorimetric measurements quantitatively confirm the enthalpy of reaction for [FeII(H2bip)3]2+ + TEMPO, thus also confirming ΔSºHAT. Calorimetry on TEMPOH + tBu3PhO• gives ΔHºHAT = 11.2 ± 0.5 kcal mol-1 which matches the enthalpy predicted from the difference in literature solution BDEs. An evaluation of the literature BDEs of both TEMPOH and tBu3PhOH is briefly presented and new estimates are included on the relative enthalpy of solvation for tBu3PhO• vs. tBu3PhOH. The primary contributor to the large magnitude of the ground-state entropy |ΔSºHAT| for the metal complexes is vibrational entropy, ΔSºvib. The common assumption that ΔSºHAT ≈ 0 for HAT reactions, developed for organic and small gas phase molecules, does not hold for transition metal based HAT reactions. The trend in magnitude of |ΔSºHAT| for reactions with TEMPO, RuII(acac)2(py-imH) << [FeII(H2bip)3]2+ = [FeII(H2bim)3]2+ < [CoII(H2bim)3]2+, is surprisingly well predicted by the trends for electron transfer half-reaction entropies, ΔSºET, in aprotic solvents. ΔSºET and

  5. Putative adverse outcome pathways relevant to neurotoxicity

    PubMed Central

    Bal-Price, Anna; Crofton, Kevin M.; Sachana, Magdalini; Shafer, Timothy J.; Behl, Mamta; Forsby, Anna; Hargreaves, Alan; Landesmann, Brigitte; Lein, Pamela J.; Louisse, Jochem; Monnet-Tschudi, Florianne; Paini, Alicia; Rolaki, Alexandra; Schrattenholz, André; Suñol, Cristina; van Thriel, Christoph; Whelan, Maurice; Fritsche, Ellen

    2016-01-01

    The Adverse Outcome Pathway (AOP) framework provides a template that facilitates understanding of complex biological systems and the pathways of toxicity that result in adverse outcomes (AOs). The AOP starts with an molecular initiating event (MIE) in which a chemical interacts with a biological target(s), followed by a sequential series of KEs, which are cellular, anatomical, and/or functional changes in biological processes, that ultimately result in an AO manifest in individual organisms and populations. It has been developed as a tool for a knowledge-based safety assessment that relies on understanding mechanisms of toxicity, rather than simply observing its adverse outcome. A large number of cellular and molecular processes are known to be crucial to proper development and function of the central (CNS) and peripheral nervous systems (PNS). However, there are relatively few examples of well-documented pathways that include causally linked MIEs and KEs that result in adverse outcomes in the CNS or PNS. As a first step in applying the AOP framework to adverse health outcomes associated with exposure to exogenous neurotoxic substances, the EU Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM) organized a workshop (March 2013, Ispra, Italy) to identify potential AOPs relevant to neurotoxic and developmental neurotoxic outcomes. Although the AOPs outlined during the workshop are not fully described, they could serve as a basis for further, more detailed AOP development and evaluation that could be useful to support human health risk assessment in a variety of ways. PMID:25605028

  6. Relevance theory: pragmatics and cognition.

    PubMed

    Wearing, Catherine J

    2015-01-01

    Relevance Theory is a cognitively oriented theory of pragmatics, i.e., a theory of language use. It builds on the seminal work of H.P. Grice(1) to develop a pragmatic theory which is at once philosophically sensitive and empirically plausible (in both psychological and evolutionary terms). This entry reviews the central commitments and chief contributions of Relevance Theory, including its Gricean commitment to the centrality of intention-reading and inference in communication; the cognitively grounded notion of relevance which provides the mechanism for explaining pragmatic interpretation as an intention-driven, inferential process; and several key applications of the theory (lexical pragmatics, metaphor and irony, procedural meaning). Relevance Theory is an important contribution to our understanding of the pragmatics of communication.

  7. [Biological weapons].

    PubMed

    Kerwat, K; Becker, S; Wulf, H; Densow, D

    2010-08-01

    Biological weapons are weapons of mass destruction that use pathogens (bacteria, viruses) or the toxins produced by them to target living organisms or to contaminate non-living substances. In the past, biological warfare has been repeatedly used. Anthrax, plague and smallpox are regarded as the most dangerous biological weapons by various institutions. Nowadays it seems quite unlikely that biological warfare will be employed in any military campaigns. However, the possibility remains that biological weapons may be used in acts of bioterrorism. In addition all diseases caused by biological weapons may also occur naturally or as a result of a laboratory accident. Risk assessment with regard to biological danger often proves to be difficult. In this context, an early identification of a potentially dangerous situation through experts is essential to limit the degree of damage.

  8. The Upside to Hg-DOM Associations for Water Quality: Removal of Hg from Solution Using Coagulaion with Metal-Based Salts

    NASA Astrophysics Data System (ADS)

    Henneberry, Y.; Kraus, T. E.; Fleck, J.; Krabbenhoft, D. P.; Horwath, W. R.

    2011-12-01

    This study assessed the potential use of metal-based coagulants to remove dissolved mercury (Hg) from natural waters and provides information regarding the importance of Hg associations with the dissolved organic matter (DOM) fraction and metal hydroxides. Previous research indicated coagulants were not effective at removing Hg from solution; however those studies used high concentrations of Hg, which did not reflect naturally occurring concentrations of Hg. Filtered water collected from an agricultural drain in the Sacramento-San Joaquin Delta (Delta) was treated with three industrial-grade coagulants (ferric chloride, ferric sulfate, and polyaluminum chloride) to determine their efficacy in removing both inroganic (IHg) and methylmercury (MeHg) from the water column. The Delta suffers from elevated surface water Hg concentrations and as a result is listed as an imparied water body. Coagulants removed up to 85% of DOM from solution. In the absence of DOM, all three coagulants released IHg into solution, however in the presence of DOM the coagulants removed up to 97% of IHg and 80% of MeHg. Results suggest that the removal of Hg is mediated by DOM-coagulant interactions. There was a preferential association of IHg with the more aromatic, higher molecular weight fraction of DOM but no such relationship was found for MeHg. This study offers new fundamental insights regarding large-scale removal of Hg at environmentally relevant concentrations. Research using isotopically labeled Hg is providing insight into whether coagulation can remove recently added Hg (e.g. atmospheric deposition) from solution and whether once formed, the floc can remove additional Hg from the water column.

  9. Systems Biology

    SciTech Connect

    Wiley, H S.

    2006-06-01

    The biology revolution over the last 50 years has been driven by the ascendancy of molecular biology. This was enthusiastically embraced by most biologists because it took us into increasingly familiar territory. It took mysterious processes, such as the replication of genetic material and assigned them parts that could be readily understood by the human mind. When we think of ''molecular machines'' as being the underlying basis of life, we are using a paradigm derived from everyday experience. However, the price that we paid was a relentless drive towards reductionism and the attendant balkanization of biology. Now along comes ''systems biology'' that promises us a solution to the problem of ''knowing more and more about less and less''. Unlike molecular biology, systems biology appears to be taking us into unfamiliar intellectual territory, such as statistics, mathematics and computer modeling. Not surprisingly, systems biology has met with widespread skepticism and resistance. Why do we need systems biology anyway and how does this new area of research promise to change the face of biology in the next couple of decades?

  10. Amyloid Polymorphism: Structural Basis and Neurobiological Relevance

    PubMed Central

    Tycko, Robert

    2015-01-01

    Summary Our understanding of the molecular structures of amyloid fibrils that are associated with neurodegenerative diseases, of mechanisms by which disease-associated peptides and proteins aggregate into fibrils, and of structural properties of aggregation intermediates has advanced considerably in recent years. Detailed molecular structural models for certain fibrils and aggregation intermediates are now available. It is now well established that amyloid fibrils are generally polymorphic at the molecular level, with a given peptide or protein being capable of forming a variety of distinct, self-propagating fibril structures. Recent results from structural studies and from studies involving cell cultures, transgenic animals, and human tissue provide initial evidence that molecular structural variations in amyloid fibrils and related aggregates may correlate with or even produce variations in disease development. This article reviews our current knowledge of the structural and mechanistic aspects of amyloid formation, as well as current evidence for the biological relevance of structural variations. PMID:25950632

  11. Mathematical modeling relevant to closed artificial ecosystems

    USGS Publications Warehouse

    DeAngelis, D.L.

    2003-01-01

    The mathematical modeling of ecosystems has contributed much to the understanding of the dynamics of such systems. Ecosystems can include not only the natural variety, but also artificial systems designed and controlled by humans. These can range from agricultural systems and activated sludge plants, down to mesocosms, microcosms, and aquaria, which may have practical or research applications. Some purposes may require the design of systems that are completely closed, as far as material cycling is concerned. In all cases, mathematical modeling can help not only to understand the dynamics of the system, but also to design methods of control to keep the system operating in desired ranges. This paper reviews mathematical modeling relevant to the simulation and control of closed or semi-closed artificial ecosystems designed for biological production and recycling in applications in space. Published by Elsevier Science Ltd on behalf of COSPAR.

  12. Evolutionary Design in Biology

    NASA Astrophysics Data System (ADS)

    Wiese, Kay C.

    computational intelligence (CI). While biological systems have helped to develop many of the computational paradigms in CI, CI is now returning the favor to help solve some of the most challenging biological mysteries itself. In many cases these probabilistic methods can produce biologically relevant results where exact deterministic methods fail. For an extensive overview of successful applications of CI algorithms to problems in bioinformatics please refer to [1].

  13. The aesthetics of chemical biology.

    PubMed

    Parsons, Glenn

    2012-12-01

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

  14. Mn in misch-metal based superlattice metal hydride alloy - Part 1 structural, hydrogen storage and electrochemical properties

    NASA Astrophysics Data System (ADS)

    Young, K.; Wong, D. F.; Wang, L.; Nei, J.; Ouchi, T.; Yasuoka, S.

    2015-03-01

    The structural, gaseous phase hydrogen storage, and electrochemical properties of a series of Mn-modified misch-metal based superlattice metal hydride alloys were investigated in part one of this two-part series of papers. X-ray diffraction analysis showed that these alloys are all multi-phased compositions with different abundances of AB2, AB3, A2B7, AB4, and AB5 phases. Substitution of Ni in the B-site by Mn promotes AB5 phase formation and decreases both gaseous phase and electrochemical capacities due to the reduction in the abundance of main hexagonal A2B7 phase. AC impedance and magnetic susceptibility measurement were employed to characterize the surface of Mn-free and Mn-modified alloys and show deterioration in surface catalytic ability as the Mn-content increases. Mn-modification adversely affected misch-metal based superlattice metal hydride alloy properties such as phase homogeneity, capacity, cycle stability, high-rate performance, and surface reaction.

  15. Interactions of metal-based engineered nanoparticles with aquatic higher plants: A review of the state of current knowledge.

    PubMed

    Thwala, Melusi; Klaine, Stephen J; Musee, Ndeke

    2016-07-01

    The rising potential for the release of engineered nanoparticles (ENPs) into aquatic environments requires evaluation of risks to protect ecological health. The present review examines knowledge pertaining to the interactions of metal-based ENPs with aquatic higher plants, identifies information gaps, and raises considerations for future research to advance knowledge on the subject. The discussion focuses on ENPs' bioaccessibility; uptake, adsorption, translocation, and bioaccumulation; and toxicity effects on aquatic higher plants. An information deficit surrounds the uptake of ENPs and associated dynamics, because the influence of ENP characteristics and water quality conditions has not been well documented. Dissolution appears to be a key mechanism driving bioaccumulation of ENPs, whereas nanoparticulates often adsorb to plant surfaces with minimal internalization. However, few reports document the internalization of ENPs by plants; thus, the role of nanoparticulates' internalization in bioaccumulation and toxicity remains unclear, requiring further investigation. The toxicities of metal-based ENPs mainly have been associated with dissolution as a predominant mechanism, although nano toxicity has also been reported. To advance knowledge in this domain, future investigations need to integrate the influence of ENP characteristics and water physicochemical parameters, as their interplay determines ENP bioaccessibility and influences their risk to health of aquatic higher plants. Furthermore, harmonization of test protocols is recommended for fast tracking the generation of comparable data. Environ Toxicol Chem 2016;35:1677-1694. © 2016 SETAC. PMID:26757140

  16. Anatomy relevant to conservative mastectomy

    PubMed Central

    O’Connell, Rachel L.

    2015-01-01

    Knowledge of the anatomy of the nipple and breast skin is fundamental to any surgeon practicing conservative mastectomies. In this paper, the relevant clinical anatomy will be described, mainly focusing on the anatomy of the “oncoplastic plane”, the ducts and the vasculature. We will also cover more briefly the nerve supply and the arrangement of smooth muscle of the nipple. Finally the lymphatic drainage of the nipple and areola will be described. An appreciation of the relevant anatomy, together with meticulous surgical technique may minimise local recurrence and ischaemic complications. PMID:26645002

  17. Anatomy relevant to conservative mastectomy.

    PubMed

    O'Connell, Rachel L; Rusby, Jennifer E

    2015-12-01

    Knowledge of the anatomy of the nipple and breast skin is fundamental to any surgeon practicing conservative mastectomies. In this paper, the relevant clinical anatomy will be described, mainly focusing on the anatomy of the "oncoplastic plane", the ducts and the vasculature. We will also cover more briefly the nerve supply and the arrangement of smooth muscle of the nipple. Finally the lymphatic drainage of the nipple and areola will be described. An appreciation of the relevant anatomy, together with meticulous surgical technique may minimise local recurrence and ischaemic complications. PMID:26645002

  18. Is synthetic biology mechanical biology?

    PubMed

    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.

  19. Recent progress in histochemistry and cell biology.

    PubMed

    Hübner, Stefan; Efthymiadis, Athina

    2012-04-01

    Studies published in Histochemistry and Cell Biology in the year 2011 represent once more a manifest of established and newly sophisticated techniques being exploited to put tissue- and cell type-specific molecules into a functional context. The review is therefore the Histochemistry and Cell Biology's yearly intention to provide interested readers appropriate summaries of investigations touching the areas of tissue biology, developmental biology, the biology of the immune system, stem cell research, the biology of subcellular compartments, in order to put the message of such studies into natural scientific-/human- and also pathological-relevant correlations.

  20. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including use of dwarf cichlids (fishes) in secondary school biology, teaching edge effects on stomatal diffusion, computer program on effects of selection on gene frequencies, biological oxidation/reduction reactions, short cuts with Drosophila, computer program…

  1. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1978

    1978-01-01

    Presents experiments, demonstrations, activities and ideas relating to various fields of biology to be used in biology courses in secondary schools. Among those experiments presented are demonstrating the early stages of ferns and mosses and simple culture methods for fern prothalli. (HM)

  2. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

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

  3. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including chi-square tests on a microcomputer, an integrated biology game, microscope slides of leaf stomata, culturing soil nematodes, technique for watering locust egg-laying tubes, hazards of biological chemicals (such as benzene, benzidene, calchicine,…

  4. Medical Scenarios Relevant to Spaceflight

    NASA Technical Reports Server (NTRS)

    Bacal, Kira; Hurs, Victor; Doerr, Harold

    2004-01-01

    The Medical Operational Support Team (MOST) was tasked by the JSC Space Medicine and Life Sciences Directorate (SLSD) to incorporate medical simulation into 1) medical training for astronaut-crew medical officers (CMO) and medical flight control teams and 2) evaluations of procedures and resources required for medical care aboard the International Space Station (ISS). Development of evidence-based medical scenarios that mimic the physiology observed during spaceflight will be needed for the MOST to complete these two tasks. The MOST used a human patient simulator, the ISS-like resources in the Medical Simulation Laboratory (MSL), and evidence from space operations, military operations and medical literature to develop space relevant medical scenarios. These scenarios include conditions concerning airway management, Advanced Cardiac Life Support (ACLS) and mitigating anaphylactic symptoms. The MOST has used these space relevant medical scenarios to develop a preliminary space medical training regimen for NASA flight surgeons, Biomedical Flight Controllers (Biomedical Engineers; BME) and CMO-analogs. This regimen is conducted by the MOST in the MSL. The MOST has the capability to develop evidence-based space-relevant medical scenarios that can help SLSD I) demonstrate the proficiency of medical flight control teams to mitigate space-relevant medical events and 2) validate nextgeneration medical equipment and procedures for space medicine applications.

  5. What's Relevant in Classical Literature?

    ERIC Educational Resources Information Center

    Hickman, Sara

    1970-01-01

    Argues the relevance of various aspects of the Thebian trilogy, "The Iliad," The Odyssey," Great Expectations," and Hamlet" to the concerns of today's high school students; a paper presented at annual convention of National Council of Teachers of English (59th, Washington, D.C., November 29, 1969). (RD)

  6. Biological clocks and the practice of psychiatry

    PubMed Central

    Schulz, Pierre

    2007-01-01

    Endogenous biological clocks enable living species to acquire some independence in relation to time. They improve the efficiency of biological systems, by allowing them to anticipate future constraints on major physyological systems and cell energy metabolism. The temporal organization of a giwen biological function can be impaired in its coordination with astronomical time or with other biological function. There are also external conditions that influence biological clocks. This temporal organization is complex, and it is possible that a series of psychiatric disorders and syndromes involve primary or secondary changes in biological clocks: seasonal and other mood disorders, premenstrual syndromes, social jet lag, free-running rhythms, and several sleep disorders are among them. In this review, we describe the main concepts relevant to chronobiology and explore the relevance of knowledge about biological clocks to the clinical practice of psychiatry PMID:17969862

  7. [Advance in the bioavailability monitoring of heavy metal based on microbial whole-cell sensor].

    PubMed

    Hou, Qi-Hui; Ma, An-Shou; Zhuang, Xiu-Liang; Zhuang, Guo-Qiang

    2013-01-01

    Microbial whole-cell biosensor is an excellent tool to assess the bioavailability of heavy metal in soil and water. However, the traditional physicochemical instruments are applied to detect the total metal. Furthermore, microbial whole-cell biosensor is simple, rapid and economical in manipulating, and is thus a highly qualified candidate for emergency detection of pollution incidents. The biological component of microbial whole-cell biosensor mostly consists of metalloregulatory proteins and reporter genes. In detail, metalloregulatory proteins mainly include the MerR family, ArsR family and RS family, and reporter genes mainly include gfp, lux and luc. Metalloregulatory protein and reporter gene are related to the sensitivity, specificity and properties in monitoring. The bioavailability of heavy metals is alterable under different conditions, influenced by pH, chelate and detection methods and so on. Increasing the accumulation of intracellular heavy metal, modifying the metalloregulatory proteins and optimizing the detecting conditions are important for improving the sensitivity, specificity and accuracy of the microbial whole-cell biosensor. The future direction of microbial whole-cell biosensor is to realize the monitoring of pollutions in situ and on line.

  8. Highly stable liquid metal-based pressure sensor integrated with a microfluidic channel.

    PubMed

    Jung, Taekeon; Yang, Sung

    2015-05-21

    Pressure measurement is considered one of the key parameters in microfluidic systems. It has been widely used in various fields, such as in biology and biomedical fields. The electrical measurement method is the most widely investigated; however, it is unsuitable for microfluidic systems because of a complicated fabrication process and difficult integration. Moreover, it is generally damaged by large deflection. This paper proposes a thin-film-based pressure sensor that is free from these limitations, using a liquid metal called galinstan. The proposed pressure sensor is easily integrated into a microfluidic system using soft lithography because galinstan exists in a liquid phase at room temperature. We investigated the characteristics of the proposed pressure sensor by calibrating for a pressure range from 0 to 230 kPa (R2 > 0.98) using deionized water. Furthermore, the viscosity of various fluid samples was measured for a shear-rate range of 30-1000 s(-1). The results of Newtonian and non-Newtonian fluids were evaluated using a commercial viscometer and normalized difference was found to be less than 5.1% and 7.0%, respectively. The galinstan-based pressure sensor can be used in various microfluidic systems for long-term monitoring with high linearity, repeatability, and long-term stability.

  9. New metal based drugs: spectral, electrochemical, DNA-binding, surface morphology and anticancer activity properties.

    PubMed

    Çeşme, Mustafa; Gölcü, Aysegul; Demirtaş, Ibrahim

    2015-01-25

    The NSAID piroxicam (PRX) drug was used for complex formation reactions with Cu(II), Zn(II) and Pt(II) metal salts have been synthesized. Then, these complexes have been characterized by spectroscopic and analytical techniques. Thermal behavior of the complexes were also investigated. The electrochemical properties of all complexes have been investigated by cyclic voltammetry (CV) using glassy carbon electrode. The biological activity of the complexes has been evaluated by examining their ability to bind to fish sperm double strand DNA (FSFSdsDNA) with UV spectroscopy. UV studies of the interaction of the PRX and its complexes with FSdsDNA have shown that these compounds can bind to FSdsDNA. The binding constants of the compounds with FSdsDNA have also been calculated. The morphology of the FSdsDNA, PRX, metal ions and metal complexes has been investigated by scanning electron microscopy (SEM). To get the SEM images, the interaction of compounds with FSdsDNA has been studied by means of differential pulse voltammetry (DPV) at FSdsDNA modified pencil graphite electrode (PGE). The decrease in intensity of the guanine oxidation signals has been used as an indicator for the interaction mechanism. The effect of proliferation PRX and complexes were examined on the HeLA and C6 cells using real-time cell analyzer with four different concentrations.

  10. Highly Stable Liquid Metal-Based Pressure Sensor Integrated with a Microfluidic Channel

    PubMed Central

    Jung, Taekeon; Yang, Sung

    2015-01-01

    Pressure measurement is considered one of the key parameters in microfluidic systems. It has been widely used in various fields, such as in biology and biomedical fields. The electrical measurement method is the most widely investigated; however, it is unsuitable for microfluidic systems because of a complicated fabrication process and difficult integration. Moreover, it is generally damaged by large deflection. This paper proposes a thin-film-based pressure sensor that is free from these limitations, using a liquid metal called galinstan. The proposed pressure sensor is easily integrated into a microfluidic system using soft lithography because galinstan exists in a liquid phase at room temperature. We investigated the characteristics of the proposed pressure sensor by calibrating for a pressure range from 0 to 230 kPa (R2 > 0.98) using deionized water. Furthermore, the viscosity of various fluid samples was measured for a shear-rate range of 30–1000 s−1. The results of Newtonian and non-Newtonian fluids were evaluated using a commercial viscometer and normalized difference was found to be less than 5.1% and 7.0%, respectively. The galinstan-based pressure sensor can be used in various microfluidic systems for long-term monitoring with high linearity, repeatability, and long-term stability. PMID:26007732

  11. Highly stable liquid metal-based pressure sensor integrated with a microfluidic channel.

    PubMed

    Jung, Taekeon; Yang, Sung

    2015-01-01

    Pressure measurement is considered one of the key parameters in microfluidic systems. It has been widely used in various fields, such as in biology and biomedical fields. The electrical measurement method is the most widely investigated; however, it is unsuitable for microfluidic systems because of a complicated fabrication process and difficult integration. Moreover, it is generally damaged by large deflection. This paper proposes a thin-film-based pressure sensor that is free from these limitations, using a liquid metal called galinstan. The proposed pressure sensor is easily integrated into a microfluidic system using soft lithography because galinstan exists in a liquid phase at room temperature. We investigated the characteristics of the proposed pressure sensor by calibrating for a pressure range from 0 to 230 kPa (R2 > 0.98) using deionized water. Furthermore, the viscosity of various fluid samples was measured for a shear-rate range of 30-1000 s(-1). The results of Newtonian and non-Newtonian fluids were evaluated using a commercial viscometer and normalized difference was found to be less than 5.1% and 7.0%, respectively. The galinstan-based pressure sensor can be used in various microfluidic systems for long-term monitoring with high linearity, repeatability, and long-term stability. PMID:26007732

  12. [Advance in the bioavailability monitoring of heavy metal based on microbial whole-cell sensor].

    PubMed

    Hou, Qi-Hui; Ma, An-Shou; Zhuang, Xiu-Liang; Zhuang, Guo-Qiang

    2013-01-01

    Microbial whole-cell biosensor is an excellent tool to assess the bioavailability of heavy metal in soil and water. However, the traditional physicochemical instruments are applied to detect the total metal. Furthermore, microbial whole-cell biosensor is simple, rapid and economical in manipulating, and is thus a highly qualified candidate for emergency detection of pollution incidents. The biological component of microbial whole-cell biosensor mostly consists of metalloregulatory proteins and reporter genes. In detail, metalloregulatory proteins mainly include the MerR family, ArsR family and RS family, and reporter genes mainly include gfp, lux and luc. Metalloregulatory protein and reporter gene are related to the sensitivity, specificity and properties in monitoring. The bioavailability of heavy metals is alterable under different conditions, influenced by pH, chelate and detection methods and so on. Increasing the accumulation of intracellular heavy metal, modifying the metalloregulatory proteins and optimizing the detecting conditions are important for improving the sensitivity, specificity and accuracy of the microbial whole-cell biosensor. The future direction of microbial whole-cell biosensor is to realize the monitoring of pollutions in situ and on line. PMID:23487961

  13. New metal based drugs: Spectral, electrochemical, DNA-binding, surface morphology and anticancer activity properties

    NASA Astrophysics Data System (ADS)

    Çeşme, Mustafa; Gölcü, Aysegul; Demirtaş, Ibrahim

    2015-01-01

    The NSAID piroxicam (PRX) drug was used for complex formation reactions with Cu(II), Zn(II) and Pt(II) metal salts have been synthesized. Then, these complexes have been characterized by spectroscopic and analytical techniques. Thermal behavior of the complexes were also investigated. The electrochemical properties of all complexes have been investigated by cyclic voltammetry (CV) using glassy carbon electrode. The biological activity of the complexes has been evaluated by examining their ability to bind to fish sperm double strand DNA (FSFSdsDNA) with UV spectroscopy. UV studies of the interaction of the PRX and its complexes with FSdsDNA have shown that these compounds can bind to FSdsDNA. The binding constants of the compounds with FSdsDNA have also been calculated. The morphology of the FSdsDNA, PRX, metal ions and metal complexes has been investigated by scanning electron microscopy (SEM). To get the SEM images, the interaction of compounds with FSdsDNA has been studied by means of differential pulse voltammetry (DPV) at FSdsDNA modified pencil graphite electrode (PGE). The decrease in intensity of the guanine oxidation signals has been used as an indicator for the interaction mechanism. The effect of proliferation PRX and complexes were examined on the HeLA and C6 cells using real-time cell analyzer with four different concentrations.

  14. The renaissance of developmental biology.

    PubMed

    St Johnston, Daniel

    2015-05-01

    Since its heyday in the 1980s and 90s, the field of developmental biology has gone into decline; in part because it has been eclipsed by the rise of genomics and stem cell biology, and in part because it has seemed less pertinent in an era with so much focus on translational impact. In this essay, I argue that recent progress in genome-wide analyses and stem cell research, coupled with technological advances in imaging and genome editing, have created the conditions for the renaissance of a new wave of developmental biology with greater translational relevance.

  15. Biological Oceanography

    NASA Astrophysics Data System (ADS)

    Dyhrman, Sonya

    2004-10-01

    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  16. BIOLOGICAL WARFARE

    PubMed Central

    Beeston, John

    1953-01-01

    The use of biological agents as controlled weapons of war is practical although uncertain. Three types of agents are feasible, including pathogenic organisms and biological pests, toxins, and synthetic hormones regulating plant growth. These agents may be chosen for selective effects varying from prolonged incipient illness to death of plants, man and domestic animals. For specific preventive and control measures required to combat these situations, there must be careful and detailed planning. The nucleus of such a program is available within the existing framework of public health activities. Additional research and expansion of established activities in time of attack are necessary parts of biological warfare defense. PMID:13059641

  17. Biological post

    PubMed Central

    Kumar, B. Suresh; Kumar, Senthil; Mohan Kumar, N. S.; Karunakaran, J. V.

    2015-01-01

    Anterior tooth fracture as a result of traumatic injuries, is frequently encountered in endodontic practice. Proper reconstruction of extensively damaged teeth can be achieved through the fragment reattachment procedure known as “biological restoration.” This case report refers to the esthetics and functional recovery of extensively damaged maxillary central incisor through the preparation and adhesive cementation of “biological post” in a young patient. Biological post obtained through extracted teeth from another individual–represent a low-cost option and alternative technique for the morphofunctional recovery of extensively damaged anterior teeth. PMID:26538952

  18. The architectural relevance of cybernetics

    SciTech Connect

    Frazer, J.H.

    1993-12-31

    This title is taken from an article by Gordon Pask in Architectural Design September 1969. It raises a number of questions which this article attempts to answer. How did Gordon come to be writing for an architectural publication? What was his contribution to architecture? How does he now come to be on the faculty of a school of architecture? And what indeed is the architectural relevance of cybernetics? 12 refs.

  19. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Twelve new experiments in biology are described by teachers for use in classrooms. Broad areas covered include enzyme action, growth regulation, microscopy, respiration, germination, plant succession, leaf structure and blood structure. Explanations are detailed. (PS)

  20. Bottle Biology.

    ERIC Educational Resources Information Center

    CSTA Journal, 1995

    1995-01-01

    Provides hands-on biology activities using plastic bottles that allow students to become engaged in asking questions, creating experiments, testing hypotheses, and generating answers. Activities explore terrestrial and aquatic systems. (MKR)

  1. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1973

    1973-01-01

    Some helpful ideas are proposed for use by biology teachers. Topics included are Food Webs,'' Key to Identification of Families,'' Viruses,'' Sieve Tube,'' Woodlice,'' Ecology of Oak Leaf Roller Moth,'' and Model Making.'' (PS)

  2. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Ten ideas that have been tried out by the authors in schools are presented for biology teachers. The areas covered include genetics, dispersal of seeds, habituation in earthworms, respiration, sensory neurons, fats and oils. A reading list is provided. (PS)

  3. Approaches to chemical synthetic biology.

    PubMed

    Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

    2012-07-16

    Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology.

  4. Biology of Pseudomonas stutzeri

    PubMed Central

    Lalucat, Jorge; Bennasar, Antoni; Bosch, Rafael; García-Valdés, Elena; Palleroni, Norberto J.

    2006-01-01

    Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri. PMID:16760312

  5. Walking: technology and biology.

    PubMed

    Pfeiffer, Friedrich; Inoue, Hirochika

    2007-01-15

    If all the signs are to be believed, then the twenty-first century will technologically be characterized by machine walking and its relevant products, which possess all chances to become real bulk goods in the course of the next decades. With several university institutes and with Honda and Sony from the industrial side, Japan is today and without any doubt the leading nation in research and development of walking machines. The US and Europe follow at some distance. Walking machines will influence all areas of daily and industrial life and, with the fast evolution of artificial intelligence, will become a real partner of human beings. All relevant technologies are highly interdisciplinary, they will push the future technologies of all technical fields. The special issue on this topic gives a selection of walking machine research and development including some aspects from biology.

  6. Biology of Immunoglobulins

    PubMed Central

    Berlot, Giorgio; Rossini, Perla; Turchet, Federica

    2015-01-01

    Intravenous Immunoglobulins (IvIg) are often administered to critically ill patients more as an act of faith than on the basis of relevant clinical studies. This particularly applies to the treatment of sepsis in adult patients, in whom the current guidelines even recommend against their use, despite that many studies demonstrated either their beneficial effects in different subsets of patients and that some preparations of IvIg are more effective than other. The biology of Ig are reviewed, aiming to a more in-depth understanding of their properties in order to clarify their possible indications in different clinical settings. PMID:25674545

  7. Industrialization of Biology.

    PubMed

    Friedman, Douglas C; Ellington, Andrew D

    2015-10-16

    The advancement of synthetic biology over the past decade has contributed substantially to the growing bioeconomy. A recent report by the National Academies highlighted several areas of advancement that will be needed for further expansion of industrial biotechnology, including new focuses on design, feedstocks, processing, organism development, and tools for testing and measurement; more particularly, a focus on expanded chassis and end-to-end design in an effort to move beyond the use of E. coli and S. cerivisiea to organisms better suited to fermentation and production; second, continued efforts in systems biology and high-throughput screening with a focus on more rapid techniques that will provide the needed information for moving to larger scale; and finally, work to accelerate the building of a holacratic community with collaboration and engagement between the relevant government agencies, industry, academia, and the public.

  8. Bayes in biological anthropology.

    PubMed

    Konigsberg, Lyle W; Frankenberg, Susan R

    2013-12-01

    In this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available.

  9. Crossing Boundaries in Undergraduate Biology Education

    ERIC Educational Resources Information Center

    Vanderklein, Dirk; Munakata, Mika; McManus, Jason

    2016-01-01

    In an effort to make mathematics relevant to biology students, the authors developed two modules that sought to integrate mathematics and ecology instruction to differing degrees. The modules were developed by a team of biology and mathematics educators and were implemented in an ecology course using three different instructional methods for three…

  10. 78 FR 16472 - Deposit of Biological Materials

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-15

    ... of the invention sufficient to enable a person (knowledgeable in the relevant science), to make and use the invention as specified by 35 U.S.C. 112. The term ``biological material'' is defined by 37 CFR... the invention involves a biological material, sometimes words and figures are not sufficient...

  11. Exemplary Programs in Secondary School Biology.

    ERIC Educational Resources Information Center

    McComas, William F.; Penick, John E.

    1989-01-01

    Summarizes 10 exemplary programs which address topics on individualized biology, a modified team approach, limnology, physical anthropology, the relevance of biology to society, ecology, and health. Provides names and addresses of contact persons for further information. Units cover a broad range of abilities and activities. (RT)

  12. The self-relevance system?

    PubMed

    Conway, Martin A; Pothos, Emmanuel M; Turk, David J

    2016-01-01

    We suggest that the Self Attention Network (SAN) maybe part of a larger self-regulatory system, which we term the Self-Relevance System (SRS) of which the "core" or default network is a major part. It is within the core network that memories are generated and the future imagined. Such memories and imaginings are the basis of preoccupations. Within the SRS then preoccupations drive the emergence of attentional biases (ABs). ABs in turn are modulated by the SAN activating and inhibiting circuits that shape behavior. We consider briefly how this might function in dysfunctional appetitive behaviors, e.g., substance abuse. PMID:26305290

  13. Relevance of nutrient media composition for hydrogen production in Chlamydomonas.

    PubMed

    Gonzalez-Ballester, David; Jurado-Oller, Jose Luis; Fernandez, Emilio

    2015-09-01

    Microalgae are capable of biological H2 photoproduction from water, solar energy, and a variety of organic substrates. Acclimation responses to different nutrient regimes finely control photosynthetic activity and can influence H2 production. Hence, nutrient stresses are an interesting scenario to study H2 production in photosynthetic organisms. In this review, we mainly focus on the H2-production mechanisms in Chlamydomonas reinhardtii and the physiological relevance of the nutrient media composition when producing H2.

  14. Relevance of nutrient media composition for hydrogen production in Chlamydomonas.

    PubMed

    Gonzalez-Ballester, David; Jurado-Oller, Jose Luis; Fernandez, Emilio

    2015-09-01

    Microalgae are capable of biological H2 photoproduction from water, solar energy, and a variety of organic substrates. Acclimation responses to different nutrient regimes finely control photosynthetic activity and can influence H2 production. Hence, nutrient stresses are an interesting scenario to study H2 production in photosynthetic organisms. In this review, we mainly focus on the H2-production mechanisms in Chlamydomonas reinhardtii and the physiological relevance of the nutrient media composition when producing H2. PMID:25952745

  15. Literature relevant to remote sensing of water quality

    NASA Technical Reports Server (NTRS)

    Middleton, E. M.; Marcell, R. F.

    1983-01-01

    References relevant to remote sensing of water quality were compiled, organized, and cross-referenced. The following general categories were included: (1) optical properties and measurement of water characteristics; (2) interpretation of water characteristics by remote sensing, including color, transparency, suspended or dissolved inorganic matter, biological materials, and temperature; (3) application of remote sensing for water quality monitoring; (4) application of remote sensing according to water body type; and (5) manipulation, processing and interpretation of remote sensing digital water data.

  16. Biological Oceanography

    NASA Technical Reports Server (NTRS)

    Abbott, M. R.

    1984-01-01

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

  17. Biological preconcentrator

    DOEpatents

    Manginell, Ronald P.; Bunker, Bruce C.; Huber, Dale L.

    2008-09-09

    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  18. Biological monitoring

    SciTech Connect

    Miller, S.

    1984-06-01

    Recent research is reviewed from books, international committees and symposia which describes the usefulness of biological monitoring for exposure to such compounds as organometallic chemicals, carbon monoxide and cyanide. The types of analyses include the following measurements: the concentration of the chemical in various biological media such as blood, urine, and expired air; the concentration of metabolites of the individual chemical in the same media; and determination of nonadverse biological changes resulting from the reaction of the organism to exposure. A main goal of such monitoring is to ensure that the current or past levels of worker exposure are safe, so that such exposure does not involve an unacceptable health risk. It considers routes other than absorption by the lungs and is a good method for evaluating individual exposures.

  19. Particulate air pollution: possible relevance in asthma.

    PubMed

    Glovsky, M M; Miguel, A G; Cass, G R

    1997-01-01

    The relative importance of air pollution in the pathogenesis of bronchial asthma has been of interest for several decades. Numerous studies on the role of gaseous air pollution containing ozone, nitrogen dioxide, sulfur dioxide, and carbon monoxide have been published. Very little attention has been focused on the role of respirable particles in the causation of asthma. In this article we summarize some of our ongoing investigations into the sources and composition of airborne particles in the Los Angeles and Pasadena atmosphere, including the search for biologically active particles that may induce asthma attacks. If is found that the urban atmosphere contains not only combustion-derived particles from diesel engine exhaust and gasoline-powered motor vehicle exhaust, but also particles formed from biological starting materials including plant debris, cigarette smoke, wood smoke, and meat smoke as well as tire debris containing some natural rubber and paved road dust. Paved road dust is a very complex mixture of particles including garden soil, tire dust, plant fragments, redeposited atmospheric particles of all types, and pollen fragments presumably ground up by passing traffic. We have shown previously that latex allergen can be extracted from tire dust, from roadside dust, and from respirable air samples taken at Los Angeles and Long Beach. At present, work is underway to identify the larger range of allergens that may be contributed by the entrainment of paved road dust into the atmosphere. The possible importance of pollen fragments present in paved road dust in very small particle sizes is discussed as well as their potential relevance in asthma.

  20. Biological rhythms

    NASA Technical Reports Server (NTRS)

    Halberg, F.

    1975-01-01

    An overview is given of basic features of biological rhythms. The classification of periodic behavior of physical and psychological characteristics as circadian, circannual, diurnal, and ultradian is discussed, and the notion of relativistic time as it applies in biology is examined. Special attention is given to circadian rhythms which are dependent on the adrenocortical cycle. The need for adequate understanding of circadian variations in the basic physiological indicators of an individual (heart rate, body temperature, systolic and diastolic blood pressure, etc.) to ensure the effectiveness of prophylactic and therapeutic measures is stressed.

  1. The Constraints of Relevance on Prevocational Curriculum

    ERIC Educational Resources Information Center

    Doherty, Catherine

    2015-01-01

    This paper reflects on how relevance has been invoked as a curricular principle, both by students and teachers, in curriculum documents and in curriculum theory, to explore its variously conceived parameters and conditions. By posing the questions "relevant to whom?", "relevant to what?", "relevant how?" and…

  2. The Need for Culturally Relevant Dance Education

    ERIC Educational Resources Information Center

    McCarthy-Brown, Nyama

    2009-01-01

    There is a need for culturally relevant teaching in dance education. Many dance teachers have heard the buzz words "culturally relevant teaching methods." Yet these dance educators acknowledge that the "dance culture" is not always synonymous with "culturally relevant." This paper examines the issue of culturally relevant teaching methods in dance…

  3. Interactive Effects of Working Memory Self-Regulatory Ability and Relevance Instructions on Text Processing

    ERIC Educational Resources Information Center

    Hamilton, Nancy Jo

    2012-01-01

    Reading is a process that requires the enactment of many cognitive processes. Each of these processes uses a certain amount of working memory resources, which are severely constrained by biology. More efficiency in the function of working memory may mediate the biological limits of same. Reading relevancy instructions may be one such method to…

  4. Systems biology of innate immunity

    PubMed Central

    Zak, Daniel E.; Aderem, Alan

    2009-01-01

    Summary Systems biology is the comprehensive and quantitative analysis of the interactions between all of the components of biological systems over time. Systems biology involves an iterative cycle, in which emerging biological problems drive the development of new technologies and computational tools. These technologies and tools then open new frontiers that revolutionize biology. Innate immunity is well suited for systems analysis, because the relevant cells can be isolated in various functional states and their interactions can be reconstituted in a biologically meaningful manner. Application of the tools of systems biology to the innate immune system will enable comprehensive analysis of the complex interactions that maintain the difficult balance between host defense and inflammatory disease. In this review, we discuss innate immunity in the context of the systems biology concepts, emergence, robustness, and modularity, and we describe emerging technologies we are applying in our systems-level analyses. These technologies include genomics, proteomics, computational analysis, forward genetics screens, and analyses that link human genetic polymorphisms to disease resistance. PMID:19120490

  5. Scaffolded biology.

    PubMed

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology. PMID:27287514

  6. Bottle Biology.

    ERIC Educational Resources Information Center

    Jager, Peter

    1993-01-01

    Describes activities which utilize plastic drink bottles and are designed to foster the development of a wide range of biological and ecological concepts. Includes instructions for making a model compost column and presents a model that illustrates open versus closed ecosystems. (DDR)

  7. Biologic Vaccines

    PubMed Central

    ADAMS, KATHERINE T.

    2009-01-01

    The threat of new disease pandemics has spurred the development of biologic vaccines, which promise tremendous improvements in global and local health. Several lend themselves to the prevention or treatment of chronic diseases. But the uncertainties of whom to vaccinate raise the question of whether the health care system can make these promising products viable. PMID:22478749

  8. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1979

    1979-01-01

    Organized by topic is a reading list for A- and S-level biology. Described are experiments for measuring rate of water uptake in a shoot; questions to aid students in designing experiments; rise of overhead projection to demonstrate osmosis and blood cell counting; and microbial manufacture of vinegar. (CS)

  9. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Describes equipment, activities, and experiments useful in biology and environmental education instruction, including, among others, sampling in ecology using an overhead projector, the slide finder as an aid to microscopy, teaching kidney function, and teaching wildlife conservation-sand dune systems. (SK)

  10. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1976

    1976-01-01

    Describes nine biology experiments, including osmosis, genetics; oxygen content of blood, enzymes in bean seedlings, preparation of bird skins, vascularization in bean seedlings, a game called "sequences" (applied to review situations), crossword puzzle for human respiration, and physiology of the woodlouse. (CS)

  11. Scaffolded biology.

    PubMed

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  12. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

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

  13. (Biological dosimetry)

    SciTech Connect

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  14. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Outlines a variety of laboratory procedures, techniques, and materials including construction of a survey frame for field biology, a simple tidal system, isolation and applications of plant protoplasts, tropisms, teaching lung structure, and a key to statistical methods for biologists. (DS)

  15. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Presents content information and/or laboratory procedures and experiments on different biology topics including small-scale cultivation of watercress and its use in water-culture experiments, microbiology of the phylloplane, use of mouthbrooders in science class, and the gene. (DC)

  16. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1984

    1984-01-01

    Presents information on the teaching of nutrition (including new information relating to many current O-level syllabi) and part 16 of a reading list for A- and S-level biology. Also includes a note on using earthworms as a source of material for teaching meiosis. (JN)

  17. Marine Biology

    ERIC Educational Resources Information Center

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  18. Cancer Biology

    ERIC Educational Resources Information Center

    Dominiecki, Mary E.

    2004-01-01

    University of Colorado's Virtual Student Fellowship available at and developed by Bakemeier, Richard F. This website is designed to give students applying for a fellowship an overview of basic topics in biology and how they are used by cancer researchers to develop new treatments.

  19. Interaction of dermatologically relevant nanoparticles with skin cells and skin

    PubMed Central

    Rancan, Fiorenza; Ahlberg, Sebastian; Nazemi, Berouz; Choe, Chun Sik; Darvin, Maxim E; Hadam, Sabrina; Blume-Peytavi, Ulrike; Loza, Kateryna; Diendorf, Jörg; Epple, Matthias; Graf, Christina; Rühl, Eckart; Meinke, Martina C; Lademann, Jürgen

    2014-01-01

    Summary The investigation of nanoparticle interactions with tissues is complex. High levels of standardization, ideally testing of different material types in the same biological model, and combinations of sensitive imaging and detection methods are required. Here, we present our studies on nanoparticle interactions with skin, skin cells, and biological media. Silica, titanium dioxide and silver particles were chosen as representative examples for different types of skin exposure to nanomaterials, e.g., unintended environmental exposure (silica) versus intended exposure through application of sunscreen (titanium dioxide) or antiseptics (silver). Because each particle type exhibits specific physicochemical properties, we were able to apply different combinations of methods to examine skin penetration and cellular uptake, including optical microscopy, electron microscopy, X-ray microscopy on cells and tissue sections, flow cytometry of isolated skin cells as well as Raman microscopy on whole tissue blocks. In order to assess the biological relevance of such findings, cell viability and free radical production were monitored on cells and in whole tissue samples. The combination of technologies and the joint discussion of results enabled us to look at nanoparticle–skin interactions and the biological relevance of our findings from different angles. PMID:25551064

  20. Macromolecules Relevant to Stone Formation

    NASA Astrophysics Data System (ADS)

    Ryall, Rosemary L.; Cook, Alison F.; Thurgood, Lauren A.; Grover, Phulwinder K.

    2007-04-01

    Despite years of research, no single macromolecule in kidney calculi or in urine has yet been shown to fulfill a specific function in stone pathogenesis. In this paper we briefly review papers investigating the urinary excretion of individual macromolecules, their effects on calcium oxalate (CaOx) crystallization and attachment of crystals to renal epithelial cells, and the influence of lithogenic conditions on their renal expression in cultured cells and animal models. Using prothrombin fragment 1 (PTF1) and human serum albumin as examples, we show the types of patterns resulting from the binding of a fluorescently tagged protein to a specific CaOx monohydrate (COM) crystal face and its incorporation into the crystal structure. Molecular modeling is also used to illustrate how PTF1 can align with the atomic array on a COM crystal surface. We conclude that although many macromolecules are, by strict definition, relevant to stone formation, very few are probably truly influential.

  1. Ancient "Observatories" - A Relevant Concept?

    NASA Astrophysics Data System (ADS)

    Belmonte, Juan Antonio

    It is quite common, when reading popular books on astronomy, to see a place referred to as "the oldest observatory in the world". In addition, numerous books on archaeoastronomy, of various levels of quality, frequently refer to the existence of "prehistoric" or "ancient" observatories when describing or citing monuments that were certainly not built with the primary purpose of observing the skies. Internet sources are also guilty of this practice. In this chapter, the different meanings of the word observatory will be analyzed, looking at how their significances can be easily confused or even interchanged. The proclaimed "ancient observatories" are a typical result of this situation. Finally, the relevance of the concept of the ancient observatory will be evaluated.

  2. Biological trade and markets.

    PubMed

    Hammerstein, Peter; Noë, Ronald

    2016-02-01

    Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other 'commodities'. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten 'terms of contract' that 'self-stabilize' trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models-often called 'Walrasian' markets-are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying 'principal-agent' problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need

  3. Biological trade and markets.

    PubMed

    Hammerstein, Peter; Noë, Ronald

    2016-02-01

    Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other 'commodities'. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten 'terms of contract' that 'self-stabilize' trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models-often called 'Walrasian' markets-are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying 'principal-agent' problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need

  4. Biological trade and markets

    PubMed Central

    2016-01-01

    Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other ‘commodities’. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten ‘terms of contract’ that ‘self-stabilize’ trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models—often called ‘Walrasian’ markets—are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying ‘principal–agent’ problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists

  5. Mars simulations relevant to planetary protection

    NASA Astrophysics Data System (ADS)

    Ehrenfreund, P.; Garry, J.; ten Kate, I.; Norberg, P.; van Sluis, K.

    We have recently investigated the native amino acid composition of two analogs of martian soil JSC-1 and Salten Skov A Mars simulation chamber has been built and used to expose samples of these analogs to temperature and lighting conditions similar to those found at low-latitudes on the martian surface We have quantified the amino acid content of these two martian regolith simulants using high performance liquid chromatography HPLC In doing so we have obtained data that are useful for biological chemical and physical studies of analogs to martian surface materials We have also investigated the influence of UV radiation low temperatures and gaseous CO 2 on the intrinsic amino acid composition of both martian soil analogs Exposure to energetic ultraviolet light in vacuum appears to cause a modest increase in the concentration of certain amino acids within the materials which has been interpreted as resulting from the degradation of microorganisms The influence of low temperatures shows that the accretion of condensed water on the soils leads to the destruction of amino acids supporting the idea that reactive chemical processes involving H 2 O are at work within the martian soil analogs We also tested the radiation resistance of Natronorubrum sp HG-1 halophilic bacteria in air and repeated those experiments in the Mars simulation chamber by mixing the halophilic microbe into martian regolith analogs In this paper we discuss the relevance of Mars simulations for life detection and for planetary protection issues

  6. Metal-based nanoparticle interactions with the nervous system: The challenge of brain entry and the risk of retention in the organism

    EPA Science Inventory

    This review of metal and metal-oxide based nanoparticles focuses on factors that influence their distribution into the nervous system, evidence that they enter brain parenchyma, and nervous system responses. Emphasis is placed on gold as a model metal-based nanoparticle and for r...

  7. Copper: Toxicological relevance and mechanisms

    PubMed Central

    Gaetke, Lisa M.; Chow-Johnson, Hannah S.; Chow, Ching K.

    2015-01-01

    Copper (Cu) is a vital mineral essential for many biological processes. The vast majority of all Cu in healthy humans is associated with enzyme prosthetic groups or bound to proteins. Cu homeostasis is tightly regulated through a complex system of Cu transporters and chaperone proteins. Excess or toxicity of Cu, which is associated with the pathogenesis of hepatic disorder, neurodegenerative changes and other disease conditions, can occur when Cu homeostasis is disrupted. The capacity to initiate oxidative damage is most commonly attributed to Cu-induced cellular toxicity. Recently, altered cellular events, including lipid metabolism, gene expression, alpha-synuclein aggregation, activation of acidic sphingomyelinase and release of ceramide, and temporal and spatial distribution of Cu in hepatocytes, as well as Cu-protein interaction in the nerve system, have been suggested to play a role in Cu toxicity. However, whether these changes are independent of, or secondary to, an altered cellular redox state of Cu remain to be elucidated. PMID:25199685

  8. Physiological relevance of dietary melanoidins.

    PubMed

    Morales, Francisco J; Somoza, Veronika; Fogliano, Vincenzo

    2012-04-01

    Melanoidins are the final products of the Maillard reaction. The main dietary sources of melanoidins are coffee, bread crust, bakery products, black beer and cocoa. Although the chemical structures of melanoidins are widely unknown, data from gravimetric techniques allow to roughly estimate a daily intake in the order of 10 g with a Western diet. Melanoidins contribute to the sensorial properties, modulating texture and flavour of foods. Growing evidence also suggests that melanoidins have health beneficial properties, such as chemopreventive, antioxidant and antimicrobial activities, and the ability to chelate different minerals. In the gastrointestinal tract, melanoidins behave not only as antioxidants, but also as dietary fibre by promoting the growth of bifidobacteria. This array of biological activities suggests the need for analytical techniques to identify the melanoidin structures and to control their formation during thermal food processing.

  9. Simulation of the light emission properties of patterned metal-based nanostructures for ultra-high density optical storage

    NASA Astrophysics Data System (ADS)

    Li, Weijun; Zhu, Yaping; Luo, Jun; Peng, Sha; Lei, Yu; Tong, Qing; Zhang, Xinyu; Xie, Changsheng

    2015-10-01

    Current researches show that the surface plasmon-polariton modes (SPPMs) in metallic nanostructures can lead to a powerful localization of guided light signals, which is generally as small as a few nanometers and thus far beyond the diffraction limit of electromagnetic waves in dielectric media. In this paper, our attention is paid to the modeling and simulation of particular kinds of patterned metal-based nanostructure fabricated over several common wafers such as typical silicon dioxide. The nanostructures are designed for concentrating and delivering incident light energy into nanoscale regions. In our research, the factors, for instance, optical materials, patterned nano-structures, the distance arrangement between adjacent single nanopattern, and the frequency of incident electromagnetic wave, are taken as variables, and further the CST microwave studio is used to simulate optical behaviors of the devices developed by us. By comparing the transmittance and electric field intensity distribution in small area, the nano-light-emission effects are analyzed, and the conditions for obtaining near-field nanospots have been chosen.

  10. Green and selective polycondensation methods toward linear sorbitol-based polyesters: enzymatic versus organic and metal-based catalysis.

    PubMed

    Gustini, Liliana; Lavilla, Cristina; Janssen, William W T J; Martínez de Ilarduya, Antxon; Muñoz-Guerra, Sebastián; Koning, Cor E

    2016-08-23

    Renewable polyesters derived from a sugar alcohol (i.e., sorbitol) were synthesized by solvent-free polycondensation. The aim was to prepare linear polyesters with pendant hydroxyl groups along the polymer backbone. The performance of the sustainable biocatalyst SPRIN liposorb CALB [an immobilized form of Candida antarctica lipase B (CALB); SPRIN technologies] and the organo-base catalyst 1,5,7-triazabicyclo[4,4,0]dec-5-ene (TBD) were compared with two metal-based catalysts: dibutyl tin oxide (DBTO) and scandium trifluoromethanesulfonate [also known as scandium triflate, Sc(OTf)3 ]. For the four catalytic systems, the efficiency and selectivity for the incorporation of sorbitol were studied, mainly using (13) C and (31) P NMR spectroscopies, whereas side reactions, such as ether formation and dehydration of sorbitol, were evaluated using MALDI-TOF-MS. Especially the biocatalyst SPRIN liposorb CALB succeeded in incorporating sorbitol in a selective way without side reactions, leading to close-to-linear polyesters. By using a renewable hydroxyl-reactive curing agent based on l-lysine, transparent and glossy poly(ester urethane) networks were successfully synthesized offering a tangible example of bio-based coatings. PMID:27406029

  11. The effect of abrasive blasting on the strength of a joint between dental porcelain and metal base.

    PubMed

    Pietnicki, Krzysztof; Wołowiec, Emilia; Klimek, Leszek

    2014-01-01

    This paper presents the effect of selected parameters of abrasive blasting on the strength of a joint between dental porcelain and metal base. Experiments were conducted for different grain sizes of abrasive material and different blasting angles, with a constant blasting pressure. InLine dental porcelain was fused on samples of cobalt-chromium alloy following abrasive blasting; they were subsequently subjected to shearing forces on a testing machine. The fractures were observed under an electron scanning microscope in order to determine the character and course of fracturing. Strength tests showed that the grain size of abrasive material was a parameter with the greatest effect on the strength. The best effects were achieved for samples subjected to abrasive blasting with material with grain size of 110 μm. No statistically significant differences were found for the strength of samples worked at different angles. The results of the fractographic examinations have shown that in all the samples, fracturing occurred mainly along the porcelain-metal boundary, with few cases of fracturing through porcelain.

  12. Noble metal-based bimetallic nanoparticles: the effect of the structure on the optical, catalytic and photocatalytic properties.

    PubMed

    Zaleska-Medynska, Adriana; Marchelek, Martyna; Diak, Magdalena; Grabowska, Ewelina

    2016-03-01

    Nanoparticles composed of two different metal elements show novel electronic, optical, catalytic or photocatalytic properties from monometallic nanoparticles. Bimetallic nanoparticles could show not only the combination of the properties related to the presence of two individual metals, but also new properties due to a synergy between two metals. The structure of bimetallic nanoparticles can be oriented in random alloy, alloy with an intermetallic compound, cluster-in-cluster or core-shell structures and is strictly dependent on the relative strengths of metal-metal bond, surface energies of bulk elements, relative atomic sizes, preparation method and conditions, etc. In this review, selected properties, such as structure, optical, catalytic and photocatalytic of noble metals-based bimetallic nanoparticles, are discussed together with preparation routes. The effects of preparation method conditions as well as metal properties on the final structure of bimetallic nanoparticles (from alloy to core-shell structure) are followed. The role of bimetallic nanoparticles in heterogeneous catalysis and photocatalysis are discussed. Furthermore, structure and optical characteristics of bimetallic nanoparticles are described in relation to the some features of monometallic NPs. Such a complex approach allows to systematize knowledge and to identify the future direction of research.

  13. Green and selective polycondensation methods toward linear sorbitol-based polyesters: enzymatic versus organic and metal-based catalysis.

    PubMed

    Gustini, Liliana; Lavilla, Cristina; Janssen, William W T J; Martínez de Ilarduya, Antxon; Muñoz-Guerra, Sebastián; Koning, Cor E

    2016-08-23

    Renewable polyesters derived from a sugar alcohol (i.e., sorbitol) were synthesized by solvent-free polycondensation. The aim was to prepare linear polyesters with pendant hydroxyl groups along the polymer backbone. The performance of the sustainable biocatalyst SPRIN liposorb CALB [an immobilized form of Candida antarctica lipase B (CALB); SPRIN technologies] and the organo-base catalyst 1,5,7-triazabicyclo[4,4,0]dec-5-ene (TBD) were compared with two metal-based catalysts: dibutyl tin oxide (DBTO) and scandium trifluoromethanesulfonate [also known as scandium triflate, Sc(OTf)3 ]. For the four catalytic systems, the efficiency and selectivity for the incorporation of sorbitol were studied, mainly using (13) C and (31) P NMR spectroscopies, whereas side reactions, such as ether formation and dehydration of sorbitol, were evaluated using MALDI-TOF-MS. Especially the biocatalyst SPRIN liposorb CALB succeeded in incorporating sorbitol in a selective way without side reactions, leading to close-to-linear polyesters. By using a renewable hydroxyl-reactive curing agent based on l-lysine, transparent and glossy poly(ester urethane) networks were successfully synthesized offering a tangible example of bio-based coatings.

  14. IKK Biology

    PubMed Central

    Liu, Fei; Xia, Yifeng; Parker, Aaron S.; Verma, Inder M.

    2012-01-01

    Summary The inhibitor of nuclear factor-κB (IκB) kinase (IKK) complex is the master regulator of the NF-κB signaling pathway. The activation of the IKK complex is a tightly regulated, highly stimulus-specific, and target-specific event that is essential for the plethora of functions attributed to NF-κB. More recently, NF-κB independent roles of IKK members have brought increased complexity to its biological function. This review highlights some of the major advances in the studies of the process of IKK activation and the biological roles of IKK family members, with a focus on NF-κB independent functions. Understanding these complex processes is essential for targeting IKK for therapeutics. PMID:22435559

  15. Crusts: biological

    USGS Publications Warehouse

    Belnap, Jayne; Elias, Scott A.

    2013-01-01

    Biological soil crusts, a community of cyanobacteria, lichens, mosses, and fungi, are an essential part of dryland ecosystems. They are critical in the stabilization of soils, protecting them from wind and water erosion. Similarly, these soil surface communities also stabilized soils on early Earth, allowing vascular plants to establish. They contribute nitrogen and carbon to otherwise relatively infertile dryland soils, and have a strong influence on hydrologic cycles. Their presence can also influence vascular plant establishment and nutrition.

  16. Marine biology

    SciTech Connect

    Thurman, H.V.; Webber, H.H.

    1984-01-01

    This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the nature of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index.

  17. Fractals in biology and medicine

    NASA Technical Reports Server (NTRS)

    Havlin, S.; Buldyrev, S. V.; Goldberger, A. L.; Mantegna, R. N.; Ossadnik, S. M.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    Our purpose is to describe some recent progress in applying fractal concepts to systems of relevance to biology and medicine. We review several biological systems characterized by fractal geometry, with a particular focus on the long-range power-law correlations found recently in DNA sequences containing noncoding material. Furthermore, we discuss the finding that the exponent alpha quantifying these long-range correlations ("fractal complexity") is smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the normal heart is characterized by long-range "anticorrelations" which are absent in the diseased heart.

  18. The NASA Space Biology Program

    NASA Technical Reports Server (NTRS)

    Halstead, T. W.

    1982-01-01

    A discussion is presented of the research conducted under the auspices of the NASA Space Biology Program. The objectives of this Program include the determination of how gravity affects and how it has shaped life on earth, the use of gravity as a tool to investigate relevant biological questions, and obtaining an understanding of how near-weightlessness affects both plants and animals in order to enhance the capability to use and explore space. Several areas of current developmental research are discussed and the future focus of the Program is considered.

  19. The meaning of biological information.

    PubMed

    Koonin, Eugene V

    2016-03-13

    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with 'meaning', i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to 'meaning' of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

  20. The meaning of biological information.

    PubMed

    Koonin, Eugene V

    2016-03-13

    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with 'meaning', i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to 'meaning' of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology. PMID:26857678

  1. The meaning of biological information

    PubMed Central

    Koonin, Eugene V.

    2016-01-01

    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to ‘meaning’ of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology. PMID:26857678

  2. On Relevance Weight Estimation and Query Expansion.

    ERIC Educational Resources Information Center

    Robertson, S. E.

    1986-01-01

    A Bayesian argument is used to suggest modifications to the Robertson and Jones relevance weighting formula to accommodate the addition to the query of terms taken from the relevant documents identified during the search. (Author)

  3. Detoxification reactions: relevance to aging

    PubMed Central

    Zimniak, Piotr

    2008-01-01

    It is widely (although not universally) accepted that organismal aging is the result of two opposing forces: (i) processes that destabilize the organism and increase the probability of death, and (ii) longevity assurance mechanisms that prevent, repair, or contain damage. Processes of the first group are often chemical and physico-chemical in nature, and are either inevitable or only under marginal biological control. In contrast, protective mechanisms are genetically determined and are subject to natural selection. Life span is therefore largely dependent on the investment into protective mechanisms which evolve to optimize reproductive fitness. Recent data indicate that toxicants, both environmental and generated endogenously by metabolism, are major contributors to macromolecular damage and physiological dysregulation that contribute to aging; electrophilic carbonyl compounds derived from lipid peroxidation appear to be particularly important. As a consequence, detoxification mechanisms, including the removal of electrophiles by glutathione transferase-catalyzed conjugation, are major longevity assurance mechanisms. The expression of multiple detoxification enzymes, each with a significant but relatively modest effect on longevity, is coordinately regulated by signaling pathways such as insulin/insulin-like signaling, explaining the large effect of such pathways on life span. The major aging-related toxicants and their cognate detoxification systems are discussed in this review. PMID:18547875

  4. IQ Predicts Biological Motion Perception in Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Rutherford, M. D.; Troje, Nikolaus F.

    2012-01-01

    Biological motion is easily perceived by neurotypical observers when encoded in point-light displays. Some but not all relevant research shows significant deficits in biological motion perception among those with ASD, especially with respect to emotional displays. We tested adults with and without ASD on the perception of masked biological motion…

  5. Bridging Physics and Biology Using Resistance and Axons

    ERIC Educational Resources Information Center

    Dyer, Joshua M.

    2014-01-01

    When teaching physics, it is often difficult to get biology-oriented students to see the relevance of physics. A complaint often heard is that biology students are required to take physics for the Medical College Admission Test (MCAT) as part of a "weeding out" process, but that they don't feel like they need physics for biology.…

  6. The Personal Relevance of the Social Studies.

    ERIC Educational Resources Information Center

    VanSickle, Ronald L.

    1990-01-01

    Conceptualizes a personal-relevance framework derived from Ronald L. VanSickle's five areas of life integrated with four general motivating goals from Abraham Maslow's hierarchy of needs and Richard and Patricia Schmuck's social motivation theory. Illustrates ways to apply the personal relevance framework to make social studies more relevant to…

  7. Grand challenges in space synthetic biology

    PubMed Central

    Montague, Michael G.; Cumbers, John; Hogan, John A.

    2015-01-01

    Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth. PMID:26631337

  8. Grand challenges in space synthetic biology.

    PubMed

    Menezes, Amor A; Montague, Michael G; Cumbers, John; Hogan, John A; Arkin, Adam P

    2015-12-01

    Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth. PMID:26631337

  9. Grand challenges in space synthetic biology.

    PubMed

    Menezes, Amor A; Montague, Michael G; Cumbers, John; Hogan, John A; Arkin, Adam P

    2015-12-01

    Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth.

  10. [Nuptiality: the most relevant changes].

    PubMed

    Quilodran, J

    1992-01-01

    Changes in family structure throughout the world have prompted research into the role of couple formation and stability as regulators of biological and social reproduction. The demographic transition has changed the demographic context of nuptiality. Mortality decline has increased survival of spouses as well as of children, and voluntary separation of couples has eclipsed widowhood as a cause of marriage dissolution. Marriage dissolution and remarriage have added complexity to family arrangements. Census data are a good source of information on nuptiality in Mexico. Around 1950, Mexico like most Latin American countries experienced an increase in nuptiality. The trend reverted after the 1960s, simultaneously with the increase in separation and divorce. Between 1970 and 1990, the proportion of Mexican men who remained single at age 45-49 declined from 6.0% to 5.6%, while the proportion of women single at the same age increased from 6.8 to 7.2%. Age at first union was 24.5 in 1970; 24.1 in 1980, and 24.7 in 1990 for men, and 21.1 in 1970, 21.6 in 1980, and 22.2 in 1990 for women. The age difference between spouses declined from 3.4 years in 1970 to 2.5 years in 1990, at least partly due to the rapid population growth of 1950-1970, which created an imbalance in the numbers of older men available for marriage to women in the larger slightly younger cohorts. Between 1970 and 1990, the proportion of women in interrupted unions increased from 5.2% to 9.5%, while the corresponding proportion for men declined from 3.3% to 2.9%. In 1990, 86% of unions among persons over age 15 were legal marriages. PMID:12158066

  11. Simple and low cost method for metal-based micro-capillary channels for heat exchanger use

    NASA Astrophysics Data System (ADS)

    Ogbonnaya, E.; Champagne, C.; Weiss, L.

    2013-11-01

    In this work, we present an alternative, low cost method for the fabrication of a heat exchanger utilizing metal-based microchannels using the UV-LiGA technique. Lithography is used to pattern dry film negative photoresist (Ordyl P-50100) on the substrate. The resist is laminated over the substrate and exposed with a UV source. The use of dry film resist allows for simple and inexpensive microchannel patterns without requiring advanced cleanroom equipment. Following the lithography process, electrodeposition of metals is used to fill the recesses patterned in the resist. In this work, nickel has been electroplated into the bounding resist structure. After electroplating, the remaining resist is dissolved leaving free standing metal structures. The fabricated exchanger is then evaluated based on thermal absorption of simulated waste heat sources and capillary action of the metal channels themselves. Channels are fabricated to heights of 60, 70 and 90 μm respectively on copper substrate using these methods. Working fluid mass transfer rate from the heated microchannel heat exchanger (MHE) is utilized as a basic metric of operation. The mass transfer rate recorded from the nickel-based MHE is 2.19, 2.81 and 3.20 mg s-1 respectively for the different channel heights. This implies an effective thermal power consumption rate of 1.66, 2.13 and 2.42 kW m-2 respectively. By contrast, an MHE fabricated with 115 and 142 μm tall channels on silicon substrate is shown to evaporate up to 2.84 and 3.04 mg s-1 respectively, giving an effective thermal power consumption of 2.15 and 2.31 kW m-2 respectively. An investigation of working fluid contact angle with the electroplated nickel surface is also presented. The surface is found to be a porous structure stemming from the electroplating process.

  12. "Gastric cytoprotection" is still relevant.

    PubMed

    Szabo, Sandor

    2014-12-01

    rapid vascular changes (e.g. increased VP and blood flow), followed by cellular events (e.g. infiltration by acute and chronic inflammatory cells). Thus, PG and histamine, by increasing VP create a perivascular edema that dilutes and delays toxic agents reaching the subepithelial capillaries. Otherwise, damaging chemicals may induce severe early vascular injury resulting in blood flow stasis, hypoxia, and necrosis of surrounding epithelial and mesenchymal cells. In this complex response, increased mucus and/or bicarbonate secretion seem to cause luminal dilution of gastrotoxic chemicals that is further reinforced by a perivascular, histodilutional component. This mechanistic explanation would encompass the protective actions of diverse agents as PG, small doses of histamine, motility stimulants, and dilute irritants (i.e. "adaptive cytoprotection"). Thus, although markedly increased VP is pathologic, slight increase in VP seems to be protective, that is, a key element in the complex pathophysiologic response during acute gastroprotection. Over the years, "gastroprotection" was also applied to accelerated healing of chronic gastroduodenal ulcers without reduction of acid secretion. The likely main mechanism here is the binding of angiogenic growth factors (e.g. basic fibroblast growth factor, vascular endothelial growth factor) to the heparin-like structures of sucralfate and sofalcone. Thus, despite intensive research of the last 30 years, gastroprotection is incompletely understood, and we are still far away from effectively treating Helicobacter pylori-negative ulcers and preventing nonsteroidal anti-inflammatory drugs-caused erosions and ulcers in the upper and lower gastrointestinal tract; hence "gastric cytoprotection" research is still relevant.

  13. The biology of family psychotherapy.

    PubMed

    Kramer, D A

    2001-07-01

    This article has presented a view of biologic psychiatry consistent with that described by Bowlby, discussed hypotheses concerning the biologic purpose of the primate brain and the human brain, and challenged standard beliefs about the identity of the patient entity in a true biologically based psychiatry. Ideas developed by Whitaker, Malone, and their colleagues almost 50 years ago are consistent with a modern biologic basis of family psychotherapy. The treatment of an anorexic family was used to illustrate possible mechanisms of psychotherapeutic treatment requiring the presence of the whole family. The role of the psychiatrist who treats a family is to understand the biologic or medical importance of treating the family as a whole, communicate this to the family, continually work toward that level of participation, suggest relevant topics for discussion, and catalyze interactions within the family. Psychotherapy with families as a whole is effective because of the power of kin selection and inclusive fitness, biologic processes not usually considered in the practice of medicine or psychiatry.

  14. Biological membranes

    PubMed Central

    Watson, Helen

    2015-01-01

    Biological membranes allow life as we know it to exist. They form cells and enable separation between the inside and outside of an organism, controlling by means of their selective permeability which substances enter and leave. By allowing gradients of ions to be created across them, membranes also enable living organisms to generate energy. In addition, they control the flow of messages between cells by sending, receiving and processing information in the form of chemical and electrical signals. This essay summarizes the structure and function of membranes and the proteins within them, and describes their role in trafficking and transport, and their involvement in health and disease. Techniques for studying membranes are also discussed. PMID:26504250

  15. Biomedically relevant chemical and physical properties of coal combustion products.

    PubMed Central

    Fisher, G L

    1983-01-01

    The evaluation of the potential public and occupational health hazards of developing and existing combustion processes requires a detailed understanding of the physical and chemical properties of effluents available for human and environmental exposures. These processes produce complex mixtures of gases and aerosols which may interact synergistically or antagonistically with biological systems. Because of the physicochemical complexity of the effluents, the biomedically relevant properties of these materials must be carefully assessed. Subsequent to release from combustion sources, environmental interactions further complicate assessment of the toxicity of combustion products. This report provides an overview of the biomedically relevant physical and chemical properties of coal fly ash. Coal fly ash is presented as a model complex mixture for health and safety evaluation of combustion processes. PMID:6337824

  16. Biological Effects of Directed Energy

    NASA Astrophysics Data System (ADS)

    Dayton, Thomas; Beason, Charles; Hitt, M. K.; Rogers, Walter; Cook, Michael

    2002-11-01

    This Final Report summarizes the biological effects research conducted by Veridian Engineering personnel under contract F41624-96-C-9009 in support of the Air Force Research Laboratory's Radio Frequency Radiation Branch from April 1997 to April 2002. Biological effects research and consultation were provided in five major areas: Active Denial System (also known as Vehicle Mounted Active Denial System), radio frequency radiation (RFR) health and safety, non-lethal weapon biological effects research, the newly formed Joint Non-Lethal Weapons Human Effects Center of Excellence, and Biotechnology. The report is organized by research efforts within the major research areas, providing title, objective, a brief description, relevance to the AF or DoD, funding, and products.

  17. NASA Workshop on Biological Adaptation

    NASA Technical Reports Server (NTRS)

    Morey-Holton, Emily (Editor); Tischler, Marc (Editor)

    1988-01-01

    A workshop was convened to review the current program in Space Biology Biological Adaptation Research and its objectives and to identify future research directions. Two research areas emerged from these deliberations: gravitational effects on structures and biomineralization and gravity affected regulatory mechanisms. The participants also recommended that research concentrate on rapidly growing animals, since gravity effects may be more pronounced during growth and development. Both research areas were defined and future research directions were identified. The recommendations of the workshop will assist the Life Sciences Division of NASA in it assessment and long-range planning of these areas of space biology. Equally important, the workshop was intended to stimulate thought and research among those attending so that they would, in turn, interest, excite, and involve other members of the academic community in research efforts relevant to these programs.

  18. How to compare biologic drugs.

    PubMed

    Calvet, Xavier; Esplugues, Juan Vicente

    2014-01-01

    This consensus document reviews the evidence on the evaluation of biological drugs. The main conclusions of the group are: a) the current evidence on biological comparisons is based on indirect comparisons and is generally unreliable and with important methodological limitations. Therefore, b) it is considered necessary to amend the regulatory directives in the sense of strongly favoring randomized non-inferiority studies comparing face to face the new biological treatment with current standards, avoiding trials versus placebo, c) A key element in this process will be determined by consensus among regulatory agencies, scientific societies, the pharmaceutical industry and health authorities regarding the clinical differences that should be considered relevant in each of the conditions tested. PMID:25043229

  19. How is physiology relevant to behavior analysis?

    PubMed Central

    Reese, Hayne W.

    1996-01-01

    Physiology is an important biological science; but behavior analysis is not a biological science, and behavior analysts can safely ignore biological processes. However, ignoring products of biological processes might be a serious mistake. The important products include behavior, instinctive drift, behavior potentials, hunger, and many developmental milestones and events. Physiology deals with the sources of such products; behavior analysis can deal with how the products affect behavior, which can be understood without understanding their sources. PMID:22478240

  20. Constitutive equations of a tensorial model for strain-induced damage of metals based on three invariants

    NASA Astrophysics Data System (ADS)

    Tutyshkin, Nikolai D.; Lofink, Paul; Müller, Wolfgang H.; Wille, Ralf; Stahn, Oliver

    2016-09-01

    On the basis of the physical concepts of void formation, nucleation, and growth, generalized constitutive equations are formulated for a tensorial model of plastic damage in metals based on three invariants. The multiplicative decomposition of the metric transformation tensor and a thermodynamically consistent formulation of constitutive relations leads to a symmetric second-order damage tensor with a clear physical meaning. Its first invariant determines the damage related to plastic dilatation of the material due to growth of the voids. The second invariant of the deviatoric damage tensor is related to the change in void shape. The third invariant of the deviatoric tensor describes the impact of the stress state on damage (Lode angle), including the effect of rotating the principal axes of the stress tensor (Lode angle change). The introduction of three measures with related physical meaning allows for the description of kinetic processes of strain-induced damage with an equivalent parameter in a three-dimensional vector space, including the critical condition of ductile failure. Calculations were performed by using experimentally determined material functions for plastic dilatation and deviatoric strain at the mesoscale, as well as three-dimensional graphs for plastic damage of steel DC01. The constitutive parameter was determined from tests in tension, compression, and shear by using scanning electron microscopy, which allowed to vary the Lode angle over the full range of its values [InlineEquation not available: see fulltext.]. In order to construct the three-dimensional plastic damage curve for a range of triaxiality parameters -1 ≤ ST ≤ 1 and of Lode angles [InlineEquation not available: see fulltext.], we used our own, as well as systematized published experimental data. A comparison of calculations shows a significant effect of the third invariant (Lode angle) on equivalent damage. The measure of plastic damage, based on three invariants, can be useful

  1. Structural Biology Fact Sheet

    MedlinePlus

    ... Home > Science Education > Structural Biology Fact Sheet Structural Biology Fact Sheet Tagline (Optional) Middle/Main Content Area What is structural biology? Structural biology is a field of science focused ...

  2. Spatial Aspects in Biological System Simulations

    PubMed Central

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

    2012-01-01

    Mathematical models of the dynamical properties of biological systems aim to improve our understanding of the studied system with the ultimate goal of being able to predict system responses in the absence of experimentation. Despite the enormous advances that have been made in biological modeling and simulation, the inherently multiscale character of biological systems and the stochasticity of biological processes continue to present significant computational and conceptual challenges. Biological systems often consist of well-organized structural hierarchies, which inevitably lead to multiscale problems. This chapter introduces and discusses the advantages and shortcomings of several simulation methods that are being used by the scientific community to investigate the spatiotemporal properties of model biological systems. We first describe the foundations of the methods and then describe their relevance and possible application areas with illustrative examples from our own research. Possible ways to address the encountered computational difficulties are also discussed. PMID:21187236

  3. Biology Cognitive Preferences of Preservice Biology Teachers.

    ERIC Educational Resources Information Center

    Cheng, Yeong-Jing

    1991-01-01

    The Biology Cognitive Preference Inventory (BCPI) for investigating the biology cognitive preference styles of 143 students in the biology teacher education program was developed and validated. The cognitive preferences include factual information or recall, principles, questioning, and applications. Preservice biology teachers exhibited a strong…

  4. Simulating Biological and Non-Biological Motion

    ERIC Educational Resources Information Center

    Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas

    2008-01-01

    It is widely accepted that the brain processes biological and non-biological movements in distinct neural circuits. Biological motion, in contrast to non-biological motion, refers to active movements of living beings. Aim of our experiment was to investigate the mechanisms underlying mental simulation of these two movement types. Subjects had to…

  5. Biological Literacy in a College Biology Classroom.

    ERIC Educational Resources Information Center

    Demastes, Sherry; Wandersee, James H.

    1992-01-01

    Examines the proposed definition of biological literacy as the understanding of a small number of pervasive biological principles appropriate to making informed personal and societal decisions. Utilizes the content of a major daily newspaper to adjust biology instruction to focus on this notion of biological literacy. Discusses benefits and…

  6. Planetary Protection: Two Relevant Terrestrial Examples

    NASA Astrophysics Data System (ADS)

    Chyba, C.

    2002-09-01

    Concerns about potential pathogens in returned samples from Mars ("Mars Sample Return: Issues and Recommendations", National Research Council, 1997) or planetary satellites ("Evaluating the Biological Potential in Samples Returned from Planetary Satellites and Small Solar System Bodies", National Research Council, 1998) focus on two potential types of pathogenesis, toxic and infectious. The National Research Council reports cited above state that the chances of extraterrestrial organisms proving either toxic or infectious to humans are extremely low, but cannot be entirely ruled out. Here I discuss recently discovered terrestrial examples relevant to each possibility, in order to make these concerns concrete. The first example concerns the production of hepatotoxins (toxins affecting the liver) and neurotoxins by cyanobacteria in glacial lakes on alpine pastures in Switzerland. In this example, mat-forming benthic cyanobacteria are implicated in a hundred cattle poisonings that have been reported from alpine pasteurs in southeastern Switzerland over the past twenty-five years (e.g. K. Mez et al, Hydrobiologia 368, 1-15 (1998)). It is unlikely that these cyanobacteria evolved the toxins in response to dairy cows; rather the susceptibility of cattle to these toxins seems simply to be an unfortunate coincidence of a toxin working across a large evolutionary distance. The second example concerns the recent demonstration that the decimation of shallow-water Caribbean elkhorn coral is due to infection by a common fecal enterobacterium associated with the human gut (K. L. Patterson et al., PNAS 99, 8725-8730 (2002)). The bacterium, Serratia marcenscens, is also a free-living microbe in water and soil, as well as an opportunistic pathogen in a variety of animal species. The distance between humans and corals emphasizes the possibility that certain organisms may prove pathogenic across a wide evolutionary divide. Of course, in neither of these cases are the evolutionary

  7. Nanoparticle-based biologic mimetics.

    PubMed

    Cliffel, David E; Turner, Brian N; Huffman, Brian J

    2009-01-01

    Centered on solid chemistry foundations, biology and materials science have reached a crossroad where bottom-up designs of new biologically important nanomaterials are a reality. The topics discussed here present the interdisciplinary field of creating biological mimics. Specifically, this discussion focuses on mimics that are developed using various types of metal nanoparticles (particularly gold) through facile synthetic methods. These methods conjugate biologically relevant molecules, e.g., small molecules, peptides, proteins, and carbohydrates, in conformationally favorable orientations on the particle surface. These new products provide stable, safe, and effective substitutes for working with potentially hazardous biologicals for applications such as drug targeting, immunological studies, biosensor development, and biocatalysis. Many standard bioanalytical techniques can be used to characterize and validate the efficacy of these new materials, including quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and enzyme-linked immunosorbent assay (ELISA). Metal nanoparticle-based biomimetics continue to be developed as potential replacements for the native biomolecule in applications of immunoassays and catalysis.

  8. Culture, Relevance, and Schooling: Exploring Uncommon Ground

    ERIC Educational Resources Information Center

    Scherff, Lisa, Ed.; Spector, Karen, Ed.

    2011-01-01

    In "Culture, Relevance, and Schooling: Exploring Uncommon Ground," Lisa Scherff, Karen Spector, and the contributing authors conceive of culturally relevant and critically minded pedagogies in terms of opening up new spatial, discursive, and/or embodied learning terrains. Readers will traverse multiple landscapes and look into a variety of spaces…

  9. The Semantic Distance Model of Relevance Assessment.

    ERIC Educational Resources Information Center

    Brooks, Terrence A.

    1998-01-01

    Presents the Semantic Distance Model (SDM) of Relevance Assessment, a cognitive model of the relationship between semantic distance and relevance assessment. Discusses premises of the model such as the subjective nature of information and the metaphor of semantic distance. Empirical results illustrate the effects of semantic distance and semantic…

  10. 12 CFR 308.157 - Relevant considerations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 5 2012-01-01 2012-01-01 false Relevant considerations. 308.157 Section 308.157 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION PROCEDURE AND RULES OF PRACTICE RULES OF PRACTICE AND PROCEDURE Procedures and Standards Applicable to an Application Pursuant to Section 19 of the FDIA § 308.157 Relevant considerations....

  11. 12 CFR 108.11 - Relevant considerations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 1 2014-01-01 2014-01-01 false Relevant considerations. 108.11 Section 108.11 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY REMOVALS, SUSPENSIONS, AND PROHIBITIONS WHERE A CRIME IS CHARGED OR PROVEN § 108.11 Relevant considerations. (a) In determining...

  12. 12 CFR 508.11 - Relevant considerations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 6 2014-01-01 2012-01-01 true Relevant considerations. 508.11 Section 508.11 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY REMOVALS, SUSPENSIONS, AND PROHIBITIONS WHERE A CRIME IS CHARGED OR PROVEN § 508.11 Relevant considerations. (a) In determining...

  13. 12 CFR 108.11 - Relevant considerations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 1 2012-01-01 2012-01-01 false Relevant considerations. 108.11 Section 108.11 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY REMOVALS, SUSPENSIONS, AND PROHIBITIONS WHERE A CRIME IS CHARGED OR PROVEN § 108.11 Relevant considerations. (a) In determining...

  14. 12 CFR 508.11 - Relevant considerations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Relevant considerations. 508.11 Section 508.11 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY REMOVALS, SUSPENSIONS, AND PROHIBITIONS WHERE A CRIME IS CHARGED OR PROVEN § 508.11 Relevant considerations. (a) In determining...

  15. System biology of gene regulation.

    PubMed

    Baitaluk, Michael

    2009-01-01

    A famous joke story that exhibits the traditionally awkward alliance between theory and experiment and showing the differences between experimental biologists and theoretical modelers is when a University sends a biologist, a mathematician, a physicist, and a computer scientist to a walking trip in an attempt to stimulate interdisciplinary research. During a break, they watch a cow in a field nearby and the leader of the group asks, "I wonder how one could decide on the size of a cow?" Since a cow is a biological object, the biologist responded first: "I have seen many cows in this area and know it is a big cow." The mathematician argued, "The true volume is determined by integrating the mathematical function that describes the outer surface of the cow's body." The physicist suggested: "Let's assume the cow is a sphere...." Finally the computer scientist became nervous and said that he didn't bring his computer because there is no Internet connection up there on the hill. In this humorous but explanatory story suggestions proposed by theorists can be taken to reflect the view of many experimental biologists that computer scientists and theorists are too far removed from biological reality and therefore their theories and approaches are not of much immediate usefulness. Conversely, the statement of the biologist mirrors the view of many traditional theoretical and computational scientists that biological experiments are for the most part simply descriptive, lack rigor, and that much of the resulting biological data are of questionable functional relevance. One of the goals of current biology as a multidisciplinary science is to bring people from different scientific areas together on the same "hill" and teach them to speak the same "language." In fact, of course, when presenting their data, most experimentalist biologists do provide an interpretation and explanation for the results, and many theorists/computer scientists aim to answer (or at least to fully describe

  16. Cell biology perspectives in phage biology.

    PubMed

    Ansaldi, Mireille

    2012-01-01

    Cellular biology has long been restricted to large cellular organisms. However, as the resolution of microscopic methods increased, it became possible to study smaller cells, in particular bacterial cells. Bacteriophage biology is one aspect of bacterial cell biology that has recently gained insight from cell biology. Despite their small size, bacteriophages could be successfully labeled and their cycle studied in the host cells. This review aims to put together, although non-extensively, several cell biology studies that recently pushed the elucidation of key mechanisms in phage biology, such as the lysis-lysogeny decision in temperate phages or genome replication and transcription, one step further.

  17. [New challenges in the biological weapons convention].

    PubMed

    Sissonen, Susanna; Raijas, Tiina; Haikala, Olli; Hietala, Heikki; Virri, Markku; Nikkari, Simo

    2012-01-01

    Microbes and their toxins are biological weapons that can cause disease in humans, animals or plants, and which can be used with hostile intent in warfare and terrorism. Biological agents can be used as weapons of mass destruction and therefore, immense human and social and major economical damage can be caused. Rapid development of life sciences and technologies during the recent decades has posed new challenges to the Biological Weapons Convention. The Convention states that the States Parties to the BWC strive to ensure that the Convention remains relevant and effective, despite changes in science, technology or politics.

  18. Phobos Sample return and Planetary Protection - Issues of relevance

    NASA Astrophysics Data System (ADS)

    Walter, Nicolas; Worms, Jean-Claude

    This presentation will cover the main issues raised during a dedicated workshop supported by ESA, NASA and COSPAR and hosted by Fraunhofer Institute for High-Speed Dynamics (EMI, Freiburg) in June 2013. The workshop discussed backward planetary protection aspects of the Phootprint Mission concept in the general context of its categorisation. The Phootprint Mission would be aimed at collecting and returning samples from the Martian moon Phobos. Although Phootprint aims at returning samples from Phobos and not Mars, recent findings indicate that Martian material can be transferred to Phobos as ejecta following meteorite impact on Mars surface. In this context, it is important to assess whether a returned Phobos sample may contain active biological system (transferred from Mars) or not. The workshop considered the following issues: - Natural transfer of material from Mars to Phobos Workshop participants discussed the conditions resulting in Mars material being transferred to Phobos and the characteristics of such transfer. - Hypervelocity impact The workshop participant discussed the result of preliminary impact tests performed by Fraunhofer EMI. These tests involved impacting a basaltic projectile into a granular target. The biological inactivation effect of high velocity impact has to be further studied using the appropriate projectiles and targets. - Ionising radiation The effect of ionising radiation on biological systems potentially transferred to Phobos is also an aspect of critical relevance to be considered. During transfer and after impact on Phobos, material transferred will be subject to different ionising radiations conditions, these would need to be further modelled. - Biological model systems It was put forward that several biological model systems (preferably wild type) would have to be selected in order to perform the impact and radiation inactivation tests. ESA is funding a dedicated test activity based on the workshop output to support the

  19. [Functionally-relevant conformational dynamics of water-soluble proteins].

    PubMed

    Novikov, G V; Sivozhelezov, V S; Shaĭtan, K V

    2013-01-01

    A study is reported of the functional-relevant dynamics of three typical water-soluble proteins: Calmodulin, Src-tyrosine kinase as well as repressor of Trp operon. Application of the state-of-art methods of structural bioinformatics allowed to identify dynamics seen in the X-ray structures of the investigated proteins associated with their specific biological functions. In addition, Normal Mode analysis technique revealed the most probable directions of the functionally-relevant motions for all that proteins were also predicted. Importantly, overall type of the motions observed on the lowest-frequency modes was very similar to the motions seen from the analysis of the X-ray data of the examined macromolecules. Thereby it was shown that the large-scale as well as local conformational motions of the proteins might be predetermined already at the level of their tertiary structures. In particular, the determining factor might be the specific fold of the alpha-helixes. Thus functionally-relevant in vivo dynamics of the investigated proteins might be evolutionally formed by means of natural selection at the level of the spatial topology. PMID:23705506

  20. Transforming Big Data into Cancer-Relevant Insight: An Initial, Multi-Tier Approach to Assess Reproducibility and Relevance.

    PubMed

    2016-08-01

    The Cancer Target Discovery and Development (CTD(2)) Network was established to accelerate the transformation of "Big Data" into novel pharmacologic targets, lead compounds, and biomarkers for rapid translation into improved patient outcomes. It rapidly became clear in this collaborative network that a key central issue was to define what constitutes sufficient computational or experimental evidence to support a biologically or clinically relevant finding. This article represents a first attempt to delineate the challenges of supporting and confirming discoveries arising from the systematic analysis of large-scale data resources in a collaborative work environment and to provide a framework that would begin a community discussion to resolve these challenges. The Network implemented a multi-tier framework designed to substantiate the biological and biomedical relevance as well as the reproducibility of data and insights resulting from its collaborative activities. The same approach can be used by the broad scientific community to drive development of novel therapeutic and biomarker strategies for cancer. Mol Cancer Res; 14(8); 675-82. ©2016 AACR. PMID:27401613

  1. Transforming Big Data into Cancer-Relevant Insight: An Initial, Multi-Tier Approach to Assess Reproducibility and Relevance.

    PubMed

    2016-08-01

    The Cancer Target Discovery and Development (CTD(2)) Network was established to accelerate the transformation of "Big Data" into novel pharmacologic targets, lead compounds, and biomarkers for rapid translation into improved patient outcomes. It rapidly became clear in this collaborative network that a key central issue was to define what constitutes sufficient computational or experimental evidence to support a biologically or clinically relevant finding. This article represents a first attempt to delineate the challenges of supporting and confirming discoveries arising from the systematic analysis of large-scale data resources in a collaborative work environment and to provide a framework that would begin a community discussion to resolve these challenges. The Network implemented a multi-tier framework designed to substantiate the biological and biomedical relevance as well as the reproducibility of data and insights resulting from its collaborative activities. The same approach can be used by the broad scientific community to drive development of novel therapeutic and biomarker strategies for cancer. Mol Cancer Res; 14(8); 675-82. ©2016 AACR.

  2. Educational Informatics for the Biology Teacher.

    ERIC Educational Resources Information Center

    Baggott, Linda; Nichol, Jon; Ellison, Paul

    1997-01-01

    Presents an introduction to the Internet and the World Wide Web showing what they can provide for the biology teacher. Discusses how to get connected, how to avoid pitfalls, and how to maximize the benefits from a growing global information system. Includes pointers to useful and relevant Internet sites. (AIM)

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

    PubMed

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

    2016-06-16

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

  4. The Importance of Biological Databases in Biological Discovery.

    PubMed

    Baxevanis, Andreas D; Bateman, Alex

    2015-01-01

    Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non-sequence-centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. PMID:26094768

  5. Biological nitric oxide signalling: chemistry and terminology

    PubMed Central

    Heinrich, Tassiele A; da Silva, Roberto S; Miranda, Katrina M; Switzer, Christopher H; Wink, David A; Fukuto, Jon M

    2013-01-01

    Biological nitrogen oxide signalling and stress is an area of extreme clinical, pharmacological, toxicological, biochemical and chemical research interest. The utility of nitric oxide and derived species as signalling agents is due to their novel and vast chemical interactions with a variety of biological targets. Herein, the chemistry associated with the interaction of the biologically relevant nitrogen oxide species with fundamental biochemical targets is discussed. Specifically, the chemical interactions of nitrogen oxides with nucleophiles (e.g. thiols), metals (e.g. hemeproteins) and paramagnetic species (e.g. dioxygen and superoxide) are addressed. Importantly, the terms associated with the mechanisms by which NO (and derived species) react with their respective biological targets have been defined by numerous past chemical studies. Thus, in order to assist researchers in referring to chemical processes associated with nitrogen oxide biology, the vernacular associated with these chemical interactions is addressed. PMID:23617570

  6. Meeting the Challenges of Diversity and Relevance.

    ERIC Educational Resources Information Center

    Schwan-Smith, Margaret; Silver, Edward A.

    1995-01-01

    Discusses the QUASAR Project, which has worked with middle school teachers in disadvantaged communities in order to help increase the relevance of mathematics by making connections between the mathematics taught in school and the lives of students. (16 references) (MKR)

  7. 33 CFR 51.8 - Relevant considerations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... GUARD DISCHARGE REVIEW BOARD § 51.8 Relevant considerations. In determining the equity and propriety of... applicant's capability to serve, the DRB considers such factors as the applicant's age and...

  8. Sandia programs relevant to microelectronics fabrication

    SciTech Connect

    Picraux, S.T.; Vook, F.L.; Gregory, B.L.

    1987-04-01

    This report was prepared for the Semiconductor Industry and the National Laboratories Workshop held at the National Academy of Sciences, Washington, DC, February 24, 1987. It details the current Sandia program activities relevant to microelectronics fabrication.

  9. Relevance is Primary in Secondary Chemistry.

    ERIC Educational Resources Information Center

    Zoller, Uri

    1985-01-01

    Describes how relevant aspects of environmental education can be integrated within the framework of contemporary high school chemistry. Examples which show how students can examine the chemical consequences of such social factors as smoking and drinking are provided. (JN)

  10. Mother Goose Is Alive and Culturally Relevant.

    ERIC Educational Resources Information Center

    Crawley, Sharon

    1992-01-01

    Asserts that Mother Goose rhymes are culturally relevant. Offers ways in which Mother Goose can be used in the classroom. Discusses activities for language arts, movement, art, music, science, and mathematics instruction. (PRA)

  11. Ontologies in biological data visualization.

    PubMed

    Carpendale, Sheelagh; Chen, Min; Evanko, Daniel; Gehlenborg, Nils; Gorg, Carsten; Hunter, Larry; Rowland, Francis; Storey, Margaret-Anne; Strobelt, Hendrik

    2014-01-01

    In computer science, an ontology is essentially a graph-based knowledge representation in which each node corresponds to a concept and each edge specifies a relation between two concepts. Ontological development in biology can serve as a focus to discuss the challenges and possible research directions for ontologies in visualization. The principle challenges are the dynamic and evolving nature of ontologies, the ever-present issue of scale, the diversity and richness of the relationships in ontologies, and the need to better understand the relationship between ontologies and the data analysis tasks scientists wish to support. Research directions include visualizing ontologies; visualizing semantically or ontologically annotated texts, documents, and corpora; automated generation of visualizations using ontologies; and visualizing ontological context to support search. Although this discussion uses issues of ontologies in biological data visualization as a springboard, these topics are of general relevance to visualization. PMID:24808195

  12. Diverse biological activities of dandelion.

    PubMed

    González-Castejón, Marta; Visioli, Francesco; Rodriguez-Casado, Arantxa

    2012-09-01

    Dandelion (Taraxacum officinale Weber) is a member of the Asteraceae (Compositae) family, native to Europe but widely distributed in the warmer temperate zones of the Northern Hemisphere. Dandelion and its parts are habitually consumed as plant foods in several areas of the world, where they are also employed in phytotherapy. Indeed, dandelion contains a wide array of phytochemicals whose biological activities are actively being explored in various areas of human health. In particular, emerging evidence suggests that dandelion and its constituents have antioxidant and anti-inflammatory activities that result in diverse biological effects. The present review provides a comprehensive analysis of the constituents of dandelion, an assessment of the pharmacological properties of dandelion, and a description of relevant studies that support the use of dandelion as a medicinal plant.

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

    PubMed

    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.

  14. Introducing systems biology for nursing science.

    PubMed

    Founds, Sandra A

    2009-07-01

    Systems biology expands on general systems theory as the "omics'' era rapidly progresses. Although systems biology has been institutionalized as an interdisciplinary framework in the biosciences, it is not yet apparent in nursing. This article introduces systems biology for nursing science by presenting an overview of the theory. This framework for the study of organisms from molecular to environmental levels includes iterations of computational modeling, experimentation, and theory building. Synthesis of complex biological processes as whole systems rather than isolated parts is emphasized. Pros and cons of systems biology are discussed, and relevance of systems biology to nursing is described. Nursing research involving molecular, physiological, or biobehavioral questions may be guided by and contribute to the developing science of systems biology. Nurse scientists can proactively incorporate systems biology into their investigations as a framework for advancing the interdisciplinary science of human health care. Systems biology has the potential to advance the research and practice goals of the National Institute for Nursing Research in the National Institutes of Health Roadmap initiative. PMID:19221104

  15. Systems biology approaches in aging research.

    PubMed

    Chauhan, Anuradha; Liebal, Ulf W; Vera, Julio; Baltrusch, Simone; Junghanß, Christian; Tiedge, Markus; Fuellen, Georg; Wolkenhauer, Olaf; Köhling, Rüdiger

    2015-01-01

    Aging is a systemic process which progressively manifests itself at multiple levels of structural and functional organization from molecular reactions and cell-cell interactions in tissues to the physiology of an entire organ. There is ever increasing data on biomedical relevant network interactions for the aging process at different scales of time and space. To connect the aging process at different structural, temporal and spatial scales, extensive systems biological approaches need to be deployed. Systems biological approaches can not only systematically handle the large-scale datasets (like high-throughput data) and the complexity of interactions (feedback loops, cross talk), but also can delve into nonlinear behaviors exhibited by several biological processes which are beyond intuitive reasoning. Several public-funded agencies have identified the synergistic role of systems biology in aging research. Using one of the notable public-funded programs (GERONTOSYS), we discuss how systems biological approaches are helping the scientists to find new frontiers in aging research. We elaborate on some systems biological approaches deployed in one of the projects of the consortium (ROSage). The systems biology field in aging research is at its infancy. It is open to adapt existing systems biological methodologies from other research fields and devise new aging-specific systems biological methodologies.

  16. Biological warfare agents.

    PubMed

    Pohanka, Miroslav; Kuca, Kamil

    2010-01-01

    Biological warfare agents are a group of pathogens and toxins of biological origin that can be potentially misused for military or criminal purposes. The present review attempts to summarize necessary knowledge about biological warfare agents. The historical aspects, examples of applications of these agents such as anthrax letters, biological weapons impact, a summary of biological warfare agents and epidemiology of infections are described. The last section tries to estimate future trends in research on biological warfare agents.

  17. A Bridge between Two Cultures: Uncovering the Chemistry Concepts Relevant to the Nursing Clinical Practice

    ERIC Educational Resources Information Center

    Brown, Corina E.; Henry, Melissa L. M.; Barbera, Jack; Hyslop, Richard M.

    2012-01-01

    This study focused on the undergraduate course that covers basic topics in general, organic, and biological (GOB) chemistry at a mid-sized state university in the western United States. The central objective of the research was to identify the main topics of GOB chemistry relevant to the clinical practice of nursing. The collection of data was…

  18. Anion binding in biological systems

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  19. Education science and biological anthropology.

    PubMed

    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.

  20. Consideration of the cellular microenvironment: physiologically relevant co-culture systems in drug discovery.

    PubMed

    L Berg, Ellen; Hsu, Yu-Chih; Lee, Jonathan A

    2014-04-01

    There is renewed interest in phenotypic approaches to drug discovery, using cell-based assays to select new drugs, with the goal of improving pharmaceutical success. Assays that are more predictive of human biology can help researchers achieve this goal. Primary cells are more physiologically relevant to human biology and advances are being made in methods to expand the available cell types and improve the potential clinical translation of these assays through the use of co-cultures or three-dimensional (3D) technologies. Of particular interest are assays that may be suitable for industrial scale drug discovery. Here we review the use of primary human cells and co-cultures in drug discovery and describe the characteristics of co-culture models for inflammation biology (BioMAP systems), neo-vascularization and tumor microenvironments. Finally we briefly describe technical trends that may enable and impact the development of physiologically relevant co-culture assays in the near future. PMID:24524933

  1. Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.

    PubMed

    Pokharel, Yuba Raj; Saarela, Jani; Szwajda, Agnieszka; Rupp, Christian; Rokka, Anne; Lal Kumar Karna, Shibendra; Teittinen, Kaisa; Corthals, Garry; Kallioniemi, Olli; Wennerberg, Krister; Aittokallio, Tero; Westermarck, Jukka

    2015-12-01

    High content protein interaction screens have revolutionized our understanding of protein complex assembly. However, one of the major challenges in translation of high content protein interaction data is identification of those interactions that are functionally relevant for a particular biological question. To address this challenge, we developed a relevance ranking platform (RRP), which consist of modular functional and bioinformatic filters to provide relevance rank among the interactome proteins. We demonstrate the versatility of RRP to enable a systematic prioritization of the most relevant interaction partners from high content data, highlighted by the analysis of cancer relevant protein interactions for oncoproteins Pin1 and PME-1. We validated the importance of selected interactions by demonstration of PTOV1 and CSKN2B as novel regulators of Pin1 target c-Jun phosphorylation and reveal previously unknown interacting proteins that may mediate PME-1 effects via PP2A-inhibition. The RRP framework is modular and can be modified to answer versatile research problems depending on the nature of the biological question under study. Based on comparison of RRP to other existing filtering tools, the presented data indicate that RRP offers added value especially for the analysis of interacting proteins for which there is no sufficient prior knowledge available. Finally, we encourage the use of RRP in combination with either SAINT or CRAPome computational tools for selecting the candidate interactors that fulfill the both important requirements, functional relevance, and high confidence interaction detection.

  2. Biological conversion system

    DOEpatents

    Scott, C.D.

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

  3. Learning Biology by Designing

    ERIC Educational Resources Information Center

    Janssen, Fred; Waarlo, Arend Jan

    2010-01-01

    According to a century-old tradition in biological thinking, organisms can be considered as being optimally designed. In modern biology this idea still has great heuristic value. In evolutionary biology a so-called design heuristic has been formulated which provides guidance to researchers in the generation of knowledge about biological systems.…

  4. Relevance and Significance of Extraterrestrial Abiological Hydrocarbon Chemistry.

    PubMed

    Olah, George A; Mathew, Thomas; Prakash, G K Surya

    2016-06-01

    Astrophysical observations show similarity of observed abiological "organics"-i.e., hydrocarbons, their derivatives, and ions (carbocations and carbanions)-with studied terrestrial chemistry. Their formation pathways, their related extraterrestrial hydrocarbon chemistry originating from carbon and other elements after the Big Bang, their parent hydrocarbon and derivative (methane and methanol, respectively), and transportation of derived building blocks of life by meteorites or comets to planet Earth are discussed in this Perspective. Their subsequent evolution on Earth under favorable "Goldilocks" conditions led to more complex molecules and biological systems, and eventually to humans. The relevance and significance of extraterrestrial hydrocarbon chemistry to the limits of science in relation to the physical aspects of evolution on our planet Earth are also discussed.

  5. Internal symmetry in protein structures: prevalence, functional relevance and evolution.

    PubMed

    Balaji, Santhanam

    2015-06-01

    Symmetry has been found at various levels of biological organization in the protein structural universe. Numerous evolutionary studies have proposed connections between internal symmetry within protein tertiary structures, quaternary associations and protein functions. Recent computational methods, such as SymD and CE-Symm, facilitate a large-scale detection of internal symmetry in protein structures. Based on the results from these methods, about 20% of SCOP folds, superfamilies and families are estimated to have structures with internal symmetry (Figure 1d). All-β and membrane proteins fold classes contain a relatively high number of unique instances of internal symmetry. In addition to the axis of symmetry, anecdotal evidence suggests that, the region of connection or contact between symmetric units could coincide with functionally relevant sites within a fold. General principles that underlie protein internal symmetry and their connections to protein structural integrity and functions remain to be elucidated.

  6. Relevance and Significance of Extraterrestrial Abiological Hydrocarbon Chemistry.

    PubMed

    Olah, George A; Mathew, Thomas; Prakash, G K Surya

    2016-06-01

    Astrophysical observations show similarity of observed abiological "organics"-i.e., hydrocarbons, their derivatives, and ions (carbocations and carbanions)-with studied terrestrial chemistry. Their formation pathways, their related extraterrestrial hydrocarbon chemistry originating from carbon and other elements after the Big Bang, their parent hydrocarbon and derivative (methane and methanol, respectively), and transportation of derived building blocks of life by meteorites or comets to planet Earth are discussed in this Perspective. Their subsequent evolution on Earth under favorable "Goldilocks" conditions led to more complex molecules and biological systems, and eventually to humans. The relevance and significance of extraterrestrial hydrocarbon chemistry to the limits of science in relation to the physical aspects of evolution on our planet Earth are also discussed. PMID:27045758

  7. Fluid mechanics relevant to flow through pretreatment of cellulosic biomass.

    PubMed

    Archambault-Léger, Véronique; Lynd, Lee R

    2014-04-01

    The present study investigates fluid mechanical properties of cellulosic feedstocks relevant to flow through (FT) pretreatment for biological conversion of cellulosic biomass. The results inform identifying conditions for which FT pretreatment can be implemented in a practical context. Measurements of pressure drop across packed beds, viscous compaction and water absorption are reported for milled and not milled sugarcane bagasse, switchgrass and poplar, and important factors impacting viscous flow are deduced. Using biomass knife-milled to pass through a 2mm sieve, the observed pressure drop was highest for bagasse, intermediate for switchgrass and lowest for poplar. The highest pressure drop was associated with the presence of more fine particles, greater viscous compaction and the degree of water absorption. Using bagasse without particle size reduction, the instability of the reactor during pretreatment above 140kg/m(3) sets an upper bound on the allowable concentration for continuous stable flow.

  8. Quantum Effects in Biological Systems

    NASA Astrophysics Data System (ADS)

    Roy, Sisir

    2014-07-01

    The debates about the trivial and non-trivial effects in biological systems have drawn much attention during the last decade or so. What might these non-trivial sorts of quantum effects be? There is no consensus so far among the physicists and biologists regarding the meaning of "non-trivial quantum effects". However, there is no doubt about the implications of the challenging research into quantum effects relevant to biology such as coherent excitations of biomolecules and photosynthesis, quantum tunneling of protons, van der Waals forces, ultrafast dynamics through conical intersections, and phonon-assisted electron tunneling as the basis for our sense of smell, environment assisted transport of ions and entanglement in ion channels, role of quantum vacuum in consciousness. Several authors have discussed the non-trivial quantum effects and classified them into four broad categories: (a) Quantum life principle; (b) Quantum computing in the brain; (c) Quantum computing in genetics; and (d) Quantum consciousness. First, I will review the above developments. I will then discuss in detail the ion transport in the ion channel and the relevance of quantum theory in brain function. The ion transport in the ion channel plays a key role in information processing by the brain.

  9. Translational environmental biology: cell biology informing conservation.

    PubMed

    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.

  10. Synthetic biology: insights into biological computation.

    PubMed

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  11. Translational environmental biology: cell biology informing conservation.

    PubMed

    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. PMID:24766840

  12. Synthetic biology: insights into biological computation.

    PubMed

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  13. New metal based drug as a therapeutic agent: Spectral, electrochemical, DNA-binding, surface morphology and photoluminescence properties

    NASA Astrophysics Data System (ADS)

    Muslu, Harun; Gölcü, Ayşegül

    2015-07-01

    Cu(II) complexes of non-steroidal anti-inflammatory drug (NSAID) Meloxicam (H2MLX) was synthesized and characterized via spectroscopic and analytical techniques. The thermal behavior of the complex was also analyzed. The photoluminescence properties of the compounds were analyzed under different conditions. The electrochemical properties of both ligand and complex have been analyzed by Cyclic Voltammetry (CV) using glassy carbon electrode. The biological activities of the compounds were evaluated through examining their capacity to bind to fish sperm double strand DNA (FSdsDNA) with absorption spectroscopy and differential pulse voltammetry (DPV). Absorption studies of the interaction of the H2MLX and its Cu(II) complex with FSdsDNA have indicated that these compounds could bind to FSdsDNA, and the binding constants were calculated. The morphology of the FSdsDNA, H2MLX, and Cu(II) complex were analyzed thanks to using scanning electron microscopy (SEM). In the DPV technique, pencil graphite electrode was used as a working electrode. The decrease in the intensity of the guanine oxidation signals was used as an indicator for the interaction mechanism.

  14. Bioavailability and bioaccumulation of metal-based engineered nanomaterials in aquatic environments: concepts and processes: chapter 5

    USGS Publications Warehouse

    Luoma, Samuel N.; Khan, Farhan R.; Croteau, Marie-Noële

    2014-01-01

    Bioavailability of Me-ENMs to aquatic organisms links their release into the environment to ecological implications. Close examination shows some important differences in the conceptual models that define bioavailability for metals and Me-ENMs. Metals are delivered to aquatic animals from Me-ENMs via water, ingestion, and incidental surface exposure. Both metal released from the Me-ENM and uptake of the nanoparticle itself contribute to bioaccumulation. Some mechanisms of toxicity and some of the metrics describing exposure may differ from metals alone. Bioavailability is driven by complex interaction of particle attributes, environmental transformations, and biological traits. Characterization of Me-ENMs is an essential part of understanding bioavailability and requires novel methodologies. The relative importance of the array of processes that could affect Me-ENM bioavailability remains poorly known, but new approaches and models are developing rapidly. Enough is known, however, to conclude that traditional approaches to exposure assessment for metals would not be adequate to assess risks from Me-ENMs.

  15. Relevant energy ranges for astrophysical reaction rates

    SciTech Connect

    Rauscher, Thomas

    2010-04-15

    Effective energy windows (Gamow windows) of astrophysical reaction rates for (p,gamma), (p,n), (p,alpha), (alpha,gamma), (alpha,n), (alpha,p), (n,gamma), (n,p), and (n,alpha) on targets with 10<=Z<=83 from proton to neutron dripline are calculated using theoretical cross sections. It is shown that widely used approximation formulas for the relevant energy ranges are not valid for a large number of reactions relevant to hydrostatic and explosive nucleosynthesis. The influence of the energy dependence of the averaged widths on the location of the Gamow windows is discussed and the results are presented in tabular form.

  16. Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance | Office of Cancer Genomics

    Cancer.gov

    The Cancer Target Discovery and Development (CTD^2) Network was established to accelerate the transformation of "Big Data" into novel pharmacological targets, lead compounds, and biomarkers for rapid translation into improved patient outcomes. It rapidly became clear in this collaborative network that a key central issue was to define what constitutes sufficient computational or experimental evidence to support a biologically or clinically relevant finding.

  17. Systems interface biology

    PubMed Central

    Doyle, Francis J; Stelling, Jörg

    2006-01-01

    The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological networks. In particular, systems engineering methods are finding unique opportunities in characterizing the rich behaviour exhibited by biological systems. In the same manner, these new classes of biological problems are motivating novel developments in theoretical systems approaches. Hence, the interface between systems and biology is of mutual benefit to both disciplines. PMID:16971329

  18. What is Systems Biology?

    PubMed Central

    Breitling, Rainer

    2010-01-01

    Systems biology is increasingly popular, but to many biologists it remains unclear what this new discipline actually encompasses. This brief personal perspective starts by outlining the asthetic qualities that motivate systems biologists, discusses which activities do not belong to the core of systems biology, and finally explores the crucial link with synthetic biology. It concludes by attempting to define systems biology as the research endeavor that aims at providing the scientific foundation for successful synthetic biology. PMID:21423352

  19. [Cross reactivity of food allergens and its clinical relevance].

    PubMed

    Moneret-Vautrin, Denise Anne

    2005-10-01

    Cross-reactions between food allergens and other allergens are a major focus of interest. They include cross-allergies between Betulaceae and Compositae pollen, and also between fruits and vegetables (Prunoideae and Apiaceae). Cross-allergies between animal allergens include mites, cockroaches and crustaceans, milk and meat, animal epithelia, meat and egg. Cross-reactivity results from homology between protein sequences, and is highly likely when this homology reaches about 70%. Phylogenetically similar proteins occur in all species and are known as pan allergens. Profilins, Bet v1 homologues, and lipid transfer proteins have varying degrees of clinical relevance. The involvement of cross-reactivity in the persistence of sensitization and in allergic disorders is unclear. The consequences of cross-reactivity during specific immunotherapy with total allergenic extracts are random. Interpretation of biological tests of IgE binding is also biased by cross-reactivity. The use of panels of major recombinant allergens should help to identify specific sensitization profiles as well as clinically relevant sensitization. Cross-reactivity between epitopes of inhalants and of food allergens may perpetuate and intensify allergic disorders. The consequences of cross-reactivity between allergens and autologous proteins are unknown. PMID:16669147

  20. Real time and label free profiling of clinically relevant exosomes.

    PubMed

    Sina, Abu Ali Ibn; Vaidyanathan, Ramanathan; Dey, Shuvashis; Carrascosa, Laura G; Shiddiky, Muhammad J A; Trau, Matt

    2016-01-01

    Tumor-derived exosomes possess significant clinical relevance due to their unique composition of genetic and protein material that is representative of the parent tumor. Specific isolation as well as identification of proportions of these clinically relevant exosomes (CREs) from biological samples could help to better understand their clinical significance as cancer biomarkers. Herein, we present a simple approach for quantification of the proportion of CREs within the bulk exosome population isolated from patient serum. This proportion of CREs can potentially inform on the disease stage and enable non-invasive monitoring of inter-individual variations in tumor-receptor expression levels. Our approach utilises a Surface Plasmon Resonance (SPR) platform to quantify the proportion of CREs in a two-step strategy that involves (i) initial isolation of bulk exosome population using tetraspanin biomarkers (i.e., CD9, CD63), and (ii) subsequent detection of CREs within the captured bulk exosomes using tumor-specific markers (e.g., human epidermal growth factor receptor 2 (HER2)). We demonstrate the isolation of bulk exosome population and detection of as low as 10% HER2(+) exosomes from samples containing designated proportions of HER2(+) BT474 and HER2(-) MDA-MB-231 cell derived exosomes. We also demonstrate the successful isolation of exosomes from a small cohort of breast cancer patient samples and identified that approximately 14-35% of their bulk population express HER2. PMID:27464736

  1. Real time and label free profiling of clinically relevant exosomes

    PubMed Central

    Sina, Abu Ali Ibn; Vaidyanathan, Ramanathan; Dey, Shuvashis; Carrascosa, Laura G.; Shiddiky, Muhammad J. A.; Trau, Matt

    2016-01-01

    Tumor-derived exosomes possess significant clinical relevance due to their unique composition of genetic and protein material that is representative of the parent tumor. Specific isolation as well as identification of proportions of these clinically relevant exosomes (CREs) from biological samples could help to better understand their clinical significance as cancer biomarkers. Herein, we present a simple approach for quantification of the proportion of CREs within the bulk exosome population isolated from patient serum. This proportion of CREs can potentially inform on the disease stage and enable non-invasive monitoring of inter-individual variations in tumor-receptor expression levels. Our approach utilises a Surface Plasmon Resonance (SPR) platform to quantify the proportion of CREs in a two-step strategy that involves (i) initial isolation of bulk exosome population using tetraspanin biomarkers (i.e., CD9, CD63), and (ii) subsequent detection of CREs within the captured bulk exosomes using tumor-specific markers (e.g., human epidermal growth factor receptor 2 (HER2)). We demonstrate the isolation of bulk exosome population and detection of as low as 10% HER2(+) exosomes from samples containing designated proportions of HER2(+) BT474 and HER2(−) MDA-MB-231 cell derived exosomes. We also demonstrate the successful isolation of exosomes from a small cohort of breast cancer patient samples and identified that approximately 14–35% of their bulk population express HER2. PMID:27464736

  2. Computational investigations of HNO in biology

    PubMed Central

    Zhang, Yong

    2013-01-01

    HNO (nitroxyl) has been found to have many physiological effects in numerous biological processes. Computational investigations have been employed to help understand the structural properties of HNO complexes and HNO reactivities in some interesting biologically relevant systems. The following computational aspects were reviewed in this work: 1) structural and energetic properties of HNO isomers; 2) interactions between HNO and non-metal molecules; 3) structural and spectroscopic properties of HNO metal complexes; 4) HNO reactions with biologically important non-metal systems; 5) involvement of HNO in reactions of metal complexes and metalloproteins. Results indicate that computational investigations are very helpful to elucidate interesting experimental phenomena and provide new insights into unique structural, spectroscopic, and mechanistic properties of HNO involvement in biology. PMID:23103077

  3. Biological organisation as closure of constraints.

    PubMed

    Montévil, Maël; Mossio, Matteo

    2015-05-01

    We propose a conceptual and formal characterisation of biological organisation as a closure of constraints. We first establish a distinction between two causal regimes at work in biological systems: processes, which refer to the whole set of changes occurring in non-equilibrium open thermodynamic conditions; and constraints, those entities which, while acting upon the processes, exhibit some form of conservation (symmetry) at the relevant time scales. We then argue that, in biological systems, constraints realise closure, i.e. mutual dependence such that they both depend on and contribute to maintaining each other. With this characterisation in hand, we discuss how organisational closure can provide an operational tool for marking the boundaries between interacting biological systems. We conclude by focusing on the original conception of the relationship between stability and variation which emerges from this framework.

  4. Ultrafast optics: Imaging and manipulating biological systems

    NASA Astrophysics Data System (ADS)

    Sheetz, Kraig E.; Squier, Jeff

    2009-03-01

    The rapid evolution of ultrafast optics technology over the past two decades has opened the window to a broad range of applications in biology and medicine. Compact, reliable, and turn-key ultrafast laser systems are enabling cutting-edge science to take place in everyday laboratories and clinics. Led by the discovery of two-photon excitation fluorescence microscopy nearly 20 years ago, the biological imaging community is exploring unique image contrast mechanisms and pushing spatial and temporal resolution to new limits. Concurrent with advancements in imaging are developments in the precision application of extremely high peak intensities available in ultrashort pulses for disrupting or manipulating targeted locations in biological systems on the submicron scale while leaving surrounding tissue healthy. The ability for scientists to selectively discriminate structures of interest at the cellular and subcellular levels under relevant physiological conditions shows tremendous promise for accelerating the path to understanding biological functions at the most fundamental level.

  5. Unleashing Optics and Optoacoustics for Developmental Biology.

    PubMed

    Ripoll, J; Koberstein-Schwarz, B; Ntziachristos, V

    2015-11-01

    The past decade marked an optical revolution in biology: an unprecedented number of optical techniques were developed and adopted for biological exploration, demonstrating increasing interest in optical imaging and in vivo interrogations. Optical methods have become faster and have reached nanoscale resolution, and are now complemented by optoacoustic (photoacoustic) methods capable of imaging whole specimens in vivo. Never before were so many optical imaging barriers broken in such a short time-frame: with new approaches to optical microscopy and mesoscopy came an increased ability to image biology at unprecedented speed, resolution, and depth. This review covers the most relevant techniques for imaging in developmental biology, and offers an outlook on the next steps for these technologies and their applications.

  6. Chemical Foundations of Hydrogen Sulfide Biology

    PubMed Central

    Li, Qian; Lancaster, Jack R.

    2013-01-01

    Following nitric oxide (nitrogen monoxide) and carbon monoxide, hydrogen sulfide (or its newer systematic name sulfane, H2S) became the third small molecule that can be both toxic and beneficial depending on the concentration. In spite of its impressive therapeutic potential, the underlying mechanisms for its beneficial effects remain unclear. Any novel mechanism has to obey fundamental chemical principles. H2S chemistry was studied long before its biological relevance was discovered, however, with a few exceptions, these past works have received relatively little attention in the path of exploring the mechanistic conundrum of H2S biological functions. This review calls attention to the basic physical and chemical properties of H2S, focuses on the chemistry between H2S and its three potential biological targets: oxidants, metals and thiol derivatives, discusses the applications of these basics into H2S biology and methodology, and introduces the standard terminology to this youthful field. PMID:23850631

  7. Unleashing Optics and Optoacoustics for Developmental Biology.

    PubMed

    Ripoll, J; Koberstein-Schwarz, B; Ntziachristos, V

    2015-11-01

    The past decade marked an optical revolution in biology: an unprecedented number of optical techniques were developed and adopted for biological exploration, demonstrating increasing interest in optical imaging and in vivo interrogations. Optical methods have become faster and have reached nanoscale resolution, and are now complemented by optoacoustic (photoacoustic) methods capable of imaging whole specimens in vivo. Never before were so many optical imaging barriers broken in such a short time-frame: with new approaches to optical microscopy and mesoscopy came an increased ability to image biology at unprecedented speed, resolution, and depth. This review covers the most relevant techniques for imaging in developmental biology, and offers an outlook on the next steps for these technologies and their applications. PMID:26435161

  8. Multiscale Computational Models of Complex Biological Systems

    PubMed Central

    Walpole, Joseph; Papin, Jason A.; Peirce, Shayn M.

    2014-01-01

    Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental platforms, has allowed multiscale modeling to expand as a means to more comprehensively investigate biological phenomena in experimentally relevant ways. This review aims to highlight recently published multiscale models of biological systems while using their successes to propose the best practices for future model development. We demonstrate that coupling continuous and discrete systems best captures biological information across spatial scales by selecting modeling techniques that are suited to the task. Further, we suggest how to best leverage these multiscale models to gain insight into biological systems using quantitative, biomedical engineering methods to analyze data in non-intuitive ways. These topics are discussed with a focus on the future of the field, the current challenges encountered, and opportunities yet to be realized. PMID:23642247

  9. Relevance of microelectronic education to industrial needs

    NASA Technical Reports Server (NTRS)

    Prince, J. L.; Lathrop, J. W.

    1977-01-01

    The relevance of microelectronic education to industrial needs was evaluated, and four categories were surveyed: (1) facts and rules; (2) skills; (3) personality; and (4) deductive-inductive reasoning. Examples of specific items in each category are given to illustrate their meaning and it was indicated as to which items in each category are strongly impacted by microelectronics courses and laboratories.

  10. Contingent Attentional Capture by Conceptually Relevant Images

    ERIC Educational Resources Information Center

    Wyble, Brad; Folk, Charles; Potter, Mary C.

    2013-01-01

    Attentional capture is an unintentional shift of visuospatial attention to the location of a distractor that is either highly salient, or relevant to the current task set. The latter situation is referred to as contingent capture, in that the effect is contingent on a match between characteristics of the stimuli and the task-defined…

  11. Making Chemistry Relevant to the Engineering Major

    ERIC Educational Resources Information Center

    Basu-Dutt, Sharmistha; Slappey, Charles; Bartley, Julie K.

    2010-01-01

    As part of a campus-wide, externally funded project to increase performance in, enthusiasm for, and retention within STEM disciplines, we developed an interdisciplinary, team-taught first-year seminar course. The construction and delivery of this course was designed to show the relevance of selected general chemistry topics such as matter and…

  12. Basic Structure of Work-Relevant Abilities.

    ERIC Educational Resources Information Center

    Prediger, Dale J.

    This study sought to determine whether the dimensions underlying a comprehensive set of 15 work-relevant abilities were similar to the Data/Ideas and Things/People Work Task Dimensions (D. J. Prediger, 1996) underlying J. L. Holland's (1997) hexagonal model of interest and occupational types. The work task dimensions and a general ability…

  13. The Relevance Aura of Bibliographic Records.

    ERIC Educational Resources Information Center

    Brooks, Terrence A.

    1997-01-01

    Analyzes relevance assessments of topical descriptors for bibliographic records for two dimensions: (1) a vertical conceptual hierarchy of broad to narrow descriptors, and (2) a horizontal linkage of related terms. The data were analyzed for a semantic distance and semantic direction effect as postulated by the Semantic Distance Model. (Author/LRW)

  14. Relevance, Pertinence and Information System Development

    ERIC Educational Resources Information Center

    Kemp, D. A.

    1974-01-01

    The difference between pertinence and relevance is discussed. Other pairs of terms and the differences between their members are examined, and the suggestion is made that such studies could increase our understanding of the theory of information systems, and thence lead to practical improvements. (Author)

  15. Achieving Relevance in Assessment through Fieldtrips

    ERIC Educational Resources Information Center

    Sutton-Brady, Catherine

    2008-01-01

    Students often bemoan the fact that they can't see the relevance of the report they are asked to write or the case study they have to analyze. This paper introduces the use of attending an industry tradeshow as a means of making assessment more interesting and meaningful. Much has been written about the need to bring reality back to management…

  16. The New FFA--Relevant, Flexible.

    ERIC Educational Resources Information Center

    Future Farmers of America, Washington, DC.

    To make education more relevant, the 1972 national seminar sought ways of integrating the Future Farmers of America (FFA) program with the broadened agricultural instruction program. Topics discussed included: (1) "Role of the FFA in the Changing Program of Agricultural Education" - William Gray (Moderator), (2) "But How Do We Get the Job Done?"…

  17. The Relevance of Cosmopolitanism for Moral Education

    ERIC Educational Resources Information Center

    Merry, Michael S.; de Ruyter, Doret J.

    2011-01-01

    In this article we defend a moral conception of cosmopolitanism and its relevance for moral education. Our moral conception of cosmopolitanism presumes that persons possess an inherent dignity in the Kantian sense and therefore they should be recognised as ends-in-themselves. We argue that cosmopolitan ideals can inspire moral educators to awaken…

  18. The Relevance of Anthropology to Language Teaching

    ERIC Educational Resources Information Center

    McLeod, Beverly

    1976-01-01

    The relevance of anthropological theory, methodology, and literature to language teaching is discussed. It is argued that culture should be taught explicitly in the language classroom, and that the anthropological theory of cultural relativity is useful in creating a judgment-free atmosphere. (Author/RM)

  19. Is Enterprise Education Relevant to Social Enterprise?

    ERIC Educational Resources Information Center

    Bridge, Simon

    2015-01-01

    Purpose: Both enterprise education and social enterprise have become fashionable but what, if any, should be the connections between them? The purpose of this paper is to explore those connections and to reflect on what relevance the two concepts might have for each other. Design/methodology/approach: Both enterprise education and social…

  20. COMPARING ENVIRONMENTALLY RELEVANT PCBS TO TCDD

    EPA Science Inventory

    COMPARING ENVIRONMENTALLY RELEVANT PCBS TO TCDD. D E Burgin1, J J Diliberto2 and L S Birnbaum3.1UNC, Chapel Hill, NC, USA; 2USEPA/ORD/NHEERL, ETD, RTP, NC, USA

    Environmental exposures to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) always occur as part of a complex mixture. ...