WorldWideScience

Sample records for biological function construction

  1. Polymer biomaterial constructs for regenerative medicine and functional biological systems

    Science.gov (United States)

    Meng, Linghui

    The use of collagen as a biomaterial is currently undergoing a renaissance in the tissue engineering field. The excellent biocompatibility and safety due to its biological characteristics, such as biodegradability and weak antigenicity, make collagen a primary material resource in medical applications. Described herein is work towards the development of novel collagen-based matrices, with additional multi-functionality imparted through a novel in-situ crosslinking approach. The process of electrospinning has become a widely used technique for the creation of fibrous scaffolds for tissue engineering applications due to its ability to rapidly create structures composed of nano-scale polymer fibers closely resembling the architecture of the extracellular matrix (ECM). Collagen-PCL sheath-core bicomponent fibrous scaffolds were fabricated using a novel variation on traditional electrospinning, known as co-axial electrospinning. The results showed that the addition of a synthetic polymer core into collagen nanofibers remarkably increased the mechanical strength of collagen matrices spun from the benign solvent system. A novel single-step, in-situ collagen crosslink approach was developed in order to solve the problems dominating traditional collagen crosslinking methods, such as dimensional shrinking and loss of porous morphology, and to simplify the crosslinking procedure for electrospun collagen scaffolds. The excess amount of NHS present in the crosslinking mixture was found to delay the EDC/collagen coupling reaction in a controlled fashion. Fundamental investigations into the development and characterization of in-situ crosslinked collagen matrices such as fibrous scaffolds, gels and sponges, as well as their biomedical applications including cell culture substrates, wound dressings, drug delivery matrices and bone regeneration substitutes, were performed. The preliminary mice studies indicated that the in-situ crosslinked collagen matrices could be good candidates

  2. Construction of Resilient Functions

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jie; WEN Qiao-yan

    2005-01-01

    Based on the relationship between nonlinearity and resiliency of a multi-output function, we present a method for constructing nonintersecting linear codes from packing design. Through these linear codes, we obtain n-variable, moutput, t-resilient functions with very high nonlinearity.Their nonlinearities are currently the best results for most of cases.

  3. Construction of optimized Boolean functions

    Institute of Scientific and Technical Information of China (English)

    CHEN Wei; YANG Yi-xian; NIU Xin-xin

    2006-01-01

    Considering connections of characteristics,this paper is aimed at the construction of optimized Boolean functions.A new method based on the Bent function,discrete Walsh spectrum and characteristics matrices are presented by concatenating,breaking,and revising output sequences conditionally.This new construction can be used to construct different kinds of functions satisfying different design criteria.

  4. Functions in Biological Kind Classification

    Science.gov (United States)

    Lombrozo, Tania; Rehder, Bob

    2012-01-01

    Biological traits that serve functions, such as a zebra's coloration (for camouflage) or a kangaroo's tail (for balance), seem to have a special role in conceptual representations for biological kinds. In five experiments, we investigate whether and why functional features are privileged in biological kind classification. Experiment 1…

  5. The relativity of biological function.

    Science.gov (United States)

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

    2015-12-01

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

  6. Imaging cellular and molecular biological functions

    Energy Technology Data Exchange (ETDEWEB)

    Shorte, S.L. [Institut Pasteur, 75 - Paris (France). Plateforme d' Imagerie Dynamique PFID-Imagopole; Frischknecht, F. (eds.) [Heidelberg Univ. Medical School (Germany). Dept. of Parasitology

    2007-07-01

    'Imaging cellular and molecular biological function' provides a unique selection of essays by leading experts, aiming at scientist and student alike who are interested in all aspects of modern imaging, from its application and up-scaling to its development. Indeed the philosophy of this volume is to provide student, researcher, PI, professional or provost the means to enter this applications field with confidence, and to construct the means to answer their own specific questions. (orig.)

  7. Understanding biological functions through molecular networks

    Institute of Scientific and Technical Information of China (English)

    Jing-Dong Jackie Han

    2008-01-01

    The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.

  8. Constructing new APN functions from known ones

    DEFF Research Database (Denmark)

    Budaghyan, L.; Carlet, C.; Leander, Gregor

    2009-01-01

    We present a method for constructing new quadratic APN functions from known ones. Applying this method to the Gold power functions we construct an APN function x(3) + tr(x(9)) over F2(n). It is proven that for n >= 7 this function is CCZ-inequivalent to the Gold functions, and in the case n = 7 i...

  9. The biological function of consciousness

    Science.gov (United States)

    Earl, Brian

    2014-01-01

    This research is an investigation of whether consciousness—one's ongoing experience—influences one's behavior and, if so, how. Analysis of the components, structure, properties, and temporal sequences of consciousness has established that, (1) contrary to one's intuitive understanding, consciousness does not have an active, executive role in determining behavior; (2) consciousness does have a biological function; and (3) consciousness is solely information in various forms. Consciousness is associated with a flexible response mechanism (FRM) for decision-making, planning, and generally responding in nonautomatic ways. The FRM generates responses by manipulating information and, to function effectively, its data input must be restricted to task-relevant information. The properties of consciousness correspond to the various input requirements of the FRM; and when important information is missing from consciousness, functions of the FRM are adversely affected; both of which indicate that consciousness is the input data to the FRM. Qualitative and quantitative information (shape, size, location, etc.) are incorporated into the input data by a qualia array of colors, sounds, and so on, which makes the input conscious. This view of the biological function of consciousness provides an explanation why we have experiences; why we have emotional and other feelings, and why their loss is associated with poor decision-making; why blindsight patients do not spontaneously initiate responses to events in their blind field; why counter-habitual actions are only possible when the intended action is in mind; and the reason for inattentional blindness. PMID:25140159

  10. Biological couplings: Function, characteristics and implementation mode

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Through rigorous natural selection, biological organisms have evolved exceptional functions highly adaptable to their living environments. Biological organisms can achieve a variety of biological functions efficiently by using the synergic actions of two or more different parts of the body, or the coupling effects of multiple factors, and demonstrate optimal adaptations to the living environment. In this paper, the function, characteristics and types of biological couplings are analyzed, the implementation mechanism and mode of biological coupling functions are revealed from the bionic viewpoint. Finally, the technological prospects of the bionic implementation of biological coupling function are predicted.

  11. Construction and Enumerating of Resilient—Functions

    Institute of Scientific and Technical Information of China (English)

    WENQiaoyan; YANGYixian

    2003-01-01

    This paper discussed construction and enumeration of resilient functions,which have widely applications in the fault-tolerant distributed computing,quantum-cryptographic key distribution,and random sequence generation for stream ciphers.It turned out that resilient functions are special case of unbiased multi-value correlation-immune functions.Resilient functions are constructed by recursive construction of orthogonal matrices and the exact number of them is found for some special cases.

  12. Construction of bent functions from near-bent functions

    DEFF Research Database (Denmark)

    Leander, Gregor; McGuire, G.

    2009-01-01

    We give a construction of bent functions in dimension 2m from near-bent functions in dimension 2m - 1. in particular, we give the first ever examples of non-weakly-normal bent functions in dimensions 10 and 12, which demonstrates the significance of our construction.......We give a construction of bent functions in dimension 2m from near-bent functions in dimension 2m - 1. in particular, we give the first ever examples of non-weakly-normal bent functions in dimensions 10 and 12, which demonstrates the significance of our construction....

  13. Constructing Ethical Principles for Synthetic Biology

    DEFF Research Database (Denmark)

    Dige, Morten

    2010-01-01

    The ethical discussion over synbio naturally raises metaquestions or questions of methodology: Which ethical principles and values could or should function as orientation or guidelines in discussing these issues?...

  14. Functional quantum biology in photosynthesis and magnetoreception

    CERN Document Server

    Lambert, Neill; Cheng, Yuan-Chung; Li, Che-Ming; Chen, Guang-Yin; Nori, Franco

    2012-01-01

    Is there a functional role for quantum mechanics or coherent quantum effects in biological processes? While this question is as old as quantum theory, only recently have measurements on biological systems on ultra-fast time-scales shed light on a possible answer. In this review we give an overview of the two main candidates for biological systems which may harness such functional quantum effects: photosynthesis and magnetoreception. We discuss some of the latest evidence both for and against room temperature quantum coherence, and consider whether there is truly a functional role for coherence in these biological mechanisms. Finally, we give a brief overview of some more speculative examples of functional quantum biology including the sense of smell, long-range quantum tunneling in proteins, biological photoreceptors, and the flow of ions across a cell membrane.

  15. BioFNet: biological functional network database for analysis and synthesis of biological systems.

    Science.gov (United States)

    Kurata, Hiroyuki; Maeda, Kazuhiro; Onaka, Toshikazu; Takata, Takenori

    2014-09-01

    In synthetic biology and systems biology, a bottom-up approach can be used to construct a complex, modular, hierarchical structure of biological networks. To analyze or design such networks, it is critical to understand the relationship between network structure and function, the mechanism through which biological parts or biomolecules are assembled into building blocks or functional networks. A functional network is defined as a subnetwork of biomolecules that performs a particular function. Understanding the mechanism of building functional networks would help develop a methodology for analyzing the structure of large-scale networks and design a robust biological circuit to perform a target function. We propose a biological functional network database, named BioFNet, which can cover the whole cell at the level of molecular interactions. The BioFNet takes an advantage in implementing the simulation program for the mathematical models of the functional networks, visualizing the simulated results. It presents a sound basis for rational design of biochemical networks and for understanding how functional networks are assembled to create complex high-level functions, which would reveal design principles underlying molecular architectures.

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

    Science.gov (United States)

    Haave, Neil

    2012-01-01

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

  17. Construction and analysis of cryptographic functions

    CERN Document Server

    Budaghyan, Lilya

    2015-01-01

    This book covers novel research on construction and analysis of optimal cryptographic functions such as almost perfect nonlinear (APN), almost bent (AB), planar and bent functions. These functions have optimal resistance to linear and/or differential attacks, which are the two most powerful attacks on symmetric cryptosystems. Besides cryptographic applications, these functions are significant in many branches of mathematics and information theory including coding theory, combinatorics, commutative algebra, finite geometry, sequence design and quantum information theory. The author analyzes equ

  18. Construction of plateaued functions satisfying multiple criteria

    Institute of Scientific and Technical Information of China (English)

    Zhang Weiguo

    2005-01-01

    A class of plateaued functions has been got by using the Maiorana-McFarland construction. A variety of desirable criteria for functions with cryptographic application could be satisfied: balancedness, high nonlinearity, correlation immunity of reasonably high order, strict avalanche criterion, non-existence of non-zero linear structures, good global avalanche characteristics, etc.

  19. Constructibility of the Universal Wave Function

    Science.gov (United States)

    Bolotin, Arkady

    2016-10-01

    This paper focuses on a constructive treatment of the mathematical formalism of quantum theory and a possible role of constructivist philosophy in resolving the foundational problems of quantum mechanics, particularly, the controversy over the meaning of the wave function of the universe. As it is demonstrated in the paper, unless the number of the universe's degrees of freedom is fundamentally upper bounded (owing to some unknown physical laws) or hypercomputation is physically realizable, the universal wave function is a non-constructive entity in the sense of constructive recursive mathematics. This means that even if such a function might exist, basic mathematical operations on it would be undefinable and subsequently the only content one would be able to deduce from this function would be pure symbolical.

  20. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  1. Construction of an efficient biologically contained Pseudomonas putida strain and its survival in outdoor assays

    DEFF Research Database (Denmark)

    Molina, Lazaro; Rodriguez, Cayo Juan Ramos; Ronchel, Maria C.;

    1998-01-01

    Active biological containment systems consist of two components, a killing element designed to induce cell death and a control element which modulates the expression of the killing function. We constructed a mini-Tn5 transposon bearing a fusion of the P(lac) promoter to the gef killing gene and a...

  2. Metacognition: computation, biology and function.

    Science.gov (United States)

    Fleming, Stephen M; Dolan, Raymond J; Frith, Christopher D

    2012-05-19

    Many complex systems maintain a self-referential check and balance. In animals, such reflective monitoring and control processes have been grouped under the rubric of metacognition. In this introductory article to a Theme Issue on metacognition, we review recent and rapidly progressing developments from neuroscience, cognitive psychology, computer science and philosophy of mind. While each of these areas is represented in detail by individual contributions to the volume, we take this opportunity to draw links between disciplines, and highlight areas where further integration is needed. Specifically, we cover the definition, measurement, neurobiology and possible functions of metacognition, and assess the relationship between metacognition and consciousness. We propose a framework in which level of representation, order of behaviour and access consciousness are orthogonal dimensions of the conceptual landscape.

  3. Personal Constructions of Biological Concepts – The Repertory Grid Approach

    Directory of Open Access Journals (Sweden)

    Thomas J. J. McCloughlin

    2017-03-01

    Full Text Available This work discusses repertory grid analysis as a tool for investigating the structures of students’ representations of biological concepts. Repertory grid analysis provides the researcher with a variety of techniques that are not associated with standard methods of concept mapping for investigating conceptual structures. It can provide valuable insights into the learning process, and can be used as a diagnostic tool in identifying problems that students have in understanding biological concepts. The biological concepts examined in this work are ‘natural kinds’: a technical class of concepts which ‘appear’ to have invisible ‘essences’ meaning carrying more perceptual weight than being perceptually similar. Because children give more weight to natural-kind membership when reasoning about traits, it would seem pertinent to apply such knowledge to deep-level research into how children reason in biology. The concept of natural kinds has a particular resonance with biology since biological kinds hold the distinction of being almost all natural kinds, such as when the same ‘stuff or thing’ takes many different forms. We have conducted a range of studies using a diversity of biological natural kinds, but in this paper, we wish to explore some of the theoretical underpinnings in more detail. To afford this exploration, we outline one case-study in a small group of secondary school students exploring the concept of ‘equine’ – that is, what is an equine? Five positive examples were chosen to engaged with by the students and one ‘outlier’ with which to compare the construction process. Recommendations are offered in applying this approach to biological education research.

  4. EV71-2A突变质粒的构建及体内外功能初探%Construction of pcDNA3 . 1-EV71-2A mutant and preliminary studying related biological functions

    Institute of Scientific and Technical Information of China (English)

    原素梅; 徐超; 张煦; 王源; 谢冰玉; 熊庆; 彭宜红

    2016-01-01

    Objective To construct EV71-2Amut(pcDNA3. 1-EV71-2A mutant plasmid)and studying its functions in vitro and in vivo, so as to provide an experiemental base for the further studying the active site and biological function of 2A pro-teinase. Methods By using of site-directed mutagenesis system based on PCR, EV71-2Amut was constructed on site-directed mutagenesis of 21His,39Asp and 110Cys genes and confirmed by sequencing analysis. Then EV71-2Amut and pRL-CMV(Cyto-megalovirus, CMV) were co-transfected to human rhabdomyosarcoma cell( RD cell) , and the enzyme activity inside cells was determined and compared with effect to pRL expression level between wild type EV71-2Apro and EV71-2Amut . EV71-2A mR-NA was detected by RT-PCR, and its effect on the quadriceps femoris of BALB/c mice was observed on histopathological changes, which reflected its transcription level and activity in vivo. Results The constructed EV71-2Amut sequence was i-dentical with we expected,the RL activity detected at cellular level from EV71-2Amut groups were significantly higher than that of EV71-2Apro groups (P<0. 05). EV71-2A-mRNA were detected by RT-PCR in quadriceps femoris from the mice injected with EV71-2Apro and EV71-2Amut . Compared with the control group injected with wild type 2A,inflammatory cell infiltration and coagulation necrosis were mild in quadriceps femoris injected with EV71-2Amut . Conclusion EV71-2Amut with H21N+D39E+C110A was successfully constructed. and its protease activity was almost abolished in RD cell and BABL/c mice. This work provides a ground work for the further studying the biological functions of EV71-2A protease.%目的:构建pcDNA3.1-EV71-2A的突变质粒(EV71-2Amut),并对其功能进行检测,为进一步研究肠道病毒71型(Enterovirus type 71,EV71)2A蛋白酶的活性位点及其生物学功能奠定实验基础。方法利用聚合酶链式反应(PCR)定点诱变技术,定点突变编码EV71-2A第21His、39Asp 和110Cys 氨基酸的位点,构建EV71

  5. ON THE CONSTRUCTION OF MAJOR AND MINOR FUNCTIONS

    Institute of Scientific and Technical Information of China (English)

    LuShipan

    1994-01-01

    In this paper,we construct directly absolutely continuous major and minor functions of a function which is Lebesque integrable ,and we also construct directly continuous major and minor functions of a function which is Henstock-Kurzweil integrable.

  6. Design principles for the analysis and construction of robustly homeostatic biological networks.

    Science.gov (United States)

    Tang, Zhe F; McMillen, David R

    2016-11-07

    Homeostatic biological systems resist external disturbances, allowing cells and organisms to maintain a constant internal state despite perturbations from their surroundings. Many biological regulatory networks are known to act homeostatically, with examples including thermal adaptation, osmoregulation, and chemotaxis. Understanding the network topologies (sets of regulatory interactions) and biological parameter regimes that can yield homeostasis in a biological system is of interest both for the study of natural biological system, and in the context of designing new biological control schemes for use in synthetic biology. Here, we examine the mathematical properties of a function that maps a biological system's inputs to its outputs, we have formulated a novel criterion (the "cofactor condition") that compactly describes the conditions for homeostasis. We further analyze the problem of robust homeostasis, wherein the system is required to maintain homeostatic behavior when its parameter values are slightly altered. We use the cofactor condition to examine previously reported examples of robust homeostasis, showing that it is a useful way to unify a number of seemingly different analyses into a single framework. Based on the observation that all previous robustly homeostatic examples fall into one of three classes, we propose a "strong cofactor condition" and use it to provide an algorithm for designing new robustly homeostatic biological networks, giving both their topologies and constraints on their parameter values. Applying the design algorithm to a three-node biological network, we construct several robustly homeostatic genetic networks, uncovering network topologies not previously identified as candidates for exhibiting robust homeostasis.

  7. Constructing biological pathways by a two-step counting approach.

    Directory of Open Access Journals (Sweden)

    Hsiuying Wang

    Full Text Available Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be characterized by two kinds of pairwise relationships: similarity and prerequisite. Many approaches have been proposed in the literature to reconstruct biological relationships. In this article, we propose a two-step method to reconstruct the biological pathway when the binary array data have measurement error. For a pair of genes in a sample, the first step of this approach is to assign counting numbers for every relationship and select the relationship with counting number greater than a threshold. The second step is to calculate the asymptotic p-values for hypotheses of possible relationships and select relationships with a large p-value. This new method has the advantages of easy calculation for the counting numbers and simple closed forms for the p-value. The simulation study and real data example show that the two-step counting method can accurately reconstruct the biological pathway and outperform the existing methods. Compared with the other existing methods, this two-step method can provide a more accurate and efficient alternative approach for reconstructing the biological network.

  8. Functional model of biological neural networks.

    Science.gov (United States)

    Lo, James Ting-Ho

    2010-12-01

    A functional model of biological neural networks, called temporal hierarchical probabilistic associative memory (THPAM), is proposed in this paper. THPAM comprises functional models of dendritic trees for encoding inputs to neurons, a first type of neuron for generating spike trains, a second type of neuron for generating graded signals to modulate neurons of the first type, supervised and unsupervised Hebbian learning mechanisms for easy learning and retrieving, an arrangement of dendritic trees for maximizing generalization, hardwiring for rotation-translation-scaling invariance, and feedback connections with different delay durations for neurons to make full use of present and past informations generated by neurons in the same and higher layers. These functional models and their processing operations have many functions of biological neural networks that have not been achieved by other models in the open literature and provide logically coherent answers to many long-standing neuroscientific questions. However, biological justifications of these functional models and their processing operations are required for THPAM to qualify as a macroscopic model (or low-order approximate) of biological neural networks.

  9. Paradigmatic List Constructions. Patterns and Functions

    Directory of Open Access Journals (Sweden)

    Valentina Benigni

    2016-02-01

    Full Text Available This paper deals with listing as a useful conceptual tool for categorization and offers an overview of the different types of lists in Russian, highlighting both universal and language-specific characteristics of this kind of construction. The data-driven approach adopted in this study allows you to identify the main criteria according to which lists can be classified (exhaustiveness of the enumeration, conjunction, types of constituents, compositionality, and so on. Particular attention is paid to paradigmatic lists, i.e. lists whose items are in a paradigmatic relationship with each other as either synonyms, co-hyponyms or co-meronyms. The features of this family of lists are dealt with in the framework of Construction Grammar, which accounts for both similarities in structure and meaning and differences in pragmatic and communicative functions.

  10. A novel construction of genome space with biological geometry.

    Science.gov (United States)

    Yu, Chenglong; Liang, Qian; Yin, Changchuan; He, Rong L; Yau, Stephen S-T

    2010-06-01

    A genome space is a moduli space of genomes. In this space, each point corresponds to a genome. The natural distance between two points in the genome space reflects the biological distance between these two genomes. Currently, there is no method to represent genomes by a point in a space without losing biological information. Here, we propose a new graphical representation for DNA sequences. The breakthrough of the subject is that we can construct the moment vectors from DNA sequences using this new graphical method and prove that the correspondence between moment vectors and DNA sequences is one-to-one. Using these moment vectors, we have constructed a novel genome space as a subspace in R(N). It allows us to show that the SARS-CoV is most closely related to a coronavirus from the palm civet not from a bird as initially suspected, and the newly discovered human coronavirus HCoV-HKU1 is more closely related to SARS than to any other known member of group 2 coronavirus. Furthermore, we reconstructed the phylogenetic tree for 34 lentiviruses (including human immunodeficiency virus) based on their whole genome sequences. Our genome space will provide a new powerful tool for analyzing the classification of genomes and their phylogenetic relationships.

  11. Research and development achievement report for fiscal 1998 on accelerated type biological function construction technologies. Development of new-type advanced-function enzyme creating technologies; 1998 nendo kasokugata seibutsu kino kochiku gijutsu no kenkyu kaihatsu seika hokokusho. Shingata kokino koso sosei gijutsu kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    An artificial mutation/selection system was constructed in a laboratory based on molecular-level findings collected about the biological evolution mechanism, and biotechnology was studied for creating excellent biological functions. In the study of novel mutation generating technologies, selection is performed after the formation of numerous chimera enzymes by a family shuffling process using resistance to heat as the index. Then, a hybrid enzyme with its resistance to heat more than 10 times higher than that of the parent enzyme was obtained. In the study of establishing coordination between genotype and phenotype, a highly sensitive bacterial coordination technology was developed, and a highly sensitive detection method was constructed using a flow cytometer. As for technologies of highly efficient selection, a research was conducted about the selection of catalytic antibodies equipped with protease and esterase activity. In the study of technologies for enhancing adaptive walk in an evolution experimenting system, the usefulness is studied of a terrain survey based on the adaptive walk theory and a high-efficiency adaptive walk method using the mutation scrambling method. (NEDO)

  12. Assessment of Constructed Wetland Biological Integrity Using Aquatic Macroinvertebrates

    Directory of Open Access Journals (Sweden)

    C. Galbrand

    2007-01-01

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

  13. Inferring Biologically Relevant Models: Nested Canalyzing Functions

    CERN Document Server

    Hinkelmann, Franziska

    2010-01-01

    Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of possible models fitting the available data is huge and identifying a biologically relevant model is of great interest. Nested canalyzing functions, where variables in a given order dominate the function, have recently been proposed as a framework for modeling gene regulatory networks. Previously we described this class of functions as an algebraic toric variety. In this paper, we present an algorithm that identifies all nested canalyzing models that fit the given data. We demonstrate our methods using a well-known Boolean model of the cell cycle in budding yeast.

  14. Physically unclonable functions constructions, properties and applications

    CERN Document Server

    Maes, Roel

    2013-01-01

    Physically unclonable functions (PUFs) are innovative physical security primitives that produce unclonable and inherent instance-specific measurements of physical objects; in many ways they are the inanimate equivalent of biometrics for human beings. Since they are able to securely generate and store secrets, they allow us to bootstrap the physical implementation of an information security system. In this book the author discusses PUFs in all their facets: the multitude of their physical constructions, the algorithmic and physical properties which describe them, and the techniques required to

  15. Biological Function of REE in Plants & Microbes

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Rare earth elements (REE) and their compounds are widely applied in agronomic and medical fields for many years. The bioinorganic chemical research of REE during the past few years indicates that REE play important roles in the promotion of photosynthetic rate as well as root absorption, regulation of hormone and nitrogen metabolism, and suppression of microbes, etc. The metallic or non-metallic targets of key biomolecule in various physiological processes can be chosen by REE for the chelation or replacement, which enables REE to regulate the biological functions or behaviors of those biomolecule and consequently leads to significant embodiment of biological function of REE in plants and microbes.Overdose of REE, however, shows an inhibitory effect on living organisms. Therefore, this paper proposes two suggestions that will be available in the extension of full use of REE's biological function. One is to obey the dose law of REE and control REE concentrations within a safe range. The other is to further test the bioaccumulation and long-period influence of REE on organisms.

  16. Functional biology of sympatric krill species

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Nielsen, Torkel Gissel

    2016-01-01

    Here we compare the functional biology of the sympatric krill species, Meganyctiphanes norvegica and Thysanoessa inermis. For M. norvegica, we investigated functional responses on diatoms and copepods, together with prey size spectra on plankton ,400 mm and copepods in the size range 500–3220 mm....... For T. inermis, only prey size spectrum on plankton ,400 mm were investigated. The prey size ranges of both species include organisms ,400 mm, and they consequently graze on several trophic levels. However, T. inermis feed on cells ,10 mm equivalent spherical diameter (ESD), whereas M. norvegica only...

  17. Marine Carotenoids: Biological Functions and Commercial Applications

    Directory of Open Access Journals (Sweden)

    José M. Vega

    2011-03-01

    Full Text Available Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for a wide range of commercial applications. Indeed, recent interest in the carotenoids has been mainly for their nutraceutical properties. A large number of scientific studies have confirmed the benefits of carotenoids to health and their use for this purpose is growing rapidly. In addition, carotenoids have traditionally been used in food and animal feed for their color properties. Carotenoids are also known to improve consumer perception of quality; an example is the addition of carotenoids to fish feed to impart color to farmed salmon.

  18. Constructions of new plateaued functions from known ones

    Institute of Scientific and Technical Information of China (English)

    Zhang Weiguo; Ding Yong; Zhang Ning; Xiao Guozhen

    2008-01-01

    A number of methods for constructing new plateaued functions from known ones are presented. By properly combining the known plateaued functions it is possible to get highly nonlinear resilient plateaued functions. The order, resiliency and propagation characteristics of the constructed plateaued functions are discussed. We show the new functions could possess the desirable cryptographic property.

  19. Biological functions of decorin in cancer

    Institute of Scientific and Technical Information of China (English)

    Xiu-Li Bi; Wancai Yang

    2013-01-01

    Decorin is a member of the extracellular matrix small leucine-rich proteoglycans family that exists and functions in stromal and epithelial cells.Accumulating evidence suggests that decorin affects the biology of various types of cancer by directly or indirectly targeting the signaling molecules involved in cell growth,survival,metastasis,and angiogenesis.More recent studies show that decorin plays important roles during tumor development and progression and is a potential cancer therapeutic agent.In this article,we summarize recent studies of decorin in cancer and discuss decorin's therapeutic and prognostic value.

  20. Flavonoids: Biosynthesis, Biological functions and Biotechnological applications

    Directory of Open Access Journals (Sweden)

    Maria Lorena eFalcone Ferreyra

    2012-09-01

    Full Text Available Flavonoids are widely distributed secondary metabolites with different metabolic functions in plants. The elucidation of the biosynthetic pathways, as well as their regulation by MYB, bHLH and WD40-type transcription factors, has allowed metabolic engineering of plants through the manipulation of the different final products with valuable applications. The present review describes the regulation of flavonoid biosynthesis, as well as the biological functions of flavonoids in plants, such as in defense against UV-B radiation and pathogen infection, nodulation, pollen fertility. In addition, we discuss different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds.

  1. Subtle Implicit Language Facts Emerge from the Functions of Constructions.

    Science.gov (United States)

    Goldberg, Adele E

    2015-01-01

    Much has been written about the unlikelihood of innate, syntax-specific, universal knowledge of language (Universal Grammar) on the grounds that it is biologically implausible, unresponsive to cross-linguistic facts, theoretically inelegant, and implausible and unnecessary from the perspective of language acquisition. While relevant, much of this discussion fails to address the sorts of facts that generative linguists often take as evidence in favor of the Universal Grammar Hypothesis: subtle, intricate, knowledge about language that speakers implicitly know without being taught. This paper revisits a few often-cited such cases and argues that, although the facts are sometimes even more complex and subtle than is generally appreciated, appeals to Universal Grammar fail to explain the phenomena. Instead, such facts are strongly motivated by the functions of the constructions involved. The following specific cases are discussed: (a) the distribution and interpretation of anaphoric one, (b) constraints on long-distance dependencies,

  2. Construction of `Wachspress Type' Rational Basis Functions over Rectangles

    Indian Academy of Sciences (India)

    P L Powar; S S Rana

    2000-02-01

    In the present paper, we have constructed rational basis functions of 0 class over rectangular elements with wider choice of denominator function. This construction yields additional number of interior nodes. Hence, extra nodal points and the flexibility of denominator function suggest better approximation.

  3. Diffusion of innovations dynamics, biological growth and catenary function

    Science.gov (United States)

    Guseo, Renato

    2016-12-01

    The catenary function has a well-known role in determining the shape of chains and cables supported at their ends under the force of gravity. This enables design using a specific static equilibrium over space. Its reflected version, the catenary arch, allows the construction of bridges and arches exploiting the dual equilibrium property under uniform compression. In this paper, we emphasize a further connection with well-known aggregate biological growth models over time and the related diffusion of innovation key paradigms (e.g., logistic and Bass distributions over time) that determine self-sustaining evolutionary growth dynamics in naturalistic and socio-economic contexts. Moreover, we prove that the 'local entropy function', related to a logistic distribution, is a catenary and vice versa. This special invariance may be explained, at a deeper level, through the Verlinde's conjecture on the origin of gravity as an effect of the entropic force.

  4. Construction of an 8-mm time-lapse camera for biological research

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report covers the construction of an 8mm camera for biological research. A time-lapse camera for use in biological research can be constructed from a super 8-mm...

  5. Frameworks for programming biological function through RNA parts and devices.

    Science.gov (United States)

    Win, Maung Nyan; Liang, Joe C; Smolke, Christina D

    2009-03-27

    One of the long-term goals of synthetic biology is to reliably engineer biological systems that perform human-defined functions. Currently, researchers face several scientific and technical challenges in designing and building biological systems, one of which is associated with our limited ability to access, transmit, and control molecular information through the design of functional biomolecules exhibiting novel properties. The fields of RNA biology and nucleic acid engineering, along with the tremendous interdisciplinary growth of synthetic biology, are fueling advances in the emerging field of RNA programming in living systems. Researchers are designing functional RNA molecules that exhibit increasingly complex functions and integrating these molecules into cellular circuits to program higher-level biological functions. The continued integration and growth of RNA design and synthetic biology presents exciting potential to transform how we interact with and program biology.

  6. Construction of Functions by Fuzzy Operators

    Directory of Open Access Journals (Sweden)

    József Dombi

    2007-12-01

    Full Text Available In this paper we present a new approach to compose and decompose functions.This technology is based on pliant concept. We use the proper transformations ofConjunction of Sigmoid function to create an effect. We aggregate the effects to composethe function. This tool is also capable for function decomposition.

  7. Effective automated feature construction and selection for classification of biological sequences.

    Directory of Open Access Journals (Sweden)

    Uday Kamath

    Full Text Available Many open problems in bioinformatics involve elucidating underlying functional signals in biological sequences. DNA sequences, in particular, are characterized by rich architectures in which functional signals are increasingly found to combine local and distal interactions at the nucleotide level. Problems of interest include detection of regulatory regions, splice sites, exons, hypersensitive sites, and more. These problems naturally lend themselves to formulation as classification problems in machine learning. When classification is based on features extracted from the sequences under investigation, success is critically dependent on the chosen set of features.We present an algorithmic framework (EFFECT for automated detection of functional signals in biological sequences. We focus here on classification problems involving DNA sequences which state-of-the-art work in machine learning shows to be challenging and involve complex combinations of local and distal features. EFFECT uses a two-stage process to first construct a set of candidate sequence-based features and then select a most effective subset for the classification task at hand. Both stages make heavy use of evolutionary algorithms to efficiently guide the search towards informative features capable of discriminating between sequences that contain a particular functional signal and those that do not.To demonstrate its generality, EFFECT is applied to three separate problems of importance in DNA research: the recognition of hypersensitive sites, splice sites, and ALU sites. Comparisons with state-of-the-art algorithms show that the framework is both general and powerful. In addition, a detailed analysis of the constructed features shows that they contain valuable biological information about DNA architecture, allowing biologists and other researchers to directly inspect the features and potentially use the insights obtained to assist wet-laboratory studies on retainment or modification

  8. Interest in biology. Part I: A multidimensional construct

    Science.gov (United States)

    Gardner, Paul L.; Tamir, Pinchas

    Interest in a school subject (e.g., biology) is conceptualized in terms of three components: topics, activities, and motives, each of which has several dimensions. In this study, seven instruments were developed and administered to grade-10 biology students in Israel. Factor analysis provided support for the conceptualization which underlies the development of the instruments. Topic dimensions included biochemical processes, nonhuman organisms, human biology, personal hygiene, and practical applications; the activity dimensions were experiential learning, reception learning, writing/summarizing and group discussion; motives included environmental issues, moral issues, examination success, personal independence, problem solving, and four career dimensions (research, high-status professions, lower-status careers, woodsy-birdsy careers). In an analysis described in Part II of this paper, the students were classified into four groups on the basis of their grade-11 subject enrollment intentions: H (high-level biology), L (low-level biology), P (physical science), and N (no science). Zero-order and multiple correlations were found between interest and other variables and membership/nonmembership of the four groups. Students in Group H were characterized by higher achievement in year-10 biology, higher levels of enjoyment of biology, career orientations towards research or high-status biology-based professions, greater interest in various biology topics, especially reproduction/cell division/genetics, and a greater tendency to regard the Bagrut (grade-12) examination as interesting. Students in Group N displayed lower levels of interest in various topics (especially the microscope, plants, and reproduction), were less motivated to solve problems, had poorer grades in biology (and chemistry), were less likely to perceive biology as useful, were less likely to regard the Bagrut examination as fair, and were less likely to be interested in social modes of learning. There

  9. Construction and Dimension Analysis for a Class of Fractal Functions

    Institute of Scientific and Technical Information of China (English)

    Hong-yong Wang; Zong-ben Xu

    2002-01-01

    In this paper, we construct a class of nowhere differentiable continuous functions by means of the Cantor series expression of real numbers. The constructed functions include some known nondifferentiable functions, such as Bush type functions. These functions are fractal functions since their graphs are in general fractal sets. Under certain conditions, we investigate the fractal dimensions of the graphs of these functions,compute the precise values of Box and Packing dimensions, and evaluate the Hausdorff dimension. Meanwhile,the Holder continuity of such functions is also discussed.

  10. A new construction of bent functions based on Z-bent functions

    DEFF Research Database (Denmark)

    Gangopadhyay, Sugata; Joshi, Anand; Leander, Gregor;

    2013-01-01

    Dobbertin has embedded the problem of construction of bent functions in a recursive framework by using a generalization of bent functions called -bent functions. Following his ideas, we generalize the construction of partial spreads bent functions to partial spreads -bent functions of arbitrary...... level. Furthermore, we show how these partial spreads -bent functions give rise to a new construction of (classical) bent functions. Further, we construct a bent function on 8 variables which is inequivalent to all Maiorana-McFarland as well as PS ap type bents. It is also shown that all bent functions...

  11. The Structure and Function of Biological Networks

    Science.gov (United States)

    Wu, Daniel Duanqing

    2010-01-01

    Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

  12. Bergman kernel function on Hua construction of the fourth type

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper introduces the Hua construction and presents the holomorphic automorphism group of the Hua construction of the fourth type. Utilizing the Bergman kernel function, under the condition of holomorphic automorphism and the standard complete orthonormal system of the semi-Reinhardt domain, the infinite series form of the Bergman kernel function is derived. By applying the properties of polynomial and Γ functions, various identification relations of the aforementioned form are developed and the explicit formula of the Bergman kernel function for the Hua construction of the fourth type is obtained, which suggest that many of the previously-reported results are only the special cases of our findings.

  13. Bioapplications of graphene constructed functional nanomaterials.

    Science.gov (United States)

    Gulzar, Arif; Yang, Piaoping; He, Fei; Xu, Jiating; Yang, Dan; Xu, Liangge; Jan, Mohammad Omar

    2017-01-25

    Graphene has distinctive mechanical, electronic, and optical properties, which researchers have applied to develop innovative electronic materials including transparent conductors and ultrafast transistors. Lately, the understanding of various chemical properties of graphene has expedited its application in high-performance devices that generate and store energy. Graphene is now increasing its terrain outside electronic and chemical applications toward biomedical areas such as precise bio sensing through graphene-quenched fluorescence, graphene-enhanced cell differentiation and growth, and graphene-assisted laser desorption/ionization for mass spectrometry. In this Account, we evaluate recent efforts to apply graphene and graphene oxides (GO) to biomedical research and a few different approaches to prepare graphene materials designed for biomedical applications and a brief perspective on their future applications. Because of its outstanding aqueous processability, amphiphilicity, surface functionalizability, surface enhanced Raman scattering (SERS), and fluorescence quenching ability, GO chemically exfoliated from oxidized graphite is considered a promising material for biological applications. In addition, the hydrophobicity and flexibility of large-area graphene synthesized by chemical vapor deposition (CVD) allow this material to play an important role in cell growth and differentiation. Graphene is considered to be an encouraging and smart candidate for numerous biomedical applications such as NIR-responsive cancer therapy and fluorescence bio-imaging and drug delivery. To that end, suitable preparation and unique approaches to utilize graphene-based materials such as graphene oxides (GOs), reduced graphene oxides (rGOs), and graphene quantum dots (GQDs) in biology and medical science are gaining growing interest.

  14. Dynamics of biomolecules, ligand binding & biological functions

    Science.gov (United States)

    Yi, Myunggi

    Proteins are flexible and dynamic. One static structure alone does not often completely explain biological functions of the protein, and some proteins do not even have high resolution structures. In order to provide better understanding to the biological functions of nicotinic acetylcholine receptor, Diphtheria toxin repressor and M2 proton channel, the dynamics of these proteins are investigated using molecular modeling and molecular dynamics (MD) simulations. With absence of high resolution structure of alpha7 receptor, the homology models of apo and cobra toxin bound forms have been built. From the MD simulations of these model structures, we observed one subunit of apo simulation moved away from other four subunits. With local movement of flexible loop regions, the whole subunit tilted clockwise. These conformational changes occurred spontaneously, and were strongly correlated with the conformational change when the channel is activated by agonists. Unlike other computational studies, we directly compared our model of open conformation with the experimental data. However, the subunits of toxin bound form were stable, and conformational change is restricted by the bound cobra toxin. These results provide activation and inhibition mechanisms of alpha7 receptors and a possible explanation for intermediate conductance of the channel. Intramolecular complex of SH3-like domain with a proline-rich (Pr) peptide segment in Diphtheria toxin repressor (DtxR) is stabilized in inactive state. Upon activation of DtxR by transition metal binding, this intramolecular complex should be dissociated. The dynamics of this intramolecular complex is investigated using MD simulations and NMR spectroscopy. We observed spontaneous opening and closing motions of the Pr segment binding pockets in both Pr-SH3 and SH3 simulations. The MD simulation results and NMR relaxation data suggest that the Pr segment exhibits a binding ↔ unbinding equilibrium. Despite a wealth of experimental

  15. Artificial Molecular Machine Immobilized Surfaces: A New Platform To Construct Functional Materials.

    Science.gov (United States)

    Zhang, Qi; Qu, Da-Hui

    2016-06-17

    Artificial molecular machines have received significant attention from chemists because of their unique ability to mimic the behaviors of biological systems. Artificial molecular machines can be easily modified with functional groups to construct new types of functional molecular switches. However, practical applications of artificial molecular machines are still challenging, because the working platform of artificial molecular machines is mostly in solution. Artificial molecular machine immobilized surfaces (AMMISs) are considered a promising platform to construct functional materials. Herein, we provide a minireview of some recent advances of functional AMMISs. The functions of AMMISs are highlighted and strategies for their construction are also discussed. Furthermore, a brief perspective of the development of artificial molecular machines towards functional materials is given.

  16. Construction and enumeration of Boolean functions with maximum algebraic immunity

    Institute of Scientific and Technical Information of China (English)

    ZHANG WenYing; WU ChuanKun; LIU XiangZhong

    2009-01-01

    Algebraic immunity is a new cryptographic criterion proposed against algebraic attacks. In order to resist algebraic attacks, Boolean functions used in many stream ciphers should possess high algebraic immunity. This paper presents two main results to find balanced Boolean functions with maximum algebraic immunity. Through swapping the values of two bits, and then generalizing the result to swap some pairs of bits of the symmetric Boolean function constructed by Dalai, a new class of Boolean functions with maximum algebraic immunity are constructed. Enumeration of such functions is also given. For a given function p(x) with deg(p(x)) < [n/2], we give a method to construct functions in the form p(x)+q(x) which achieve the maximum algebraic immunity, where every term with nonzero coefficient in the ANF of q(x) has degree no less than [n/2].

  17. Constructive feedforward neural networks using hermite polynomial activation functions.

    Science.gov (United States)

    Ma, Liying; Khorasani, K

    2005-07-01

    In this paper, a constructive one-hidden-layer network is introduced where each hidden unit employs a polynomial function for its activation function that is different from other units. Specifically, both a structure level as well as a function level adaptation methodologies are utilized in constructing the network. The functional level adaptation scheme ensures that the "growing" or constructive network has different activation functions for each neuron such that the network may be able to capture the underlying input-output map more effectively. The activation functions considered consist of orthonormal Hermite polynomials. It is shown through extensive simulations that the proposed network yields improved performance when compared to networks having identical sigmoidal activation functions.

  18. Construct validity of functional capacity tests in healthy workers

    NARCIS (Netherlands)

    Lakke, Sandra E.; Soer, Remko; Geertzen, Jan H.B.; Wiitink, Harriët; Douma, Rob K.W.; Schans, Cees P. van der; Reneman, Michiel F.

    2013-01-01

    Background: Functional Capacity (FC) is a multidimensional construct within the activity domain of the International Classification of Functioning, Disability and Health framework (ICF). Functional capacity evaluations (FCEs) are assessments of work-related FC. The extent to which these work-related

  19. Subtle implicit language facts emerge from the functions of constructions

    Directory of Open Access Journals (Sweden)

    Adele Eva Goldberg

    2016-01-01

    Full Text Available Much has been written about the unlikelihood of innate, syntax-specific, universal knowledge of language (Universal Grammar on the grounds that it is biologically implausible, unresponsive to cross-linguistic facts, theoretically inelegant, and implausible and unnecessary from the perspective of language acquisition. While relevant, much of this discussion fails to address the sorts of facts that generative linguists often take as evidence in favor of the Universal Grammar Hypothesis: subtle, intricate, knowledge about language that speakers implicitly know without being taught. This paper revisits a few often-cited such cases and argues that, although the facts are sometimes even more complex and subtle than is generally appreciated, appeals to Universal Grammar fail to explain the phenomena. Instead, such facts are strongly motivated by the functions of the constructions involved. The following specific cases are discussed: a the distribution and interpretation of anaphoric one, b constraints on long-distance dependencies, c subject-auxiliary inversion, and d cross-linguistic linking generalizations between semantics and syntax.

  20. Construction of high order balanced multiscaling functions via PTST

    Institute of Scientific and Technical Information of China (English)

    YANG Shouzhi; PENG Lizhong

    2006-01-01

    The concept of paraunitary two-scale similarity transform (PTST) is introduced. We discuss the property of PTST, and prove that PTST preserves the orthogonal, approximation order and smoothness of the given orthogonal multiscaling functions. What is more, by applying PTST, we present an algorithm of constructing high order balanced multiscaling functions by balancing the already existing orthogonal nonbalanced multi- scaling functions. The corresponding transform matrix is given explicitly. In addition, we also investigate the symmetry of the balanced multiscaling functions. Finally, construction examples are given.

  1. Fibroblast Growth Factors: Biology, Function, and Application for Tissue Regeneration

    Directory of Open Access Journals (Sweden)

    Ye-Rang Yun

    2010-01-01

    Full Text Available Fibroblast growth factors (FGFs that signal through FGF receptors (FGFRs regulate a broad spectrum of biological functions, including cellular proliferation, survival, migration, and differentiation. The FGF signal pathways are the RAS/MAP kinase pathway, PI3 kinase/AKT pathway, and PLCγ pathway, among which the RAS/MAP kinase pathway is known to be predominant. Several studies have recently implicated the in vitro biological functions of FGFs for tissue regeneration. However, to obtain optimal outcomes in vivo, it is important to enhance the half-life of FGFs and their biological stability. Future applications of FGFs are expected when the biological functions of FGFs are potentiated through the appropriate use of delivery systems and scaffolds. This review will introduce the biology and cellular functions of FGFs and deal with the biomaterials based delivery systems and their current applications for the regeneration of tissues, including skin, blood vessel, muscle, adipose, tendon/ligament, cartilage, bone, tooth, and nerve tissues.

  2. Interspecific variation in beeswax as a biological construction material.

    Science.gov (United States)

    Buchwald, Robert; Breed, Michael D; Greenberg, Alan R; Otis, Gard

    2006-10-01

    Beeswax is a multicomponent material used by bees in the genus Apis to house larvae and store honey and pollen. We characterized the mechanical properties of waxes from four honeybee species: Apis mellifera L., Apis andreniformis L., Apis dorsata L. and two subspecies of Apis cerana L. In order to isolate the material effects from the architectural properties of nest comb, we formed raw wax in to right, circular cylindrical samples, and compressed them in an electromechanical tensometer. From the resulting stress-strain curves, values for yield stress, yield strain, stress and strain at the proportional limit, stiffness, and resilience were obtained. Apis dorsata wax was stiffer and had a higher yield stress and stress at the proportional limit than all of the other waxes. The waxes of A. cerana and A. mellifera had intermediate strength and stiffness, and A. andreniformis wax was the least strong, stiff and resilient. All of the waxes had similar strain values at the proportional limit and yield point. The observed differences in wax mechanical properties correlate with the nesting ecology of these species. A. mellifera and A. cerana nest in cavities that protect the nest from environmental stresses, whereas the species with the strongest and stiffest wax, A. dorsata, constructs relatively heavy nests attached to branches of tall trees, exposing them to substantially greater mechanical forces. The wax of A. andreniformis was the least strong, stiff and resilient, and their nests have low masses relative to other species in the genus and, although not built in cavities, are constructed on lower, often shielded branches that can absorb the forces of wind and rain.

  3. Functionalized Nanodiamonds for Biological and Medical Applications.

    Science.gov (United States)

    Lai, Lin; Barnard, Amanda S

    2015-02-01

    Nanodiamond is a promising material for biological and medical applications, owning to its relatively inexpensive and large-scale synthesis, unique structure, and superior optical properties. However, most biomedical applications, such as drug delivery and bio-imaging, are dependent upon the precise control of the surfaces, and can be significantly affected by the type, distribution and stability of chemical funtionalisations of the nanodiamond surface. In this paper, recent studies on nanodiamonds and their biomedical applications by conjugating with different chemicals are reviewed, while highlighting the critical importance of surface chemical states for various applications.

  4. Constructions of vector output Boolean functions with high generalized nonlinearity

    Institute of Scientific and Technical Information of China (English)

    KE Pin-hui; ZHANG Sheng-yuan

    2008-01-01

    Carlet et al. recently introduced generalized nonlinearity to measure the ability to resist the improved correlation attack of a vector output Boolean function. This article presents a construction of vector output Boolean functions with high generalized nonlinearity using the sample space. The relation between the resilient order and generalized nonlinearity is also discussed.

  5. On the construction of double group molecular symmetry functions

    NARCIS (Netherlands)

    Visscher, L

    1996-01-01

    A new procedure for constructing double group symmetry functions is presented. Using this method integrals over Hermitian operators can become real quantities, even though the integrand and the functions themselves are complex. This is especially of interest to 4-component relativistic methods that

  6. FUNCTION IN BIOLOGY: ETIOLOGICAL AND ORGANIZATIONAL PERSPECTIVES

    Directory of Open Access Journals (Sweden)

    Nunes Neto Nei Freitas Freitas

    2009-12-01

    -ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

    ABSTRACT. In this paper, we argue for a taxonomy of approaches to function based on different epistemological perspectives assumed with regard to the treatment of this central concept in the life sciences. We distinguish between etiological and organizational perspectives on function, analyzing two distinct theories related to each perspective: Wright’s selectionist etiological approach and Godfrey-Smith’s modern history theory of functions, in the case of the etiological perspective; and Cummins’ functional analysis and Collier’s interactivist approach to function, among organizational accounts. We explain differences and similarities between these theories and the broader perspectives on function, arguing for a particular way of understanding the consensus without unity in debates about function. While explaining the accounts of function, we also deal with the relationship between this concept and other important biological concepts, such as adaptation, selection, complexity, and autonomy. We also advance an argument for the limits and prospects of the explanatory role of function in evolution. By arguing that changes in functionality are always grounded on changes in systems’ organization, we show that function can never explain the origins of traits. Nevertheless, it can explain the spread of traits in populations, but only when we are dealing with functionally novel traits. Finally, we stress that organizational accounts of function are needed to understand how new functions appear by means of changes in systems

  7. Relative constructions in Portuguese varieties: a functional-discursive interpretation

    Directory of Open Access Journals (Sweden)

    Roberto Gomes Camacho

    2013-02-01

    Full Text Available This work examines relative constructions in Portuguese varieties based on the principle that Portuguese has a set of relativization strategies that are recognized in typological linguistics as constructions that define related groups of languages. It is postulated that these different strategies, when employed by the same linguistic system, do not really constitute variants of the same syntactic variable, but they are the speaker’s actual choices facing the necessity to perform different social and discursive functions.

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

    Directory of Open Access Journals (Sweden)

    Taishin eNomura

    2010-12-01

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

  9. YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae.

    Science.gov (United States)

    Guo, Yakun; Dong, Junkai; Zhou, Tong; Auxillos, Jamie; Li, Tianyi; Zhang, Weimin; Wang, Lihui; Shen, Yue; Luo, Yisha; Zheng, Yijing; Lin, Jiwei; Chen, Guo-Qiang; Wu, Qingyu; Cai, Yizhi; Dai, Junbiao

    2015-07-27

    It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts.

  10. Autofluorescence: Biological functions and technical applications.

    Science.gov (United States)

    García-Plazaola, José Ignacio; Fernández-Marín, Beatriz; Duke, Stephen O; Hernández, Antonio; López-Arbeloa, Fernando; Becerril, José María

    2015-07-01

    Chlorophylls are the most remarkable examples of fluorophores, and their fluorescence has been intensively studied as a non-invasive tool for assessment of photosynthesis. Many other fluorophores occur in plants, such as alkaloids, phenolic compounds and porphyrins. Fluorescence could be more than just a physicochemical curiosity in the plant kingdom, as several functional roles in biocommunication occur or have been proposed. Besides, fluorescence emitted by secondary metabolites can convert damaging blue and UV into wavelengths potentially useful for photosynthesis. Detection of the fluorescence of some secondary phytochemicals may be a cue for some pollinators and/or seed dispersal organisms. Independently of their functions, plant fluorophores provide researchers with a tool that allows the visualization of some metabolites in plants and cells, complementing and overcoming some of the limitations of the use of fluorescent proteins and dyes to probe plant physiology and biochemistry. Some fluorophores are influenced by environmental interactions, allowing fluorescence to be also used as a specific stress indicator.

  11. Genomic Functionalization: The Next Revolution In Biology

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Peter [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Schoeniger, Joseph S. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Imbro, Paula M. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2014-07-01

    We have implemented a ligand-alignment algorithm into our developed computational pipeline for identifying specificity-determining features (SDFs) in protein-ligand complexes. Given a set of protein-ligand complex structures, the algorithm aligns the complexes by ligand rather than by the C -RMSD or standard approach, providing a single reference frame for extracting SDFs. We anticipate that this ligand-alignment capability will be highly useful for protein function prediction. We already have a database containing > 20 K ligand-protein complex crystal structures taken from the Protein Data Bank. By aligning these proteins to single reference frames using ligand alignment, we can submit the complexes to our pipeline for SDF extraction. The SDFs derived from this training procedure can be used as thumbprints that are hallmarks of individual enzyme classes. These SDF thumbprints may then serve as guides to the prediction of function of new unknown proteins.

  12. A Threshold Pseudorandom Function Construction and Its Applications

    DEFF Research Database (Denmark)

    Nielsen, Jesper Buus

    2002-01-01

    We give the first construction of a practical threshold pseudo- random function.The protocol for evaluating the function is efficient enough that it can be used to replace random oracles in some protocols relying on such oracles. In particular, we show how to transform the efficient...... cryptographically secure Byzantine agreement protocol by Cachin, Kursawe and Shoup for the random oracle model into a cryptographically secure protocol for the complexity theoretic model without loosing efficiency or resilience,thereby constructing an efficient and optimally resilient Byzantine agreement protocol...

  13. Construction of Lyapunov Function for Dissipative Gyroscopic System

    Institute of Scientific and Technical Information of China (English)

    XU Wei; YUAN Bo; AO Ping

    2011-01-01

    @@ We introduce a force decomposition to construct a potential function in deterministic dynamics described by ordinary differential equations in the context of dissipative gyroscopic systems.Such a potential function serves as the corresponding Lyapunov function for the dynamics,hence it gives both quantitative and qualitative descriptions for stability of motion.As an example we apply our force decomposition to a four-dimensional dissipative gyroscopic system.We explicitly obtain the potential function for all parameter regimes in the linear limit,including those regimes where the Lyapunov function was previously believed not to exist.%We introduce a force decomposition to construct a potential function in deterministic dynamics described by ordinary differential equations in the context of dissipative gyroscopic systems. Such a potential function serves as the corresponding Lyapunov function for the dynamics, hence it gives both quantitative and qualitative descriptions for stability of motion. As an example we apply our force decomposition to a four-dimensional dissipative gyroscopic system. We explicitly obtain the potential function for all parameter regimes in the linear limit, including those regimes where the Lyapunov function was previously believed not to exist.

  14. Multi-functional Anti-pollution Construction Structure for Drilling

    Institute of Scientific and Technical Information of China (English)

    Chen Lirong; Yin Weidong; Yang Ping; Wang Rong

    1997-01-01

    @@ Treatment of drilling waste water is the focus of environmental protection for the East Sichuan Drilling Corporation. The three-functional (consists of settling pit, oil interceptor,cistern) construction structure against pollution from drilling waste water was preliminarily improved in 1989.

  15. Bergman kernel function on Hua Construction of the second type

    Institute of Scientific and Technical Information of China (English)

    ZHANG Liyou

    2005-01-01

    In this paper, we give an explicit formula of the Bergman kernel function on Hua Construction of the second type when the parameters 1/p1,…, 1/pr-1 are positive integers and 1/pr is an arbitrary positive real number.

  16. Evidence for a Role of Executive Functions in Learning Biology

    Science.gov (United States)

    Rhodes, Sinéad M.; Booth, Josephine N.; Campbell, Lorna Elise; Blythe, Richard A.; Wheate, Nial J.; Delibegovic, Mirela

    2014-01-01

    Research examining cognition and science learning has focused on working memory, but evidence implicates a broader set of executive functions. The current study examined executive functions and learning of biology in young adolescents. Fifty-six participants, aged 12-13?years, completed tasks of working memory (Spatial Working Memory), inhibition…

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

    Science.gov (United States)

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

    2015-12-15

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking.

  18. ASSESSMENT CRITERIA OF FUNCTIONALITY GEOTEXTILES USED IN ROAD CONSTRUCTION

    Directory of Open Access Journals (Sweden)

    LUCA Cristinel

    2016-05-01

    Full Text Available This work was performed in order to assess the functionality of geotextiles used in road construction. To increase the quality of road works requires the use of geotextiles in their structure. Depending on the role and the benefits they offer, geotextiles have a number of physical properties, hydraulic, endurance and optimal characteristics regarding their degradation. Geotextile properties were identified and divided according to their characteristics area. Thus, there were obtained textile properties oriented towards geotextiles and properties geared to the application field respectively reinforcement, drainage, and filtration. Value engineering works at the level of constructive product conception and production. The instrumentation is done by functional analysis, value functions and design or redesign of geotextile based on the necessary functions. Systematic research method allowed geotextiles dimensioning functions in order to obtain products in terms of quality, reliability and maximum operational performance. Functions obtained from the analysis are appropriate for a single property. After obtaining the set of decisions was possible functions geotextiles hierarchy after the significance of their use. Establishing the importance of the coefficients or characteristics hierarchy after their weight requires the comparison of the features between them and grading them in proportion to their degree of importance. The ranking of these functions is beneficial when designing or redesigning geotextiles.

  19. Mimicking biological functionality with polymers for biomedical applications

    Science.gov (United States)

    Green, Jordan J.; Elisseeff, Jennifer H.

    2016-12-01

    The vast opportunities for biomaterials design and functionality enabled by mimicking nature continue to stretch the limits of imagination. As both biological understanding and engineering capabilities develop, more sophisticated biomedical materials can be synthesized that have multifaceted chemical, biological and physical characteristics designed to achieve specific therapeutic goals. Mimicry is being used in the design of polymers for biomedical applications that are required locally in tissues, systemically throughout the body, and at the interface with tissues.

  20. Carbohydrate nanocarriers in biomedical applications: functionalization and construction.

    Science.gov (United States)

    Kang, Biao; Opatz, Till; Landfester, Katharina; Wurm, Frederik R

    2015-11-21

    The specific targeting of either tumor cells or immune cells in vivo by carefully designed and appropriately surface-functionalized nanocarriers may become an effective therapeutic treatment for a variety of diseases. Carbohydrates, which are prominent biomolecules, have shown their outstanding ability in balancing the biocompatibility, stability, biodegradability, and functionality of nanocarriers. The recent applications of sugar (mono/oligosaccharides and/or polysaccharides) for the development of nanomedicines are summarized in this review, including the application of carbohydrates for the surface-functionalization of various nanocarriers and for the construction of the nanocarrier itself. Current problems and challenges are also addressed.

  1. Construction Learning as a Function of Frequency, Frequency Distribution, and Function

    Science.gov (United States)

    Ellis, Nick C.; Ferreira-Junior, Fernando

    2009-01-01

    This article considers effects of construction frequency, form, function, and prototypicality on second language acquisition (SLA). It investigates these relationships by focusing on naturalistic SLA in the European Science Foundation corpus (Perdue, 1993) of the English verb-argument constructions (VACs): verb locative (VL), verb object locative…

  2. Development of functional geopolymers for water purification, and construction purposes

    OpenAIRE

    M. Alshaaer; B. El-Eswed; R.I. Yousef; Khalili, F.; Rahier, H

    2016-01-01

    This paper deals with the development of functional geopolymers based on local resources such as kaolinitic soil and zeolitic tuff for the construction of water storage containers and water transfer channels. The effect of water content on the mechanical performance and physical properties of synthesized geopolymers was evaluated. The results confirmed that the optimum ratio of water is 28% of clay fraction, which revealed observable improvements of physical, mechanical, and adsorption proper...

  3. Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients

    Institute of Scientific and Technical Information of China (English)

    Lianshuo Li; Zicheng Wang; Peng He; Shining Ma; Jie Du; Rui Jiang

    2016-01-01

    Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, includ-ing KEGG orthologous groups and the evolutionary genealogy of genes:Non-supervised Ortholo-gous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network. We devised two statistical methods to infer pairwise relationships between microbial functional units based on a deep sequencing dataset of gut microbiome from type 2 dia-betes (T2D) patients as well as healthy controls. Networks containing such functional units and their significant interactions were constructed subsequently. We conducted a variety of analyses of global properties, local properties, and functional modules in the resulting functional networks. Our data indicate that besides the observations consistent with the current knowledge, this study provides novel biological insights into the gut microbiome associated with T2D.

  4. Uncovering Biological Network Function via Graphlet Degree Signatures

    Directory of Open Access Journals (Sweden)

    Nataša Pržulj

    2008-01-01

    Full Text Available Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker’s yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.Results: We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein’s local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Availability: Data is available upon request.

  5. Biological ensilage of fish - optimization of stability, safety and functionality

    NARCIS (Netherlands)

    Enes Dapkevicius, M.L.N.

    2002-01-01

    This thesis deals with stability, safety, and functionality aspects of biological fish silage (BFS) obtained by lactic acid fermentation. BFS may provide an economically viable, environment friendly way of upgrading fish waste.BFS has been found advantageous when compared to the so-called acid proce

  6. Functional and biological characteristics of asthma in cleaning workers.

    NARCIS (Netherlands)

    Vizcaya, D.; Mirabelli, M.C.; Orriols, R.; Antó, J.M.; Barreiro, E.; Burgos, F.; Arjona, L.; Gomez, F.; Zock, J.P.

    2013-01-01

    Objectives: Cleaning workers have an increased risk of asthma but the underlying mechanisms are largely unknown. We studied functional and biological characteristics in asthmatic cleaners and compared these to healthy cleaners. Methods: Forty-two cleaners with a history of asthma and/or recent respi

  7. Assessing the Effectiveness of a Constructed Arctic Stream Using Multiple Biological Attributes

    Science.gov (United States)

    Jones, Nicholas E.; Scrimgeour, Garry J.; Tonn, William M.

    2008-12-01

    Objective assessment of habitat compensation is a central yet challenging issue for restoration ecologists. In 1997, a 3.4-km stream channel, designed to divert water around an open pit diamond mine, was excavated in the Barrenlands region of the Canadian Arctic to create productive stream habitat. We evaluated the initial success of this compensation program by comparing multiple biological attributes of the constructed stream during its first three years to those of natural reference streams in the area. The riparian zone of the constructed stream was largely devoid of vegetation throughout the period, in contrast to the densely vegetated zones of reference streams. The constructed stream also contained lower amounts of woody debris, coarse particulate organic matter (CPOM), and epilithon; had lower coverage by macrophytes and bryophytes; and processed leaf litter at a lower rate than reference streams. Species richness and densities of macroinvertebrates were consistently lower in the constructed stream compared to natural streams. This contributed to differences in macroinvertebrate assemblage structure throughout the period, although assemblages showed some convergence by year 3. The effectiveness of the constructed stream to emulate natural streams varied somewhat depending on the biological attribute being evaluated. Assessments based on individual attributes showed that minimal to moderate levels of similarity between the constructed stream and natural streams were achieved. A collective assessment of all biological and ecosystem attributes suggested that the constructed stream was not a good surrogate for natural streams during these first years. Additional time would be required before many characteristics of the constructed stream would resemble those of reference streams. Because initial efforts to improve fish habitat in the constructed stream focused on physical structures (e.g., weirs, vanes, rock, groins), ecological factors limiting fish growth

  8. Evaluation of gene association methods for coexpression network construction and biological knowledge discovery.

    Directory of Open Access Journals (Sweden)

    Sapna Kumari

    Full Text Available BACKGROUND: Constructing coexpression networks and performing network analysis using large-scale gene expression data sets is an effective way to uncover new biological knowledge; however, the methods used for gene association in constructing these coexpression networks have not been thoroughly evaluated. Since different methods lead to structurally different coexpression networks and provide different information, selecting the optimal gene association method is critical. METHODS AND RESULTS: In this study, we compared eight gene association methods - Spearman rank correlation, Weighted Rank Correlation, Kendall, Hoeffding's D measure, Theil-Sen, Rank Theil-Sen, Distance Covariance, and Pearson - and focused on their true knowledge discovery rates in associating pathway genes and construction coordination networks of regulatory genes. We also examined the behaviors of different methods to microarray data with different properties, and whether the biological processes affect the efficiency of different methods. CONCLUSIONS: We found that the Spearman, Hoeffding and Kendall methods are effective in identifying coexpressed pathway genes, whereas the Theil-sen, Rank Theil-Sen, Spearman, and Weighted Rank methods perform well in identifying coordinated transcription factors that control the same biological processes and traits. Surprisingly, the widely used Pearson method is generally less efficient, and so is the Distance Covariance method that can find gene pairs of multiple relationships. Some analyses we did clearly show Pearson and Distance Covariance methods have distinct behaviors as compared to all other six methods. The efficiencies of different methods vary with the data properties to some degree and are largely contingent upon the biological processes, which necessitates the pre-analysis to identify the best performing method for gene association and coexpression network construction.

  9. Construction and use of numerical-analytical approximating functions

    Science.gov (United States)

    Serazutdinov, M. N.

    2016-11-01

    The article goes over the methodology of constructing numerical-analytical approximating functions, satisfying the given boundary conditions for the function of its derivatives in the circuit areas of various shapes. The methodology is based on presenting the unknown function as a series in a complete set of functions that do not satisfy the given boundary conditions on the contour of the area, but additionally numerically defined near the contour to satisfy the boundary conditions. The additional definition of the functions near the area contour is performed numerically based on finite-difference relations. The main advantage of the stated method is the ability to build a relatively simple approximating functions satisfying the given boundary conditions on the boundary of complex shaped areas. The examples of applying the described method for solving the boundary value problem of a plate of different shapes. The possibility of using numerical-analytical functions for solving boundary value problems that contain higher derivatives up to fourth order is shown.

  10. CONSTRUCTION, EXPRESSION AND BIOLOGICAL ASSESSMENT OF BPI23-Fcγ 1 RECOMBINANT PROTEIN PROKARYOTIC EXPRESSION VECTOR

    Institute of Scientific and Technical Information of China (English)

    安云庆; 管远志; 柯岩; 杨贵贞

    2002-01-01

    Objective. To construct pBV-BPI600-Fcγ 1700 recombinant expression vector, to transform it into Escherichia coli DH5α , and to induce the expression of BPI23-Fcγ 1 anti-bacterial recombinant protein. Methods. Genes coding for BPI23 and Fcγ 1 were amplified by RT-PCR from mRNA extracted from HL-60 cell and normal human leukocytes; recombinant cloning vector and recombinant expression vector were then constructed. pBV-BPI600-Fcγ 1700 recombinant expression vector was transformed into the competent Escherichia coli DH5α and BPI23-Fcγ 1 recombinant protein was expressed by a temperature-induced method. Results. (1) Expected amplified products BPI600bp and Fcγ 1700bp were obtained by RT-PCR method. (2) pUC18-BPI180, pUC18-BPI420 and pUC18-Fcγ 1700 recombinant cloning vectors were successfully constructed, and sequences were identical with the reported ones. (3) pBV-BPI600-Fcγ 1700 recombinant expression vector was successfully constructed, and the enzyme digestion analysis showed an expected result. (4) The expression level of BPI23-Fcγ 1 recombinant protein accounted for 20% of total bacterial proteins. (5) The renatured BPI23-Fcγ 1 recombinant protein showed bacteriocidal activity and biological function of complement fixation, and opsonization. Conclusion. pBV-BPI600-Fcγ 1700 recombinant expression vector was successfully constructed, and BPI23-Fcγ 1 recombinant protein with double biological activity of BPI and IgGFc was expressed in Escherichia coli.

  11. Milk protein tailoring to improve functional and biological properties

    Directory of Open Access Journals (Sweden)

    JEAN-MARC CHOBERT

    2012-01-01

    Full Text Available Proteins are involved in every aspects of life: structure, motion, catalysis, recognition and regulation. Today's highly sophisticated science of the modifications of proteins has ancient roots. The tailoring of proteins for food and medical uses precedes the beginning of what is called biochemistry. Chemical modification of proteins was pursued early in the twentieth century as an analytical procedure for side-chain amino acids. Later, methods were developed for specific inactivation of biologically active proteins and titration of their essential groups. Enzymatic modifications were mainly developed in the seventies when many more enzymes became economically available. Protein engineering has become a valuable tool for creating or improving proteins for practical use and has provided new insights into protein structure and function. The actual and potential use of milk proteins as food ingredients has been a popular topic for research over the past 40 years. With today's sophisticated analytical, biochemical and biological research tools, the presence of compounds with biological activity has been demonstrated. Improvements in separation techniques and enzyme technology have enabled efficient and economic isolation and modification of milk proteins, which has made possible their use as functional foods, dietary supplements, nutraceuticals and medical foods. In this review, some chemical and enzymatic modifications of milk proteins are described, with particular focus on their functional and biological properties.

  12. Applications of large-scale density functional theory in biology

    Science.gov (United States)

    Cole, Daniel J.; Hine, Nicholas D. M.

    2016-10-01

    Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

  13. A structural biology perspective on NMDA receptor pharmacology and function.

    Science.gov (United States)

    Regan, Michael C; Romero-Hernandez, Annabel; Furukawa, Hiro

    2015-08-01

    N-methyld-aspartate receptors (NMDARs) belong to the large family of ionotropic glutamate receptors (iGluRs), which are critically involved in basic brain functions as well as multiple neurological diseases and disorders. The NMDARs are large heterotetrameric membrane protein complexes. The extensive extracellular domains recognize neurotransmitter ligands and allosteric compounds and translate the binding information to regulate activity of the transmembrane ion channel. Here, we review recent advances in the structural biology of NMDARs with a focus on pharmacology and function. Structural analysis of the isolated extracellular domains in combination with the intact heterotetrameric NMDAR structure provides important insights into how this sophisticated ligand-gated ion channel may function.

  14. Neuroscience in the era of functional genomics and systems biology.

    Science.gov (United States)

    Geschwind, Daniel H; Konopka, Genevieve

    2009-10-15

    Advances in genetics and genomics have fuelled a revolution in discovery-based, or hypothesis-generating, research that provides a powerful complement to the more directly hypothesis-driven molecular, cellular and systems neuroscience. Genetic and functional genomic studies have already yielded important insights into neuronal diversity and function, as well as disease. One of the most exciting and challenging frontiers in neuroscience involves harnessing the power of large-scale genetic, genomic and phenotypic data sets, and the development of tools for data integration and mining. Methods for network analysis and systems biology offer the promise of integrating these multiple levels of data, connecting molecular pathways to nervous system function.

  15. Recursive random forest algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways

    Science.gov (United States)

    Zhang, Kui; Busov, Victor; Wei, Hairong

    2017-01-01

    Background Present knowledge indicates a multilayered hierarchical gene regulatory network (ML-hGRN) often operates above a biological pathway. Although the ML-hGRN is very important for understanding how a pathway is regulated, there is almost no computational algorithm for directly constructing ML-hGRNs. Results A backward elimination random forest (BWERF) algorithm was developed for constructing the ML-hGRN operating above a biological pathway. For each pathway gene, the BWERF used a random forest model to calculate the importance values of all transcription factors (TFs) to this pathway gene recursively with a portion (e.g. 1/10) of least important TFs being excluded in each round of modeling, during which, the importance values of all TFs to the pathway gene were updated and ranked until only one TF was remained in the list. The above procedure, termed BWERF. After that, the importance values of a TF to all pathway genes were aggregated and fitted to a Gaussian mixture model to determine the TF retention for the regulatory layer immediately above the pathway layer. The acquired TFs at the secondary layer were then set to be the new bottom layer to infer the next upper layer, and this process was repeated until a ML-hGRN with the expected layers was obtained. Conclusions BWERF improved the accuracy for constructing ML-hGRNs because it used backward elimination to exclude the noise genes, and aggregated the individual importance values for determining the TFs retention. We validated the BWERF by using it for constructing ML-hGRNs operating above mouse pluripotency maintenance pathway and Arabidopsis lignocellulosic pathway. Compared to GENIE3, BWERF showed an improvement in recognizing authentic TFs regulating a pathway. Compared to the bottom-up Gaussian graphical model algorithm we developed for constructing ML-hGRNs, the BWERF can construct ML-hGRNs with significantly reduced edges that enable biologists to choose the implicit edges for experimental

  16. Morpho-chemistry and functionality of diseased biological tissues

    Science.gov (United States)

    Lange, Marta; Cicchi, Riccardo; Pavone, Francesco

    2014-09-01

    Heart and cardiovascular diseases are one of the most common in the world, in particular - arthrosclerosis. The aim of the research is to distinguish pathological and healthy tissue regions in biological samples, in this case - to distinguish collagen and lipid rich regions within the arterial wall. In the work a specific combination of such methods are used: FLIM and SHG in order to evaluate the biological tissue morphology and functionality, so that this research could give a contribution for creating a new biological tissue imaging standard in the closest future. During the study the most appropriate parameter for fluorescence lifetime decay was chosen in order to evaluate lifetime decay parameters and the isotropy of the arterial wall and deposition, using statistical methods FFT and GLCM. The research gives a contribution or the future investigations for evaluating lipid properties when it can de-attach from the arterial wall and cause clotting in the blood vessel or even a stroke.

  17. Biological mechanisms associated with triazophos (TAP) removal by horizontal subsurface flow constructed wetlands (HSFCW)

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Juan; Feng, Yuqin; Dai, Yanran; Cui, Naxin [State Key Laboratory of Pollution Control and ResourceReuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092 (China); Anderson, Bruce [Department of Civil Engineering, Queen' s University, Kingston K7L3N6 (Canada); Cheng, Shuiping, E-mail: shpcheng@tongji.edu.cn [State Key Laboratory of Pollution Control and ResourceReuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092 (China)

    2016-05-15

    Triazophos (TAP) is a widely used pesticide that is easily accumulated in the environment due to its relatively high stability: this accumulation from agricultural runoff results in potential hazards to aquatic ecosystems. Constructed wetlands are generally considered to be an effective technology for treating TAP polluted surface water. However, knowledge about the biological mechanisms of TAP removal is still lacking. This study investigates the responses of a wetland plant (Canna indica), substrate enzymes and microbial communities in bench-scale horizontal subsurface-flow constructed wetlands (HSCWs) loaded with different TAP concentrations (0, 0.1, 0.5 and 5 mg·L{sup −1}). The results indicate that TAP stimulated the activities of superoxide dismutase (SOD) and peroxidase (POD) in the roots of C. indica. The highest TAP concentrations significantly inhibited photosynthetic activities, as shown by a reduced effective quantum yield of PS II (Φ{sub PSII}) and lower electron transport rates (ETR). However, interestingly, the lower TAP loadings exhibited some favorable effects on these two variables, suggesting that C. indica is a suitable species for use in wetlands designed for treatment of low TAP concentrations. Urease and alkaline phosphatase (ALP) in the wetland substrate were activated by TAP. Two-way ANOVA demonstrated that urease activity was influenced by both the TAP concentrations and season, while acidphosphatase (ACP) only responded to seasonal variations. Analysis of high throughput sequencing of 16S rRNA revealed seasonal variations in the microbial community structure of the wetland substrate at the phylum and family levels. In addition, urease activity had a greater correlation with the relative abundance of some functional microbial groups, such as the Bacillaceae family, and the ALP and ACP may be influenced by the plant more than substrate microbial communities. - Highlights: • Physiological responses of the wetland plant to triazophos

  18. Engineering multiple biological functional motifs into a blank collagen-like protein template from Streptococcus pyogenes.

    Science.gov (United States)

    Peng, Yong Y; Stoichevska, Violet; Schacht, Kristin; Werkmeister, Jerome A; Ramshaw, John A M

    2014-07-01

    Bacterially derived triple-helical, collagen-like proteins are attractive as potential biomedical materials. The collagen-like domain of the Scl2 protein from S. pyogenes lacks any specific binding sites for mammalian cells yet possesses the inherent structural integrity of the collagen triple-helix of animal collagens. It can, therefore, be considered as a structurally-stable "blank slate" into which various defined, biological sequences, derived from animal collagens, can be added by substitutions or insertions, to enable production of novel designed materials to fit specific functional requirements. In the present study, we have used site directed mutagenesis to substitute two functional sequences, one for heparin binding and the other for integrin binding, into different locations in the triple-helical structure. This provided three new constructs, two containing the single substitutions and one containing both substitutions. The stability of these constructs was marginally reduced when compared to the unmodified sequence. When compared to the unmodified bacterial collagen, both the modified collagens that contain the heparin binding site showed marked binding of fluorescently labeled heparin. Similarly, the modified collagens from both constructs containing the integrin binding site showed significant adhesion of L929 cells that are known to possess the appropriate integrin receptor. C2C12 cells that lack any appropriate integrins did not bind. These data show that bacterial collagen-like sequences can be modified to act like natural extracellular matrix collagens by inserting one or more unique biological domains with defined function.

  19. SU-E-T-54: Benefits of Biological Cost Functions

    Energy Technology Data Exchange (ETDEWEB)

    Demirag, N [Elekta CMS GmbH, Freiburg Im Breisgau, baden wurttemberg (Germany)

    2014-06-01

    Purpose: To verify the benefits of the biological cost functions. Methods: TG166 patients were used for the test case scenarios. Patients were planned using Monaco V5.0 (CMS/Elekta, St.Louis, MO) Monaco has 3 biological and 8 physical CFs. In this study the plans were optimized using 3 different scenarios. 1- Biological CFs only 2-Physical CFs only 3- Combination of Physical and Biological CFsMonaco has 3 biological CFs. Target EUD used for the targets, derived from the poisson cell kill model, has an α value that controls the cold spots inside the target. α values used in the optimization were 0.5 and 0.8. if cold spots needs to be penalized α value increased. Serial CF: it's called serial to mimic the behaviour of the serial organs, if a high k value like 12 or 14 is used it controls the maximum dose. Serial CF has a k parameter that is used to shape the whole dvh curve. K value ranges between 1–20. k:1 is used to control the mean dose, lower k value controls the mean dose, higher k value controls the higher dose, using 2 serial CFs with different k values controls the whole DVH. Paralel CF controls the percentage of the volume that tolerates higher doses than the reference dose to mimic the behaviour of the paralel organs. Results: It was possible to achive clinically accepted plans in all 3 scenarios. The benefit of the biological cost functions were to control the mean dose for target and OAR, to shape the DVH curve using one EUD value and one k value simplifies the optimization process. Using the biological CFs alone, it was hard to control the dose at a point. Conclusion: Biological CFs in Monaco doesn't require the ntcp/tcp values from the labs and useful to shape the whole dvh curve. I work as an applications support specialist for Elekta and I am a Ph.D. Student in Istanbul University for radiation therapy physics.

  20. Recursive confidence band construction for an unknown distribution function.

    Science.gov (United States)

    Kiatsupaibul, Seksan; Hayter, Anthony J

    2015-01-01

    Given a sample X1,...,Xn of independent observations from an unknown continuous distribution function F, the problem of constructing a confidence band for F is considered, which is a fundamental problem in statistical inference. This confidence band provides simultaneous inferences on all quantiles and also on all of the cumulative probabilities of the distribution, and so they are among the most important inference procedures that address the issue of multiplicity. A fully nonparametric approach is taken where no assumptions are made about the distribution function F. Historical approaches to this problem, such as Kolmogorov's famous () procedure, represent some of the earliest inference methodologies that address the issue of multiplicity. This is because a confidence band at a given confidence level 1-α allows inferences on all of the quantiles of the distribution, and also on all of the cumulative probabilities, at that specified confidence level. In this paper it is shown how recursive methodologies can be employed to construct both one-sided and two-sided confidence bands of various types. The first approach operates by putting bounds on the cumulative probabilities at the data points, and a recursive integration approach is described. The second approach operates by providing bounds on certain specified quantiles of the distribution, and its implementation using recursive summations of multinomial probabilities is described. These recursive methodologies are illustrated with examples, and R code is available for their implementation.

  1. Biological framework for soil aggregation: Implications for ecological functions.

    Science.gov (United States)

    Ghezzehei, Teamrat; Or, Dani

    2016-04-01

    Soil aggregation is heuristically understood as agglomeration of primary particles bound together by biotic and abiotic cementing agents. The organization of aggregates is believed to be hierarchical in nature; whereby primary particles bond together to form secondary particles and subsequently merge to form larger aggregates. Soil aggregates are not permanent structures, they continuously change in response to internal and external forces and other drivers, including moisture, capillary pressure, temperature, biological activity, and human disturbances. Soil aggregation processes and the resulting functionality span multiple spatial and temporal scales. The intertwined biological and physical nature of soil aggregation, and the time scales involved precluded a universally applicable and quantifiable framework for characterizing the nature and function of soil aggregation. We introduce a biophysical framework of soil aggregation that considers the various modes and factors of the genesis, maturation and degradation of soil aggregates including wetting/drying cycles, soil mechanical processes, biological activity and the nature of primary soil particles. The framework attempts to disentangle mechanical (compaction and soil fragmentation) from in-situ biophysical aggregation and provides a consistent description of aggregate size, hierarchical organization, and life time. It also enables quantitative description of biotic and abiotic functions of soil aggregates including diffusion and storage of mass and energy as well as role of aggregates as hot spots of nutrient accumulation, biodiversity, and biogeochemical cycles.

  2. Deducing protein function by forensic integrative cell biology.

    Directory of Open Access Journals (Sweden)

    William C Earnshaw

    2013-12-01

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

  3. Deducing protein function by forensic integrative cell biology.

    Science.gov (United States)

    Earnshaw, William C

    2013-12-01

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

  4. Content-rich biological network constructed by mining PubMed abstracts

    Directory of Open Access Journals (Sweden)

    Sharp Burt M

    2004-10-01

    Full Text Available Abstract Background The integration of the rapidly expanding corpus of information about the genome, transcriptome, and proteome, engendered by powerful technological advances, such as microarrays, and the availability of genomic sequence from multiple species, challenges the grasp and comprehension of the scientific community. Despite the existence of text-mining methods that identify biological relationships based on the textual co-occurrence of gene/protein terms or similarities in abstract texts, knowledge of the underlying molecular connections on a large scale, which is prerequisite to understanding novel biological processes, lags far behind the accumulation of data. While computationally efficient, the co-occurrence-based approaches fail to characterize (e.g., inhibition or stimulation, directionality biological interactions. Programs with natural language processing (NLP capability have been created to address these limitations, however, they are in general not readily accessible to the public. Results We present a NLP-based text-mining approach, Chilibot, which constructs content-rich relationship networks among biological concepts, genes, proteins, or drugs. Amongst its features, suggestions for new hypotheses can be generated. Lastly, we provide evidence that the connectivity of molecular networks extracted from the biological literature follows the power-law distribution, indicating scale-free topologies consistent with the results of previous experimental analyses. Conclusions Chilibot distills scientific relationships from knowledge available throughout a wide range of biological domains and presents these in a content-rich graphical format, thus integrating general biomedical knowledge with the specialized knowledge and interests of the user. Chilibot http://www.chilibot.net can be accessed free of charge to academic users.

  5. Biological properties of extracellular vesicles and their physiological functions

    Directory of Open Access Journals (Sweden)

    María Yáñez-Mó

    2015-05-01

    Full Text Available In the past decade, extracellular vesicles (EVs have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

  6. Biological properties of extracellular vesicles and their physiological functions

    Science.gov (United States)

    Yáñez-Mó, María; Siljander, Pia R.-M.; Andreu, Zoraida; Zavec, Apolonija Bedina; Borràs, Francesc E.; Buzas, Edit I.; Buzas, Krisztina; Casal, Enriqueta; Cappello, Francesco; Carvalho, Joana; Colás, Eva; Silva, Anabela Cordeiro-da; Fais, Stefano; Falcon-Perez, Juan M.; Ghobrial, Irene M.; Giebel, Bernd; Gimona, Mario; Graner, Michael; Gursel, Ihsan; Gursel, Mayda; Heegaard, Niels H. H.; Hendrix, An; Kierulf, Peter; Kokubun, Katsutoshi; Kosanovic, Maja; Kralj-Iglic, Veronika; Krämer-Albers, Eva-Maria; Laitinen, Saara; Lässer, Cecilia; Lener, Thomas; Ligeti, Erzsébet; Linē, Aija; Lipps, Georg; Llorente, Alicia; Lötvall, Jan; Manček-Keber, Mateja; Marcilla, Antonio; Mittelbrunn, Maria; Nazarenko, Irina; Hoen, Esther N.M. Nolte-‘t; Nyman, Tuula A.; O'Driscoll, Lorraine; Olivan, Mireia; Oliveira, Carla; Pállinger, Éva; del Portillo, Hernando A.; Reventós, Jaume; Rigau, Marina; Rohde, Eva; Sammar, Marei; Sánchez-Madrid, Francisco; Santarém, N.; Schallmoser, Katharina; Ostenfeld, Marie Stampe; Stoorvogel, Willem; Stukelj, Roman; Van der Grein, Susanne G.; Vasconcelos, M. Helena; Wauben, Marca H. M.; De Wever, Olivier

    2015-01-01

    In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system. PMID:25979354

  7. Mnk kinase pathway: Cellular functions and biological outcomes

    Institute of Scientific and Technical Information of China (English)

    Sonali; Joshi; Leonidas; C; Platanias

    2014-01-01

    The mitogen-activated protein kinase(MAPK) interacting protein kinases 1 and 2(Mnk1 and Mnk2) play important roles in controlling signals involved in mRNA translation. In addition to the MAPKs(p38 or Erk), multiple studies suggest that the Mnk kinases can be regulated by other known kinases such as Pak2 and/or other unidentified kinases by phosphorylation of residues distinct from the sites phosphorylated by the MAPKs. Several studies have established multiple Mnk protein targets, including PSF, heterogenous nuclear ribonucleoprotein A1, Sprouty 2 and have lead to the identification of distinct biological functions and substrate specificity for the Mnk kinases. In this review we discuss the pathways regulating the Mnk kinases, their known substrates as well as the functional consequences of engagement of pathways controlled by Mnk kinases. These kinases play an important role in mRNA translation via their regulation of eukaryotic initiation factor 4E(eIF4E) and their functions have important implications in tumor biology as well as the regulation of drug resistance to anti-oncogenic therapies. Other studies have identified a role for the Mnk kinases in cap-independent mRNA translation, suggesting that the Mnk kinases can exert important functional effects independently of the phosphorylation of eIF4 E. The role of Mnk kinases in inflammation and inflammationinduced malignancies is also discussed.

  8. Design in nature how the constructal law governs evolution in biology, physics, technology, and social organization

    CERN Document Server

    Bejan, Adrian

    2013-01-01

    In this groundbreaking book, Adrian Bejan takes the recurring patterns in nature—trees, tributaries, air passages, neural networks, and lightning bolts—and reveals how a single principle of physics, the constructal law, accounts for the evolution of these and many other designs in our world. Everything—from biological life to inanimate systems—generates shape and structure and evolves in a sequence of ever-improving designs in order to facilitate flow. River basins, cardiovascular systems, and bolts of lightning are very efficient flow systems to move a current—of water, blood, or electricity. Likewise, the more complex architecture of animals evolve to cover greater distance per unit of useful energy, or increase their flow across the land. Such designs also appear in human organizations, like the hierarchical “flowcharts” or reporting structures in corporations and political bodies. All are governed by the same principle, known as the constructal law, and configure and reconfigure themselves...

  9. Probing the Xenopus laevis inner ear transcriptome for biological function

    Directory of Open Access Journals (Sweden)

    Powers TuShun R

    2012-06-01

    Full Text Available Abstract Background The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Results Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization. Conclusions We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome

  10. On The Construction of Models for Electrical Conduction in Biological Tissues

    Science.gov (United States)

    Gómez-Aguilar, F.; Bernal-Alvarado, J.; Cordova-Fraga, T.; Rosales-García, J.; Guía-Calderón, M.

    2010-12-01

    Applying RC circuit theory, a theoretical representation for the electrical conduction in a biological multilayer system was developed. In particular an equivalent circuit for the epidermis, dermis and the subcutaneous tissue was constructed. This model includes an equivalent circuit, inside the dermis, in order to model a small formation like tumor. This work shows the feasibility to apply superficial electrodes to detect subcutaneous abnormalities. The behavior of the model is shown in the form of a frequency response chart. The Bode and Nyquist plots are also obtained. This theoretical frame is proposed to be a general treatment to describe the bioelectrical transport in a three layer bioelectrical system.

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  12. Click Chemistry Mediated Functionalization of Vertical Nanowires for Biological Applications.

    Science.gov (United States)

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica; Buch-Månson, Nina; Bovet, Nicolas; Nygård, Jesper; Martinez, Karen L; Meldal, Morten

    2016-01-11

    Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use of the Cu(I) -catalyzed alkyne-azide cycloaddition and its strain-promoted variant for the covalent functionalization of vertical NWs with peptides and proteins. The potential of the approach was demonstrated in two complementary applications of measuring enzyme activity and protein binding, which is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use of covalently modified NWs for diagnostic purposes using minute amounts of material.

  13. Quality function deployment for buildable and sustainable construction

    CERN Document Server

    Natee, Singhaputtangkul; Teo, Evelyn A L

    2016-01-01

    This book focuses on the implementation of Quality Function Deployment (QFD) in the construction industry as a tool to help building designers arrive at optimal decisions for external envelope systems with sustainable and buildable design goals. In particular, the book integrates special features into the conventional QFD tool to enhance its performance. These features include a fuzzy multi-criteria decision-making method, fuzzy consensus scheme, and Knowledge Management System (KMS). This integration results in a more robust decision support tool, known as the Knowledge-based Decision Support System QFD (KBDSS-QFD) tool. As an example, the KBDSS-QFD tool is used for the assessment of building envelope materials and designs for high-rise residential buildings in Singapore in the early design stage. The book provides the reader with a conceptual framework for understanding the development of the KBDSS-QFD tool. The framework is presented in a generalized form in order to benefit building professionals, decisio...

  14. Development of functional geopolymers for water purification, and construction purposes

    Directory of Open Access Journals (Sweden)

    M. Alshaaer

    2016-09-01

    Full Text Available This paper deals with the development of functional geopolymers based on local resources such as kaolinitic soil and zeolitic tuff for the construction of water storage containers and water transfer channels. The effect of water content on the mechanical performance and physical properties of synthesized geopolymers was evaluated. The results confirmed that the optimum ratio of water is 28% of clay fraction, which revealed observable improvements of physical, mechanical, and adsorption properties of the geopolymeric products. Such geopolymers showed the highest compressive strength, density, and maximum adsorption capacity toward cadmium among the products and precursors tested. The residual soluble salts in produced geopolymers were markedly reduced by using this optimum water content.

  15. Hash function construction using weighted complex dynamical networks

    Institute of Scientific and Technical Information of China (English)

    Song Yu-Rong; Jiang Guo-Ping

    2013-01-01

    A novel scheme to construct a hash function based on a weighted complex dynamical network (WCDN) generated from an original message is proposed in this paper.First,the original message is divided into blocks.Then,each block is divided into components,and the nodes and weighted edges are well defined from these components and their relations.Namely,the WCDN closely related to the original message is established.Furthermore,the node dynamics of the WCDN are chosen as a chaotic map.After chaotic iterations,quantization and exclusive-or operations,the fixed-length hash value is obtained.This scheme has the property that any tiny change in message can be diffused rapidly through the WCDN,leading to very different hash values.Analysis and simulation show that the scheme possesses good statistical properties,excellent confusion and diffusion,strong collision resistance and high efficiency.

  16. IQGAP1 and its binding proteins control diverse biological functions.

    Science.gov (United States)

    White, Colin D; Erdemir, Huseyin H; Sacks, David B

    2012-04-01

    IQGAP proteins have been identified in a wide spectrum of organisms, ranging from yeast to humans. The most extensively studied family member is the ubiquitously expressed scaffold protein IQGAP1, which participates in multiple essential aspects of mammalian biology. IQGAP1 mediates these effects by binding to and regulating the function of numerous interacting proteins. Over ninety proteins have been reported to associate with IQGAP1, either directly or as part of a larger complex. In this review, we summarise those IQGAP1 binding partners that have been identified in the last five years. The molecular mechanisms by which these interactions contribute to the functions of receptors and their signalling cascades, small GTPase function, cytoskeletal dynamics, neuronal regulation and intracellular trafficking are evaluated. The evidence that has accumulated recently validates the role of IQGAP1 as a scaffold protein and expands the repertoire of cellular activities in which it participates.

  17. Biomarkers of Aging: From Function to Molecular Biology.

    Science.gov (United States)

    Wagner, Karl-Heinz; Cameron-Smith, David; Wessner, Barbara; Franzke, Bernhard

    2016-06-02

    Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products.

  18. Functionalization of hydroxyl terminated polybutadiene with biologically active fluorescent molecule

    Indian Academy of Sciences (India)

    R Murali Sankar; Subhadeep Saha; K Seeni Meera; Tushar Jana

    2009-10-01

    A biologically active molecule, 2-chloro-4,6-bis(dimethylamino)-1,3,5-triazine (CBDT), has been covalently attached at the terminal carbon atoms of the hydroxyl terminated polybutadiene (HTPB) backbone. The modification of HTPB backbone by CBDT molecule does not affect the unique physico-chemical properties such as fluidity, hydroxyl value and microstructure of the parent HTPB. The formation of hydrogen bonding between the terminal hydroxyl groups and the nitrogen atoms of triazine moiety is the driving force for the terminal attachment chemistry. The functionalized HTPB (HTPB–CBDT) shows a strong fluorescence emission at 385 nm.

  19. Functionalization of polydopamine coated magnetic nanoparticles with biological entities

    Science.gov (United States)

    Mǎgeruşan, Lidia; Mrówczyński, Radosław; Turcu, Rodica

    2015-12-01

    New hybrid materials, obtained through introduction of cysteine, lysine and folic acid as biological entities into polydopamine-coated magnetite nanoparticles, are reported. The syntheses are straight forward and various methods were applied for structural and morphological characterization of the resulting nanoparticles. XPS proved a very powerful tool for surface chemical analysis and it evidences the functionalization of polydopamine coated magnetite nanoparticles. The superparamagnetic behavior and the high values of saturation magnetization recommend all products for further application where magnetism is important for targeting, separation, or heating by alternative magnetic fields.

  20. A Model-Based Approach to Constructing Music Similarity Functions

    Directory of Open Access Journals (Sweden)

    Lamere Paul

    2007-01-01

    Full Text Available Several authors have presented systems that estimate the audio similarity of two pieces of music through the calculation of a distance metric, such as the Euclidean distance, between spectral features calculated from the audio, related to the timbre or pitch of the signal. These features can be augmented with other, temporally or rhythmically based features such as zero-crossing rates, beat histograms, or fluctuation patterns to form a more well-rounded music similarity function. It is our contention that perceptual or cultural labels, such as the genre, style, or emotion of the music, are also very important features in the perception of music. These labels help to define complex regions of similarity within the available feature spaces. We demonstrate a machine-learning-based approach to the construction of a similarity metric, which uses this contextual information to project the calculated features into an intermediate space where a music similarity function that incorporates some of the cultural information may be calculated.

  1. Superior drainage treated by combinational technique of biologic contact oxidation and constructed wetland

    Institute of Scientific and Technical Information of China (English)

    胡学斌; 徐志恒; 柴宏祥; 龙腾锐

    2009-01-01

    The superior drainage was pre-treated by biologic contact oxidation on BOD5 load of 0.72 kg/(m3·d),and then post-treated by constructed wetland. The results about the effect on the constructed wetland post-treatment show that the total nitrogen (TN) is the restrictive index of the combinational technique treatment effect. To meet the reclaimed water quality standard and reuse for waterscape,the peak hydraulic load of constructed wetland is 0.50 m/d in summer (30-36 ℃) and 0.33 m/d in winter (8-12℃),and the load ratio of the peak hydraulic under the two temperature conditions is 3-2. The results are combined of reclaimed water quantity requirements in different seasons of green building. Reasonable scale of the reclaimed water treatment systems can be determined. The treatment efficacy can be well predicted,and both the design and operations can be effectively guided,by which the reclaimed water treatment systems regard superior drainage as the source and are purified by combinational technique of contact oxidation and artificial wetland.

  2. STAT6: its role in interleukin 4-mediated biological functions.

    Science.gov (United States)

    Takeda, K; Kishimoto, T; Akira, S

    1997-05-01

    Interleukin (IL) 4 is known to be a cytokine which plays a central role in the regulation of immune response. Studies on cytokine signal transduction have clarified the mechanism by which IL4 exerts its functions. Two cytoplasmic proteins, signal transducer and activator of transcription (STAT) 6 and IL4-induced phosphotyrosine substrate/insulin receptor substrate 2 (4PS/IRS2), are activated in IL4 signal transduction. Recent studies from STAT6-deficient mice have revealed the essential role of STAT6 in IL4-mediated biological actions. In addition, STAT6 has also been demonstrated to be important for the functions mediated by IL13, which is related to IL4. IL4 and IL13 have been shown to induce the production of IgE, which is a major mediator in an allergic response. These findings indicate that STAT6 activation is involved in IL4- and IL13-mediated disorders such as allergy.

  3. Current studies on physiological functions and biological production of lactosucrose.

    Science.gov (United States)

    Mu, Wanmeng; Chen, Qiuming; Wang, Xiao; Zhang, Tao; Jiang, Bo

    2013-08-01

    Lactosucrose (O-β-D-galactopyranosyl-(1,4)-O-α-D-glucopyranosyl-(1,2)-β-D-fructofuranoside) is a trisaccharide formed from lactose and sucrose by enzymatic transglycosylation. This rare trisaccharide is a kind of indigestible carbohydrate, has good prebiotic effect, and promotes intestinal mineral absorption. It has been used as a functional ingredient in a range of food products which are approved as foods for specified health uses in Japan. Using lactose and sucrose as substrates, lactosucrose can be produced through transfructosylation by β-fructofuranosidase from Arthrobacter sp. K-1 or a range of levansucrases, or through transgalactosylation by β-galactosidase from Bacillus circulans. This article presented a review of recent studies on the physiological functions of lactosucrose and the biological production from lactose and sucrose by different enzymes.

  4. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials

    Science.gov (United States)

    McDougall, Carmel; Woodcroft, Ben J.

    2016-01-01

    In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of

  5. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

    Science.gov (United States)

    McDougall, Carmel; Woodcroft, Ben J; Degnan, Bernard M

    2016-01-01

    In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of

  6. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

    Directory of Open Access Journals (Sweden)

    Carmel McDougall

    Full Text Available In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the

  7. Construction of short hairpin RNA eukaryotic expression vectors targeting peroxire- doxin Ⅰ and identification of their biological functions%靶向PeroxiredoxinⅠ基因的shRNA真核表达载体的构建及生物学功能鉴定

    Institute of Scientific and Technical Information of China (English)

    郭启帅; 黄曦; 张俊; 李少林

    2011-01-01

    Objective To construct short hairpin RNA (shRNA) eukaryotic expression vectors targeting peroxiredoxin Ⅰ ( Prx Ⅰ ) gene and investigate the effect of down-regulating Prx Ⅰ expression on the biological functions of breast carcinoma MCF-7 cells. Methods The eukaryotic expression vectors targeting Prx Ⅰ gene were constructed and then transfected into MCF-7 cells. Transfection efficiency was evaluated by flow cytometry. The mRNA and protein expressions of Prx Ⅰ in MCF-7 cells were detected by RT-PCR and Western blotting. The proliferation of MCF-7 cells was determined by MTT assay. The cell cycle and apoptosis were evaluated by flow cytometry. Results The eukaryotic expression vectors pGPU6-HK (negative control), pGPU6-Prxl, pGPU6-Prx2, pGPU6-Prx3 and pGPU6-Prx4 were successfully constructed and then transfected into MCF-7 cells respectively. Transfection efficiency was about 80%. The expression of Prx Ⅰ in MCF-7 cells transfected with 4 Prx vectors were inhibited significantly at both mRNA and protein levels, especially in the cells with pGPU6-Prx3, whose inhibitory rates were 82.6% and 80.5% respectively at mRNA and protein levels. When pGPU6-Prx3 group was compared with untransfected group and the group transfected with pGPU6HK, the cell proliferation was markedly delayed (P < 0. 05 ), the cell apoptosis rate was significantly increased, and the cells were arrested in G1 phase and S phase were significantly decreased (P < 0. 05 ).Conclusion Eukaryotic expression vectors of shRNA Prx Ⅰ is successfully constructed, and specifically downregulate the Prx Ⅰ expression at mRNA and protein levels. Transfection of pGPU6-Prx3 vector significantly inhibits cell proliferation, induces cell apoptosis, and regulates cell phase redistribution in MCF-7 cells.%目的 构建针对PeroxiredoxinⅠ(PrxⅠ)基因的短发夹RNA(short hairpin RNA, shRNA)真核表达载体,观察下调PrxⅠ基因表达后对乳腺癌MCF-7细胞生物学功能的影响.方法

  8. Sucrose metabolism gene families and their biological functions.

    Science.gov (United States)

    Jiang, Shu-Ye; Chi, Yun-Hua; Wang, Ji-Zhou; Zhou, Jun-Xia; Cheng, Yan-Song; Zhang, Bao-Lan; Ma, Ali; Vanitha, Jeevanandam; Ramachandran, Srinivasan

    2015-11-30

    Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.

  9. Event-based text mining for biology and functional genomics.

    Science.gov (United States)

    Ananiadou, Sophia; Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B

    2015-05-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research.

  10. Streamlined Construction of the Cyanobacterial CO2-Fixing Organelle via Protein Domain Fusions for Use in Plant Synthetic Biology.

    Science.gov (United States)

    Gonzalez-Esquer, C Raul; Shubitowski, Tyler B; Kerfeld, Cheryl A

    2015-09-01

    Bacterial microcompartments (BMCs) are self-assembling organelles that sequester segments of biochemical pathways within a protein shell. Given their functional diversity, BMCs constitute a rich source of metabolic modules for applications in synthetic biology. The carboxysome, the cyanobacterial BMC for CO(2) fixation, has attracted significant attention as a target for installation into chloroplasts and serves as the foundation for introducing other types of BMCs into plants. Carboxysome assembly involves a series of protein-protein interactions among at least six gene products to form a metabolic core, around which the shell assembles. This complexity creates significant challenges for the transfer, regulation, and assembly of carboxysomes, or any of the myriad of functionally distinct BMCs, into heterologous systems. To overcome this bottleneck, we constructed a chimeric protein in the cyanobacterium Synechococcus elongatus that structurally and functionally replaces four gene products required for carboxysome formation. The protein was designed based on protein domain interactions in the carboxysome core. The resulting streamlined carboxysomes support photosynthesis. This strategy obviates the need to regulate multiple genes and decreases the genetic load required for carboxysome assembly in heterologous systems. More broadly, the reengineered carboxysomes represent a proof of concept for a domain fusion approach to building multifunctional enzymatic cores that should be generally applicable to the engineering of BMCs for new functions and cellular contexts.

  11. Modular construction of a functional artificial epothilone polyketide pathway.

    Science.gov (United States)

    Osswald, Corina; Zipf, Gregor; Schmidt, Gisela; Maier, Josef; Bernauer, Hubert S; Müller, Rolf; Wenzel, Silke C

    2014-10-17

    Natural products of microbial origin continue to be an important source of pharmaceuticals and agrochemicals exhibiting potent activities and often novel modes of action. Due to their inherent structural complexity chemical synthesis is often hardly possible, leaving fermentation as the only viable production route. In addition, the pharmaceutical properties of natural products often need to be optimized for application by sophisticated medicinal chemistry and/or biosynthetic engineering. The latter requires a detailed understanding of the biosynthetic process and genetic tools to modify the producing organism that are often unavailable. Consequently, heterologous expression of complex natural product pathways has been in the focus of development over recent years. However, piecing together existing DNA cloned from natural sources and achieving efficient expression in heterologous circuits represent several limitations that can be addressed by synthetic biology. In this work we have redesigned and reassembled the 56 kb epothilone biosynthetic gene cluster from Sorangium cellulosum for expression in the high GC host Myxococcus xanthus. The codon composition was adapted to a modified codon table for M. xanthus, and unique restriction sites were simultaneously introduced and others eliminated from the sequence in order to permit pathway assembly and future interchangeability of modular building blocks from the epothilone megasynthetase. The functionality of the artificial pathway was demonstrated by successful heterologous epothilone production in M. xanthus at significant yields that have to be improved in upcoming work. Our study sets the stage for future engineering of epothilone biosynthesis and production optimization using a highly flexible assembly strategy.

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

    Science.gov (United States)

    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…

  13. Fine tuning points of generating function construction for linear recursions

    Science.gov (United States)

    Yolcu, Bahar; Demiralp, Metin

    2014-10-01

    Recursions are quite important mathematical tools since many systems are mathematically modelled to ultimately take us to these equations because of their rather easy algebraic natures. They fit computer programming needs quite well in many circumstances to produce solutions. However, it is generally desired to find the asymptotic behaviour of the general term in the relevant sequence for convergence and therefore practicality issues. One of the general tendencies to find the general term asymptotic behaviour, when its ordering number grows unboundedly, is the integral representation over a generating function which does not depend on individual sequence elements. This is tried to be done almost for all types of recursions, even though the linear cases gain more importance than the others because they can be more effectively investigated by using many linear algebraic tools. Despite this may seem somehow to be rather trivial, there are a lot of theoretical fine tuning issues in the construction of true integral representations over true intervals on real axis or paths in complex domains. This work is devoted to focus on this issue starting from scratch for better understanding of the matter. The example cases are chosen to best illuminate the situations to get information for future generalization even though the work can be considered at somehow introductory level.

  14. DMPD: Type I interferon receptors: biochemistry and biological functions. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17502368 Type I interferon receptors: biochemistry and biological functions. de Wee...(.html) (.csml) Show Type I interferon receptors: biochemistry and biological functions. PubmedID 17502368 T...itle Type I interferon receptors: biochemistry and biological functions. Authors

  15. Biological performance of functionalized biomedical polymers for potential applications as intraocular lens.

    Science.gov (United States)

    Zheng, Zhiwen; Wang, Yingjun; Jiao, Yan; Zhai, Zhichen

    2016-08-01

    To study the biological performance of surface-modified biomedical polymer materials, a model of the functional mechanism of nonspecific adsorption resistance was constructed. Cell behavior on the surface and in vivo transplantation features of intraocular lens (IOL) materials, such as hydrophobic acrylic ester and polymethyl methacrylate (PMMA), were investigated. The results of cell adhesion and proliferation studies showed that the addition of hirudin can significantly resist epithelial cell adhesion, better than the pure amination process, and thereby inhibit excessive proliferation on the surface. Experiments on the eyes of rabbits indicated that the IOL surfaces with hirudin modification reduced the incidence of cell aggregation and inflammation. Combined with a study of protein-resistant layer construction with recombinant hirudin on the material surface, the mechanism of surface functionalization was determined. The biological performance indicated that nonspecific adsorption is greatly decreased due to the existence of amphiphilic ions or hydration layers, which lead to stability and long-term resistance to nonspecific adsorption. These results offer a theoretical basis for the use of traditional biomedical polymer materials in long-term clinical applications. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1961-1967, 2016.

  16. Construction of DNA damage response gene pprI function-deficient and function-complementary mutants in Deinococcus radiodurans

    Institute of Scientific and Technical Information of China (English)

    GAO Guanjun; LU Huiming; HUANG Lifen; HUA Yuejin

    2005-01-01

    PprI, a DNA damage response factor from the extraordinary radioresistant bacterium Deinococcus radiodurans, plays a central regulatory role in multiple DNA damage repair. In this study, a fusion DNA fragment carrying kanamycin resistance gene with the D. Radiodurans groEL promoter was cloned by PCR amplification and reversely inserted into the pprI locus in the genome of the wild-type strain R1. The resulting pprI-deficient strain, designated YR1, was very sensitive to ionizing radiation. Meanwhile, the re- combinant DNA fragment was cloned into the shuttle vector pRADZ3, and resulted in plasmid pRADK with kanamycin resistance in D. Radiodurans. The fragments containing complete pprI gene and 3'-terminal deletion pprI△ were cloned into plasmid pRADK. The resulted plasmids designated pRADKpprI and pRADKpprI△ were then transformed to YR1. Results show that YR1 carrying pRADKpprI was able to fully restore the extreme radioresistance to the same level as the wild-type D. Raiodurans R1, whereas YR1 pRADKpprI△ failed to do so. Construction of DNA repair switch PprI function-deficient and function-complementary mutants in D. Radiodurans is not only useful to elucidating the relationship between domains and functions of PprI protein, but also opens the door to the further studies of the biological functions of PprI protein in vivo.

  17. Biological sulfate removal from construction and demolition debris leachate: Effect of bioreactor configuration

    Energy Technology Data Exchange (ETDEWEB)

    Kijjanapanich, Pimluck, E-mail: som_cheng00@hotmail.com [Pollution Prevention and Resource Recovery Chair Group, UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft (Netherlands); Do, Anh Tien [Civil and Environmental Engineering, University of South Florida, Tampa, FL 33620 (United States); Annachhatre, Ajit P. [Environmental Engineering and Management, Asian Institute of Technology, PO Box 4, Klongluang, Pathumthani 12120 (Thailand); Esposito, Giovanni [Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043 Cassino (Italy); Yeh, Daniel H. [Civil and Environmental Engineering, University of South Florida, Tampa, FL 33620 (United States); Lens, Piet N.L. [Pollution Prevention and Resource Recovery Chair Group, UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft (Netherlands)

    2014-03-01

    Highlights: • Novel biological technique for gypsum removal from CDD. • CDDS leachate treatment performed using different sulfate reducing bioreactors. • Gypsum in CDD can be used as a source of sulfate for sulfate reducing bacteria. • High calcium concentration (1000 mg L{sup −1}) did not affect the bioreactor performance. - Abstract: Due to the contamination of construction and demolition debris (CDD) by gypsum drywall, especially, its sand fraction (CDD sand, CDDS), the sulfate content in CDDS exceeds the posed limit of the maximum amount of sulfate present in building sand (1.73 g sulfate per kg of sand for the Netherlands). Therefore, the CDDS cannot be reused for construction. The CDDS has to be washed in order to remove most of the impurities and to obtain the right sulfate content, thus generating a leachate, containing high sulfate and calcium concentrations. This study aimed at developing a biological sulfate reduction system for CDDS leachate treatment and compared three different reactor configurations for the sulfate reduction step: the upflow anaerobic sludge blanket (UASB) reactor, inverse fluidized bed (IFB) reactor and gas lift anaerobic membrane bioreactor (GL-AnMBR). This investigation demonstrated that all three systems can be applied for the treatment of CDDS leachate. The highest sulfate removal efficiency of 75–85% was achieved at a hydraulic retention time (HRT) of 15.5 h. A high calcium concentration up to 1000 mg L{sup −1} did not give any adverse effect on the sulfate removal efficiency of the IFB and GL-AnMBR systems.

  18. Discoveries of rhythms in human biological functions: a historical review.

    Science.gov (United States)

    Lemmer, Björn

    2009-08-01

    Though there are very early and ancient observations on the daily variation in physiological and pathophysiological functions (e.g., bronchial asthma), more detailed and scientific reports were not published until the beginning of the 17th century. The aim of this review is to bring those reports to the attention of researchers of chronobiology and chronopharmacology. The ancient books and their contents, which constitute the basis for this review, are part of the personal library collection of the author; numerous observations and reports on biologic rhythms in man are presented here for the first time. The intent of this review is to demonstrate that the fields of chronobiology and chronopharmacology are not only a new and modern branch of science, but that it stands on the shoulders of wonderful and insightful observations and explanations made by our scientific forefathers. It is the hope that the reader will enjoy the richness of the ancient reports that contribute to our present knowledge achieved through astute early biologic rhythm research.

  19. Linking biological soil crust diversity to ecological functions

    Science.gov (United States)

    Glaser, Karin; Borchhardt, Nadine; Schulz, Karoline; Mikhailyuk, Tatiana; Baumann, Karen; Leinweber, Peter; Ulf, Karsten

    2016-04-01

    Biological soil crusts (BSCs) are an association of different microorganisms and soil particles in the top millimeters of the soil. They are formed by algae, cyanobacteria, microfungi, bacteria, bryophytes and lichens in various compositions. Our aim was to determine and compare the biodiversity of all occurring organisms in biogeographically different habitats, ranging from polar (both Arctic and Antarctic), subpolar (Scandinavia), temperate (Germany) to dry regions (Chile). The combination of microscopy and molecular techniques (next-generation sequencing) revealed highly diverse crust communities, whose composition clustered by region and correlates with habitat characteristics such as water content. The BSC biodiversity was then linked to the ecological function of the crusts. The functional role of the BSCs in the biogeochemical cycles of carbon, nitrogen and phosphorous is evaluated using an array of state of the art soil chemistry methods including Py-FIMS (pyrolysis field ionization mass spectrometry) and XANES (x-ray absorbance near edge structure). Total P as well as P fractions were quantified in all BSCs, adjacent soil underneath and comparable nearby soil of BSC-free areas revealing a remarkable accumulation of total phosphorous and a distinct pattern of P fractions in the crust. Further, we observed an indication of a different P-speciation composition in the crust compared with BSC-free soil. The data allow answering the question whether BSCs act as sink or source for these compounds, and how biodiversity controls the biogeochemical function of BSCs.

  20. Genome-wide survey for biologically functional pseudogenes.

    Directory of Open Access Journals (Sweden)

    Orjan Svensson

    2006-05-01

    Full Text Available According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological function. Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the human-mouse species split, and also a larger group of primate-specific ones found from human-chimpanzee searches. Two processed sequences are notable, their conservation since the human-mouse split being as high as most protein-coding genes; one is derived from the protein Ataxin 7-like 3 (ATX7NL3, and one from the Spinocerebellar ataxia type 1 protein (ATX1. Our approach is comparative and can be applied to any pair of species. It is implemented by a semi-automated pipeline based on cross-species BLAST comparisons and maximum-likelihood phylogeny estimations. To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios.

  1. Twenty years of protein interaction studies for biological function deciphering.

    Science.gov (United States)

    Legrain, Pierre; Rain, Jean-Christophe

    2014-07-31

    Intensive methodological developments and technology innovation have been devoted to protein-protein interaction studies over 20years. Genetic indirect assays and sophisticated large scale biochemical analyses have jointly contributed to the elucidation of protein-protein interactions, still with a lot of drawbacks despite heavy investment in human resources and technologies. With the most recent developments in mass spectrometry and computational tools for studying protein content of complex samples, the initial goal of deciphering molecular bases of biological functions is now within reach. Here, we described the various steps of this process and gave examples of key milestones in this scientific story line. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.

  2. Structure, Function, and Biology of the Enterococcus faecalis Cytolysin

    Directory of Open Access Journals (Sweden)

    Daria Van Tyne

    2013-04-01

    Full Text Available Enterococcus faecalis is a Gram-positive commensal member of the gut microbiota of a wide range of organisms. With the advent of antibiotic therapy, it has emerged as a multidrug resistant, hospital-acquired pathogen. Highly virulent strains of E. faecalis express a pore-forming exotoxin, called cytolysin, which lyses both bacterial and eukaryotic cells in response to quorum signals. Originally described in the 1930s, the cytolysin is a member of a large class of lanthionine-containing bacteriocins produced by Gram-positive bacteria. While the cytolysin shares some core features with other lantibiotics, it possesses unique characteristics as well. The current understanding of cytolysin biosynthesis, structure/function relationships, and contribution to the biology of E. faecalis are reviewed, and opportunities for using emerging technologies to advance this understanding are discussed.

  3. Biological Functional Relevance of Asymmetric Dimethylarginine (ADMA in Cardiovascular Disease

    Directory of Open Access Journals (Sweden)

    Sara Franceschelli

    2013-12-01

    Full Text Available There is growing evidence that increased levels of the endogenous NO synthase inhibitor asymmetric dimethylarginine (ADMA may contribute to endothelial dysfunction. Studies in animal models as well as in humans have suggested that the increase in ADMA occurs at a time when vascular disease has not yet become clinically evident. ADMA competitively inhibits NO elaboration by displacing L-arginine from NO synthase. In a concentration-dependent manner, it thereby interferes not only with endothelium-dependent, NO-mediated vasodilation, but also with other biological functions exerted by NO. The upshot may be a pro-atherogenic state. Recently, several studies have investigated the effect of various therapeutical interventions on ADMA plasma concentrations.

  4. CONSTRUCTING A FLEXIBLE LIKELIHOOD FUNCTION FOR SPECTROSCOPIC INFERENCE

    Energy Technology Data Exchange (ETDEWEB)

    Czekala, Ian; Andrews, Sean M.; Mandel, Kaisey S.; Green, Gregory M. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Hogg, David W., E-mail: iczekala@cfa.harvard.edu [Center for Cosmology and Particle Physics, Department of Physics, New York University, 4 Washington Place, New York, NY, 10003 (United States)

    2015-10-20

    We present a modular, extensible likelihood framework for spectroscopic inference based on synthetic model spectra. The subtraction of an imperfect model from a continuously sampled spectrum introduces covariance between adjacent datapoints (pixels) into the residual spectrum. For the high signal-to-noise data with large spectral range that is commonly employed in stellar astrophysics, that covariant structure can lead to dramatically underestimated parameter uncertainties (and, in some cases, biases). We construct a likelihood function that accounts for the structure of the covariance matrix, utilizing the machinery of Gaussian process kernels. This framework specifically addresses the common problem of mismatches in model spectral line strengths (with respect to data) due to intrinsic model imperfections (e.g., in the atomic/molecular databases or opacity prescriptions) by developing a novel local covariance kernel formalism that identifies and self-consistently downweights pathological spectral line “outliers.” By fitting many spectra in a hierarchical manner, these local kernels provide a mechanism to learn about and build data-driven corrections to synthetic spectral libraries. An open-source software implementation of this approach is available at http://iancze.github.io/Starfish, including a sophisticated probabilistic scheme for spectral interpolation when using model libraries that are sparsely sampled in the stellar parameters. We demonstrate some salient features of the framework by fitting the high-resolution V-band spectrum of WASP-14, an F5 dwarf with a transiting exoplanet, and the moderate-resolution K-band spectrum of Gliese 51, an M5 field dwarf.

  5. Constructing a Flexible Likelihood Function for Spectroscopic Inference

    Science.gov (United States)

    Czekala, Ian; Andrews, Sean M.; Mandel, Kaisey S.; Hogg, David W.; Green, Gregory M.

    2015-10-01

    We present a modular, extensible likelihood framework for spectroscopic inference based on synthetic model spectra. The subtraction of an imperfect model from a continuously sampled spectrum introduces covariance between adjacent datapoints (pixels) into the residual spectrum. For the high signal-to-noise data with large spectral range that is commonly employed in stellar astrophysics, that covariant structure can lead to dramatically underestimated parameter uncertainties (and, in some cases, biases). We construct a likelihood function that accounts for the structure of the covariance matrix, utilizing the machinery of Gaussian process kernels. This framework specifically addresses the common problem of mismatches in model spectral line strengths (with respect to data) due to intrinsic model imperfections (e.g., in the atomic/molecular databases or opacity prescriptions) by developing a novel local covariance kernel formalism that identifies and self-consistently downweights pathological spectral line “outliers.” By fitting many spectra in a hierarchical manner, these local kernels provide a mechanism to learn about and build data-driven corrections to synthetic spectral libraries. An open-source software implementation of this approach is available at http://iancze.github.io/Starfish, including a sophisticated probabilistic scheme for spectral interpolation when using model libraries that are sparsely sampled in the stellar parameters. We demonstrate some salient features of the framework by fitting the high-resolution V-band spectrum of WASP-14, an F5 dwarf with a transiting exoplanet, and the moderate-resolution K-band spectrum of Gliese 51, an M5 field dwarf.

  6. Functionalized nanoparticles for biological imaging and detection applications

    Science.gov (United States)

    Mei, Bing C.

    Semiconductor quantum dots (QDs) and gold nanoparticles (AuNPs) have gained tremendous attention in the last decade as a result of their size-dependent spectroscopic properties. These nanoparticles have been a subject of intense study to bridge the gap between macroscopic and atomic behavior, as well as to generate new materials for novel applications in therapeutics, biological sensing, light emitting devices, microelectronics, lasers, and solar cells. One of the most promising areas for the use of these nanoparticles is in biotechnology, where their size-dependent optical properties are harnessed for imaging and sensing applications. However, these nanoparticles, as synthesized, are often not stable in aqueous media and lack simple and reliable means of covalently linking to biomolecules. The focus of this work is to advance the progress of these nanomaterials for biotechnology by synthesizing them, characterizing their optical properties and rendering them water-soluble and functional while maintaining their coveted optical properties. QDs were synthesized by an organometallic chemical procedure that utilizes coordinating solvents to provide brightly luminescent nanoparticles. The optical interactions of these QDs were studied as a function of concentration to identify particle size-dependent optimal concentrations, where scattering and indirection excitation are minimized and the amount light observed per particle is maximized. Both QDs and AuNPs were rendered water-soluble and stable in a broad range of biologically relevant conditions by using a series of ligands composed of dihydrolipoic acid (DHLA) appended to poly(ethylene glycol) methyl ether. By studying the stability of the surface modified AuNPs, we revealed some interesting information regarding the role of the surface ligand on the nanoparticle stability (i.e. solubility in high salt concentration, resistance to dithiothreitol competition and cyanide decomposition). Furthermore, the nanoparticles

  7. Developmental self-construction and -configuration of functional neocortical neuronal networks.

    Science.gov (United States)

    Bauer, Roman; Zubler, Frédéric; Pfister, Sabina; Hauri, Andreas; Pfeiffer, Michael; Muir, Dylan R; Douglas, Rodney J

    2014-12-01

    The prenatal development of neural circuits must provide sufficient configuration to support at least a set of core postnatal behaviors. Although knowledge of various genetic and cellular aspects of development is accumulating rapidly, there is less systematic understanding of how these various processes play together in order to construct such functional networks. Here we make some steps toward such understanding by demonstrating through detailed simulations how a competitive co-operative ('winner-take-all', WTA) network architecture can arise by development from a single precursor cell. This precursor is granted a simplified gene regulatory network that directs cell mitosis, differentiation, migration, neurite outgrowth and synaptogenesis. Once initial axonal connection patterns are established, their synaptic weights undergo homeostatic unsupervised learning that is shaped by wave-like input patterns. We demonstrate how this autonomous genetically directed developmental sequence can give rise to self-calibrated WTA networks, and compare our simulation results with biological data.

  8. Constructing Soliton and Kink Solutions of PDE Models in Transport and Biology

    Directory of Open Access Journals (Sweden)

    Vsevolod A. Vladimirov

    2006-06-01

    Full Text Available We present a review of our recent works directed towards discovery of a periodic, kink-like and soliton-like travelling wave solutions within the models of transport phenomena and the mathematical biology. Analytical description of these wave patterns is carried out by means of our modification of the direct algebraic balance method. In the case when the analytical description fails, we propose to approximate invariant travelling wave solutions by means of an infinite series of exponential functions. The effectiveness of the method of approximation is demonstrated on a hyperbolic modification of Burgers equation.

  9. Multifunctional surfaces with discrete functionalized regions for biological applications.

    Science.gov (United States)

    Ghosh, Moniraj; Alves, Christina; Tong, Ziqiu; Tettey, Kwadwo; Konstantopoulos, Konstantinos; Stebe, Kathleen J

    2008-08-05

    In this paper we describe a method for creating multifunctional glass surfaces presenting discrete patches of different proteins on an inert PEG-functionalized background. Microcontact printing is used to stamp the substrate with octadecyltrichlorosilane to define the active regions. The substrate is then back-filled with PEG-silane {[[2-methoxypoly(ethyleneoxy)]propyl]trimethoxysilane} to define passive regions. A microfluidics device is subsequently affixed to the substrate to deliver proteins to the active regions, with as many channels as there are proteins to be patterned. Examples of trifunctional surfaces are given which present three terminating functional groups, i.e., protein 1, protein 2, and PEG. These surfaces should be broadly useful in biological studies, as patch size is well established to influence cell viability, growth, and differentiation. Three examples of cellular interactions with the surfaces are demonstrated, including the capture of cells from a single cell suspension, the selective sorting of cells from a mixed suspension, and the adhesion of cells to ligand micropatches at critical shear stresses. Within these examples, we demonstrate that the patterned immobilized proteins are active, as they retain their ability to interact with either antibodies in solution or receptors presented by cells. When appropriate (e.g., for E-selectin), proteins are patterned in their physiological orientations using a sandwich immobilization technique, which is readily accommodated within our method. The protein surface densities are highly reproducible in the patches, as supported by fluorescence intensity measurements. Potential applications include biosensors based on the interaction of cells or of marker proteins with protein patches, fundamental studies of cell adhesion as a function of patch size and shear stress, and studies of cell differentiation as a function of surface cues.

  10. Quality Function Deployment For Row House Construction In Real Estate

    Directory of Open Access Journals (Sweden)

    Sukhlal Mujalda

    2015-06-01

    Full Text Available Abstract House construction for real state is the current demand to satisfy the different categories of customer. Various techniques are available to satisfy the customer demand like QFD. Using the QFD house of quality modal we were able to understand the fundamental customer quality and care requirement within the real estate construction. This paper represent a simple case using QFD on the design phase of a real estate construction project as a tool of improvement for feature of middle class row house unit.

  11. Biosynthesis and biological functions of terpenoids in plants.

    Science.gov (United States)

    Tholl, Dorothea

    2015-01-01

    Terpenoids (isoprenoids) represent the largest and most diverse class of chemicals among the myriad compounds produced by plants. Plants employ terpenoid metabolites for a variety of basic functions in growth and development but use the majority of terpenoids for more specialized chemical interactions and protection in the abiotic and biotic environment. Traditionally, plant-based terpenoids have been used by humans in the food, pharmaceutical, and chemical industries, and more recently have been exploited in the development of biofuel products. Genomic resources and emerging tools in synthetic biology facilitate the metabolic engineering of high-value terpenoid products in plants and microbes. Moreover, the ecological importance of terpenoids has gained increased attention to develop strategies for sustainable pest control and abiotic stress protection. Together, these efforts require a continuous growth in knowledge of the complex metabolic and molecular regulatory networks in terpenoid biosynthesis. This chapter gives an overview and highlights recent advances in our understanding of the organization, regulation, and diversification of core and specialized terpenoid metabolic pathways, and addresses the most important functions of volatile and nonvolatile terpenoid specialized metabolites in plants.

  12. Wartime Construction Project Outcomes as a Function of Contract Type

    Science.gov (United States)

    2016-07-01

    Engineering Management at the Air Force Institute of Technology . He teaches courses and advises research students in con- struction and crisis management ...the firm-fixed-price (FFP) norm. Using a dataset of 25 wartime construction projects managed by the Air Force Civil Engineer Center, the authors...projects in wartime environments. Keywords: firm-fixed-price, cost-plus-fixed-fee, Afghanistan, construction management , contract structure 332 Defense ARJ

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

    Directory of Open Access Journals (Sweden)

    C. C. Galbrand

    2007-01-01

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

  14. Natural killer cells: Biology, functions and clinical relevance

    Directory of Open Access Journals (Sweden)

    Vojvodić Svetlana

    2010-01-01

    Full Text Available Introduction. Natural Killer cells (NK cells represent the subset of peripheral lymphocytes that play critical role in the innate immune response to virus-infected and tumor transformed cells. Lysis of NK sensitive target cells could be mediated independently of antigen stimulation and without requirement of peptide presentation by the major histocompatibility complex (MHC molecules. NK cell activity and functions are controlled by a considerable number of cell surface receptors, which exist in both inhibitory and activating isoforms. There are several groups of NK cell surface receptors: 1 killer immunoglobulin like receptors-KIR, 2 C-type lectin receptors,3natural citotoxicity receptors-NCR and 4 Toll-like receptors-TLR. Functions of NK receptors. Defining the biology of NK cell surface receptors has contributed to the concept of the manner how NK cells selectively recognize and lyse tumor and virally infected cells while sparing normal cells. Further, identification of NK receptor ligands and their expression on the normal and transformed cells has led to the development of clinical approaches to manipulating receptor/ligand interactions that showed clinical benefit. NK cells are the first lymphocyte subset that reconstitute the peripheral blood following allogeneic HSCT and multiple roles for alloreactive donor NK cells have been demonstrated, in diminishing Graft vs. Host Disease (GvHD through selective killing recipient dendritic cells, prevention of graft rejection by killing recipient T cells and participation in Graft vs. Leukaemia (GvL effect through destruction of residual host tumor cells. Conclusion. Besides their role in HSCT, NK cell receptors have an important clinical relevance that reflects from the fact that they play a crucial role in the development of some diseases as well as in possibilities of managing all NK receptors through selective expansion and usage of NK cells in cancer immunotherapy.

  15. Function and regulation of lipid biology in Caenorhabditis elegans aging

    Directory of Open Access Journals (Sweden)

    Nicole Shangming Hou

    2012-05-01

    Full Text Available Rapidly expanding aging populations and a concomitant increase in the prevalence of age-related diseases are global health problems today. Over the past three decades, a large body of work has led to the identification of genes and regulatory networks that affect longevity and health span, often benefitting from the tremendous power of genetics in vertebrate and invertebrate model organisms. Interestingly, many of these factors appear linked to lipids, important molecules that participate in cellular signaling, energy metabolism, and structural compartmentalization. Despite the putative link between lipids and longevity, the role of lipids in aging remains poorly understood. Emerging data from the model organism Caenorhabditis elegans suggest that lipid composition may change during aging, as several pathways that influence aging also regulate lipid metabolism enzymes; moreover, some of these enzymes apparently play key roles in the pathways that affect the rate of aging. By understanding how lipid biology is regulated during C. elegans aging, and how it impacts molecular, cellular and organismal function, we may gain insight into novel ways to delay aging using genetic or pharmacological interventions. In the present review we discuss recent insights into the roles of lipids in C. elegans aging, including regulatory roles played by lipids themselves, the regulation of lipid metabolic enzymes, and the roles of lipid metabolism genes in the pathways that affect aging.

  16. Function and Regulation of Lipid Biology in Caenorhabditis elegans Aging

    Science.gov (United States)

    Hou, Nicole Shangming; Taubert, Stefan

    2012-01-01

    Rapidly expanding aging populations and a concomitant increase in the prevalence of age-related diseases are global health problems today. Over the past three decades, a large body of work has led to the identification of genes and regulatory networks that affect longevity and health span, often benefiting from the tremendous power of genetics in vertebrate and invertebrate model organisms. Interestingly, many of these factors appear linked to lipids, important molecules that participate in cellular signaling, energy metabolism, and structural compartmentalization. Despite the putative link between lipids and longevity, the role of lipids in aging remains poorly understood. Emerging data from the model organism Caenorhabditis elegans suggest that lipid composition may change during aging, as several pathways that influence aging also regulate lipid metabolism enzymes; moreover, some of these enzymes apparently play key roles in the pathways that affect the rate of aging. By understanding how lipid biology is regulated during C. elegans aging, and how it impacts molecular, cellular, and organismal function, we may gain insight into novel ways to delay aging using genetic or pharmacological interventions. In the present review we discuss recent insights into the roles of lipids in C. elegans aging, including regulatory roles played by lipids themselves, the regulation of lipid metabolic enzymes, and the roles of lipid metabolism genes in the pathways that affect aging. PMID:22629250

  17. Construction of a novel oncolytic adenoviral vector and its biological characteristics.

    Science.gov (United States)

    Zhang, Mingzhi; Zhang, Xudong; Han, Zhiqiang; Chen, Xinfeng; Yang, Li; Sheng, Yuqiao; Wen, Jianguo

    2013-02-01

    In this study, we aimed to construct an effective and safe oncolytic adenoviral vector for cancer treatment with gene therapy. First, the promoter of the catalytic subunit of human telomerase (hTERTp), adenovirus early region 1a gene (E1A) and thymidine kinase gene of human herpes virus type 1 (HSV-1-TK) were amplified by using PCR from genomic DNA of 293A cells and wild-type HSV-1 (wHSV-1). These specially-prepared elements were inserted into an adenoviral shuttle vector in the opposite and the same directions of left inverted terminal repeat (L-ITR), respectively, to construct pENTR-E1A-IRES-TK-hTERTp (pEITH) and pENTR-hTERTp-E1A-IRES-TK (pHEIT). LR reaction between adenoviral shuttle vectors (pEITH and pHEIT) and the backbone vector DEST was carried out to establish adenoviral expression vectors pAd-E1A-IRES-TK-hTERTp (pAd-EITH) and pAd-hTERTp-E1A-IRES-TK (pAd-HEIT). Recombinant adenovirus Ad-EITH and Ad-HEIT were produced by transfecting 293A cells and purified for the subsequent studies of titer measurement, replication capability with and without acyclovir (ACV) and antitumor ability with and without ganciclovir (GCV) to evaluate the biological characteristics. Adenoviral shuttle vectors pEITH and pHEIT and expression vectors pAd-EITH and pAd-HEIT were successfully constructed, and recombinant adenoviruses Ad-EITH and Ad-HEIT with high titer were produced. The results of replication and cytotoxicity assays showed that Ad-EITH and Ad-HEIT replicated in the hTERTp (+) human nasopharyngeal carcinoma cell line CNE and expressed the TK gene effectively leading to the death of tumor cells. In addition, there were still some Ad-HEIT particles replicating in the hTERTp (-) human osteosarcoma U-2OS cells and human lung HFL-1 fibroblasts compared to Ad-EITH which was hardly able to replicate in U-2OS and HFL-1 cells. In addition, we also observed an interesting phenomenon, that the replication of Ad-EITH could be inhibited by antiviral drug ACV on account of the

  18. CONSTRUCTION OF A FUNCTIONAL LACTOSE PERMEASE DEVOID OF CYSTEINE RESIDUES

    NARCIS (Netherlands)

    VANIWAARDEN, PR; PASTORE, JC; KONINGS, WN; KABACK, HR

    1991-01-01

    By use of oligonucleotide-directed, site-specific mutagenesis, a lactose (lac) permease molecule was constructed in which all eight cysteinyl residues were simultaneously mutagenized (C-less permease). Cys154 was replaced with valine, and Cys117, -148, -176, -234, -333, -353, and -355 were replaced

  19. Endogenous nitric oxide synthesis: biological functions and pathophysiology.

    Science.gov (United States)

    Bredt, D S

    1999-12-01

    Modern molecular biology has revealed vast numbers of large and complex proteins and genes that regulate body function. By contrast, discoveries over the past ten years indicate that crucial features of neuronal communication, blood vessel modulation and immune response are mediated by a remarkably simple chemical, nitric oxide (NO). Endogenous NO is generated from arginine by a family of three distinct calmodulin- dependent NO synthase (NOS) enzymes. NOS from endothelial cells (eNOS) and neurons (nNOS) are both constitutively expressed enzymes, whose activities are stimulated by increases in intracellular calcium. Immune functions for NO are mediated by a calcium-independent inducible NOS (iNOS). Expression of iNOS protein requires transcriptional activation, which is mediated by specific combinations of cytokines. All three NOS use NADPH as an electron donor and employ five enzyme cofactors to catalyze a five-electron oxidation of arginine to NO with stoichiometric formation of citrulline. The highest levels of NO throughout the body are found in neurons, where NO functions as a unique messenger molecule. In the autonomic nervous system NO functions NO functions as a major non-adrenergic non-cholinergic (NANC) neurotransmitter. This NANC pathway plays a particularly important role in producing relaxation of smooth muscle in the cerebral circulation and the gastrointestinal, urogenital and respiratory tracts. Dysregulation of NOS activity in autonomic nerves plays a major role in diverse pathophysiological conditions including migraine headache, hypertrophic pyloric stenosis and male impotence. In the brain, NO functions as a neuromodulator and appears to mediate aspects of learning and memory. Although endogenous NO was originally appreciated as a mediator of smooth muscle relaxation, NO also plays a major role in skeletal muscle. Physiologically muscle-derived NO regulates skeletal muscle contractility and exercise-induced glucose uptake. nNOS occurs at the

  20. Biologically inspired information theory: Adaptation through construction of external reality models by living systems.

    Science.gov (United States)

    Nakajima, Toshiyuki

    2015-12-01

    Higher animals act in the world using their external reality models to cope with the uncertain environment. Organisms that have not developed such information-processing organs may also have external reality models built in the form of their biochemical, physiological, and behavioral structures, acquired by natural selection through successful models constructed internally. Organisms subject to illusions would fail to survive in the material universe. How can organisms, or living systems in general, determine the external reality from within? This paper starts with a phenomenological model, in which the self constitutes a reality model developed through the mental processing of phenomena. Then, the it-from-bit concept is formalized using a simple mathematical model. For this formalization, my previous work on an algorithmic process is employed to constitute symbols referring to the external reality, called the inverse causality, with additional improvements to the previous work. Finally, as an extension of this model, the cognizers system model is employed to describe the self as one of many material entities in a world, each of which acts as a subject by responding to the surrounding entities. This model is used to propose a conceptual framework of information theory that can deal with both the qualitative (semantic) and quantitative aspects of the information involved in biological processes.

  1. Construction of secure and fast hash functions using nonbinary error-correcting codes

    DEFF Research Database (Denmark)

    Knudsen, Lars Ramkilde; Preneel, Bart

    2002-01-01

    This paper considers iterated hash functions. It proposes new constructions of fast and secure compression functions with nl-bit outputs for integers n>1 based on error-correcting codes and secure compression functions with l-bit outputs. This leads to simple and practical hash function construct......, some new attacks are presented that essentially match the presented lower bounds. The constructions allow for a large degree of internal parallelism. The limits of this approach are studied in relation to bounds derived in coding theory.......This paper considers iterated hash functions. It proposes new constructions of fast and secure compression functions with nl-bit outputs for integers n>1 based on error-correcting codes and secure compression functions with l-bit outputs. This leads to simple and practical hash function...

  2. Construction of 1-Resilient Boolean Functions with Optimal Algebraic Immunity and Good Nonlinearity

    Institute of Scientific and Technical Information of China (English)

    Sen-Shan Pan; Xiao-Tong Fu; Wei-Guo Zhangx

    2011-01-01

    This paper presents a construction for a class of 1-resilient functions with optimal algebraic immunity on an even number of variables. The construction is based on the concatenation of two balanced functions in associative classes. For some n, a part of 1-resilient functions with maximum algebraic immunity constructed in the paper can achieve almost optimal nonlinearity. Apart from their high nonlinearity, the functions reach Siegenthaler's upper bound of algebraic degree. Also a class of 1-resilient functions on any number n > 2 of variables with at least sub-optimal algebraic immunity is provided.

  3. Phytochrome from Green Plants: Properties and biological Function

    Energy Technology Data Exchange (ETDEWEB)

    Quail, Peter H.

    2014-07-25

    Pfr conformer reverses this activity upon initial light exposure, inducing the switch to photomorphogenic development. This reversal involves light-triggered translocation of the photoactivated phy molecule into the nucleus where it interacts with PIF-family members, inducing rapid phosphorylation and degradation of the PIFs via the ubiquitin-proteasome system. This degradation in turn elicits rapid alterations in gene expression that drive the deetiolation transition. This project has made considerable progress in defining phy-PIF signaling activity in controlling the SAR. The biological functions of the multiple PIF-family members in controlling the SAR, including dissection of the relative contributions of the individual PIFs to this process, as well as to diurnal growth-control oscillations, have been investigated using higher-order pif-mutant combinations. Using microarray analysis of a quadruple pif mutant we have defined the shade-induced, PIF-regulated transcriptional network genome-wide. This has revealed that a dynamic antagonism between the phys and PIFs generates selective reciprocal responses during deetiolation and the SAR in a rapidly light-responsive transcriptional network. Using integrated RNA-seq and ChIP-seq analysis of higher order pif-mutant combinations, we have defined the direct gene-targets of PIF transcriptional regulation, and have obtained evidence that this regulation involves differential direct targeting of rapidly light-responsive genes by the individual PIF-family members. This project has provided significant advances in our understanding of the molecular mechanisms by which the phy-PIF photosensory signaling pathway regulates an important bioenergy-related plant response to the light environment. The identification of molecular targets in the primary transcriptional-regulatory circuitry of this pathway has the potential to enable genetic or reverse-genetic manipulation of the partitioning of carbon between reproductive and

  4. Construction of membrane-bound artificial cells using microfluidics: a new frontier in bottom-up synthetic biology.

    Science.gov (United States)

    Elani, Yuval

    2016-06-15

    The quest to construct artificial cells from the bottom-up using simple building blocks has received much attention over recent decades and is one of the grand challenges in synthetic biology. Cell mimics that are encapsulated by lipid membranes are a particularly powerful class of artificial cells due to their biocompatibility and the ability to reconstitute biological machinery within them. One of the key obstacles in the field centres on the following: how can membrane-based artificial cells be generated in a controlled way and in high-throughput? In particular, how can they be constructed to have precisely defined parameters including size, biomolecular composition and spatial organization? Microfluidic generation strategies have proved instrumental in addressing these questions. This article will outline some of the major principles underpinning membrane-based artificial cells and their construction using microfluidics, and will detail some recent landmarks that have been achieved.

  5. Constructive tissue remodeling of biologic scaffolds: A phenomenon associated with scaffold characteristics and distinctive macrophage phenotypes

    Science.gov (United States)

    Brown, Bryan Nicklaus

    Scaffolds composed of extracellular matrix (ECM) have been shown to promote formation of site-specific, functional host tissue following implantation in a number of preclinical and clinical settings. However, the exact mechanisms by which ECM scaffolds are able to promote this type of "constructive tissue remodeling" are unknown. Further, the ability of ECM scaffolds to promote constructive tissue remodeling appears to be dependent on the methods used in their production and the applications in which they are utilized. Therefore, a comprehensive understanding of ECM scaffold characteristics and their effects upon the host response and subsequent tissue remodeling outcome is essential to the design of intelligent scaffolds for specific clinical applications. The present work investigated the effects of tissue source and chemical cross-linking upon the resulting ECM scaffolds, showing that ECM scaffold materials have distinct ultrastructural and compositional characteristics which are dependant on the anatomic location from which the scaffolds are derived and the methods used in their production. These characteristics were associated with distinct patterns of cell behavior in vitro. Distinct tissue remodeling outcomes were observed following implantation of a subset of these scaffold materials in a rat abdominal wall musculature reconstruction model. Acellular, non-cross-linked ECM was associated with constructive tissue remodeling while scaffolds that contained cellular components or were chemically cross-linked resulted in dense connective tissue deposition or encapsulation, respectively. Despite differences in the tissue remodeling outcome, a histologically similar population of macrophages was observed following implantation in each of these cases. Therefore, the phenotype of the macrophage population participating in the host response was investigated. It was shown that scaffolds which resulted in constructive tissue remodeling were associated with an increase

  6. Recombinant expression library of Pyrococcus furiosus constructed by high-throughput cloning: a useful tool for functional and structural genomics

    Directory of Open Access Journals (Sweden)

    Hui eYuan

    2015-09-01

    Full Text Available Hyperthermophile Pyrococcus furiosus grows optimally near 100°C and is an important resource of many industrial and molecular biological enzymes. To study the structure and function of Pyrococcus furiosus proteins at whole genome level, we constructed expression plasmids of each Pyrococcus furiosus gene using a ligase-independent cloning method, which was based on amplifying target gene and vector by PCR using phosphorothioate-modified primers and digesting PCR products by λ exonuclease. Our cloning method had a positive clone percentage of ≥ 80% in 96-well plate cloning format. Small-scale expression experiment showed that 55 out of 80 genes were efficiently expressed in Escherichia coli Strain Rosetta 2(DE3pLysS. In summary, this recombinant expression library of Pyrococcus furiosus provides a platform for functional and structural studies, as well as developing novel industrial enzymes. Our cloning scheme is adaptable to constructing recombinant expression library of other sequenced organisms.

  7. Alterations in immune function with biologic therapies for autoimmune disease.

    Science.gov (United States)

    Her, Minyoung; Kavanaugh, Arthur

    2016-01-01

    Autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, psoriasis, and others, are characterized by dysregulation of various aspects of normal immunity and inflammation. Biologic agents targeting key components of the dysregulated immune response have dramatically improved patient outcomes and transformed treatment paradigms for a number of systemic inflammatory autoimmune diseases. Despite their excellent efficacy, because they do affect normal immune responsiveness, biologic agents can potentially be associated with a variety of adverse effects. Important potential adverse effects related to the use of biologic agents include immunosuppression, which might result in outcomes such as infection, and autoimmunity, that could result in paradoxical inflammation or even autoimmune disease. In this article the current clinical evidence and immunologic mechanisms of the adverse effects related to biologic agents are discussed.

  8. Laser Direct Writing of Idealized Cellular and Biologic Constructs for Tissue Engineering and Regenerative Medicine

    Science.gov (United States)

    Schiele, Nathan R.; Corr, David T.; Chrisey, Douglas B.

    Conventional tissue engineering typically involves homogenously seeding cells into a scaffold, then manipulating the scaffold either mechanically, using bioreactors, or chemically, using growth factors, in an attempt to tailor the mechanical and biological properties of the engineered tissue. The material composition of the scaffold gives the construct its initial strength; then the scaffold either remodels or dissolves when implanted in the body. An ideal tissue replacement scaffold would be biocompatible, biodegradable, implantable, and would match the strength of the tissue it is replacing, and would remodel by natural mechanisms [1]. Finding or creating scaffold materials that meet all these specifications while providing an environment for cell attachment and proliferation is one of the main goals of conventional tissue engineering. Popular current scaffold materials include poly-l-lactic acid (PLLA) [2] and collagen [3]. Typically, the utilization of scaffolds in tissue engineering employs a top-down approach in which cells are seeded homogenously into the scaffold, then incubated in vitro prior to implantation. Scaffold properties, such as geometric dimensions (e.g., thickness) and cellular in-growth, are limited by the diffusion of nutrients, since these scaffolds do not incorporate vascular structures to transport nutrients and remove wastes deep into the scaffold as in native tissue [4]. Although seeded scaffolds have proven successful in some cases, there remains the need to have greater control of cell placement as well as the placement of additional features such as vascular structures, multiple cell types, growth factors, and extracellular matrix proteins that will aid in the fabrication of the next generation of engineered tissues.

  9. Construction of Transgenic Crop Germplasm Effective Function and Characteristic Analysis

    Institute of Scientific and Technical Information of China (English)

    DING Guangzhou; WANG Xiaowei

    2008-01-01

    Germplasm effect reflects the quantitative relation between production ability of gennplasm elements and yield (quality) of a certain crop, which can be shown by mathematic function, namely, germplasm effect function. Germplasm effect of a crop variety is an aggregation of many effective factors, and is restrained by different effective factors;constant increase of any one effect of germplasm elements would lead to law of effect decline, therefore, possible modes of transgenic crops effect function were deduced according to the law of effect decline. The possible modes of single transgenic germplasm effect function and multi-transgenic germplasm effect regression equation were discussed, and the characteristics of germplasm effect regression equation were analyzed in this paper.

  10. Constructing and Counting Even-Variable Symmetric Boolean Functions with Algebraic Immunity not Less Than $d$

    CERN Document Server

    Li, Yuan; Kan, Haibin

    2011-01-01

    In this paper, we explicitly construct a large class of symmetric Boolean functions on $2k$ variables with algebraic immunity not less than $d$, where integer $k$ is given arbitrarily and $d$ is a given suffix of $k$ in binary representation. If let $d = k$, our constructed functions achieve the maximum algebraic immunity. Remarkably, $2^{\\lfloor \\log_2{k} \\rfloor + 2}$ symmetric Boolean functions on $2k$ variables with maximum algebraic immunity are constructed, which is much more than the previous constructions. Based on our construction, a lower bound of symmetric Boolean functions with algebraic immunity not less than $d$ is derived, which is $2^{\\lfloor \\log_2{d} \\rfloor + 2(k-d+1)}$. As far as we know, this is the first lower bound of this kind.

  11. New Construction Approach of Basic Belief Assignment Function Based on Confusion Matrix

    Directory of Open Access Journals (Sweden)

    Jing Zhu

    2012-08-01

    Full Text Available In the application of belief function theory, the first problem is the construction of the basic belief assignment. This study presents a new construction approach based on the confusion matrix. The method starts from the output of the confusion matrix and then designs construction strategy for basic belief assignment functions based on the expectation vector of the confusion matrix. Comparative tests of several other construction methods on the U.C.I database show that our proposed method can achieve higher target classification accuracy, lower computational complexity, which has a strong ability to promote the application.

  12. Superatomic Boolean algebras constructed from strongly unbounded functions

    CERN Document Server

    Martinez, Juan Carlos

    2010-01-01

    Using Koszmider's strongly unbounded functions, we show the following consistency result: Suppose that $\\kappa,\\lambda$ are infinite cardinals such that $\\kappa^{+++} \\leq \\lambda$, $\\kappa^{_{{\\omega}_1}\\concatenation \\$ and $\\_{{\\omega}_2}\\concatenation \\$ can be cardinal sequences of superatomic Boolean algebras.

  13. Constructing and Deriving Reciprocal Trigonometric Relations: A Functional Analytic Approach

    Science.gov (United States)

    Ninness, Chris; Dixon, Mark; Barnes-Holmes, Dermot; Rehfeldt, Ruth Anne; Rumph, Robin; McCuller, Glen; Holland, James; Smith, Ronald; Ninness, Sharon K.; McGinty, Jennifer

    2009-01-01

    Participants were pretrained and tested on mutually entailed trigonometric relations and combinatorially entailed relations as they pertained to positive and negative forms of sine, cosine, secant, and cosecant. Experiment 1 focused on training and testing transformations of these mathematical functions in terms of amplitude and frequency followed…

  14. Monthly Monetary Planning for China via Applying Method of Constructing Objective Function

    Institute of Scientific and Technical Information of China (English)

    ZENG Jian-hua; YANG Xiao-guang; XU Shan-ying

    2001-01-01

    Many economic problems can be formulated as optimization problems. Econometricians have long devoted their efforts to construct the econometric equation systems, while the corresponding objective functions receive few attentions. In recent twenty years, some techniques to construct the objective functions with economic implications have been developed, which might have a potential in economic decision-making.In the paper we apply the method of constructing objective function to design an optimization model for monthly monetary planning of China. The real monthly data from 1991 to 1999 are used to evaluate the monthly economic situation. Our empirical experiment shows that the model gives a good short-term forecasting.

  15. Gastrointestinal function and metabolic control after construction of an orthotopic ileal neobladder in bladder cancer

    DEFF Research Database (Denmark)

    Thorstenson, Andreas; Jacobsson, Hans; Onelöv, Erik

    2007-01-01

    OBJECTIVE: To investigate the effects of ileum resection in orthotopic neobladder construction on gastrointestinal function and metabolic control. MATERIAL AND METHODS: We included 28 patients who underwent radical cystectomy and construction of an orthotopic neobladder or continent ileal reservoir...... were unchanged. CONCLUSIONS: Using the distal ileum for orthotopic neobladder construction causes bowel disorders in a quarter of cystectomy patients. Diarrhoea and faecal urgency are probably caused by decreased reabsorption of bile and are not due to changes in gastrointestinal hormones. A sizeable...

  16. The social construction of literacy in a high school biology class

    Science.gov (United States)

    Thomas, Heather K.

    2000-10-01

    The purpose of this classroom case study was to explore the social construction of literacy in a high school biology class with a constructivist teacher. The teacher, Mr. Green, believed strongly in active student engagement. A social constructionist, interpretivist approach provided a framework for data collection and analysis. Field notes of one semester of participant observation and interviews of the teacher and students served as primary data sources. Supplemental data were derived from document analysis of classroom materials. Data were categorized and analyzed for patterns within or between categories. These patterns formed the basis for several assertions about literacy and science activities in this classroom. Results suggested that Mr. Green orchestrated the talk in the classroom but did not do all of the talking; there was a large quantity of varied student talk in this classroom atmosphere of shared authority. When Mr. Green talked with his students, he focused on building science concepts. He created opportunities for students to work together and engage in scientist-like activities, but students talked to each other mostly about "getting the work done." Reading and writing were embedded in most classroom tasks, for example, taking notes from textbooks and reading lab directions. Most students could complete these literacy tasks, but many had difficulty doing them in a meaningful way. They preferred to use oral rather than written language. Students responded positively when Mr. Green provided a greater degree of teacher guidance for reading and writing tasks. This study suggests that sharing authority with students may help create a language-rich environment in which students use language to meet their perceived learning needs. It also suggests that as teachers share authority they would do well to maintain responsibility for showing students how to use reading and writing to develop conceptual understandings. Future research might engage teachers in

  17. Cell biology and functional dynamics of the mammalian sperm surface

    NARCIS (Netherlands)

    Gadella, B.M.; Luna, C.

    2014-01-01

    Theriogenology has now a 40-year rich history on covering sperm biological aspects with a special emphasis on farm and husbandry animals. The major and most influential of these contributions will be placed into an evolutionary perspective of ongoing and intriguing progresses made in this field. Alt

  18. Design of Functional Polyesters for Electronic and Biological Applications

    OpenAIRE

    Nelson, Ashley Marie

    2015-01-01

    Melt polymerization and novel monomers enabled the synthesis of polyesters for electronic and biological applications. Inspiration from nature and a passion for environmental preservation instigated an emphasis on the incorporation of renewable resources into polymeric materials. Critical analysis of current research surrounding bisphenol-A replacements and ion-containing segmented polyurethanes aided in identifying benchmark polymers, including limitations, challenges, and future needs. S...

  19. Click chemistry mediated functionalization of vertical nanowires for biological applications

    DEFF Research Database (Denmark)

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica;

    2016-01-01

    is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use...

  20. Oxidative metabolites of lycopene and their biological functions

    Science.gov (United States)

    To gain a better understanding of the beneficial biological activities of lycopene on cancer prevention, a greater knowledge of the metabolism of lycopene is needed. In particular, the identification of lycopene metabolites and oxidation products in vivo; the importance of tissue specific lycopene c...

  1. Respiratory Symptoms and Lung Function among Danish Construction Workers. A Cross-Sectional Study

    DEFF Research Database (Denmark)

    Hanskov, Dorte Jessing Agerby; Brauer, Charlotte; Breinegaard, Nina;

    2015-01-01

    Objective:This study investigated whether Danish construction workers had an increased prevalence of chronic obstructive pulmonary disease (COPD) or affected lung function and if the prevalence differed between types of jobs within construction. Methods:A cross-sectional study of 899 Danish male ...

  2. Flexible gateway constructs for functional analyses of genes in plant pathogenic fungi

    NARCIS (Netherlands)

    Mehrabi, Rahim; Mirzadi Gohari, Amir; Silva, da Gilvan Ferreira; Steinberg, Gero; Kema, Gert H.J.; Wit, de Pierre J.G.M.

    2015-01-01

    Genetic manipulation of fungi requires quick, low-cost, efficient, high-throughput and molecular tools. In this paper, we report 22 entry constructs as new molecular tools based on the Gateway technology facilitating rapid construction of binary vectors that can be used for functional analysis of

  3. Constructing Knowledge about the Trigonometric Functions and Their Geometric Meaning on the Unit Circle

    Science.gov (United States)

    Altman, Renana; Kidron, Ivy

    2016-01-01

    Processes of knowledge construction are investigated. A learner is constructing knowledge about the trigonometric functions and their geometric meaning on the unit circle. The analysis is based on the dynamically nested epistemic action model for abstraction in context. Different tasks are offered to the learner. In his effort to perform the…

  4. In search of lipid translocases and their biological functions

    NARCIS (Netherlands)

    Hoekstra, D; van Ijzendoorn, SCD

    2003-01-01

    In plasma membranes, lipids distribute asymmetrically across the bilayer, a process that requires proteins. Recent work identified novel lipid translocators in yeast, and their activity was functionally correlated to endocytosis, thus boosting investigations on identity, mechanism, and function of l

  5. Construction

    Science.gov (United States)

    2002-01-01

    Harbor Deepening Project, Jacksonville, FL Palm Valley Bridge Project, Jacksonville, FL Rotary Club of San Juan, San Juan, PR Tren Urbano Subway...David. What is nanotechnology? What are its implications for construction?, Foresight/CRISP Workshop on Nanotechnology, Royal Society of Arts

  6. SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities.

    Science.gov (United States)

    Martínez-García, Esteban; Aparicio, Tomás; Goñi-Moreno, Angel; Fraile, Sofía; de Lorenzo, Víctor

    2015-01-01

    The Standard European Vector Architecture 2.0 database (SEVA-DB 2.0, http://seva.cnb.csic.es) is an improved and expanded version of the platform released in 2013 (doi: 10.1093/nar/gks1119) aimed at assisting the choice of optimal genetic tools for de-constructing and re-constructing complex prokaryotic phenotypes. By adopting simple compositional rules, the SEVA standard facilitates combinations of functional DNA segments that ease both the analysis and the engineering of diverse Gram-negative bacteria for fundamental or biotechnological purposes. The large number of users of the SEVA-DB during its first two years of existence has resulted in a valuable feedback that we have exploited for fixing DNA sequence errors, improving the nomenclature of the SEVA plasmids, expanding the vector collection, adding new features to the web interface and encouraging contributions of materials from the community of users. The SEVA platform is also adopting the Synthetic Biology Open Language (SBOL) for electronic-like description of the constructs available in the collection and their interfacing with genetic devices developed by other Synthetic Biology communities. We advocate the SEVA format as one interim asset for the ongoing transition of genetic design of microorganisms from being a trial-and-error endeavor to become an authentic engineering discipline.

  7. Opposing Biological Functions of Tryptophan Catabolizing Enzymes During Intracellular Infection

    Science.gov (United States)

    Divanovic, Senad; Sawtell, Nancy M.; Trompette, Aurelien; Warning, Jamie I.; Dias, Alexandra; Cooper, Andrea M.; Yap, George S.; Arditi, Moshe; Shimada, Kenichi; DuHadaway, James B.; Prendergast, George C.; Basaraba, Randall J.; Mellor, Andrew L.; Munn, David H.; Aliberti, Julio

    2012-01-01

    Recent studies have underscored physiological and pathophysiological roles for the tryptophan-degrading enzyme indolamine 2,3-dioxygenase (IDO) in immune counterregulation. However, IDO was first recognized as an antimicrobial effector, restricting tryptophan availability to Toxoplasma gondii and other pathogens in vitro. The biological relevance of these findings came under question when infectious phenotypes were not forthcoming in IDO-deficient mice. The recent discovery of an IDO homolog, IDO-2, suggested that the issue deserved reexamination. IDO inhibition during murine toxoplasmosis led to 100% mortality, with increased parasite burdens and no evident effects on the immune response. Similar studies revealed a counterregulatory role for IDO during leishmaniasis (restraining effector immune responses and parasite clearance), and no evident role for IDO in herpes simplex virus type 1 (HSV-1) infection. Thus, IDO plays biologically important roles in the host response to diverse intracellular infections, but the dominant nature of this role—antimicrobial or immunoregulatory—is pathogen-specific. PMID:21990421

  8. Cerenkov Radiation: A Multi-functional Approach for Biological Sciences

    Directory of Open Access Journals (Sweden)

    Xiaowei eMa

    2014-02-01

    Full Text Available Cerenkov radiation (CR has been used in various biological research fields, which has aroused lots of attention in recent years. Combining optical imaging instruments and most of nuclear medicine imaging or radiotherapy probes, the CR was developed as a new imaging modality for biology studies, called Cerenkov luminescence imaging (CLI. On the other hand, it was novelly used as an internal excitation source to activate some fluorophores for energy transfer imaging. However, it also has some shortages such as relatively weak luminescence intensity and low penetration in tissue. Thus some scientific groups demonstrated to optimize the CLI and demonstrated it to three-dimension tomography. In this article, we elaborate on its principle, history, and applications and discuss a number of directions for technical improvements. Then concluded some advantages and shortages of CR and discuss some prospects of it.

  9. Constructing analytically mode functions of inflation with trans-Planckian physics

    CERN Document Server

    Zhu, Tao; Cleaver, Gerald; Kirsten, Klaus; Sheng, Qin

    2013-01-01

    We present a technique, {\\em the uniform asymptotic approximation}, to construct analytically solutions of the mode functions of inflation with trans-Planckian physics, in which the dispersion relations are nonlinear and have various turning points (zeros). Each turning point can be a single, double or higher multiple zero. Error bounds are constructed explicitly. It is shown that the analytical solutions describe the exact evolution of the mode function extremely well even only to the first-order approximations.

  10. FUSE: a profit maximization approach for functional summarization of biological networks

    Directory of Open Access Journals (Sweden)

    Seah Boon-Siew

    2012-03-01

    Full Text Available Abstract Background The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL principle to maximize information gain of the summary graph while satisfying the level of detail constraint. Results We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. Conclusion By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

  11. Trigonometric and hyperbolic functions method for constructing analytic solutions to nonlinear plane magnetohydrodynamics equilibrium equations

    Energy Technology Data Exchange (ETDEWEB)

    Moawad, S. M., E-mail: smmoawad@hotmail.com [Department of Mathematics, Faculty of Science, Beni-Suef University, Beni-Suef (Egypt)

    2015-02-15

    In this paper, we present a solution method for constructing exact analytic solutions to magnetohydrodynamics (MHD) equations. The method is constructed via all the trigonometric and hyperbolic functions. The method is applied to MHD equilibria with mass flow. Applications to a solar system concerned with the properties of coronal mass ejections that affect the heliosphere are presented. Some examples of the constructed solutions which describe magnetic structures of solar eruptions are investigated. Moreover, the constructed method can be applied to a variety classes of elliptic partial differential equations which arise in plasma physics.

  12. Expression of Recombinant Human Amelogenin in Iranian Lizard Leishmania and Its Biological Function Assay

    Directory of Open Access Journals (Sweden)

    Zahra YADEGARI

    2015-10-01

    Full Text Available Background: Amelogenins are the major components of enamel matrix proteins. Enamel matrix derivatives (EMD can be used in periodontal diseases to regenerate periodontal tissues. The main aim of this study was to evaluate ex-pression of full-length functional recombinant human amelogenin (rhAm in Iranian lizard Leishmania (I.L.L. as an alternative eukaryotic expression system.Methods: Human cDNA encoding a 175-amino acid amelogenin expression cassette was sub cloned into a pLEXSY vector. The construct was transferred into Leishmania cells by electroporation. The protein production was surveyed in the transcription and the translation levels. The expressed protein was purified and some of its biological properties were investigated in comparison to EMD and negative control.Results: Expression of rhAm was confirmed by RT-PCR and western blot test in Leishmania cells. Purified rhAm sig-nificantly inhibited the formation of tartrate-resistant acid phosphatase positive (TRAP+ multinuclear cells in calcitriol stimulated mouse marrow cultures. Moreover, it significantly promoted proliferation and DNA synthesis in L929 mouse fibroblast cells.Conclusion: Functional rhAm was successfully expressed in I.L.L. Easy handling and post translation modification were the main advantages of this expression system. It is suggested to investigate molecular properties of this rhAm in the future.

  13. Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

    Science.gov (United States)

    Li, Jun; Zhao, Patrick X

    2016-01-01

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

  14. The SHP-2 tyrosine phosphatase: Signaling mechanisms and biological functions

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Cellular biological activities are tightly controlled by intracellular signaling processes initiated by extracellular signals.Protein tyrosine phosphatases, which remove phosphate groups from phosphorylated signaling molecules, play equally important tyrosine roles as protein tyrosine kinases in signal transduction.SHP-2, a cytoplasmic SH2 domain containing protein tyrosine phosphatase, is involved in the signaling pathways of a variety of growth factors and cytokines. Recent studies have clearly demonstrated that this phosphatase plays an important role in transducing signal relay from the cell surface to the nucleus, and is a critical intracellular regulator in mediating cell proliferation and differentiation.

  15. Inferring biological functions of guanylyl cyclases with computational methods

    KAUST Repository

    Alquraishi, May Majed

    2013-09-03

    A number of studies have shown that functionally related genes are often co-expressed and that computational based co-expression analysis can be used to accurately identify functional relationships between genes and by inference, their encoded proteins. Here we describe how a computational based co-expression analysis can be used to link the function of a specific gene of interest to a defined cellular response. Using a worked example we demonstrate how this methodology is used to link the function of the Arabidopsis Wall-Associated Kinase-Like 10 gene, which encodes a functional guanylyl cyclase, to host responses to pathogens. © Springer Science+Business Media New York 2013.

  16. Constructal law of design and evolution: Physics, biology, technology, and society

    Science.gov (United States)

    Bejan, Adrian; Lorente, Sylvie

    2013-04-01

    This is a review of the theoretical and applied progress made based on the Constructal law of design and evolution in nature, with emphasis on the last decade. The Constructal law is the law of physics that accounts for the natural tendency of all flow systems (animate and inanimate) to change into configurations that offer progressively greater flow access over time. The progress made with the Constructal law covers the broadest range of science, from heat and fluid flow and geophysics, to animal design, technology evolution, and social organization (economics, government). This review presents the state of this fast growing field, and draws attention to newly opened directions for original research. The Constructal law places the concepts of life, design, and evolution in physics.

  17. Neuroscience in the era of functional genomics and systems biology

    OpenAIRE

    Geschwind, Daniel H.; Konopka, Genevieve

    2009-01-01

    Advances in genetics and genomics have fuelled a revolution in discovery-based, or hypothesis-generating, research that provides a powerful complement to the more directly hypothesis-driven molecular, cellular and systems neuroscience. Genetic and functional genomic studies have already yielded important insights into neuronal diversity and function, as well as disease. One of the most exciting and challenging frontiers in neuroscience involves harnessing the power of large-scale genetic, gen...

  18. Exosome Function: From Tumor Immunology to Pathogen Biology

    OpenAIRE

    Schorey, Jeffrey S; Bhatnagar, Sanchita

    2008-01-01

    Exosomes are the newest family member of ‘bioactive vesicles’ that function to promote intercellular communication. Exosomes are derived from the fusion of multi-vesicular bodies with the plasma membrane and extracellular release of the intraluminal vesicles. Recent studies have focused on the biogenesis and composition of exosomes as well as regulation of exosome release. Exosomes have been shown to be released by cells of hematopoietic and non-hematopoietic origin, yet their function remain...

  19. Construction of new synthetic biology tools for the control of gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002.

    Science.gov (United States)

    Zess, Erin K; Begemann, Matthew B; Pfleger, Brian F

    2016-02-01

    Predictive control of gene expression is an essential tool for developing synthetic biological systems. The current toolbox for controlling gene expression in cyanobacteria is a barrier to more in-depth genetic analysis and manipulation. Towards relieving this bottleneck, this work describes the use of synthetic biology to construct an anhydrotetracycline-based induction system and adapt a trans-acting small RNA (sRNA) system for use in the cyanobacterium Synechococcus sp. strain PCC 7002. An anhydrotetracycline-inducible promoter was developed to maximize intrinsic strength and dynamic range. The resulting construct, PEZtet , exhibited tight repression and a maximum 32-fold induction upon addition of anhydrotetracycline. Additionally, a sRNA system based on the Escherichia coli IS10 RNA-IN/OUT regulator was adapted for use in Synechococcus sp. strain PCC 7002. This system exhibited 70% attenuation of target gene expression, providing a demonstration of the use of sRNAs for differential gene expression in cyanobacteria. These systems were combined to produce an inducible sRNA system, which demonstrated 59% attenuation of target gene expression. Lastly, the role of Hfq, a critical component of sRNA systems in E. coli, was investigated. Genetic studies showed that the Hfq homolog in Synechococcus sp. strain PCC 7002 did not impact repression by the engineered sRNA system. In summary, this work describes new synthetic biology tools that can be applied to physiological studies, metabolic engineering, or sRNA platforms in Synechococcus sp. strain PCC 7002.

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

    OpenAIRE

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

    2015-01-01

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

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

    Science.gov (United States)

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

  2. The suffix-free-prefix-free hash function construction and its indifferentiability security analysis

    DEFF Research Database (Denmark)

    Bagheri, Nasour; Gauravaram, Praveen; Knudsen, Lars R.

    2012-01-01

    is indifferentiable from a random oracle (RO) when the compression function is viewed as a fixed input-length random oracle (FIL-RO). We show that some hash function constructions proposed in the literature fit in the SFPF framework while others that do not fit in this framework are not indifferentiable from a RO. We...

  3. Universal construction of control Lyapunov functions for a class of nonlinear systems

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A method is developed by which control Lyapunov functions of a class of nonlinear systems can be constructed systematically.Based on the control Lyapunov function,a feedback control is obtained to stabilize the closed-loop system.In addition,this method is applied to stabilize the Benchmark system.A simulation shows the effectiveness of the method.

  4. Three New Construction Methods of the Highly Nonlinear Balanced Boolean Function

    Institute of Scientific and Technical Information of China (English)

    TANXinglie; SHEKun; JIQingbing; ZHOUMingtian; SHENChangxiang

    2003-01-01

    Nonlinearity is a nonlinear criterion of Boolean function. In this paper, some useful definitions and theorems are introduced, and then three new ways to construct the highly nonlinear balanced boolean function are given by ways of concatenating, dividing, modifying and alternating, which are proven to be very effective.

  5. Construct validation and the Rasch model: functional ability of healthy elderly people

    DEFF Research Database (Denmark)

    Avlund, K; Kreiner, S; Schultz-Larsen, K

    1993-01-01

    The purpose of this study was to test the construct validity of a measure of functional ability, developed with the intention of achieving a high degree of variability and capacity for discriminating among a group of healthy elderly people. Data were collected from 734 70-year-old people in Denmark...... functional ability can appear by either tiredness or reduced speed....

  6. Sensitivity analysis applied to the construction of radial basis function networks.

    Science.gov (United States)

    Shi, D; Yeung, D S; Gao, J

    2005-09-01

    Conventionally, a radial basis function (RBF) network is constructed by obtaining cluster centers of basis function by maximum likelihood learning. This paper proposes a novel learning algorithm for the construction of radial basis function using sensitivity analysis. In training, the number of hidden neurons and the centers of their radial basis functions are determined by the maximization of the output's sensitivity to the training data. In classification, the minimal number of such hidden neurons with the maximal sensitivity will be the most generalizable to unknown data. Our experimental results show that our proposed sensitivity-based RBF classifier outperforms the conventional RBFs and is as accurate as support vector machine (SVM). Hence, sensitivity analysis is expected to be a new alternative way to the construction of RBF networks.

  7. Use of Constructed-Response Questions to Support Learning of Cell Biology during Lectures

    Directory of Open Access Journals (Sweden)

    Foong May Yeong

    2015-02-01

    Full Text Available The use of class-response systems such as the Clickers to promote active-learning during lectures has been wide-spread. However, the often-used MCQ format in class activities as well as in assessments for large classes might lower students’ expectations and attitudes towards learning. Here, I describe my experience converting MCQs to constructed-response questions for in-class learning activities by removing cues from the MCQs. From the responses submitted, students seemed capable of providing answers without the need for cues. Using class-response systems such as Socrative for such constructed-response questions could be useful to challenge students to express their ideas in their own words. Moreover, by constructing their own answers, mis-conceptions could be revealed and corrected in a timely manner.

  8. Novel ESCRT functions in cell biology: spiraling out of control?

    Science.gov (United States)

    Campsteijn, Coen; Vietri, Marina; Stenmark, Harald

    2016-08-01

    The endosomal sorting complex required for transport (ESCRT), originally identified for its role in endosomal protein sorting and biogenesis of multivesicular endosomes (MVEs), has proven to be a versatile machinery for involution and scission of narrow membrane invaginations filled with cytosol. Budding of enveloped viruses and cytokinetic abscission were early described functions for the ESCRT machinery, and recently a number of new ESCRT functions have emerged. These include cytokinetic abscission checkpoint control, plasma membrane repair, exovesicle release, quality control of nuclear pore complexes, neuron pruning, and sealing of the newly formed nuclear envelope. Here we review these novel ESCRT mechanisms and discuss similarities and differences between the various ESCRT-dependent activities.

  9. Molecular structure and biological function of proliferating cell nuclear antigen

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proliferating cell nuclear antigen (PCNA) is the core component of replication complex in eukaryote.As a processive factor of DNA polymerase delta, PCNA coordinates the replication process by interacting with various replication proteins. PCNA appears to play an essential role in many cell events, such as DNA damage repair, cell cycle regulation, and apoptosis, through the coordination or organization of different partners. PCNA is an essential factor in cell proliferation, and has clinical significance in tumor research. In this article we review the functional structure of PCNA, which acts as a function switch in different cell events.

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

    NARCIS (Netherlands)

    Mazereeuw, M.

    2013-01-01

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

  11. Construction of tunable radial basis function networks using orthogonal forward selection.

    Science.gov (United States)

    Chen, Sheng; Hong, Xia; Luk, Bing L; Harris, Chris J

    2009-04-01

    An orthogonal forward selection (OFS) algorithm based on leave-one-out (LOO) criteria is proposed for the construction of radial basis function (RBF) networks with tunable nodes. Each stage of the construction process determines an RBF node, namely, its center vector and diagonal covariance matrix, by minimizing the LOO statistics. For regression application, the LOO criterion is chosen to be the LOO mean-square error, while the LOO misclassification rate is adopted in two-class classification application. This OFS-LOO algorithm is computationally efficient, and it is capable of constructing parsimonious RBF networks that generalize well. Moreover, the proposed algorithm is fully automatic, and the user does not need to specify a termination criterion for the construction process. The effectiveness of the proposed RBF network construction procedure is demonstrated using examples taken from both regression and classification applications.

  12. Construction and behavior of biologically contained bacteria for environmental applications in bioredemiation

    DEFF Research Database (Denmark)

    Ronchel, M. C.; Ramos, C.; Jensen, Lars Bogø;

    1995-01-01

    . Expression from P-lac is controlled through a regulatory cascade, so that P-lac is snitched on or off by the absence or presence of alkylbenzoates, respectively. Similar uncontained strains were also constructed and tested as a control. Contained and uncontained strains were genetically stable...

  13. UNIFORM ANALYTIC CONSTRUCTION OF WAVELET ANALYSIS FILTERS BASED ON SINE AND COSINE TRIGONOMETRIC FUNCTIONS

    Institute of Scientific and Technical Information of China (English)

    李建平; 唐远炎; 严中洪; 张万萍

    2001-01-01

    Based on sine and cosine functions, the compactly supported orthogonal wavelet filter coefficients with arbitrary length are constructed for the first time. When/N = 2k- 1 and N = 2k , the unified analytic constructions of orthogonal wavelet filters are put forward,respectively. The famous Daubechies filter and some other well-known wavelet filters are tested by the proposed novel method which is very useful for wavelet theory research and many application areas such as pattern recognition.

  14. Social inclusion enhances biological motion processing: a functional near-infrared spectroscopy study.

    Science.gov (United States)

    Bolling, Danielle Z; Pelphrey, Kevin A; Kaiser, Martha D

    2013-04-01

    Humans are especially tuned to the movements of other people. Neural correlates of this social attunement have been proposed to lie in and around the right posterior superior temporal sulcus (STS) region, which robustly responds to biological motion in contrast to a variety of non-biological motions. This response persists even when no form information is provided, as in point-light displays (PLDs). The aim of the current study was to assess the ability of functional near-infrared spectroscopy (fNIRS) to reliably measure brain responses to PLDs of biological motion, and determine the sensitivity of these responses to interpersonal contextual factors. To establish reliability, we measured brain activation to biological motion with fNIRS and functional magnetic resonance imaging (fMRI) during two separate sessions in an identical group of 12 participants. To establish sensitivity, brain responses to biological motion measured with fNIRS were subjected to an additional social manipulation where participants were either socially included or excluded before viewing PLDs of biological motion. Results revealed comparable brain responses to biological motion using fMRI and fNIRS in the right supramarginal gyrus. Further, social inclusion increased brain responses to biological motion in right supramarginal gyrus and posterior STS. Thus, fNIRS can reliably measure brain responses to biological motion and can detect social experience-dependent modulations of these brain responses.

  15. Constructing exact solutions to discrete systems with the trial function method

    Institute of Scientific and Technical Information of China (English)

    Taogetusang Sirendaoerji

    2008-01-01

    Based on the homogenous balance method and the trial function method, several trial function methods composed of exponential functions are proposed and applied to nonlinear discrete systems. With the help of symbolic computation system, the new exact solitary wave solutions to discrete nonlinear mKdV lattice equation, discrete nonlinear (2+1) dimensional Toda lattice equation, Ablowitz-Ladik-lattice system are constructed.The method is of significance to seek exact solitary wave solutions to other nonlinear discrete systems.

  16. Constructing knowledge about the trigonometric functions and their geometric meaning on the unit circle

    Science.gov (United States)

    Altman, Renana; Kidron, Ivy

    2016-10-01

    Processes of knowledge construction are investigated. A learner is constructing knowledge about the trigonometric functions and their geometric meaning on the unit circle. The analysis is based on the dynamically nested epistemic action model for abstraction in context. Different tasks are offered to the learner. In his effort to perform the different tasks, he has the opportunity to understand the process used to create unit circle representations of trigonometric expressions. The theoretical framework of abstraction in context is used to analyse the evolution of the learner's construction of knowledge in the transition from 'triangle' trigonometry to 'circle' trigonometry.

  17. Functional Nanostructured Platforms for Chemical and Biological Sensing

    Energy Technology Data Exchange (ETDEWEB)

    Letant, S E

    2006-03-20

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

  18. Density functional theory across chemistry, physics and biology.

    Science.gov (United States)

    van Mourik, Tanja; Bühl, Michael; Gaigeot, Marie-Pierre

    2014-03-13

    The past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg-Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT.

  19. Critical Quality Source Diagnosis for Dam Concrete Construction Based on Quality Gain-loss Function

    Directory of Open Access Journals (Sweden)

    Bo Wang

    2014-06-01

    Full Text Available In dam concrete construction process, it not only has quality loss arising from quality fluctuation, but also gains quality compensation effect due to the mutual cooperation and adaptation coupling between working procedures (WPs. The calculation and transmission complexity of the quality loss and quality compensation affect the quality management of dam concrete construction. As the quality compensation effect existing in the production practice cannot be described by Taguchi quality loss function, the concept of quality gain-loss function was presented in this paper, which was based on endowing the constant term in the expansion of Taylor series with physical meaning—quality compensation. Based on quality gain-loss function theory, a new quality gain-loss transmission model of dam concrete construction based on GERT network was constructed and its effective algorithm was designed. WP quality gain-loss and its impact on the final product were reasonably measured, and the critical quality routes and critical quality WPs were detected and diagnosed in dam concrete construction network. Summer temperature-controlled concrete construction in the third phase of Three Gorges Project (TGP was taken as an example to carry out the study, and the calculation results showed the validity and practicability of the presented model and algorithm.

  20. Teacher and student actions to construct biology literacy at a community college: A bounded case study

    Science.gov (United States)

    Griesel, Patricia

    2000-10-01

    Science content area literacy, particularly literacy development in college level biology, is the focus of this study. The study investigates the actions and activities of an instructor and six students over the course of 16 weeks. The study is in response to interest in the literate practices in science classes (NSES, 1996) and to the call for contextual studies that facilitate the learning of science (Borasi & Siegel, 1999; Moje, 1996; Nist & Holschuh, 1996; Prentiss, 1998). A collaborative study between the biology teacher and the researcher, this study investigates the practices believed to be effective for the development of biology literacy. Data sources, in the qualitative bounded case study (Bogdin & Biklin, 1982; Glaser & Strauss, 1967; Miles & Huberman, 1994), include: field notes of classroom observations, in-depth interviews (Seidman, 1992), class surveys, and literate artifacts. The data were coded and analyzed using a constant comparative method (Glaser & Strauss, 1967). The six students reveal similarities and differences regarding the actions, patterns, practices and use of materials and their beliefs about effective practice in the development of biology literacy. The results indicate that a variety of actions and activities are needed to facilitate the development of biology literacy. The common themes to develop from the students' data about effective teacher actions are the following: (a) involves and engages students in inquiry learning through group projects, hands-on, and group discussions; (b) relates examples, experiences, and stories; (c) exhibits expertise; (d) encourages a relaxed classroom atmosphere; (e) facilitates and coaches students; and (f) credits creativity. Further, students report their teacher to be an expert, in terms of science knowledge and literate practices, and that her expertise contributes to their understanding of biology literacy. The teachers' data reveals three themes embedded in her classroom actions: science as

  1. On the construction of CASCI-type wave functions for very large active spaces

    CERN Document Server

    Boguslawski, Katharina; Reiher, Markus

    2011-01-01

    We present an efficient procedure to construct configuration-interaction-type electronic wave functions of molecular systems that require very large active spaces for a qualitatively correct description of their electronic structure. Our procedure is based on the density-matrix renormalization group algorithm that provides the necessary information in terms of the eigenstates of the reduced density matrices to calculate the coefficient of any basis state in the many-particle Hilbert space of the molecular system under study. Since the dimension of the Hilbert space scales factorially with the size of the active space, a sophisticated Monte Carlo sampling routine has been implemented that constructs an accurate representation of the electronic wave function. We emphasize that our sampling routine can also construct complete-active-space configuration-interaction-type wave functions from any other type of tensor network states, such as the complete-graph tensor network states or the correlator product states.

  2. Biological functions of iduronic acid in chondroitin/dermatan sulfate.

    Science.gov (United States)

    Thelin, Martin A; Bartolini, Barbara; Axelsson, Jakob; Gustafsson, Renata; Tykesson, Emil; Pera, Edgar; Oldberg, Åke; Maccarana, Marco; Malmstrom, Anders

    2013-05-01

    The presence of iduronic acid in chondroitin/dermatan sulfate changes the properties of the polysaccharides because it generates a more flexible chain with increased binding potentials. Iduronic acid in chondroitin/dermatan sulfate influences multiple cellular properties, such as migration, proliferation, differentiation, angiogenesis and the regulation of cytokine/growth factor activities. Under pathological conditions such as wound healing, inflammation and cancer, iduronic acid has diverse regulatory functions. Iduronic acid is formed by two epimerases (i.e. dermatan sulfate epimerase 1 and 2) that have different tissue distribution and properties. The role of iduronic acid in chondroitin/dermatan sulfate is highlighted by the vast changes in connective tissue features in patients with a new type of Ehler-Danlos syndrome: adducted thumb-clubfoot syndrome. Future research aims to understand the roles of the two epimerases and their interplay with the sulfotransferases involved in chondroitin sulfate/dermatan sulfate biosynthesis. Furthermore, a better definition of chondroitin/dermatan sulfate functions using different knockout models is needed. In this review, we focus on the two enzymes responsible for iduronic acid formation, as well as the role of iduronic acid in health and disease.

  3. Biochemical and biological functions of class I phosphatidylinositol transfer proteins.

    Science.gov (United States)

    Cockcroft, Shamshad; Carvou, Nicolas

    2007-06-01

    Phosphoinositides function in a diverse array of cellular activities. They include a role as substrate for lipid kinases and phospholipases to generate second messengers, regulators of the cytoskeleton, of enzymes and of ion channels, and docking sites for reversible recruitment of proteins to membranes. Mammalian phosphatidylinositol transfer proteins, PITPalpha and PITPbeta are paralogs that share 77% sequence identity and contain a hydrophobic cavity that can sequester either phosphatidylinositol or phosphatidylcholine. A string of 11 amino acid residues at the C-terminal acts as a "lid" which shields the lipid from the aqueous environment. PITPs in vitro can facilitate inter-membrane lipid transfer and this requires the movement of the "lid" to allow the lipid cargo to be released. Thus PITPs are structurally designed for delivering lipid cargo and could thus participate in cellular events that are dependent on phosphatidylinositol or derivatives of phosphatidylinositol. Phosphatidylinositol, the precursor for all phosphoinositides is synthesised at the endoplasmic reticulum and its distribution to other organelles could be facilitated by PITPs. Here we highlight recent studies that report on the three-dimensional structures of the different PITP forms and suggest how PITPs are likely to dock at the membrane surface for lipid delivery and extraction. Additionally we discuss whether PITPs are important regulators of sphingomyelin metabolism, and finally describe recent studies that link the association of PITPs with diverse functions including membrane traffic at the Golgi, neurite outgrowth, cytokinesis and stem cell growth.

  4. [Adipogenic function and other biologic effects of insulin].

    Science.gov (United States)

    Pankov, Y A

    2016-01-01

    Studies on experimental animals with knockout of the insulin receptor gene Insr (in the whole body or in certain tissues) and/or related genes encoding proteins involved in realization of insulin signal transduction in target cells, have made an important contribution to the elucidation of insulin regulation of metabolism, particularly fat metabolism. Since the whole insulin secreted by b-cells, together with the products of gastrointestinal tract digestion of proteins, fats, and carbohydrates reach the liver, the latter is the first organ on which this hormone acts. The liver employs released amino acids for synthesis of proteins, including apoproteins for various lipoproteins. Glucose is used for synthesis of glycogen, fatty acids, and triglycerides, which enter all the organs in very low density lipoproteins (VLDL). The LIRKO mice with knockout of the Insr gene in the liver demonstrated inhibition of synthesis of macromolecular compounds from amino acids, glucose, and fatty acids. Low molecular weight substances demonstrated increased entry to circulation, and together with other disorders induced hyperglycemia. In LIRKO mice blood glucose levels and glucose tolerance demonstrated time-dependent normalization and at later stages the increase in glucose levels was replaced by hypoglycemia. These changes can be well explained if we take into consideration that one of the main functions of insulin consists in stimulation of energy accumulation by means of activation of triglyceride deposition in adipose tissue. FIRKO mice with selective knockout of adipose tissue Insr were characterized by decreased uptake of glucose in adipocytes, and its transformation into lipids. However, the level of body fat in animals remained normal, possibly due to preserved insulin receptor in the liver and insulin-induced activation of triglyceride production which maintained normal levels of body fat stores, the effective functioning of adipose tissue and secretion of leptin by

  5. Application of Angular Momentum Theory to Constructing Basis Functions of Irreducible Representations of Icosahedral Group

    Institute of Scientific and Technical Information of China (English)

    LI An-yong

    2004-01-01

    A new method based on angular momentum theory was proposed to construct the basis functions of the irreducible representations(IRs) of point groups. The transformation coefficients, i. e. , coefficients S, are the components of the eigenvectors of some Hermitian matrices, and can be made as real numbers for all pure rotation point groups. The general formula for coefficient S was deduced, and applied to constructing the basis functions of single-valued irreducible representations of icosahedral group from the spherical harmonics with angular momentum j≤7.

  6. Constructive Function Theory on Sets of the Complex Plane through Potential Theory and Geometric Function Theory

    OpenAIRE

    Andrievskii, Vladimir

    2006-01-01

    This is a survey of some recent results concerning polynomial inequalities and polynomial approximation of functions in the complex plane. The results are achieved by the application of methods and techniques of modern geometric function theory and potential theory.

  7. Development of biological functional material and product from Nelumbo nucifera

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Il Yun; Park, Yong Dae; Jin, Chang Hyun; Choi, Dae Seong

    2008-01-15

    The solvent extracts of Nelumbo nucifera G. were investigated for the activities of antioxidant, whitening, anti-wrinkle and antimicrobial effects to apply as a functional ingredient for cosmetic products. The electron donating ability of irradiated NN-L extract was above 85% at the concentration of 50ppm. The superoxide dismutase(SOD)-like activity of irradiated NN-L extract was about 76% at 1,000ppm concentration. The xanthine oxidase inhibitory effect of irradiated NN-L extract was about 15% at 1,000ppm. The tyrosinase inhibitory effect of irradiated NN-L extract was about 18% at 1,000ppm. Anti-wrinkle effect, the elastase inhibition activity of irradiated NN-L extract was about 45% at 1,000ppm concentration. All these findings suggested that Nelumbo nucifera G. has a great potential as a cosmeceutical ingredient.

  8. The biology and function of exosomes in cancer.

    Science.gov (United States)

    Kalluri, Raghu

    2016-04-01

    Humans circulate quadrillions of exosomes at all times. Exosomes are a class of extracellular vesicles released by all cells, with a size range of 40-150 nm and a lipid bilayer membrane. Exosomes contain DNA, RNA, and proteins. Exosomes likely remove excess and/or unnecessary constituents from the cells, functioning like garbage bags, although their precise physiological role remains unknown. Additionally, exosomes may mediate specific cell-to-cell communication and activate signaling pathways in cells they fuse or interact with. Exosomes are detected in the tumor microenvironment, and emerging evidence suggests that they play a role in facilitating tumorigenesis by regulating angiogenesis, immunity, and metastasis. Circulating exosomes can be used as liquid biopsies and noninvasive biomarkers for early detection, diagnosis, and treatment of cancer patients.

  9. Biological function of activation-induced cytidine deaminase (AID

    Directory of Open Access Journals (Sweden)

    Ritu Kumar

    2014-10-01

    Full Text Available Activation-induced Cytidine Deaminase (AID is an essential regulator of B cell diversification, but its full range of action has until recently been an enigma. Based on homology, it was originally proposed to be an RNA-editing enzyme, but so far, no RNA substrates are known. Rather, it functions by deaminating cytidine, and in this manner, coupled with base-excision repair or mismatch repair machinery, it is a natural mutator. This allows it to play a central role in adaptive immunity, whereby it initiates the processes of class switch recombination and somatic hypermutation to help generate a diverse and high-affinity repertoire of immunoglobulin isotypes. More recently, it has been appreciated that methylated cytidine, already known as a key epigenetic mark on DNA controlling gene expression, can also be a target for AID modification. Coupled with repair machinery, this can facilitate the active removal of methylated DNA. This activity can impact the process of cellular reprogramming, including transition of a somatic cell to pluripotency, which requires major reshuffling of epigenetic memory. Thus, seemingly disparate roles for AID in controlling immune diversity and epigenetic memory have a common mechanistic basis. However, the very activity that is so useful for B cell diversity and cellular reprogramming is dangerous for the integrity of the genome. Thus, AID expression and activity is tightly regulated, and deregulation is associated with diseases including cancer. Here, we review the range of AID functions with a focus on its mechanisms of action and regulation. Major questions remain to be answered concerning how and when AID is targeted to specific loci and how this impacts development and disease.

  10. GSK-3: functional insights from cell biology and animal models

    Directory of Open Access Journals (Sweden)

    Oksana eKaidanovich-Beilin

    2011-11-01

    Full Text Available Glycogen synthase kinase-3 (GSK-3 is a widely expressed and highly conserved serine/threonine protein kinase encoded in mammals by two genes that generate two related proteins: GSK-3α and GSK-3β. GSK-3 is active in cells under resting conditions and is primarily regulated through inhibition or diversion of its activity. While GSK-3 is one of the few protein kinases that can be inactivated by phosphorylation, the mechanisms of GSK-3 regulation are more varied and not fully understood. Precise control appears to be achieved by a combination of phosphorylation, localization, and sequestration by a number of GSK-3-binding proteins. GSK-3 lies downstream of several major signaling pathways including the phosphatidylinositol 3’ kinase pathway, the Wnt pathway, Hedgehog signaling and Notch. Specific pools of GSK-3, which differ in intracellular localization, binding partner affinity and relative amount are differentially sensitized to several distinct signaling pathways and these sequestration mechanisms contribute to pathway insulation and signal specificity. Dysregulation of signaling pathways involving GSK-3 is associated with the pathogenesis of numerous neurological and psychiatric disorders and there are data suggesting GSK-3 isoform-selective roles in several of these. Here, we review the current knowledge of GSK-3 regulation and targets and discuss the various animal models that have been employed to dissect the functions of GSK-3 in brain development and function through the use of conventional or conditional knock-out mice as well as transgenic mice. These studies have revealed fundamental roles for these protein kinases in memory, behavior and neuronal fate determination and provide insights into possible therapeutic interventions.

  11. Biological function of activation-induced cytidine deaminase (AID).

    Science.gov (United States)

    Kumar, Ritu; DiMenna, Lauren J; Chaudhuri, Jayanta; Evans, Todd

    2014-01-01

    Activation-induced Cytidine Deaminase (AID) is an essential regulator of B cell diversification, but its full range of action has until recently been an enigma. Based on homology, it was originally proposed to be an RNA-editing enzyme, but so far, no RNA substrates are known. Rather, it functions by deaminating cytidine, and in this manner, coupled with base-excision repair or mismatch repair machinery, it is a natural mutator. This allows it to play a central role in adaptive immunity, whereby it initiates the processes of class switch recombination and somatic hypermutation to help generate a diverse and high-affinity repertoire of immunoglobulin isotypes. More recently, it has been appreciated that methylated cytidine, already known as a key epigenetic mark on DNA controlling gene expression, can also be a target for AID modification. Coupled with repair machinery, this can facilitate the active removal of methylated DNA. This activity can impact the process of cellular reprogramming, including transition of a somatic cell to pluripotency, which requires major reshuffling of epigenetic memory. Thus, seemingly disparate roles for AID in controlling immune diversity and epigenetic memory have a common mechanistic basis. However, the very activity that is so useful for B cell diversity and cellular reprogramming is dangerous for the integrity of the genome. Thus, AID expression and activity is tightly regulated, and deregulation is associated with diseases including cancer. Here, we review the range of AID functions with a focus on its mechanisms of action and regulation. Major questions remain to be answered concerning how and when AID is targeted to specific loci and how this impacts development and disease.

  12. The reflection of life functional entailment and imminence in relational biology

    CERN Document Server

    Louie, A H

    2013-01-01

    A. H. Louie’s The Reflection of Life: Functional Entailment and Imminence in Relational Biology is a continuation of the exploratory journey in relational biology which began with his 2009 monograph More Than Life Itself: A Synthetic Continuation in Relational Biology. The theme of his first book was ‘What is life?’; the theme of this sequel is “How do two life forms interact?” Biology is a subject concerned with organization of relations. Relational biology is the approach that advocates ‘function dictates structure”, rather than ‘structure implies function’. It is mathematics decoded into biological realizations. The book demonstrates some of the powers of the approach of relational biology, and illustrates how pertinent problems in biology can be better addressed this way. In the first volume the theory was developed by using partially ordered sets, lattices, simulations, models, Aristotle’s four causes, graphs, categories, simple and complex systems, anticipatory systems, and metabolis...

  13. Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch.

    Science.gov (United States)

    Holmstrom, Erik D; Polaski, Jacob T; Batey, Robert T; Nesbitt, David J

    2014-12-03

    Riboswitches represent a family of highly structured regulatory elements found primarily in the leader sequences of bacterial mRNAs. They function as molecular switches capable of altering gene expression; commonly, this occurs via a conformational change in a regulatory element of a riboswitch that results from ligand binding in the aptamer domain. Numerous studies have investigated the ligand binding process, but little is known about the structural changes in the regulatory element. A mechanistic description of both processes is essential for deeply understanding how riboswitches modulate gene expression. This task is greatly facilitated by studying all aspects of riboswitch structure/dynamics/function in the same model system. To this end, single-molecule fluorescence resonance energy transfer (smFRET) techniques have been used to directly observe the conformational dynamics of a hydroxocobalamin (HyCbl) binding riboswitch (env8HyCbl) with a known crystallographic structure.1 The single-molecule RNA construct studied in this work is unique in that it contains all of the structural elements both necessary and sufficient for regulation of gene expression in a biological context. The results of this investigation reveal that the undocking rate constant associated with the disruption of a long-range kissing-loop (KL) interaction is substantially decreased when the ligand is bound to the RNA, resulting in a preferential stabilization of the docked conformation. Notably, the formation of this tertiary KL interaction directly sequesters the Shine-Dalgarno sequence (i.e., the ribosome binding site) via base-pairing, thus preventing translation initiation. These results reveal that the conformational dynamics of this regulatory switch are quantitatively described by a four-state kinetic model, whereby ligand binding promotes formation of the KL interaction. The results of complementary cell-based gene expression experiments conducted in Escherichia coli are highly

  14. Chemical construction and structural permutation of potent cytotoxin polytheonamide B: discovery of artificial peptides with distinct functions.

    Science.gov (United States)

    Itoh, Hiroaki; Inoue, Masayuki

    2013-07-16

    Polytheonamide B (1), isolated from the marine sponge Theonella swinhoei, is a posttranslationally modified ribosomal peptide (MW 5030 Da) that displays extraordinary cytotoxicity. Among its 48 amino acid residues, this peptide includes a variety D- and L-amino acids that do not occur in proteins, and the chiralities of these amino acids alternate in sequence. These structural features induce the formation of a stable β6.3-helix, giving rise to a tubular structure of over 4 nm in length. In the biological setting, this fold is believed to transport cations across the lipid bilayer through a pore, thereby acting as an ion channel. In this Account, we discuss the construction and structural permutations of this potent cytotoxin. First we describe the 161-step chemical construction of this unusual peptide 1. By developing a synthetic route to 1, we established the chemical basis for subsequent SAR studies to pinpoint the proteinogenic and nonproteinogenic building blocks within the molecule that confer its toxicity and channel function. Using fully synthetic 1, we generated seven analogues with point mutations, and studies of their activity revealed the importance of the N-terminal moiety. Next, we simplified the structure of 1 by substituting six amino acid residues of 1 to design a more synthetically accessible analogue 9. This dansylated polytheonamide mimic 9 was synthesized in 127 total steps, and we evaluated its function to show that it can emulate the toxic and ion channel activities of 1 despite its multiple structural modifications. Finally, we applied a highly automated synthetic route to 48-mer 9 to generate 13 substructures of 27-39-mers. The 37-mer 12 exhibited nanomolar level toxicity through a potentially distinct mode of action from 1 and 9. The SAR studies of polytheonamide B and the 21 artificial analogues have deepened our understanding of the precise structural requirements for the biological functions of 1. They have also led to the discovery of

  15. Biological catalysis of the hydrological cycle: life's thermodynamic function

    Directory of Open Access Journals (Sweden)

    K. Michaelian

    2011-01-01

    Full Text Available Darwinian theory depicts life as being overwhelmingly consumed by a fight for survival in a hostile environment. However, from a thermodynamic perspective, life is a dynamic out of equilibrium process, stabilizing and coevolving in concert with its abiotic environment. The living component of the biosphere on the surface of the Earth of greatest biomass, the plants and cyanobacteria, are involved in the transpiration of a vast amount of water. Transpiration is part of the global water cycle, and it is this cycle that distinguishes Earth from its apparently life barren neighboring planets, Venus and Mars. The dissipation of sunlight into heat by organic molecules in the biosphere and its coupling to the water cycle (as well as other abiotic processes, is by far the greatest entropy producing process occurring on Earth. Life, from this perspective, can be viewed as performing an important thermodynamic function; acting as a dynamic catalyst by aiding irreversible abiotic process such as the water cycle, hurricanes, and ocean and wind currents to produce entropy. The role of animals in this view is that of unwitting but dedicated servants of the plants and cyanobacteria, helping them to grow and to spread into initially inhospitable areas.

  16. Functionalized diamond nanopowder for phosphopeptides enrichment from complex biological fluids

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Dilshad [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Najam-ul-Haq, Muhammad, E-mail: najamulhaq@bzu.edu.pk [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, A-6020 Innsbruck (Austria); Jabeen, Fahmida; Ashiq, Muhammad N.; Athar, Muhammad [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Rainer, Matthias; Huck, Christian W.; Bonn, Guenther K. [Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, A-6020 Innsbruck (Austria)

    2013-05-02

    Graphical abstract: -- Highlights: •Derivatization of diamond nanopowder as IMAC and RP. •Characterization with SEM, EDX and FT-IR. •Phosphopeptide enrichment from standard as well as real samples. •Desalting and human serum profiling with reproducible results. •MALDI-MS analysis with database identification. -- Abstract: Diamond is known for its high affinity and biocompatibility towards biomolecules and is used exclusively in separation sciences and life science research. In present study, diamond nanopowder is derivatized as Immobilized Metal Ion Affinity Chromatographic (IMAC) material for the phosphopeptides enrichment and as Reversed Phase (C-18) media for the desalting of complex mixtures and human serum profiling through MALDI-TOF-MS. Functionalized diamond nanopowder is characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Diamond-IMAC is applied to the standard protein (β-casein), spiked human serum, egg yolk and non-fat milk for the phosphopeptides enrichment. Results show the selectivity of synthesized IMAC-diamond immobilized with Fe{sup 3+} and La{sup 3+} ions. To comprehend the elaborated use, diamond-IMAC is also applied to the serum samples from gall bladder carcinoma for the potential biomarkers. Database search is carried out by the Mascot program ( (www.matrixscience.com)) for the assignment of phosphorylation sites. Diamond nanopowder is thus a separation media with multifunctional use and can be applied to cancer protein profiling for the diagnosis and biomarker identification.

  17. The biological effect and medical functions of the Infrared Rays

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-feng

    2001-01-01

    The quantum vibrational energy-spectra including high excited states of the protein molecules have been calculated by new theory of bio-energy transport along the protein molecules and its dynamic equation, discrete nonlinear Schrodinger equation, appropriate to the protein molecules on the basis of the level of molecular structure. This energy-spectra obtained are basically consistent with the experimental values by infrared absorption and radiated measurement of person's hands and laser-Raman spectrum from metabolically active E. Coli.. From this energy-spectra we know that the infrared lights with (1-3)x1000nm and (5-7)x1000nm wavelength can be absorbed by the protein molecules in the living systems.In accordance with the non-linear theory of the bio-energy transport we know that the energy of the infrared light absorbed by the proteins can result in vibrations of amide-I in amino acids and can facilitate the bio-energy transport along the protein molecular chains from one place to other for the growth of living bodies. This processe is non-thermal. This is just non-thermal effect of the infrared lights. According to the mechanism we explained further the medical functions of the infrared lights absorbed.

  18. Towards understanding the biological function of hopanoids (Invited)

    Science.gov (United States)

    Doughty, D. M.; Hunter, R.; Summons, R. E.; Newman, D. K.

    2010-12-01

    Rhodopseudomonas palustris TIE-1 expresses bacterial hopanoid lipids that are structurally similar and evolutionarily related to eukaryotic sterols. The genome of R. palustris TIE-1 contains two copies of the hpnN gene (hpnN1 and hpnN2) that are orthologs of genes encoding eukaryotic sterol and lipid transporters. Hopanoid localization to the outer membrane was found to be dependent upon hpnN1. Since the cell cycle of R. palustris TIE-1 is obligately bimodal with each cell division resulting in the generation of one mother and one swarmer cell, evidence was obtained that hopanoids where specifically localized to the outer membrane of mother cells. The sequestration of hopanoids to the mother cells was also disrupted by the deletion of the hpnN1 gene. Mutants lacking the hopanoid transporters were able to grow normally at 30 °C but showed decreased growth at 38 °C. The hopanoid transporter mutant formed cellular filaments when grown at elevated temperature. Because sedimentary steranes and hopanes comprise some of the earliest evidence for the emergence of distinct bacteria and eukaryotic phyla, a better appreciation of the function of hopanoids will improve our ability to interpret the evolution of life on Earth.

  19. Strigolactone biology: genes, functional genomics, epigenetics and applications.

    Science.gov (United States)

    Makhzoum, Abdullah; Yousefzadi, Morteza; Malik, Sonia; Gantet, Pascal; Tremouillaux-Guiller, Jocelyne

    2017-03-01

    Strigolactones (SLs) represent an important new plant hormone class marked by their multifunctional role in plant and rhizosphere interactions. These compounds stimulate hyphal branching in arbuscular mycorrhizal fungi (AMF) and seed germination of root parasitic plants. In addition, they are involved in the control of plant architecture by inhibiting bud outgrowth as well as many other morphological and developmental processes together with other plant hormones such as auxins and cytokinins. The biosynthetic pathway of SLs that are derived from carotenoids was partially decrypted based on the identification of mutants from a variety of plant species. Only a few SL biosynthetic and regulated genes and related regulatory transcription factors have been identified. However, functional genomics and epigenetic studies started to give first elements on the modality of the regulation of SLs related genes. Since they control plant architecture and plant-rhizosphere interaction, SLs start to be used for agronomical and biotechnological applications. Furthermore, the genes involved in the SL biosynthetic pathway and genes regulated by SL constitute interesting targets for plant breeding. Therefore, it is necessary to decipher and better understand the genetic determinants of their regulation at different levels.

  20. Human Dopamine Receptors Interaction Network (DRIN): a systems biology perspective on topology, stability and functionality of the network.

    Science.gov (United States)

    Podder, Avijit; Jatana, Nidhi; Latha, N

    2014-09-21

    Dopamine receptors (DR) are one of the major neurotransmitter receptors present in human brain. Malfunctioning of these receptors is well established to trigger many neurological and psychiatric disorders. Taking into consideration that proteins function collectively in a network for most of the biological processes, the present study is aimed to depict the interactions between all dopamine receptors following a systems biology approach. To capture comprehensive interactions of candidate proteins associated with human dopamine receptors, we performed a protein-protein interaction network (PPIN) analysis of all five receptors and their protein partners by mapping them into human interactome and constructed a human Dopamine Receptors Interaction Network (DRIN). We explored the topology of dopamine receptors as molecular network, revealing their characteristics and the role of central network elements. More to the point, a sub-network analysis was done to determine major functional clusters in human DRIN that govern key neurological pathways. Besides, interacting proteins in a pathway were characterized and prioritized based on their affinity for utmost drug molecules. The vulnerability of different networks to the dysfunction of diverse combination of components was estimated under random and direct attack scenarios. To the best of our knowledge, the current study is unique to put all five dopamine receptors together in a common interaction network and to understand the functionality of interacting proteins collectively. Our study pinpointed distinctive topological and functional properties of human dopamine receptors that have helped in identifying potential therapeutic drug targets in the dopamine interaction network.

  1. Functional or constructive attitudes: Which type drives consumers' evaluation of meat products?

    Science.gov (United States)

    Hamlin, Robert

    2016-07-01

    Consumer attitudes towards meat can be divided up into two types: Functional attitudes which are stable and exist over long periods of time, and constructive attitudes which are ephemeral and usually constructed at the point of sale. This research investigated the temporal and situational stability of meat consumers' attitudes by using the same established functional, multidimensional attitude instrument to generate attitude profiles for the four meat types: chicken/beef/lamb/poultry both as an abstracted construct and as a cue on a range of meat and meat-based products. The results showed that strong attitude profile was generated by the meat types as abstracted constructs, but that this profile broke down completely when the food products carrying the same meat types were evaluated. This result indicates that consumer attitudes may not be temporally or situationally stable, which in turn suggests that consumers' evaluation and choice of meat products may be driven to a greater or lesser extent by constructive rather than functional attitudes.

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

    Science.gov (United States)

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

    2016-10-20

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

  3. Biological image construction by using Raman radiation and Pca: preliminary results

    Energy Technology Data Exchange (ETDEWEB)

    Martinez E, J. C. [IPN, Unidad Profesional Interdisciplinaria de Ingenieria, Campus Guanajuato, Av. Mineral de Valenciana 200, Col. Fracc. Industrial Puerto Interior, 36275 Silao, Guanajuato (Mexico); Cordova F, T. [Universidad de Guanajuato, DIC, Departamento de Ingenieria Fisica, Loma del Bosque No. 103, Col. Lomas del Campestre, 37150 Leon, Guanajuato (Mexico); Hugo R, V., E-mail: jcmartineze@ipn.mx [Universidad de Guadalajara, Centro Universitario de Tonala, Morelos No. 180, 69584 Tonala, Jalisco (Mexico)

    2015-10-15

    Full text: In the last years, the Raman spectroscopy (Rs) technique has had some applications in the study and analysis of biological samples, due to it is able to detect concentrations or presence of certain organic and inorganic compounds of medical interest. In this work, raw data were obtained through measurements in selected points on a square regions in order to detect specific organic / inorganic compounds on biological samples. Gold nano stars samples were prepared and coated with membrane markers (CD 10+ and CD 19+) and diluted in leukemic B lymphocytes. Each data block was evaluated independently by the method of principal component analysis (Pca) in order to find representative dimensionless values (Cp) for each Raman spectrum in a specific coordinate. Each Cp was normalized in a range of 0-255 in order to generate a representative image of 8 bits of the region under study. Data acquisition was performed with Raman microscopy system Renishaw in Via in the range of 550 to 1700 cm-1 with a 785 nm laser source, with a power of 17 m W and 15 s of exposure time were used for each spectrum. In preliminary results could detect the presence of molecular markers CD 10+ and CD 19+ with gold nano stars and discrimination between both markers. The results suggest conducting studies with specific concentrations organic and inorganic materials. (Author)

  4. Construction of a Smooth Lyapunov Function for the Robust and Exact Second-Order Differentiator

    OpenAIRE

    2016-01-01

    Differentiators play an important role in (continuous) feedback control systems. In particular, the robust and exact second-order differentiator has shown some very interesting properties and it has been used successfully in sliding mode control, in spite of the lack of a Lyapunov based procedure to design its gains. As contribution of this paper, we provide a constructive method to determine a differentiable Lyapunov function for such a differentiator. Moreover, the Lyapunov function is used...

  5. Constructing the probability distribution function for the total capacity of a power system

    Energy Technology Data Exchange (ETDEWEB)

    Vasin, V.P.; Prokhorenko, V.I.

    1980-01-01

    The difficulties involved in constructing the probability distribution function for the total capacity of a power system consisting of numerous power plants are discussed. A method is considered for the approximate determination of such a function by a Monte Carlo method and by exact calculation based on special recursion formulas on a particular grid of argument values. It is shown that there may be significant deviations between the true probability distribution and a normal distribution.

  6. Esthetic-functional recovery of permanent posterior tooth using autogenous biological restoration

    Directory of Open Access Journals (Sweden)

    A M Botelho

    2012-01-01

    Full Text Available Occlusal morphology and difficult access for cleaning permanent molars result in the buildup of bacterial plaque and the development of caries. One method known as biological restoration was carried out. This technique known as biological restoration, has as main restorative material a fragment obtained from a duly donated extracted human tooth. This case report describes the restoration of an extensively decayed molar through the bonding of a fragment obtained from a third molar extracted from the patient himself. Biological restoration is a low-cost option that offers satisfactory aesthetic, morphological and functional results.The morphological/functional reestablishment of posterior teeth can be obtained through biological restoration, which allows the recovery of properties inherent to the dental structure, offers satisfactory aesthetic results and low cost.

  7. Bioactive Components and Functional Properties of Biologically Activated Cereal Grains: A Bibliographic Review.

    Science.gov (United States)

    Singh, Arashdeep; Sharma, Savita

    2015-10-14

    Whole grains provide energy, nutrients, fibres and bioactive compounds that may synergistically contribute to their protective effects. A wide range of these compounds is affected by germination. While some compounds, such as β-glucans are degraded, others, like antioxidants and total phenolics are increased by means of biological activation of grains. The water and oil absorption capacity as well as emulsion and foaming capacity of biologically activated grains are also improved. Application of biological activation of grains is of emerging interest, which may significantly enhance the nutritional, functional and bioactive content of grains, as well as improve palatability of grain foods in a natural way. Therefore, biological activation of cereals can be a way to produce food grains enriched with health promoting compounds and enhanced functional attributes.

  8. Sharing Structure and Function in Biological Design with SBOL 2.0.

    Science.gov (United States)

    Roehner, Nicholas; Beal, Jacob; Clancy, Kevin; Bartley, Bryan; Misirli, Goksel; Grünberg, Raik; Oberortner, Ernst; Pocock, Matthew; Bissell, Michael; Madsen, Curtis; Nguyen, Tramy; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Densmore, Douglas; Gennari, John H; Wipat, Anil; Sauro, Herbert M; Myers, Chris J

    2016-06-17

    The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.

  9. Construct Validity of Functional Capacity Evaluation in Patients with Whiplash-Associated Disorders

    NARCIS (Netherlands)

    Trippolini, M. A.; Dijkstra, P. U.; Geertzen, J. H. B.; Reneman, M. F.

    2015-01-01

    Purpose The construct validity of functional capacity evaluations (FCE) in whiplash-associated disorders (WAD) is unknown. The aim of this study was to analyse the validity of FCE in patients with WAD with cultural differences within a workers' compensation setting. Methods 314 participants (42 % fe

  10. The MOX/SUC precursor strategies: robust ways to construct functionalized oligonucleotides.

    Science.gov (United States)

    Polushin, N

    2001-01-01

    The use of phosphoramidites bearing one or more methoxyoxalamido (MOX) or succinimido (SUC) reactive groups for construction of functionalized oligonucleotides is described. The efficiency of the new precursor strategy was demonstrated in the synthesis of oligonucleotide containing up to 16 imidazole residues.

  11. Construction of Lyapunov functions for some models of infectious diseases in vivo: from simple models to complex models.

    Science.gov (United States)

    Kajiwara, Tsuyoshi; Sasaki, Toru; Takeuchi, Yasuhiro

    2015-02-01

    We present a constructive method for Lyapunov functions for ordinary differential equation models of infectious diseases in vivo. We consider models derived from the Nowak-Bangham models. We construct Lyapunov functions for complex models using those of simpler models. Especially, we construct Lyapunov functions for models with an immune variable from those for models without an immune variable, a Lyapunov functions of a model with absorption effect from that for a model without absorption effect. We make the construction clear for Lyapunov functions proposed previously, and present new results with our method.

  12. Construction of a microbial natural product library for chemical biology studies.

    Science.gov (United States)

    Kato, Naoki; Takahashi, Shunji; Nogawa, Toshihiko; Saito, Tamio; Osada, Hiroyuki

    2012-04-01

    The RIKEN Natural Products Depository (NPDepo) is a public depository of small molecules. Currently, the NPDepo chemical library contains 39,200 pure compounds, half of which are natural products and their derivatives. In order to reinforce the uniqueness of our chemical library, we have improved our strategies for the collection of microbial natural products. Firstly, a microbial metabolite fraction library coupled with an MP (microbial products) plot database provides a powerful resource for the efficient isolation of microbial metabolites. Secondly, biosynthetic studies of microbial metabolites have enabled us to not only access ingenious biosynthetic machineries, but also obtain a variety of biosynthetic intermediates. Our chemical library contributes to the discovery of molecular probes for increasing our understanding of complex biological processes and for eventually developing new drug leads.

  13. Chemical Construction of Polyfunctional Nanocomposites and Nanorobots for Medico-biological Applications

    Science.gov (United States)

    Gorbyk, P. P.; Dubrovin, I. V.; Petranovska, A. L.; Abramov, M. V.; Usov, D. G.; Storozhuk, L. P.; Turanska, S. P.; Turelyk, M. P.; Chekhun, V. F.; Lukyanova, N. Yu.; Shpak, A. P.; Korduban, O. M.

    A method for preparation of magnetosensitive nanocomposites on the basis of surface-modified magnetite carrying immobilized cisplatin and monoclonal antibody CD 95 (a medico-biological nanorobot model) was developed. Adsorption and covalent immobilization of monoclonal antibody CD 95 and human normal immunoglobulin on nanocomposites comprising magnetite coated with poly(acryl amide) and γ-aminopropylsiloxane was studied. Isotherms of covalent attachment of oxidized immunoglobulin via formation of Schiff bases and non-specific (physical) adsorption of the normal immunoglobulin were compared. Kinetics of release of the immunoglobulin to a model environment was studied. Interaction of the prepared models of nanorobots with the cell line MCF-7 was studied. It was shown that use of magnetically driven nanocomposites carrying the anti-tumour drug and the monoclonal antibody CD 95 causes a synergic cytotoxic effect which exceeds the influence of the control doses up to 50%.

  14. Constructing failure in big biology: The socio-technical anatomy of Japan's Protein 3000 Project.

    Science.gov (United States)

    Fukushima, Masato

    2016-02-01

    This study focuses on the 5-year Protein 3000 Project launched in 2002, the largest biological project in Japan. The project aimed to overcome Japan's alleged failure to contribute fully to the Human Genome Project, by determining 3000 protein structures, 30 percent of the global target. Despite its achievement of this goal, the project was fiercely criticized in various sectors of society and was often branded an awkward failure. This article tries to solve the mystery of why such failure discourse was prevalent. Three explanatory factors are offered: first, because some goals were excluded during project development, there was a dynamic of failed expectations; second, structural genomics, while promoting collaboration with the international community, became an 'anti-boundary object', only the absence of which bound heterogeneous domestic actors; third, there developed an urgent sense of international competition in order to obtain patents on such structural information.

  15. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  16. Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors.

    Science.gov (United States)

    Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

    2013-05-01

    In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids.

  17. N-acylation of phosphatidylethanolamine and its biological functions in mammals

    DEFF Research Database (Denmark)

    Wellner, Niels; Diep, Thi Ai; Janfelt, Christian;

    2013-01-01

    N-acylphosphatidylethanolamine (NAPE) and N-acylplasmenylethanolamine (pNAPE) are widely found phospholipids, and they are precursors for N-acylethanolamines, a group of compounds that has a variety of biological effects and encompasses the endocannabinoid anandamide. NAPE and pNAPE are synthesiz...... reviews the metabolism, occurrence and assay of NAPE and pNAPE, and discusses the putative biological functions in mammals of these phospholipids. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism....

  18. Functional Richness and Identity Do Not Strongly Affect Invasibility of Constructed Dune Communities.

    Science.gov (United States)

    Mason, Tanya J; French, Kristine; Jolley, Dianne F

    2017-01-01

    Biotic effects are often used to explain community structure and invasion resistance. We evaluated the contribution of functional richness and identity to invasion resistance and abiotic resource availability using a mesocosm experiment. We predicted that higher functional richness would confer greater invasion resistance through greater resource sequestration. We also predicted that niche pre-emption and invasion resistance would be higher in communities which included functional groups similar to the invader than communities where all functional groups were distinct from the invader. We constructed communities of different functional richness and identity but maintained constant species richness and numbers of individuals in the resident community. The constructed communities represented potential fore dune conditions following invader control activities along the Australian east coast. We then simulated an invasion event by bitou (Chrysanthemoides monilifera ssp. rotundata DC. Norl.), a South African shrub invader. We used the same bitou propagule pressure across all treatments and monitored invasion success and resource availability for 13 months. Contrary to our predictions, we found that functional richness did not mediate the number of bitou individuals or bitou cover and functional identity had little effect on invasion success: there was a trend for the grass single functional group treatment to supress bitou individuals, but this trend was obscured when grasses were in multi functional group treatments. We found that all constructed communities facilitated bitou establishment and suppressed bitou cover relative to unplanted mesocosms. Abiotic resource use was either similar among planted communities, or differences did not relate to invasion success (with the exception of light availability). We attribute invasion resistance to bulk plant biomass across planted treatments rather than their functional group arrangement.

  19. Constructing a one-way hash function one-way function based on the unified Chaotic system

    Institute of Scientific and Technical Information of China (English)

    Long Min; Peng Fei; Chen Guan-Rong

    2008-01-01

    A new one-way hash function based on the unified chaotic system is constructed.With different values of a key parameter,the unified chaotic system represents different chaotic systems,based on which the one-way hash function algorithm is constructed with three round operations and an initial vector on an input message.In each round operation,the parameters are processed by three different chaotic systems generated from the unified chaotic system.Feed-forwards are used at the end of each round operation and at the end of each element of the message processing.Meanwhile,in each round operation,parameter-exchanging operations are implemented.Then,the hash value of length 160 bits is obtained from the last six parameters.Simulation and analysis both demonstrate that the algorithm has great flexibility,satisfactory hash performance,weak collision property,and high security.

  20. Priority of TCM in Regulating Gene Function as a Whole Through Development of Modern Biology

    Institute of Scientific and Technical Information of China (English)

    Hu zuo-wei; zhou yan-ping; Shen zi-yin

    2004-01-01

    Molecular Biology based on the DNA Double-helix structure has made great progress in 20 century.After Human Genome Project (HGP) completed, Molecular Biology is faced upon more and more challenges, andtake changes from protion concept to integration concept, from linear thinking to complicated thinking. so post-genomics, including functional genomics, proteomics, is gradually established. Among them, System Biology is themost prominent. It is becoming to tend to integration, and infiltrate to each other for the two thinking of genomeand TCM in studying life science, which reflect the inevitablility and importance of integration of TCM and West-ern Medicine. The priority of TCM in treatment as a whole, and regulating functional gene and functional networkmay take greater achievement in post - genomic time.

  1. One-way hash function construction based on the spatiotemporal chaotic system

    Institute of Scientific and Technical Information of China (English)

    Luo Yu-Ling; Du Ming-Hui

    2012-01-01

    Based on the spatiotemporal chaotic system,a novel algorithm for constructing a one-way hash function is proposed and analysed.The message is divided into fixed length blocks.Each message block is processed by the hash compression function in parallel.The hash compression is constructed based on the spatiotemporal chaos.In each message block,the ASCII code and its position in the whole message block chain constitute the initial conditions and the key of the hash compression function.The final hash value is generated by further compressing the mixed result of all the hash compression values.Theoretic analyses and numerical simulations show that the proposed algorithm presents high sensitivity to the message and key,good statistical properties,and strong collision resistance.

  2. Electromagnetic fields as structure-function zeitgebers in biological systems: environmental orchestrations of morphogenesis and consciousness.

    Science.gov (United States)

    Rouleau, Nicolas; Dotta, Blake T

    2014-01-01

    Within a cell system structure dictates function. Any interaction between cells, or a cell and its environment, has the potential to have long term implications on the function of a given cell and emerging cell aggregates. The structure and function of cells are continuously subjected to modification by electrical and chemical stimuli. However, biological systems are also subjected to an ever-present influence: the electromagnetic (EM) environment. Biological systems have the potential to be influenced by subtle energies which are exchanged at atomic and subatomic scales as EM phenomena. These energy exchanges have the potential to manifest at higher orders of discourse and affect the output (behavior) of a biological system. Here we describe theoretical and experimental evidence of EM influence on cells and the integration of whole systems. Even weak interactions between EM energies and biological systems display the potential to affect a developing system. We suggest the growing literature of EM effects on biological systems has significant implications to the cell and its functional aggregates.

  3. The Functional Model Approach to the Consulting for Vertically - Integrated Construction Group

    Directory of Open Access Journals (Sweden)

    Pimenova Anna

    2016-01-01

    Full Text Available Managerial decision making in the framework of functional modeling of the consulting process have a direct effect on other business - processes of vertically - integrated group of construction companies. As a result, the experience of consulting companies tends to be used for the making managerial solutions. Consultancy is known as one of the most complicated types of buisiness process. It requires a huge and deep examines and researches of targeting area, therefore need to be provided with special methodology, included internal standards of the consulting companies. Correct methodological support, planning process and implementation of managerial solutions should be based on the survey of the direct and inverse connections and interdependence of all group’s business – processes. Functional - process modeling of the vertically - integrated construction group could be considered as an instrument of examination and analysis of the issue how the managerial solution impact on the business-process for the construction group functioning. The main result of the research is the formalized process-oriented model – prototype of the business - processes of vertically - integrated group of construction companies.

  4. 3D Cell Printing of Functional Skeletal Muscle Constructs Using Skeletal Muscle-Derived Bioink.

    Science.gov (United States)

    Choi, Yeong-Jin; Kim, Taek Gyoung; Jeong, Jonghyeon; Yi, Hee-Gyeong; Park, Ji Won; Hwang, Woonbong; Cho, Dong-Woo

    2016-10-01

    Engineered skeletal muscle tissues that mimic the structure and function of native muscle have been considered as an alternative strategy for the treatment of various muscular diseases and injuries. Here, it is demonstrated that 3D cell-printing of decellularized skeletal muscle extracellular matrix (mdECM)-based bioink facilitates the fabrication of functional skeletal muscle constructs. The cellular alignment and the shape of the tissue constructs are controlled by 3D cell-printing technology. mdECM bioink provides the 3D cell-printed muscle constructs with a myogenic environment that supports high viability and contractility as well as myotube formation, differentiation, and maturation. More interestingly, the preservation of agrin is confirmed in the mdECM, and significant increases in the formation of acetylcholine receptor clusters are exhibited in the 3D cell-printed muscle constructs. In conclusion, mdECM bioink and 3D cell-printing technology facilitate the mimicking of both the structural and functional properties of native muscle and hold great promise for producing clinically relevant engineered muscle for the treatment of muscular injuries.

  5. Enhancement of methane production from cassava residues by biological pretreatment using a constructed microbial consortium.

    Science.gov (United States)

    Zhang, Qinghua; He, Jiang; Tian, Min; Mao, Zhonggui; Tang, Lei; Zhang, Jianhua; Zhang, Hongjian

    2011-10-01

    In the study, a stable thermophilic microbial consortium with high cellulose-degradation ability was successfully constructed. That several species of microbes coexisted in this consortium was proved by DGGE (denaturing gradient gel electrophoresis) and sequence analysis. The cooperation and symbiosis of these microbes in this consortium enhanced their cellulose-degradation ability. The pretreatment of cassava residues mixing with distillery wastewater prior to anaerobic digestion was investigated by using this microbial consortium as inoculums in batch bioreactors at 55 °C. The experimental results showed that the maximum methane yield (259.46 mL/g-VS) of cassava residues was obtained through 12h of pretreatment by this microbial consortium, which was 96.63% higher than the control (131.95 mL/g-VS). In addition, it was also found that the maximum methane yield is obtained when the highest filter paper cellulase (FPase), carboxymethyl cellulase (CMCase) and xylanase activity and soluble COD (sCOD) are produced.

  6. Justifying molecular images in cell biology textbooks: From constructions to primary data.

    Science.gov (United States)

    Serpente, Norberto

    2016-02-01

    For scientific claims to be reliable and productive they have to be justified. However, on the one hand little is known on what justification precisely means to scientists, and on the other the position held by philosophers of science on what it entails is rather limited; for justifications customarily refer to the written form (textual expressions) of scientific claims, leaving aside images, which, as many cases from the history of science show are relevant to this process. The fact that images can visually express scientific claims independently from text, plus their vast variety and origins, requires an assessment of the way they are currently justified and in turn used as sources to justify scientific claims in the case of particular scientific fields. Similarly, in view of the different nature of images, analysis is required to determine on what side of the philosophical distinction between data and phenomena these different kinds of images fall. This paper historicizes and documents a particular aspect of contemporary life sciences research: the use of the molecular image as vehicle of knowledge production in cell studies, a field that has undergone a significant shift in visual expressions from the early 1980s onwards. Focussing on textbooks as sources that have been overlooked in the historiography of contemporary biomedicine, the aim is to explore (1) whether the shift of cell studies, entailing a superseding of the optical image traditionally conceptualised as primary data, by the molecular image, corresponds with a shift of justificatory practices, and (2) to assess the role of the molecular image as primary data. This paper also explores the dual role of images as teaching resources and as resources for the construction of knowledge in cell studies especially in its relation to discovery and justification. Finally, this paper seeks to stimulate reflection on what kind of archival resources could benefit the work of present and future epistemic

  7. BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.

    Science.gov (United States)

    Sen Sarma, Moushumi; Arcoleo, David; Khetani, Radhika S; Chee, Brant; Ling, Xu; He, Xin; Jiang, Jing; Mei, Qiaozhu; Zhai, ChengXiang; Schatz, Bruce

    2011-07-01

    With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments can be analyzed to extract concepts that are computational equivalents of a classification such as Gene Ontology, yielding discriminating concepts that differentiate gene mentions from other mentions. The functions of individual genes can be summarized from sentences in biological literature, to produce results resembling a model organism database entry that is automatically computed. Statistical frequency analysis based on literature phrase extraction generates offline semantic indexes to support these gene function services. The website with BeeSpace Navigator is free and open to all; there is no login requirement at www.beespace.illinois.edu for version 4. Materials from the 2010 BeeSpace Software Training Workshop are available at www.beespace.illinois.edu/bstwmaterials.php.

  8. One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy.

    Science.gov (United States)

    Casini, Arturo; MacDonald, James T; De Jonghe, Joachim; Christodoulou, Georgia; Freemont, Paul S; Baldwin, Geoff S; Ellis, Tom

    2014-01-01

    Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications.

  9. One-pot sequential alkynylation and cycloaddition: regioselective construction and biological evaluation of novel benzoxazole-triazole derivatives.

    Science.gov (United States)

    Srivastava, Ananya; Aggarwal, Leena; Jain, Nidhi

    2015-01-12

    Individually, benzoxazole and triazole moieties are of significant biological interest owing to their importance in drugs and pharmaceuticals. To assess their combined biological impact when woven into one molecule, we designed a novel, regioselective, multicomponent, one-pot (MCOP) approach for the construction of benzoxazole-linked triazoles. The synthesis has been achieved in two sequential steps involving copper-catalyzed alkynylation of benzoxazole followed by a 1,3-dipolar cycloaddition reaction. By combination of these two bioactive units into one core, a series of new benzoxazole-triazole scaffolds has been synthesized and subjected to in vitro antibacterial and anticancer evaluation. Tests against clinical isolates of Staphylococcus aureus and Escherichia coli showed potent Gram-negative activity for compounds 4{1,1,1}, 4{1,1,4}, and 4{1,2,1}. The cytotoxicity of the synthesized library was determined against three cancer cell lines: HeLa, SKBr3, and Hep G2. Compound 4{2,2,2} showed significant cytotoxicity against all the cell lines. These preliminary bioassay evaluations strongly suggest the promise and scope of these novel molecules as therapeutic agents in medical science.

  10. Arrival order among native plant functional groups does not affect invasibility of constructed dune communities.

    Science.gov (United States)

    Mason, T J; French, K; Jolley, D

    2013-10-01

    Different arrival order scenarios of native functional groups to a site may influence both resource use during development and final community structure. Arrival order may then indirectly influence community resistance to invasion. We present a mesocosm experiment of constructed coastal dune communities that monitored biotic and abiotic responses to different arrival orders of native functional groups. Constructed communities were compared with unplanted mesocosms. We then simulated a single invasion event by bitou (Chrysanthemoides monilifera ssp. rotundata), a dominant exotic shrub of coastal communities. We evaluated the hypothesis that plantings with simultaneous representation of grass, herb and shrub functional groups at the beginning of the experiment would more completely sequester resources and limit invasion than staggered plantings. Staggered plantings in turn would offer greater resource use and invasion resistance than unplanted mesocosms. Contrary to our expectations, there were few effects of arrival order on abiotic variables for the duration of the experiment and arrival order was unimportant in final community invasibility. All planted mesocosms supported significantly more invader germinants and significantly less invader abundance than unplanted mesocosms. Native functional group plantings may have a nurse effect during the invader germination and establishment phase and a competitive function during the invader juvenile and adult phase. Arrival order per se did not affect resource use and community invasibility in our mesocosm experiment. While grass, herb and shrub functional group plantings will not prevent invasion success in restored communities, they may limit final invader biomass.

  11. Searching for Electrical Properties, Phenomena and Mechanisms in the Construction and Function of Chromosomes

    Directory of Open Access Journals (Sweden)

    Ivan Kanev

    2013-03-01

    Full Text Available Our studies reveal previously unidentified electrical properties of chromosomes: (1 chromosomes are amazingly similar in construction and function to electrical transformers; (2 chromosomes possess in their construction and function, components similar to those of electric generators, conductors, condensers, switches, and other components of electrical circuits; (3 chromosomes demonstrate in nano-scale level electromagnetic interactions, resonance, fusion and other phenomena similar to those described by equations in classical physics. These electrical properties and phenomena provide a possible explanation for unclear and poorly understood mechanisms in clinical genetics including: (a electrically based mechanisms responsible for breaks, translocations, fusions, and other chromosomal abnormalities associated with cancer, intellectual disability, infertility, pregnancy loss, Down syndrome, and other genetic disorders; (b electrically based mechanisms involved in crossing over, non-disjunction and other events during meiosis and mitosis; (c mechanisms demonstrating heterochromatin to be electrically active and genetically important.

  12. Design and construction of higher-order structure and function in proteinosome-based protocells.

    Science.gov (United States)

    Huang, Xin; Patil, Avinash J; Li, Mei; Mann, Stephen

    2014-06-25

    The design and construction of higher-order structure and function in proteinosome microcompartments enclosed by a cross-linked membrane of amphiphilic bovine serum albumin/poly(N-isopropylacrylamide) (BSA-NH2/PNIPAAm) nanoconjugates is described. Three structure/function relationships are investigated: (i) differential chemical cross-linking for the control of membrane disassembly and regulated release of encapsulated genetic polymers; (ii) enzyme-mediated hydrogel structuring of the internal microenvironment to increase mechanical robustness and generate a molecularly crowded reaction environment; and (iii) self-production of a membrane-enclosing outer hydrogel wall for generating protease-resistant forms of the protein-polymer protocells. Our results highlight the potential of integrating aspects of supramolecular and polymer chemistry into the design and construction of novel bioinspired microcompartments as a step toward small-scale materials systems based on synthetic cellularity.

  13. Functional genomics bridges the gap between quantitative genetics and molecular biology.

    Science.gov (United States)

    Lappalainen, Tuuli

    2015-10-01

    Deep characterization of molecular function of genetic variants in the human genome is becoming increasingly important for understanding genetic associations to disease and for learning to read the regulatory code of the genome. In this paper, I discuss how recent advances in both quantitative genetics and molecular biology have contributed to understanding functional effects of genetic variants, lessons learned from eQTL studies, and future challenges in this field.

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

    Science.gov (United States)

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

    2015-05-01

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

  15. Determining the impacts of trawling on benthic function in European waters : a biological traits approach

    DEFF Research Database (Denmark)

    Bolam, Stefan; Kenny, Andrew; Garcia, Clement;

    on benthic ecosystem functioning over much larger spatial scales than previously undertaken. Biological traits information from 887 stations across European waters (Norwegian, UK, Belgian, Dutch, Danish waters, the Mediterranean and Black Sea) were analysed to: i) quantify the relationships between infaunal...

  16. A comprehensive software suite for protein family construction and functional site prediction

    Science.gov (United States)

    Haft, David Renfrew; Haft, Daniel H.

    2017-01-01

    In functionally diverse protein families, conservation in short signature regions may outperform full-length sequence comparisons for identifying proteins that belong to a subgroup within which one specific aspect of their function is conserved. The SIMBAL workflow (Sites Inferred by Metabolic Background Assertion Labeling) is a data-mining procedure for finding such signature regions. It begins by using clues from genomic context, such as co-occurrence or conserved gene neighborhoods, to build a useful training set from a large number of uncharacterized but mutually homologous proteins. When training set construction is successful, the YES partition is enriched in proteins that share function with the user’s query sequence, while the NO partition is depleted. A selected query sequence is then mined for short signature regions whose closest matches overwhelmingly favor proteins from the YES partition. High-scoring signature regions typically contain key residues critical to functional specificity, so proteins with the highest sequence similarity across these regions tend to share the same function. The SIMBAL algorithm was described previously, but significant manual effort, expertise, and a supporting software infrastructure were required to prepare the requisite training sets. Here, we describe a new, distributable software suite that speeds up and simplifies the process for using SIMBAL, most notably by providing tools that automate training set construction. These tools have broad utility for comparative genomics, allowing for flexible collection of proteins or protein domains based on genomic context as well as homology, a capability that can greatly assist in protein family construction. Armed with this new software suite, SIMBAL can serve as a fast and powerful in silico alternative to direct experimentation for characterizing proteins and their functional interactions. PMID:28182651

  17. Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

    Science.gov (United States)

    St Laurent, Georges; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J L; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R R; Nicolas, Estelle; McCaffrey, Timothy A; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

    2016-04-20

    Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs.

  18. A data-driven approach to reverse engineering customer engagement models: towards functional constructs.

    Directory of Open Access Journals (Sweden)

    Natalie Jane de Vries

    Full Text Available Online consumer behavior in general and online customer engagement with brands in particular, has become a major focus of research activity fuelled by the exponential increase of interactive functions of the internet and social media platforms and applications. Current research in this area is mostly hypothesis-driven and much debate about the concept of Customer Engagement and its related constructs remains existent in the literature. In this paper, we aim to propose a novel methodology for reverse engineering a consumer behavior model for online customer engagement, based on a computational and data-driven perspective. This methodology could be generalized and prove useful for future research in the fields of consumer behaviors using questionnaire data or studies investigating other types of human behaviors. The method we propose contains five main stages; symbolic regression analysis, graph building, community detection, evaluation of results and finally, investigation of directed cycles and common feedback loops. The 'communities' of questionnaire items that emerge from our community detection method form possible 'functional constructs' inferred from data rather than assumed from literature and theory. Our results show consistent partitioning of questionnaire items into such 'functional constructs' suggesting the method proposed here could be adopted as a new data-driven way of human behavior modeling.

  19. A data-driven approach to reverse engineering customer engagement models: towards functional constructs.

    Science.gov (United States)

    de Vries, Natalie Jane; Carlson, Jamie; Moscato, Pablo

    2014-01-01

    Online consumer behavior in general and online customer engagement with brands in particular, has become a major focus of research activity fuelled by the exponential increase of interactive functions of the internet and social media platforms and applications. Current research in this area is mostly hypothesis-driven and much debate about the concept of Customer Engagement and its related constructs remains existent in the literature. In this paper, we aim to propose a novel methodology for reverse engineering a consumer behavior model for online customer engagement, based on a computational and data-driven perspective. This methodology could be generalized and prove useful for future research in the fields of consumer behaviors using questionnaire data or studies investigating other types of human behaviors. The method we propose contains five main stages; symbolic regression analysis, graph building, community detection, evaluation of results and finally, investigation of directed cycles and common feedback loops. The 'communities' of questionnaire items that emerge from our community detection method form possible 'functional constructs' inferred from data rather than assumed from literature and theory. Our results show consistent partitioning of questionnaire items into such 'functional constructs' suggesting the method proposed here could be adopted as a new data-driven way of human behavior modeling.

  20. Deconstructing and constructing innate immune functions using molecular sensors and actuators

    Science.gov (United States)

    Coutinho, Kester; Inoue, Takanari

    2016-05-01

    White blood cells such as neutrophils and macrophages are made competent for chemotaxis and phagocytosis -- the dynamic cellular behaviors that are hallmarks of their innate immune functions -- by the reorganization of complex biological circuits during differentiation. Conventional loss-of-function approaches have revealed that more than 100 genes participate in these cellular functions, and we have begun to understand the intricate signaling circuits that are built up from these gene products. We now appreciate: (1) that these circuits come in a variety of flavors -- so that we can make a distinction between genetic circuits, metabolic circuits and signaling circuits; and (2) that they are usually so complex that the assumption of multiple feedback loops, as well as that of crosstalk between seemingly independent pathways, is now routine. It has not escaped our notice, however, that just as physicists and electrical engineers have long been able to disentangle complex electric circuits simply by repetitive cycles of probing and measuring electric currents using a voltmeter, we might similarly be able to dissect these intricate biological circuits by incorporating equivalent approaches in the fields of cell biology and bioengineering. Existing techniques in biology for probing individual circuit components are unfortunately lacking, so that the overarching goal of drawing an exact circuit diagram for the whole cell -- complete with kinetic parameters for connections between individual circuit components -- is not yet in near sight. My laboratory and others have thus begun the development of a new series of molecular tools that can measurably investigate the circuit connectivity inside living cells, as if we were doing so on a silicon board. In these proceedings, I will introduce some of these techniques, provide examples of their implementation, and offer a perspective on directions moving forward.

  1. To be well - to function well. Health biology at Copenhagen University

    DEFF Research Database (Denmark)

    Rosenkilde, Per

    1995-01-01

    Human Fysiologi, Health biology, Public health, Biology Curriculum, University curriculum, Health promotion.......Human Fysiologi, Health biology, Public health, Biology Curriculum, University curriculum, Health promotion....

  2. Functional Genomics Assistant (FUGA: a toolbox for the analysis of complex biological networks

    Directory of Open Access Journals (Sweden)

    Ouzounis Christos A

    2011-10-01

    Full Text Available Abstract Background Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of these patterns is critical for the assessment of fundamental processes in cell biology and pathology. Representation and analysis of cellular constituents through network principles is a promising and popular analytical avenue towards a deeper understanding of molecular mechanisms in a system-wide context. Findings We present Functional Genomics Assistant (FUGA - an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics. In contrast to conventional differential expression analysis of individual genes, FUGA offers a framework for the study of system-wide properties of biological networks and highlights putative molecular targets using concepts of systems biology. Conclusion FUGA offers a simple and customizable framework for network analysis in a variety of systems biology applications. It is freely available for individual or academic use at http://code.google.com/p/fuga.

  3. Construction of a Smooth Lyapunov Function for the Robust and Exact Second-Order Differentiator

    Directory of Open Access Journals (Sweden)

    Tonametl Sanchez

    2016-01-01

    Full Text Available Differentiators play an important role in (continuous feedback control systems. In particular, the robust and exact second-order differentiator has shown some very interesting properties and it has been used successfully in sliding mode control, in spite of the lack of a Lyapunov based procedure to design its gains. As contribution of this paper, we provide a constructive method to determine a differentiable Lyapunov function for such a differentiator. Moreover, the Lyapunov function is used to provide a procedure to design the differentiator’s parameters. Also, some sets of such parameters are provided. The determination of the positive definiteness of the Lyapunov function and negative definiteness of its derivative is converted to the problem of solving a system of inequalities linear in the parameters of the Lyapunov function candidate and also linear in the gains of the differentiator, but bilinear in both.

  4. Assembly of a functional 3D primary cardiac construct using magnetic levitation

    Directory of Open Access Journals (Sweden)

    Glauco Souza

    2016-07-01

    Full Text Available Easily assembled organotypic co-cultures have long been sought in medical research. In vitro tissue constructs with faithful representation of in vivo tissue characteristics are highly desirable for screening and characteristic assessment of a variety of tissue types. Cardiac tissue analogs are particularly sought after due to the phenotypic degradation and difficulty of culture of primary cardiac myocytes. This study utilized magnetic nanoparticles and primary cardiac myocytes in order to levitate and culture multicellular cardiac aggregates (MCAs. Cells were isolated from 2 day old Sprague Dawley rat hearts and subsequently two groups were incubated with either C1: 33 µL nanoshell/million cells or C2: 50 µL nanoshell/million cells. Varying numbers of cells for each concentration were cultured in a magnetic field in a 24 well plate and observed over a period of 12 days. Constructs generally formed spherical structures. Masson’s trichrome staining of a construct shows the presence of extracellular matrix protein, indicating the presence of functional fibroblasts. Many constructs exhibited noticeable contraction after 4 days of culture and continued contracting noticeably past day 9 of culture. Noticeable contractility indicates the presence of functional primary cardiac myocytes in culture. Phenotypic conservation of cardiac cells was ascertained using IHC staining by α-actinin and collagen. CD31 and fibrinogen were probed in order to assess localization of fibroblasts and endothelial cells. The study verifies a protocol for the use of magnetic levitation in order to rapidly assemble 3D cardiac like tissue with phenotypic and functional stability.

  5. Morphological and functional characteristics of three-dimensional engineered bone-ligament-bone constructs following implantation.

    Science.gov (United States)

    Ma, Jinjin; Goble, Kristen; Smietana, Michael; Kostrominova, Tatiana; Larkin, Lisa; Arruda, Ellen M

    2009-10-01

    The incidence of ligament injury has recently been estimated at 400,000/year. The preferred treatment is reconstruction using an allograft, but outcomes are limited by donor availability, biomechanical incompatibility, and immune rejection. The creation of an engineered ligament in vitro solely from patient bone marrow stromal cells (has the potential to greatly enhance outcomes in knee reconstructions. Our laboratory has developed a scaffoldless method to engineer three-dimensional (3D) ligament and bone constructs from rat bone marrow stem cells in vitro. Coculture of these two engineered constructs results in a 3D bone-ligament-bone (BLB) construct with viable entheses, which was successfully used for medial collateral ligament (MCL) replacement in a rat model. 1 month and 2 month implantations were applied to the engineered BLBs. Implantation of 3D BLBs in a MCL replacement application demonstrated that our in vitro engineered tissues grew and remodeled quickly in vivo to an advanced phenotype and partially restored function of the knee. The explanted 3D BLB ligament region stained positively for type I collagen and elastin and was well vascularized after 1 and 2 months in vivo. Tangent moduli of the ligament portion of the 3D BLB 1 month explants increased by a factor of 2.4 over in vitro controls, to a value equivalent to those observed in 14-day-old neonatal rat MCLs. The 3D BLB 1 month explants also exhibited a functionally graded response that closely matched native MCL inhomogeneity, indicating the constructs functionally adapted in vivo.

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

    Science.gov (United States)

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

    2006-03-01

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

  7. CONSTRUCTION OF DIDACTIC MODEL OF MEMBRANE AND EXTRACELLULAR MATRIX TO FACILITATE THE TEACHING/LEARNING BY BIOLOGICAL SCIENCES STUDENTS AT UFRN

    Directory of Open Access Journals (Sweden)

    M. V.S. Medeiros et al

    2015-08-01

    Full Text Available This work was developed in the course of MOLECULAR DIVERSITY, required curricular component for the courses of Biological Sciences at UFRN. This course intends to encourage the study of the chemical structure and function of biomolecules using lectures and practical classes. Looking at the evaluations from previous semesters, it became evident that the subjects of the membrane and extracellular matrix were not being learned in a meaningful way. We also noticed lack of motivation from students due to difficulties in understanding molecules, weakening the teaching/learning process. Given this situation, our work aimed to encourage students to construct the constituent molecules of the membrane and extracellular matrix and assemble these structures, in order to understand molecular interactions, improve understanding of the subject and facilitate the learning process. This was accomplished through a monitoring project with the help of monitors. The proposed methodology consisted of separating the class into groups, where each would be responsible for making and exposing the other students to one of the molecules (Membrane Lipids, integrins, fibronectin, collagen, elastin, laminin, hyaluronic acid, and then discussing these molecules’ structural characteristics and interactions. The students could use various types of materials like cardboard, colored pens and polystyrene. The molecules were presented to the class, and the groups had set up the membrane and the matrix indicating the location of molecules and their possible interactions. All groups created their molecules according to given specifications. They created didactic and colorful molecules and positively interacted with all other groups during the assembly of the membrane and extracellular matrix; they also discussed molecules functions and interactions. We noticed during presentations and evaluation a strong performance in the subjects in question, as well as the construction of a

  8. The functional biology and trophic role of krill (Thysanoessa raschii) in a Greenlandic fjord

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Nielsen, Torkel Gissel; Munk, Peter

    2011-01-01

    Despite being a key zooplankton group, knowledge on krill biology from the Arctic is inadequate. The present study examine the functional biology and evaluate the trophic role of krill in the GodthAyenbsfjord (64 degrees N, 51 degrees W) SW Greenland, through a combination of fieldwork...... ration of 1% body C d(-1). Furthermore, T. raschii was capable of exploiting plankton cells from 5 to 400 mu m, covering several trophic levels of the pelagic food web. The calculated grazing impact by T. raschii on the fjord plankton community was negligible. However, the schooling and migratory...

  9. Biological dosimetry of ionizing radiation: Evaluation of the dose with cytogenetic methodologies by the construction of calibration curves

    Science.gov (United States)

    Zafiropoulos, Demetre; Facco, E.; Sarchiapone, Lucia

    2016-09-01

    In case of a radiation accident, it is well known that in the absence of physical dosimetry biological dosimetry based on cytogenetic methods is a unique tool to estimate individual absorbed dose. Moreover, even when physical dosimetry indicates an overexposure, scoring chromosome aberrations (dicentrics and rings) in human peripheral blood lymphocytes (PBLs) at metaphase is presently the most widely used method to confirm dose assessment. The analysis of dicentrics and rings in PBLs after Giemsa staining of metaphase cells is considered the most valid assay for radiation injury. This work shows that applying the fluorescence in situ hybridization (FISH) technique, using telomeric/centromeric peptide nucleic acid (PNA) probes in metaphase chromosomes for radiation dosimetry, could become a fast scoring, reliable and precise method for biological dosimetry after accidental radiation exposures. In both in vitro methods described above, lymphocyte stimulation is needed, and this limits the application in radiation emergency medicine where speed is considered to be a high priority. Using premature chromosome condensation (PCC), irradiated human PBLs (non-stimulated) were fused with mitotic CHO cells, and the yield of excess PCC fragments in Giemsa stained cells was scored. To score dicentrics and rings under PCC conditions, the necessary centromere and telomere detection of the chromosomes was obtained using FISH and specific PNA probes. Of course, a prerequisite for dose assessment in all cases is a dose-effect calibration curve. This work illustrates the various methods used; dose response calibration curves, with 95% confidence limits used to estimate dose uncertainties, have been constructed for conventional metaphase analysis and FISH. We also compare the dose-response curve constructed after scoring of dicentrics and rings using PCC combined with FISH and PNA probes. Also reported are dose response curves showing scored dicentrics and rings per cell, combining

  10. A biologically inspired psychometric function for accuracy of visual identification as a function of exposure duration

    DEFF Research Database (Denmark)

    Petersen, Anders; Andersen, Tobias

    in modelling human performance in whole and partial report tasks in which multiple simultaneously presented letters are to be reported (Shibuya & Bundesen, 1988). Therefore, we investigated visual letter identification as a function of exposure duration. On each trial, a single randomly chosen letter (A......The psychometric function of letter identification is typically described as a function of stimulus intensity. However, the effect of stimulus exposure duration on letter identification remains poorly described. This is surprising because the effect of exposure duration has played a central role......-Z) was presented at the centre of the screen. Exposure duration was varied from 5 to 210 milliseconds. The letter was followed by a pattern mask. Three subjects each completed 54,080 trials in a 26-Alternative Forced Choice procedure. We compared the exponential, the gamma and the Weibull psychometric functions...

  11. Closure, function, emergence, semiosis, and life: the same idea? Reflections on the concrete and the abstract in theoretical biology.

    Science.gov (United States)

    Emmeche, C

    2000-01-01

    In this note epistemological problems in general theories about living systems are considered; in particular, the question of hidden connections between different areas of experience, such as folk biology and scientific biology, and hidden connections between central concepts of theoretical biology, such as function, semiosis, closure, and life.

  12. Construction of homogeneous loading functions for elastoplastic damage models for concrete

    Science.gov (United States)

    Zhang, Ji; Li, Jie

    2014-03-01

    Over the past 2 decades, tight restriction has been imposed on strength criteria of concrete by the combination of plasticity and damage in one theory. The present study aims at constructing plastic/damage loading functions for elastoplastic damage models for concrete that can perform more satisfactorily in 3D stress states. Numerous strength criteria of concrete are reorganized according to their simplest representations as Cartesian, cylindrical, mixed cylindrical-Cartesian, and other forms, and the homogeneity of loading functions discussed. It is found that under certain supplementary conditions from physical meanings, an unambiguous definition of the cohesion in a strength criterion, which is demanded in an elastoplastic damage model, is usually available in an explicit or implicit form, and in each case the loading function is still homogeneous. To apply and validate the presented theory, we construct the respective homogeneous damage and plastic loading functions and implant them into some widely used elastoplastic damage models for concrete, and their performances in triaxial compression prove to have improved significantly.

  13. Constructing a working taxonomy of functional Ada software components for real-time embedded system applications

    Science.gov (United States)

    Wallace, Robert

    1986-01-01

    A major impediment to a systematic attack on Ada software reusability is the lack of an effective taxonomy for software component functions. The scope of all possible applications of Ada software is considered too great to allow the practical development of a working taxonomy. Instead, for the purposes herein, the scope of Ada software application is limited to device and subsystem control in real-time embedded systems. A functional approach is taken in constructing the taxonomy tree for identified Ada domain. The use of modular software functions as a starting point fits well with the object oriented programming philosophy of Ada. Examples of the types of functions represented within the working taxonomy are real time kernels, interrupt service routines, synchronization and message passing, data conversion, digital filtering and signal conditioning, and device control. The constructed taxonomy is proposed as a framework from which a need analysis can be performed to reveal voids in current Ada real-time embedded programming efforts for Space Station.

  14. A Novel Human Tissue-Engineered 3-D Functional Vascularized Cardiac Muscle Construct

    Science.gov (United States)

    Valarmathi, Mani T.; Fuseler, John W.; Davis, Jeffrey M.; Price, Robert L.

    2017-01-01

    Organ tissue engineering, including cardiovascular tissues, has been an area of intense investigation. The major challenge to these approaches has been the inability to vascularize and perfuse the in vitro engineered tissue constructs. Attempts to provide oxygen and nutrients to the cells contained in the biomaterial constructs have had varying degrees of success. The aim of this current study is to develop a three-dimensional (3-D) model of vascularized cardiac tissue to examine the concurrent temporal and spatial regulation of cardiomyogenesis in the context of postnatal de novo vasculogenesis during stem cell cardiac regeneration. In order to achieve the above aim, we have developed an in vitro 3-D functional vascularized cardiac muscle construct using human induced pluripotent stem cell-derived embryonic cardiac myocytes (hiPSC-ECMs) and human mesenchymal stem cells (hMSCs). First, to generate the prevascularized scaffold, human cardiac microvascular endothelial cells (hCMVECs) and hMSCs were co-cultured onto a 3-D collagen cell carrier (CCC) for 7 days under vasculogenic culture conditions. In this milieu, hCMVECs/hMSCs underwent maturation, differentiation, and morphogenesis characteristic of microvessels, and formed extensive plexuses of vascular networks. Next, the hiPSC-ECMs and hMSCs were co-cultured onto this generated prevascularized CCCs for further 7 or 14 days in myogenic culture conditions. Finally, the vascular and cardiac phenotypic inductions were analyzed at the morphological, immunological, biochemical, molecular, and functional levels. Expression and functional analyses of the differentiated cells revealed neo-angiogenesis and neo-cardiomyogenesis. Thus, our unique 3-D co-culture system provided us the apt in vitro functional vascularized 3-D cardiac patch that can be utilized for cellular cardiomyoplasty. PMID:28194397

  15. The bottom-up approach to defining life : deciphering the functional organization of biological cells via multi-objective representation of biological complexity from molecules to cells

    Directory of Open Access Journals (Sweden)

    Sathish ePeriyasamy

    2013-12-01

    Full Text Available In silico representation of cellular systems needs to represent the adaptive dynamics of biological cells, recognizing a cell’s multi-objective topology formed by spatially and temporally cohesive intracellular structures. The design of these models needs to address the hierarchical and concurrent nature of cellular functions and incorporate the ability to self-organise in response to transitions between healthy and pathological phases, and adapt accordingly. The functions of biological systems are constantly evolving, due to the ever changing demands of their environment. Biological systems meet these demands by pursuing objectives, aided by their constituents, giving rise to biological functions. A biological cell is organised into an objective/task hierarchy. These objective hierarchy corresponds to the nested nature of temporally cohesive structures and representing them will facilitate in studying pleiotropy and polygeny by modeling causalities propagating across multiple interconnected intracellular processes. Although biological adaptations occur in physiological, developmental and reproductive timescales, the paper is focused on adaptations that occur within physiological timescales, where the biomolecular activities contributing to functional organisation, play a key role in cellular physiology. The paper proposes a multi-scale and multi-objective modelling approach from the bottom-up by representing temporally cohesive structures for multi-tasking of intracellular processes. Further the paper characterises the properties and constraints that are consequential to the organisational and adaptive dynamics in biological cells.

  16. Colorimetric detection of biological hydrogen sulfide using fluorosurfactant functionalized gold nanorods.

    Science.gov (United States)

    Zhang, Xuan; Zhou, Wenjuan; Yuan, Zhiqin; Lu, Chao

    2015-11-07

    As a well-known environmental pollutant but also an important gaseous transmitter, the specific detection of hydrogen sulfide (H2S) is significant in biological systems. In this study, fluorosurfactant functionalized gold nanorods (FSN-AuNRs) have been proposed to act as selective colorimetric nanoprobes for H2S. With the combination of strong gold-S interactions and small FSN bilayer interstices, FSN-AuNRs demonstrate favorable selectivity and sensitivity toward H2S over other anions and small biological molecules. The practical application of the present method in biological H2S detection was validated with human and mouse serum samples. Moreover, the proposed nanoprobe can also be used for evaluating the activity of H2S synthetase.

  17. Construction of Green's Functions for the Two-Dimensional Static Klein-Gordon Equation

    Institute of Scientific and Technical Information of China (English)

    MELNIKOV Yu. A.

    2011-01-01

    In contrast to the cognate Laplace equation, for which a vast number of Green's functions is available, the field is not that developed for the static Klein-Gordon equation. The latter represents, nonetheless, a natural area for application of some of the methods that are proven productive for the Laplace equation. The perspective looks especially attractive for the methods of images and eigenfunction expansion.This study is based on our experience recently gained on the construction of Green's functions for elliptic partial differential equations. An extensive list of boundary-value problems formulated for the static Klein-Gordon equation is considered. Computerfriendly representations of their Green's functions are obtained, most of which have never been published before.

  18. Functionalized nanoporous silica for the removal of heavy metals from biological systems: adsorption and application.

    Science.gov (United States)

    Yantasee, Wassana; Rutledge, Ryan D; Chouyyok, Wilaiwan; Sukwarotwat, Vichaya; Orr, Galya; Warner, Cynthia L; Warner, Marvin G; Fryxell, Glen E; Wiacek, Robert J; Timchalk, Charles; Addleman, R Shane

    2010-10-01

    Surface-functionalized nanoporous silica, often referred to as self-assembled monolayers on mesoporous supports (SAMMS), has previously demonstrated the ability to serve as very effective heavy metal sorbents in a range of aquatic and environmental systems, suggesting that they may be advantageously utilized for biomedical applications such as chelation therapy. Herein we evaluate surface chemistries for heavy metal capture from biological fluids, various facets of the materials' biocompatibility, and the suitability of these materials as potential therapeutics. Of the materials tested, thiol-functionalized SAMMS proved most capable of removing selected heavy metals from biological solutions (i.e., blood, urine, etc.) Consequentially, thiol-functionalized SAMMS was further analyzed to assess the material's performance under a number of different biologically relevant conditions (i.e., variable pH and ionic strength) to gauge any potentially negative effects resulting from interaction with the sorbent, such as cellular toxicity or the removal of essential minerals. Additionally, cellular uptake studies demonstrated no cell membrane permeation by the silica-based materials generally highlighting their ability to remain cellularly inert and thus nontoxic. The results show that organic ligand functionalized nanoporous silica could be a valuable material for a range of detoxification therapies and potentially other biomedical applications.

  19. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry.

    Science.gov (United States)

    Kalay, Ziya

    2011-08-01

    How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.

  20. Enhanced cytocompatibility of silver-containing biointerface by constructing nitrogen functionalities

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei, E-mail: weizhang@mail.ipc.ac.cn [Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Liu, Jun [Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Wang, Huaiyu [Department of Physics & Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong (China); Xu, Ying; Wang, Pingli [Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Ji, Junhui, E-mail: jhji@mail.ipc.ac.cn [Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Chu, Paul K. [Department of Physics & Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong (China)

    2015-09-15

    Graphical abstract: Constructing nitrogen functionalities is promising method to enhance cytocompatibility of the biointerface by simultaneous Ag and N{sub 2} plasma modification. - Highlights: • N{sub 2} plasma immersion ion implantation (PIII) treatment generates plenty of nitrogen functionalities on polymer substrate. • N{sub 2} PIII treatment increases surface roughness and hydrophilicity and improves its capability to adsorb protein. • Simultaneous Ag and N{sub 2} plasma modification constructs nitrogen functionalities to enhance cytocompatibility of the biointerface. - Abstract: Silver (Ag) has recently been introduced into polymeric biomedical implants by plasma immersion ion implantation (PIII) to enhance the antibacterial capability. However, Ag ions and nanoparticles can increase the cytotoxicity and inhibit cellular proliferation and the relationship is time- and dose-dependent. In this study, Ag and N{sub 2} PIII is conducted in concert to produce nitrogen functional groups as well as Ag-containing biointerface. In addition to the creation of nitrogen functionalities, the surface roughness and hydrophilicity are improved in favor of protein adsorption. Compared to the biointerface created by Ag PIII only, the nitrogen functionalities generated by N{sub 2} co-PIII do not affect DNA synthesis and the total protein level but evidently enhance cellular adhesion, viability, and proliferation at the biointerface. The modified surface is observed to upregulate the osteogenesis-related marker expression of bone cells in contact. Our findings suggest that dual Ag and N{sub 2} PIII is a desirable technique to enhance both the cytocompatibility and antibacterial capability of medical polymers.

  1. Syntheses of biologically active natural products and leading compounds for new pharmaceuticals employing effective construction of a polycyclic skeleton.

    Science.gov (United States)

    Ihara, Masataka

    2006-06-01

    Cascade reactions are useful methods for the construction of polycyclic skeletons, which are important cores for biological activities. A variety of cascade reactions carried out under multiple reaction conditions, such as pericyclic, polar, radical, and transition metal-catalyzed reaction conditions, have been investigated. Culmorin, pentalenene, pentalenic acid, deoxypentalenic acid, longiborneol, cedrandiol, 8,14-cedranoxide, atisirene, atisine, and estrane-type steroids were synthesized via the intramolecular double Michael reaction. Aza double Michael reaction was applied to the syntheses of tylophorine, epilupinine, tacamonine, and paroxetine. Furthermore, sequential Michael and aldol reactions were performed in both intramolecular and intermolecular manners, leading to the formation of polycyclic compounds fused to a four-membered ring. Synthesis of paesslerin A utilizing a multicomponent cascade reaction revealed an error in the proposed structure. Unique cascade reactions carried out under radical and transition metal-catalyzed reaction conditions were also investigated. With the combination of several cascade reactions, serofendic acids and methyl 7beta-hydroxykaurenoate, both of which have neuroprotective activity, were synthesized in a selective manner.

  2. High performance hybrid functional Petri net simulations of biological pathway models on CUDA.

    Science.gov (United States)

    Chalkidis, Georgios; Nagasaki, Masao; Miyano, Satoru

    2011-01-01

    Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand for performance accelerations by efficient and inexpensive parallel computation solutions. Recent developments in the field of general-purpose computation on graphics processing units (GPGPU) enabled the scientific community to port a variety of compute intensive algorithms onto the graphics processing unit (GPU). This work presents the first scheme for mapping biological hybrid functional Petri net models, which can handle both discrete and continuous entities, onto compute unified device architecture (CUDA) enabled GPUs. GPU accelerated simulations are observed to run up to 18 times faster than sequential implementations. Simulating the cell boundary formation by Delta-Notch signaling on a CUDA enabled GPU results in a speedup of approximately 7x for a model containing 1,600 cells.

  3. Form and function: Perspectives on structural biology and resources for the future

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, D. (ed.)

    1990-12-01

    The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs.

  4. Mediating objects: scientific and public functions of models in nineteenth-century biology.

    Science.gov (United States)

    Ludwig, David

    2013-01-01

    The aim of this article is to examine the scientific and public functions of two- and three-dimensional models in the context of three episodes from nineteenth-century biology. I argue that these models incorporate both data and theory by presenting theoretical assumptions in the light of concrete data or organizing data through theoretical assumptions. Despite their diverse roles in scientific practice, they all can be characterized as mediators between data and theory. Furthermore, I argue that these different mediating functions often reflect their different audiences that included specialized scientists, students, and the general public. In this sense, models in nineteenth-century biology can be understood as mediators between theory, data, and their diverse audiences.

  5. Cognitive-graphic method for constructing of hierarchical forms of basic functions of biquadratic finite element

    Science.gov (United States)

    Astionenko, I. O.; Litvinenko, O. I.; Osipova, N. V.; Tuluchenko, G. Ya.; Khomchenko, A. N.

    2016-10-01

    Recently the interpolation bases of the hierarchical type have been used for the problem solving of the approximation of multiple arguments functions (such as in the finite-element method). In this work the cognitive graphical method of constructing of the hierarchical form bases on the serendipity finite elements is suggested, which allowed to get the alternative bases on a biquadratic finite element from the serendipity family without internal knots' inclusion. The cognitive-graphic method allowed to improve the known interpolation procedure of Taylor and to get the modified elements with irregular arrangement of knots. The proposed procedures are universal and are spread in the area of finite-elements.

  6. Collaborative role construction in a conversation with dementia: an application of systemic functional linguistics.

    Science.gov (United States)

    Müller, Nicole; Wilson, Brent T

    2008-01-01

    This study applies the tools provided by Systemic Functional Linguistics (SFL) to the description of patterns in a conversation between a person with dementia and a person without. It shows how, in the presence of, on the one hand, considerable communicative and cognitive deficits, and on the other, a collaborative interlocutor, a person with dementia succeeds in leading and sustaining a lengthy conversation, and of constructing for himself a positive role in the interaction, namely that of the elder advising a much younger man.

  7. Applying systemic functional linguistics to conversations with dementia: the linguistic construction of relationships between participants.

    Science.gov (United States)

    Müller, Nicole; Mok, Zaneta

    2012-02-01

    Social isolation in dementia is a growing concern as the incidence and prevalence of dementing conditions is on the rise in many societies. Positive social interactions, which foster the construction and enactment of positive interpersonal relationships and therefore positive discursive identities, make an important contribution to emotional well-being. In this article, we investigate how two women diagnosed with dementia of the Alzheimer's type use language to relate to each other and two visiting graduate students. We use Systemic Functional Linguistics as an analytical framework, specifically investigating the use of vocatives and naming, and conversational moves and exchanges.

  8. Construction of Canonical Polynomial Basis Functions for Solving Special Nth -Order Linear Integro-Differential Equations

    Directory of Open Access Journals (Sweden)

    1 Taiwo O. A

    2013-01-01

    Full Text Available The problem of solving special nth-order linear integro-differential equations has special importance in engineering and sciences that constitutes a good model for many systems in various fields. In this paper, we construct canonical polynomial from the differential parts of special nth-order integro-differential equations and use it as our basis function for the numerical solutions of special nth-order integro-differential equations. The results obtained by this method are compared with those obtained by Adomian Decomposition method. It is also observed that the new method is an effective method with high accuracy. Some examples are given to illustrate the method.

  9. A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology

    OpenAIRE

    Carbonell-Ballestero, M.; Duran-Nebreda, S.; Montanez, R.; Sole, R.; Macia, J.; Rodriguez-Caso, C.

    2014-01-01

    Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses-the so-called transfer function-and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the in...

  10. New insights in the biology of BDNF synthesis and release: implications in CNS function

    OpenAIRE

    Greenberg, Michael E.; Xu, Baoji; Lu, Bai; Hempstead, Barbara L.

    2009-01-01

    BDNF has pleiotrophic effects on neuronal development and synaptic plasticity that underlie circuit formation and cognitive function. Recent breakthroughs reveal that neuronal activity regulates BDNF cell biology, including Bdnf transcription, dendritic targeting and trafficking of BDNF mRNA and protein, and secretion and extracellular conversion of proBDNF to mature BDNF. Defects in these mechanisms contribute differentially to cognitive dysfunction and anxiety–like behaviors. Here we review...

  11. Nanoelectromechanics of Inorganic and Biological Systems: From Structural Imaging to Local Functionalities

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, Brian [University College, Dublin; Kalinin, Sergei V [ORNL; Jesse, Stephen [ORNL; Thompson, G. L. [Clemson University; Vertegel, Alexey [ORNL; Hohlbauch, Sophia [Asylum Research, Santa Barbara, CA; Proksch, Roger [Asylum Research, Santa Barbara, CA

    2008-01-01

    Coupling between electrical and mechanical phenomena is extremely common in inorganic materials, and nearly ubiquitous in biological systems, underpinning phenomena and devices ranging from SONAR to cardiac activity and hearing. This paper briefly summarizes the Scanning Probe Microscopy (SPM) approach, referred to as Piezoresponse Force Microscopy (PFM), for probing electromechanical coupling on the nanometer scales, and delineates some existing and emerging applications to probe local structure and functionality in inorganic ferroelectrics, calcified and connective tissues, and complex biosystems based on electromechanical detection.

  12. Validation of Procedures for Monitoring Crewmember Immune Function - Short Duration Biological Investigation

    Science.gov (United States)

    Sams, Clarence; Crucian, Brian; Stowe, Raymond; Pierson, Duane; Mehta, Satish; Morukov, Boris; Uchakin, Peter; Nehlsen-Cannarella, Sandra

    2008-01-01

    Validation of Procedures for Monitoring Crew Member Immune Function - Short Duration Biological Investigation (Integrated Immune-SDBI) will assess the clinical risks resulting from the adverse effects of space flight on the human immune system and will validate a flightcompatible immune monitoring strategy. Immune system changes will be monitored by collecting and analyzing blood, urine and saliva samples from crewmembers before, during and after space flight.

  13. Functionalized Nanoporous Silica for Removal of Heavy Metals from Biological Systems; Adsorption and Application

    Energy Technology Data Exchange (ETDEWEB)

    Yantasee, Wassana; Rutledge, Ryan D.; Chouyyok, Wilaiwan; Sukwarotwat, Vichaya; Orr, Galya; Warner, Cynthia L.; Warner, Marvin G.; Fryxell, Glen E.; Wiacek, Robert J.; Timchalk, Charles; Addleman, Raymond S.

    2010-10-01

    Functionalized nanoporous silica, often referred to as self-assembled monolayers on mesoporous supports (SAMMS) have previously demonstrated the ability to serve as very effective heavy metal sorbents in a range of aquatic and environmental systems suggesting they may be advantageously utilized for biomedical applications such as chelation therapy. Herein we evaluate surface chemistries for heavy metal capture from biological fluids, various facets of the materials biocompatibility and the suitability of these materials as potential therapeutics. Of the materials tested, thiol-functionalized SAMMS proved most capable of removing selected heavy metals from biological solutions (i.e. blood, urine, etc.) As a result, thiol SAMMS was further analyzed to assess the material’s performance under a number of different biologically relevant conditions (i.e. variable pH and ionic strength) as well to gauge any potentially negative cellular effects resulting from interaction with the sorbent, such as cellular toxicity or possible chelation of essential minerals. Additionally, cellular uptake studies demonstrated no cell membrane permeation by the silica-based materials generally highlighting their ability to remain cellularly inert and thus non-toxic. As a result, it has been determined that organic ligand-functionalized nanoporous silica materials could be a valuable material for detoxification therapeutics and potentially other biomedical applications as needed.

  14. Biological roles and functional mechanisms of arenavirus Z protein in viral replication.

    Science.gov (United States)

    Wang, Jialong; Danzy, Shamika; Kumar, Naveen; Ly, Hinh; Liang, Yuying

    2012-09-01

    Arenaviruses can cause severe hemorrhagic fever diseases in humans, with limited prophylactic or therapeutic measures. A small RING-domain viral protein Z has been shown to mediate the formation of virus-like particles and to inhibit viral RNA synthesis, although its biological roles in an infectious viral life cycle have not been directly addressed. By taking advantage of the available reverse genetics system for a model arenavirus, Pichinde virus (PICV), we provide the direct evidence for the essential biological roles of the Z protein's conserved residues, including the G2 myristylation site, the conserved C and H residues of RING domain, and the poorly characterized C-terminal L79 and P80 residues. Dicodon substitutions within the late (L) domain (PSAPPYEP) of the PICV Z protein, although producing viable mutant viruses, have significantly reduced virus growth, a finding suggestive of an important role for the intact L domain in viral replication. Further structure-function analyses of both PICV and Lassa fever virus Z proteins suggest that arenavirus Z proteins have similar molecular mechanisms in mediating their multiple functions, with some interesting variations, such as the role of the G2 residue in blocking viral RNA synthesis. In summary, our studies have characterized the biological roles of the Z protein in an infectious arenavirus system and have shed important light on the distinct functions of its domains in virus budding and viral RNA regulation, the knowledge of which may lead to the development of novel antiviral drugs.

  15. Emerging Molecular and Biological Functions of MBD2, a Reader of DNA Methylation

    Directory of Open Access Journals (Sweden)

    Kathleen H Wood

    2016-05-01

    Full Text Available DNA methylation is an epigenetic mark that is essential for many biological processes and is linked to diseases such as cancer. Methylation is usually associated with transcriptional silencing, but new research has challenged this model. Both transcriptional activation and repression have recently been found to be associated with DNA methylation in a context-specific manner. How DNA methylation patterns are interpreted into different functional output remains poorly understood. One mechanism involves the protein ‘readers’ of methylation, which includes the methyl-CpG binding domain (MBD family of proteins. This review examines the molecular and biological functions of MBD2, which binds to CpG methylation and is an integral part of the nucleosome remodeling and histone deacetylation (NuRD complex. MBD2 has been linked to immune system function and tumorigenesis, yet little is known about its functions in vivo. Recent studies have found the MBD2 protein is ubiquitously expressed, with relatively high levels in the lung, liver and colon. Mbd2 null mice surprisingly show relatively mild phenotypes compared to mice with loss of function of other MBD proteins. This evidence has previously been interpreted as functional redundancy between the MBD proteins. Here we examine and contextualize research that suggests MBD2 has unique properties and functions among the MBD proteins. These functions translate to recently described roles in the development and differentiation of multiple cell lineages, including pluripotent stem cells and various cell types of the immune system, as well as in tumorigenesis. We also consider possible models for the dynamic interactions between MBD2 and NuRD in different tissues in vivo. The functions of MBD2 may have direct therapeutic implications for several areas of human disease, including autoimmune conditions and cancer, in addition to providing insights into the actions of NuRD and chromatin regulation.

  16. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory

    Directory of Open Access Journals (Sweden)

    Gao Haichun

    2007-08-01

    Full Text Available Abstract Background Large-scale sequencing of entire genomes has ushered in a new age in biology. One of the next grand challenges is to dissect the cellular networks consisting of many individual functional modules. Defining co-expression networks without ambiguity based on genome-wide microarray data is difficult and current methods are not robust and consistent with different data sets. This is particularly problematic for little understood organisms since not much existing biological knowledge can be exploited for determining the threshold to differentiate true correlation from random noise. Random matrix theory (RMT, which has been widely and successfully used in physics, is a powerful approach to distinguish system-specific, non-random properties embedded in complex systems from random noise. Here, we have hypothesized that the universal predictions of RMT are also applicable to biological systems and the correlation threshold can be determined by characterizing the correlation matrix of microarray profiles using random matrix theory. Results Application of random matrix theory to microarray data of S. oneidensis, E. coli, yeast, A. thaliana, Drosophila, mouse and human indicates that there is a sharp transition of nearest neighbour spacing distribution (NNSD of correlation matrix after gradually removing certain elements insider the matrix. Testing on an in silico modular model has demonstrated that this transition can be used to determine the correlation threshold for revealing modular co-expression networks. The co-expression network derived from yeast cell cycling microarray data is supported by gene annotation. The topological properties of the resulting co-expression network agree well with the general properties of biological networks. Computational evaluations have showed that RMT approach is sensitive and robust. Furthermore, evaluation on sampled expression data of an in silico modular gene system has showed that under

  17. Effective dielectric properties of biological cells: generalization of the spectral density function approach.

    Science.gov (United States)

    Goncharenko, Anatoliy V; Chang, Yia-Chung

    2009-07-23

    We suggest an extension of the spectral density function approach to describe the complex dielectric response of suspensions of arbitrarily shaped particles having a thin shell, in particular, biological cells. The approach is shown to give analytical results in some simple but practically important cases. In the general case, for the 3-phase systems it reduces to determination of the spectral density function for the suspension of a certain kind. Prospects and limitations of the approach, as well as practical examples, are also considered.

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

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

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

  19. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth.

    Directory of Open Access Journals (Sweden)

    Timothy G Bromage

    Full Text Available The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the

  20. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth.

    Science.gov (United States)

    Bromage, Timothy G; Idaghdour, Youssef; Lacruz, Rodrigo S; Crenshaw, Thomas D; Ovsiy, Olexandra; Rotter, Björn; Hoffmeier, Klaus; Schrenk, Friedemann

    2016-01-01

    The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that

  1. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth

    Science.gov (United States)

    Bromage, Timothy G.; Idaghdour, Youssef; Lacruz, Rodrigo S.; Crenshaw, Thomas D.; Ovsiy, Olexandra; Rotter, Björn; Hoffmeier, Klaus; Schrenk, Friedemann

    2016-01-01

    The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that

  2. High yield of functional metagenomic library from mangroves constructed in fosmid vector.

    Science.gov (United States)

    Gonçalves, A C S; dos Santos, A C F; dos Santos, T F; Pessoa, T B A; Dias, J C T; Rezende, R P

    2015-10-02

    In the present study, metagenomic technique and fosmid vectors were used to construct a library of clones for exploring the biotechnological potential of mangrove soils by isolation of functional genes encoding hydrolytic enzymes. The library was built with genomic DNA from the soil samples of mangrove sediments and the functional screening of 1824 clones (~64 Mbp) was performed to detect the hydrolytic activity specific for cellulases, amylases (at acidic, neutral and basic pH), lipases/esterases, proteases, and nitrilases. Significant numbers of clones, positive for the tested enzyme activities were obtained. Our results indicate the importance and biotechnological potential of mangrove soils especially when compared to those obtained using other soil metagenomic libraries.

  3. Functionalized olefin cross-coupling to construct carbon-carbon bonds

    Science.gov (United States)

    Lo, Julian C.; Gui, Jinghan; Yabe, Yuki; Pan, Chung-Mao; Baran, Phil S.

    2014-12-01

    Carbon-carbon (C-C) bonds form the backbone of many important molecules, including polymers, dyes and pharmaceutical agents. The development of new methods to create these essential connections in a rapid and practical fashion has been the focus of numerous organic chemists. This endeavour relies heavily on the ability to form C-C bonds in the presence of sensitive functional groups and congested structural environments. Here we report a chemical transformation that allows the facile construction of highly substituted and uniquely functionalized C-C bonds. Using a simple iron catalyst, an inexpensive silane and a benign solvent under ambient atmosphere, heteroatom-substituted olefins are easily reacted with electron-deficient olefins to create molecular architectures that were previously difficult or impossible to access. More than 60 examples are presented with a wide array of substrates, demonstrating the chemoselectivity and mildness of this simple reaction.

  4. A New Method of Constructing Bivariate Vector Valued Rational Interpolation Function

    Institute of Scientific and Technical Information of China (English)

    Lin ZHENGI; Gong Qin ZHU

    2011-01-01

    At present,the methods of constructing vector valued rational interpolation function in rectangular mesh are mainly presented by means of the branched continued fractions.In order to get vector valued rational interpolation function with lower degree and better approximation effect,the paper divides rectangular mesh into pieces by choosing nonnegative integer parameters d1(0≤di ≤ m) and d2 (0≤d2 ≤n),builds bivariate polynomial vector interpolation for each piece,then combines with them properly.As compared with previous methods,the new method given by this paper is easy to compute and the degree for the interpolants is lower.

  5. Relationship between Architectural Outer Shape and Function of Buildings: Behaviour Study on Building Constructed in China

    Directory of Open Access Journals (Sweden)

    ISSA. A.M. Al-Kahtani

    2008-01-01

    Full Text Available The present study attempted to investigate the behaviour of some projects designed and constructed in China during the last decades from an architectural view point and their compatibility with respect to the relationship between the outer shape and function of the building. The study includes different groups of architectural works including; Culture architecture, Education architecture, Office architecture and Hotel architecture surveying about 60 projects divided into four groups. Four types of relationship were adopted depending on score given to each building. The statistical tools also used to classify and specify accurately the relationship between the buildings and the groups. The study concluded that most of the buildings give good relationship and express the function of the building in addition to aesthetics considerations but the educational architecture give the best representation.

  6. Toward total synthesis of cell function: Reconstituting cell dynamics with synthetic biology.

    Science.gov (United States)

    Kim, Allen K; DeRose, Robert; Ueno, Tasuku; Lin, Benjamin; Komatsu, Toru; Nakamura, Hideki; Inoue, Takanari

    2016-02-09

    Biological phenomena, such as cellular differentiation and phagocytosis, are fundamental processes that enable cells to fulfill important physiological roles in multicellular organisms. In the field of synthetic biology, the study of these behaviors relies on the use of a broad range of molecular tools that enable the real-time manipulation and measurement of key components in the underlying signaling pathways. This Review will focus on a subset of synthetic biology tools known as bottom-up techniques, which use technologies such as optogenetics and chemically induced dimerization to reconstitute cellular behavior in cells. These techniques have been crucial not only in revealing causal relationships within signaling networks but also in identifying the minimal signaling components that are necessary for a given cellular function. We discuss studies that used these systems in a broad range of cellular and molecular phenomena, including the time-dependent modulation of protein activity in cellular proliferation and differentiation, the reconstitution of phagocytosis, the reconstitution of chemotaxis, and the regulation of actin reorganization. Finally, we discuss the potential contribution of synthetic biology to medicine.

  7. MOBILE HOUSING AS A FUNCTIONAL-TYPOLOGICAL VARIETY OF THE INDUSTRY OF MODERN CONSTRUCTION

    Directory of Open Access Journals (Sweden)

    MIRONENKO V. P.

    2015-09-01

    Full Text Available Problem statement. Current socio-demographic conditions in Ukraine and the level of housing of different types and quality suggest the possibility of active development mobile home construction. Practical advantages of mobile homes in various regions of the world reflected in the popularity of their use, especially as a temporary, recreational, holiday and tourist accommodation. The use of mobile housing in Ukraine currently is limited functional-typological composition. Aim. Identify the features of the design and construction of mobile homes on the basis of studying the world and domestic experience based integrated assessment formative factors (environmental and fire safety, energy efficiency, reliability and sustainability, etc.. Analyzing of the resent research. In research on mobility and transform element residential buildings addressed such issues: the experience of adaptation of housing to changes in the life of their inhabitants in the form of transformation of the internal space and its versatility [1; 11]; the methodology and design of constructions differing movable , collapsible or foldable parts and features of formation of mobile home recreational purpose[19]; the evolution of human dwellings and projected a futuristic look at the structure of the living environment [14]. In the scientific development of modern authors on architectural topics most relevant topics related to energy issues: a study of the historical background of the development of energy efficient housing, development of the basic requirements and solutions, their formation, and the creation of engineering and efficient method of designing low-rise architecture [15]; an analysis of the use of alternative energy sources, identify the main ways of saving energy and the development of architecture energy-saving residential buildings of low and medium-rise [16]; the development of an integrated approach to the ecological – economic substantiation of creation of

  8. Preliminary Discussion on Construction of Biological Fire Prevention Forest Belts in Kecun Township%浅谈柯村镇生物防火林带建设

    Institute of Scientific and Technical Information of China (English)

    许亮明

    2016-01-01

    营造生物防火林带,既有预防和阻隔林火的作用,又有社会效益和生态效益。本文从必要性、建设目标、技术措施、建设的主要做法及效益分析等方面入手,论述了柯村镇建设生物防火林带的可行性,在实现主动、高效森林防火的前提下,达到巩固造林成果、维护区域森林生态安全的目的。%Construction of biological fire prevention forest belts can not only prevent and hinder forest fire, but also produce social and economic benefits. In this paper, the feasibility for constructing biological fire prevention forest belts in Kecun Township was expounded from the aspects of the necessity, construction goal, technical measures, main construction practices and benefit analysis. The aim of consolidating afforestation achievements and safeguarding regional biological security could be achieved with realization of active and highly efficient forest fire prevention.

  9. Applications of post-translational modifications of FoxO family proteins in biological functions

    Institute of Scientific and Technical Information of China (English)

    Ying Zhao; Yachen Wang; Wei-Guo Zhu

    2011-01-01

    The functions of the FoxO family proteins, in particular their transcriptional activities, are modulated by post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, methylation and glycosylation. These PTMs occur in response to different cellular stresses, which in turn regulate the subcellular localization of FoxO family proteins, as well as their half-life, DNA binding, transcriptional activity and ability to interact with other cellular proteins. In this review, we summarize the role of PTMs of FoxO family proteins in linking their biological and functional relevance with various diseases.%The functions of the FoxO family proteins,in particular their transcriptional activities,are modulated by post-translational modifications (PTMs),including phosphorylation,acetylation,ubiquitination,methylation and glycosylation.These PTMs occur in response to different cellular stresses,which in turn regulate the subceilular localization of FoxO family proteins,as well as their half-life,DNA binding,transcriptional activity and ability to interact with other cellular proteins.In this review,we summarize the role of PTMs of FoxO family proteins in linking their biological and functional relevance with various diseases.

  10. Constructing Ionic Liquid-Filled Proton Transfer Channels within Nanocomposite Membrane by Using Functionalized Graphene Oxide.

    Science.gov (United States)

    Wu, Wenjia; Li, Yifan; Chen, Pingping; Liu, Jindun; Wang, Jingtao; Zhang, Haoqin

    2016-01-13

    Herein, nanocomposite membranes are fabricated based on functionalized graphene oxides (FGOs) and sulfonated poly(ether ether ketone) (SPEEK), followed by being impregnated with imidazole-type ionic liquid (IL). The functional groups (acidic group or basic group) on FGOs generate strong interfacial interactions with SPEEK chains and then adjust their motion and stacking. As a result, the nanocomposite membranes possess tunable interfacial domains as determined by its free volume characteristic, which provides regulated location for IL storage. The stored ILs act as hopping sites for water-free proton conduction along the FGO-constructed interfacial channels. The microstructure at SPEEK-FGO interface governs the IL uptake and distribution in nanocomposite membrane. Different from GO and vinyl imidazole functionalized GO (VGO), the presence of acidic (-SO3H) groups confers the p-styrenesulfonic acid functionalized GO (SGO) incorporated nanocomposite membrane loose interface and strong electrostatic attraction with imidazole-type IL, imparting an enhanced IL uptake and anhydrous proton conductivity. Nanocomposite membrane containing 7.5% SGO attains the maximum IL uptake of 73.7% and hence the anhydrous conductivity of 21.9 mS cm(-1) at 150 °C, more than 30 times that of SPEEK control membrane (0.69 mS cm(-1)). In addition, SGOs generate electrostatic attractions to the ILs confined within SGO-SPEEK interface, affording the nanocomposite membrane enhanced IL retention ability.

  11. Functional results after repair of large hiatal hernia by use of a biologic mesh

    Directory of Open Access Journals (Sweden)

    Filimon eAntonakis

    2016-03-01

    Full Text Available Background: The aim of this observational study is to analyze the results of patients with large hiatal hernia and upside-down stomach after surgical closure with a biologic mesh (Permacol®, Covidien, Neustadt an der Donau, Germany. Biologic mesh is used to prevent long-term detrimental effects of artificial meshes and to reduce recurrence rates. Methods: A total of 13 patients with a large hiatal hernia and endothoracic stomach, who underwent surgery between 2010 and 2014, were included. Interviews and upper endoscopy were conducted to determine recurrence, lifestyle restrictions and current complaints. Results: After a mean follow-up of 26+18 months (range 3-58 months 10 patients (three men, mean age 73+13, range 26-81 years were evaluated. A small recurrent axial hernia was found in one patient postoperatively. Dysphagia was the most common complaint (four cases, while in one case the problem was solved after endoscopic dilatation. In three cases bloat and postprandial pain were documented. In one case explantation of the mesh was necessary due to mesh migration and painful adhesions. In one further case with gastroparesis pyloroplasty was performed without success.Conclusion: Recurrence was rare after hernia repair with the biologic mesh Permacol®. Dysphagia, gas bloat and intraabdominal pain were frequent complaints. Despite the small number of patients it can be concluded that a biologic mesh may be an alternative to synthetic meshes to reduce recurrences. Long-term results should be studied in the future in order to assess the potential of biologic meshes to preserve esophageal function as well. This is important since artificial meshes are known to erode the esophagus after 5–10 years.

  12. A Critical Role for Cysteine 57 in the Biological Functions of Selenium Binding Protein-1

    Directory of Open Access Journals (Sweden)

    Qi Ying

    2015-11-01

    Full Text Available The concentration of selenium-binding protein1 (SBP1 is often lower in tumors than in the corresponding tissue and lower levels have been associated with poor clinical outcomes. SBP1 binds tightly selenium although what role selenium plays in its biological functions remains unknown. Previous studies indicated that cysteine 57 is the most likely candidate amino acid for selenium binding. In order to investigate the role of cysteine 57 in SBP1, this amino acid was altered to a glycine and the mutated protein was expressed in human cancer cells. The SBP1 half-life, as well as the cellular response to selenite cytotoxicity, was altered by this change. The ectopic expression of SBP1GLY also caused mitochondrial damage in HCT116 cells. Taken together, these results indicated that cysteine 57 is a critical determinant of SBP1 function and may play a significant role in mitochondrial function.

  13. Functional profiles reveal unique ecological roles of various biological soil crust organisms

    Science.gov (United States)

    Bowker, M.A.; Mau, R.L.; Maestre, F.T.; Escolar, C.; Castillo-Monroy, A. P.

    2011-01-01

    1. At the heart of the body of research on biodiversity effects on ecosystem function is the debate over whether different species tend to be functionally singular or redundant. When we consider ecosystem multi-function, the provision of multiple ecosystem functions simultaneously, we may find that seemingly redundant species may in fact play unique roles in ecosystems. 2. Over the last few decades, the significance of biological soil crusts (BSCs) as ecological boundaries and ecosystem engineers, and their multi-functional nature, has become increasingly well documented. We compiled 'functional profiles' of the organisms in this understudied community, to determine whether functional singularity emerges when multiple ecosystem functions are considered. 3. In two data sets, one representing multiple sites around the semi-arid regions of Spain (regional scale), and another from a single site in central Spain (local scale), we examined correlations between the abundance or frequency of BSC species in a community, and multiple surrogates of ecosystem functioning. There was a wide array of apparent effects of species on specific functions. 4. Notably, in gypsiferous soils and at regional scale, we found that indicators of carbon (C) and phosphorus cycling were apparently suppressed and promoted by the lichens Diploschistes diacapsis and Squamarina lentigera, respectively. The moss Pleurochaete squarrosa appears to promote C cycling in calcareous soils at this spatial scale. At the local scale in gypsiferous soils, D. diacapsis positively correlated with carbon cycling, but negatively with nitrogen cycling, whereas numerous lichens exhibited the opposite profile. 5. We found a high degree of functional singularity, i.e. that species were highly individualistic in their effects on multiple functions. Many functional attributes were not easily predictable from existing functional grouping systems based primarily on morphology. 6. Our results suggest that maintaining

  14. A new discrete-continuous algorithm for radial basis function networks construction.

    Science.gov (United States)

    Zhang, Long; Li, Kang; He, Haibo; Irwin, George W

    2013-11-01

    The construction of a radial basis function (RBF) network involves the determination of the model size, hidden nodes, and output weights. Least squares-based subset selection methods can determine a RBF model size and its parameters simultaneously. Although these methods are robust, they may not achieve optimal results. Alternatively, gradient methods are widely used to optimize all the parameters. The drawback is that most algorithms may converge slowly as they treat hidden nodes and output weights separately and ignore their correlations. In this paper, a new discrete-continuous algorithm is proposed for the construction of a RBF model. First, the orthogonal least squares (OLS)-based forward stepwise selection constructs an initial model by selecting model terms one by one from a candidate term pool. Then a new Levenberg-Marquardt (LM)-based parameter optimization is proposed to further optimize the hidden nodes and output weights in the continuous space. To speed up the convergence, the proposed parameter optimization method considers the correlation between the hidden nodes and output weights, which is achieved by translating the output weights to dependent parameters using the OLS method. The correlation is also used by the previously proposed continuous forward algorithm (CFA). However, unlike the CFA, the new method optimizes all the parameters simultaneously. In addition, an equivalent recursive sum of squared error is derived to reduce the computation demanding for the first derivatives used in the LM method. Computational complexity is given to confirm the new method is much more computationally efficient than the CFA. Different numerical examples are presented to illustrate the effectiveness of the proposed method. Further, Friedman statistical tests on 13 classification problems are performed, and the results demonstrate that RBF networks built by the new method are very competitive in comparison with some popular classifiers.

  15. A streptavidin functionalized graphene oxide/Au nanoparticles composite for the construction of sensitive chemiluminescent immunosensor

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Zhanjun, E-mail: zjyang@yzu.edu.cn [Key Laboratory of Environmental Material and Environmental Engineering of Jiangsu Province, College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002 (China); Luo, Shufen; Li, Juan; Shen, Juan; Yu, Suhua; Hu, Xiaoya [Key Laboratory of Environmental Material and Environmental Engineering of Jiangsu Province, College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002 (China); Dionysiou, Dionysios D. [Environmental Engineering and Science Program, School of Energy Environmental, Biological and Medical Engineering, University of Cincinnati, Cincinnati, OH 45221-0012 (United States)

    2014-08-11

    Highlights: • A novel streptavidin/GO/AuNPs composite is prepared for immobilizing antibody. • A highly sensitive chemiluminescent immunosensor is constructed for tumor marker. • The immunoassay system shows extremely low detection limit down to picogram level. • This work provides a promising approach for ultrasensitive biosensing applications. - Abstract: In this work, a novel streptavidin functionalized graphene oxide/Au nanoparticles (streptavidin/GO/AuNPs) composite is prepared and for the first time used to construct sensitive chemiluminescent immunosensor for the detection of tumor marker. The streptavidin/GO/AuNPs composite and the immunosensor are characterized using scanning electron microscopy, static water contact angle measurement and electrochemical impedance spectroscopy. The biofunctionalized composite has large reactive surface area and excellent biocompatibility, thus the capture antibody can be efficiently immobilized on its surface based on the highly selective recognition of streptavidin to biotinylated antibody. Using α-fetoprotein (AFP) as a model, the proposed chemiluminescent immunosensor shows a wide linear range from 0.001 to 0.1 ng mL{sup −1} with an extremely low detection limit down to 0.61 pg mL{sup −1}. The resulting AFP immunosensor shows high detection sensitivity, fast assay speed, acceptable detection and fabrication reproducibility, good specificity and stability. The assay results of serum samples with the proposed method are in an acceptable agreement with the reference values. This work provides a promising biofunctionalized nanostructure for sensitive biosensing applications.

  16. Coset construction of logarithmic minimal models: branching rules and branching functions

    CERN Document Server

    Pearce, Paul A

    2013-01-01

    Working in the Virasoro picture, it is argued that the logarithmic minimal models LM(p,p')=LM(p,p';1) can be extended to an infinite hierarchy of logarithmic conformal field theories LM(p,p';n) at higher fusion levels n=1,2,3,.... From the lattice, these theories are constructed by fusing together n x n elementary faces of the appropriate LM(p,p') models. It is further argued that all of these logarithmic theories are realized as diagonal cosets (A_1^{(1)})_k \\oplus (A_1^{(1)})_n / (A_1^{(1)})_{k+n} where n is the integer fusion level and k=np/(p'-p)-2 is a fractional level. These cosets mirror the cosets of the higher fusion level minimal models of the form M(m,m';n), but are associated with certain reducible representations. We present explicit branching rules for characters in the form of multiplication formulas arising in the logarithmic limit of the usual Goddard-Kent-Olive coset construction of the non-unitary minimal models M(m,m';n). The limiting branching functions play the role of Kac characters for...

  17. A primer on molecular biology for imagers: III. Proteins: structure and function.

    Science.gov (United States)

    Pandit, Sunil D; Li, King C P

    2004-04-01

    This article along with the first 2 in this series (4,12) completes the discussion on the key molecules and process inside the cell namely, DNA, RNA, and proteins. These 3 articles provide a very basic foundation for understanding molecular biology concepts and summarize some of the work of numerous scientists over the past century. We understand these processes far better now than we did in the past, but clearly this knowledge is by no means complete and a number of basic scientists are working hard to elucidate and understand the fundamental mechanisms that operate within a cell. Genes and gene products work with each other in complex, interconnected pathways, and in perfect harmony to make a functional cell, tissue, and an organism as a whole. There is a lot of cross-talk that happens between different proteins that interact with various other proteins, DNA, and RNA to establish pathways, networks, and molecular systems as a team working to perfection. The past 15 years have seen the rapid development of systems biology approaches. We live in an era that emphasizes multi-disciplinary, cross-functional teams to perform science rather than individual researchers working on the bench on a very specific problem. Global approaches have become more common and the amount of data generated must be managed by trained bioinformatics personnel and large computers. In our subsequent articles, we will discuss these global approaches and the areas of genomics, functional genomics, and proteomics that have revolutionized the way we perform science.

  18. Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions

    Directory of Open Access Journals (Sweden)

    Werner Mark

    2008-08-01

    Full Text Available Abstract Background Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions. Results 14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites. Conclusion Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.

  19. A Gaussian mixture model based cost function for parameter estimation of chaotic biological systems

    Science.gov (United States)

    Shekofteh, Yasser; Jafari, Sajad; Sprott, Julien Clinton; Hashemi Golpayegani, S. Mohammad Reza; Almasganj, Farshad

    2015-02-01

    As we know, many biological systems such as neurons or the heart can exhibit chaotic behavior. Conventional methods for parameter estimation in models of these systems have some limitations caused by sensitivity to initial conditions. In this paper, a novel cost function is proposed to overcome those limitations by building a statistical model on the distribution of the real system attractor in state space. This cost function is defined by the use of a likelihood score in a Gaussian mixture model (GMM) which is fitted to the observed attractor generated by the real system. Using that learned GMM, a similarity score can be defined by the computed likelihood score of the model time series. We have applied the proposed method to the parameter estimation of two important biological systems, a neuron and a cardiac pacemaker, which show chaotic behavior. Some simulated experiments are given to verify the usefulness of the proposed approach in clean and noisy conditions. The results show the adequacy of the proposed cost function.

  20. Functional Interfaces Constructed by Controlled/Living Radical Polymerization for Analytical Chemistry.

    Science.gov (United States)

    Wang, Huai-Song; Song, Min; Hang, Tai-Jun

    2016-02-10

    The high-value applications of functional polymers in analytical science generally require well-defined interfaces, including precisely synthesized molecular architectures and compositions. Controlled/living radical polymerization (CRP) has been developed as a versatile and powerful tool for the preparation of polymers with narrow molecular weight distributions and predetermined molecular weights. Among the CRP system, atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT) are well-used to develop new materials for analytical science, such as surface-modified core-shell particles, monoliths, MIP micro- or nanospheres, fluorescent nanoparticles, and multifunctional materials. In this review, we summarize the emerging functional interfaces constructed by RAFT and ATRP for applications in analytical science. Various polymers with precisely controlled architectures including homopolymers, block copolymers, molecular imprinted copolymers, and grafted copolymers were synthesized by CRP methods for molecular separation, retention, or sensing. We expect that the CRP methods will become the most popular technique for preparing functional polymers that can be broadly applied in analytical chemistry.

  1. Construction and screening of a functional metagenomic library to identify novel enzymes produced by Antarctic bacteria

    Institute of Scientific and Technical Information of China (English)

    Ignacio Ferrés; Vanesa Amarelle; Francisco Noya; Elena Fabiano

    2015-01-01

    A metagenomic fosmid library of approximately 52 000 clones was constructed to identify functional genes encoding cold-adapted enzymes. Metagenomic DNA was extracted from a sample of glacial meltwater, collected on the Antarctic Peninsula during the ANTARKOS XXIX Expedition during the austral summer of 2012–2013. Each clone contained an insert of about 35–40 kb, so the library represented almost 2 Gb of genetic information from metagenomic DNA. Activity-driven screening was used to detect the cold-adapted functions expressed by the library. Fifty lipase/esterase and two cellulase-producing clones were isolated, and two clones able to grow on Avicel® as the sole carbon source. Interestingly, three clones formed a brown precipitate in the presence of manganese (II). Accumulation of manganese oxides was determined with a leucoberbelin blue assay, indicating that these three clones had manganese-oxidizing activity. To the best of our knowledge, this is the first report of a manganese oxidase activity detected with a functional metagenomic strategy.

  2. Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sumino, Ayumi; Dewa, Takehisa; Takeuchi, Toshikazu; Sugiura, Ryuta; Sasaki, Nobuaki; Misawa, Nobuo; Tero, Ryugo; Urisu, Tsuneo; Gardiner, Alastair T; Cogdell, Richard J; Hashimoto, Hideki; Nango, Mamoru

    2011-07-11

    The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAY), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.

  3. Learning can be all Fun and Games: Constructing and Utilizing a Biology Taboo Wiktionary to Enhance Student Learning in an Introductory Biology Course

    Directory of Open Access Journals (Sweden)

    Jeffrey T. Olimpo

    2010-10-01

    Full Text Available Most introductory courses in the biological sciences are inherently content-dense and rich with jargon—jargon that is often confusing and nonsensical to novice students. These characteristics present an additional paradox to instructors, who strive to achieve a balance between simply promoting passive, rote memorization of facts and engaging students in developing true, concrete understanding of the terminology. To address these concerns, we developed and implemented a Biology Taboo Wiktionary that provided students with an interactive opportunity to review and describe concepts they had encountered during their first semester of introductory biology. However, much like the traditional Taboo game, the rules were such that students could not use obvious terms to detail the main term. It was our belief that if the student could synthesize a thoughtful, scientific explanation of the term under these conditions, he or she demonstrated a true understanding of the conceptual context and meaning of the term.

  4. Synthesis, characterization, and in vitro biological evaluation of highly stable diversely functionalized superparamagnetic iron oxide nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Dipsikha; Sahu, Sumanta K. [Indian Institute of Technology Kharagpur, Department of Chemistry (India); Banerjee, Indranil [Indian Institute of Technology Kharagpur, Department of Biotechnology (India); Das, Manasmita [Indian Institute of Technology Kharagpur, Department of Chemistry (India); Mishra, Debashish; Maiti, Tapas K. [Indian Institute of Technology Kharagpur, Department of Biotechnology (India); Pramanik, Panchanan, E-mail: dipsikha.chem@gmail.com [Indian Institute of Technology Kharagpur, Department of Chemistry (India)

    2011-09-15

    In this article, we report the design and synthesis of a series of well-dispersed superparamagnetic iron oxide nanoparticles (SPIONs) using chitosan as a surface modifying agent to develop a potential T{sub 2} contrast probe for magnetic resonance imaging (MRI). The amine, carboxyl, hydroxyl, and thiol functionalities were introduced on chitosan-coated magnetic probe via simple reactions with small reactive organic molecules to afford a series of biofunctionalized nanoparticles. Physico-chemical characterizations of these functionalized nanoparticles were performed by TEM, XRD, DLS, FTIR, and VSM. The colloidal stability of these functionalized iron oxide nanoparticles was investigated in presence of phosphate buffer saline, high salt concentrations and different cell media for 1 week. MRI analysis of human cervical carcinoma (HeLa) cell lines treated with nanoparticles elucidated that the amine-functionalized nanoparticles exhibited higher amount of signal darkening and lower T{sub 2} relaxation in comparison to the others. The cellular internalization efficacy of these functionalized SPIONs was also investigated with HeLa cancer cell line by magnetically activated cell sorting (MACS) and fluorescence microscopy and results established selectively higher internalization efficacy of amine-functionalized nanoparticles to cancer cells. These positive attributes demonstrated that these nanoconjugates can be used as a promising platform for further in vitro and in vivo biological evaluations.

  5. New insights in the biology of BDNF synthesis and release: implications in CNS function.

    Science.gov (United States)

    Greenberg, Michael E; Xu, Baoji; Lu, Bai; Hempstead, Barbara L

    2009-10-14

    BDNF has pleiotropic effects on neuronal development and synaptic plasticity that underlie circuit formation and cognitive function. Recent breakthroughs reveal that neuronal activity regulates BDNF cell biology, including Bdnf transcription, dendritic targeting and trafficking of BDNF mRNA and protein, and secretion and extracellular conversion of proBDNF to mature BDNF. Defects in these mechanisms contribute differentially to cognitive dysfunction and anxiety-like behaviors. Here we review recent studies, presented at a symposium at Neuroscience 2009, that describe regulatory mechanisms that permit rapid and dynamic refinement of BDNF actions in neurons.

  6. Systems biology: Functional analysis of natural microbial consortia using community proteomics.

    Science.gov (United States)

    VerBerkmoes, Nathan C; Denef, Vincent J; Hettich, Robert L; Banfield, Jillian F

    2009-03-01

    We know very little about the metabolic functioning and evolutionary dynamics of microbial communities. Recent advances in comprehensive, sequencing-based methods, however, are laying a molecular foundation for new insights into how microbial communities shape the Earth's biosphere. Here we explore the convergence of microbial ecology, genomics, biological mass spectrometry and informatics that form the new field of microbial community proteogenomics. We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities.

  7. Late-stage functionalization of biologically active heterocycles through photoredox catalysis.

    Science.gov (United States)

    Dirocco, Daniel A; Dykstra, Kevin; Krska, Shane; Vachal, Petr; Conway, Donald V; Tudge, Matthew

    2014-05-05

    The direct CH functionalization of heterocycles has become an increasingly valuable tool in modern drug discovery. However, the introduction of small alkyl groups, such as methyl, by this method has not been realized in the context of complex molecule synthesis since existing methods rely on the use of strong oxidants and elevated temperatures to generate the requisite radical species. Herein, we report the use of stable organic peroxides activated by visible-light photoredox catalysis to achieve the direct methyl-, ethyl-, and cyclopropylation of a variety of biologically active heterocycles. The simple protocol, mild reaction conditions, and unique tolerability of this method make it an important tool for drug discovery.

  8. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

    Directory of Open Access Journals (Sweden)

    Christopher Y Park

    Full Text Available A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics

  9. The origin of neutron biological effectiveness as a function of energy

    Science.gov (United States)

    Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

    2016-01-01

    The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data. PMID:27654349

  10. Automated methods of predicting the function of biological sequences using GO and BLAST

    Directory of Open Access Journals (Sweden)

    Baumann Ute

    2005-11-01

    Full Text Available Abstract Background With the exponential increase in genomic sequence data there is a need to develop automated approaches to deducing the biological functions of novel sequences with high accuracy. Our aim is to demonstrate how accuracy benchmarking can be used in a decision-making process evaluating competing designs of biological function predictors. We utilise the Gene Ontology, GO, a directed acyclic graph of functional terms, to annotate sequences with functional information describing their biological context. Initially we examine the effect on accuracy scores of increasing the allowed distance between predicted and a test set of curator assigned terms. Next we evaluate several annotator methods using accuracy benchmarking. Given an unannotated sequence we use the Basic Local Alignment Search Tool, BLAST, to find similar sequences that have already been assigned GO terms by curators. A number of methods were developed that utilise terms associated with the best five matching sequences. These methods were compared against a benchmark method of simply using terms associated with the best BLAST-matched sequence (best BLAST approach. Results The precision and recall of estimates increases rapidly as the amount of distance permitted between a predicted term and a correct term assignment increases. Accuracy benchmarking allows a comparison of annotation methods. A covering graph approach performs poorly, except where the term assignment rate is high. A term distance concordance approach has a similar accuracy to the best BLAST approach, demonstrating lower precision but higher recall. However, a discriminant function method has higher precision and recall than the best BLAST approach and other methods shown here. Conclusion Allowing term predictions to be counted correct if closely related to a correct term decreases the reliability of the accuracy score. As such we recommend using accuracy measures that require exact matching of predicted

  11. Importance of N-Glycosylation on CD147 for Its Biological Functions

    Directory of Open Access Journals (Sweden)

    Yang Bai

    2014-04-01

    Full Text Available Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation.

  12. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    . With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available...... function, and this leads to an expanded role of the classical approach applied in microbial physiology. With the increased understanding of the molecular mechanisms it is envisaged that in the future it will be possible to describe the interaction between all the components in the system (the cell), also......Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function...

  13. Biological Sensitivity to Family Income: Differential Effects on Early Executive Functioning.

    Science.gov (United States)

    Obradović, Jelena; Portilla, Ximena A; Ballard, Parissa J

    2016-01-01

    The study examined how the interplay between children's cortisol response and family income is related to executive function (EF) skills. The sample included one hundred and two 5- to 6-year-olds (64% minority). EF skills were measured using laboratory tasks and observer ratings. Physiological reactivity was assessed via cortisol response during a laboratory visit. A consistent, positive association between family income and EF skills emerged only for children who showed high cortisol response, a marker of biological sensitivity to context. In contrast, family income was not related to EF skills in children who displayed low cortisol response. Follow-up analyses revealed a disordinal interaction, suggesting that differential susceptibility can be detected at the level of basic cognitive and self-regulatory skills that support adaptive functioning.

  14. Enzymes for ecdysteroid biosynthesis: their biological functions in insects and beyond.

    Science.gov (United States)

    Niwa, Ryusuke; Niwa, Yuko S

    2014-01-01

    Steroid hormones are responsible for the coordinated regulation of many aspects of biological processes in multicellular organisms. Since the last century, many studies have identified and characterized steroidogenic enzymes in vertebrates, including mammals. However, much less is known about invertebrate steroidogenic enzymes. In the last 15 years, a number of steroidogenic enzymes and their functions have been characterized in ecdysozoan animals, especially in the fruit fly Drosophila melanogaster. In this review, we summarize the latest knowledge of enzymes crucial for synthesizing ecdysteroids, the principal insect steroid hormones. We also discuss the functional conservation and diversity of ecdysteroidogenic enzymes in other insects and even non-insect species, such as nematodes, vertebrates, and lower eukaryotes.

  15. Importance of N-glycosylation on CD147 for its biological functions.

    Science.gov (United States)

    Bai, Yang; Huang, Wan; Ma, Li-Tian; Jiang, Jian-Li; Chen, Zhi-Nan

    2014-04-15

    Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation.

  16. Landscape Construction in Dynamical Systems

    Science.gov (United States)

    Tang, Ying; Yuan, Ruoshi; Wang, Gaowei; Ao, Ping

    The idea of landscape has been recently applied to study various of biological problems. We demonstrate that a dynamical structure built into nonlinear dynamical systems allows us to construct such a global optimization landscape, which serves as the Lyapunov function for the ordinary differential equation. We find exact constructions on the landscape for a class of dynamical systems, including a van der Pol type oscillator, competitive Lotka-Volterra systems, and a chaotic system. The landscape constructed provides a new angle for understanding and modelling biological network dynamics.

  17. Gene-Set Local Hierarchical Clustering (GSLHC--A Gene Set-Based Approach for Characterizing Bioactive Compounds in Terms of Biological Functional Groups.

    Directory of Open Access Journals (Sweden)

    Feng-Hsiang Chung

    Full Text Available Gene-set-based analysis (GSA, which uses the relative importance of functional gene-sets, or molecular signatures, as units for analysis of genome-wide gene expression data, has exhibited major advantages with respect to greater accuracy, robustness, and biological relevance, over individual gene analysis (IGA, which uses log-ratios of individual genes for analysis. Yet IGA remains the dominant mode of analysis of gene expression data. The Connectivity Map (CMap, an extensive database on genomic profiles of effects of drugs and small molecules and widely used for studies related to repurposed drug discovery, has been mostly employed in IGA mode. Here, we constructed a GSA-based version of CMap, Gene-Set Connectivity Map (GSCMap, in which all the genomic profiles in CMap are converted, using gene-sets from the Molecular Signatures Database, to functional profiles. We showed that GSCMap essentially eliminated cell-type dependence, a weakness of CMap in IGA mode, and yielded significantly better performance on sample clustering and drug-target association. As a first application of GSCMap we constructed the platform Gene-Set Local Hierarchical Clustering (GSLHC for discovering insights on coordinated actions of biological functions and facilitating classification of heterogeneous subtypes on drug-driven responses. GSLHC was shown to tightly clustered drugs of known similar properties. We used GSLHC to identify the therapeutic properties and putative targets of 18 compounds of previously unknown characteristics listed in CMap, eight of which suggest anti-cancer activities. The GSLHC website http://cloudr.ncu.edu.tw/gslhc/ contains 1,857 local hierarchical clusters accessible by querying 555 of the 1,309 drugs and small molecules listed in CMap. We expect GSCMap and GSLHC to be widely useful in providing new insights in the biological effect of bioactive compounds, in drug repurposing, and in function-based classification of complex diseases.

  18. Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax Hemophore

    Energy Technology Data Exchange (ETDEWEB)

    Ekworomadu, MarCia T.; Poor, Catherine B.; Owens, Cedric P.; Balderas, Miriam A.; Fabian, Marian; Olson, John S.; Murphy, Frank; Balkabasi, Erol; Honsa, Erin S.; He, Chuan; Goulding, Celia W.; Maresso, Anthony W. (Baylor); (UCI); (Cornell); (Rice); (UC)

    2014-10-02

    To replicate in mammalian hosts, bacterial pathogens must acquire iron. The majority of iron is coordinated to the protoporphyrin ring of heme, which is further bound to hemoglobin. Pathogenic bacteria utilize secreted hemophores to acquire heme from heme sources such as hemoglobin. Bacillus anthracis, the causative agent of anthrax disease, secretes two hemophores, IsdX1 and IsdX2, to acquire heme from host hemoglobin and enhance bacterial replication in iron-starved environments. Both proteins contain NEAr-iron Transporter (NEAT) domains, a conserved protein module that functions in heme acquisition in Gram-positive pathogens. Here, we report the structure of IsdX1, the first of a Gram-positive hemophore, with and without bound heme. Overall, IsdX1 forms an immunoglobin-like fold that contains, similar to other NEAT proteins, a 3{sub 10}-helix near the heme-binding site. Because the mechanistic function of this helix in NEAT proteins is not yet defined, we focused on the contribution of this region to hemophore and NEAT protein activity, both biochemically and biologically in cultured cells. Site-directed mutagenesis of amino acids in and adjacent to the helix identified residues important for heme and hemoglobin association, with some mutations affecting both properties and other mutations affecting only heme stabilization. IsdX1 with mutations that reduced the ability to associate with hemoglobin and bind heme failed to restore the growth of a hemophore-deficient strain of B. anthracis on hemoglobin as the sole iron source. These data indicate that not only is the 3{sub 10}-helix important for NEAT protein biology, but also that the processes of hemoglobin and heme binding can be both separate as well as coupled, the latter function being necessary for maximal heme-scavenging activity. These studies enhance our understanding of NEAT domain and hemophore function and set the stage for structure-based inhibitor design to block NEAT domain interaction with

  19. Functional and molecular characterization of the role of CTCF in human embryonic stem cell biology.

    Directory of Open Access Journals (Sweden)

    Sri Kripa Balakrishnan

    Full Text Available The CCCTC-binding factor CTCF is the only known vertebrate insulator protein and has been shown to regulate important developmental processes such as imprinting, X-chromosome inactivation and genomic architecture. In this study, we examined the role of CTCF in human embryonic stem cell (hESC biology. We demonstrate that CTCF associates with several important pluripotency genes, including NANOG, SOX2, cMYC and LIN28 and is critical for hESC proliferation. CTCF depletion impacts expression of pluripotency genes and accelerates loss of pluripotency upon BMP4 induced differentiation, but does not result in spontaneous differentiation. We find that CTCF associates with the distal ends and internal sites of the co-regulated 160 kb NANOG-DPPA3-GDF3 locus. Each of these sites can function as a CTCF-dependent enhancer-blocking insulator in heterologous assays. In hESCs, CTCF exists in multisubunit protein complexes and can be poly(ADPribosylated. Known CTCF cofactors, such as Cohesin, differentially co-localize in the vicinity of specific CTCF binding sites within the NANOG locus. Importantly, the association of some cofactors and protein PARlation selectively changes upon differentiation although CTCF binding remains constant. Understanding how unique cofactors may impart specialized functions to CTCF at specific genomic locations will further illuminate its role in stem cell biology.

  20. Strategies for the chemical and biological functionalization of scaffolds for cardiac tissue engineering: a review.

    Science.gov (United States)

    Tallawi, Marwa; Rosellini, Elisabetta; Barbani, Niccoletta; Cascone, Maria Grazia; Rai, Ranjana; Saint-Pierre, Guillaume; Boccaccini, Aldo R

    2015-07-06

    The development of biomaterials for cardiac tissue engineering (CTE) is challenging, primarily owing to the requirement of achieving a surface with favourable characteristics that enhances cell attachment and maturation. The biomaterial surface plays a crucial role as it forms the interface between the scaffold (or cardiac patch) and the cells. In the field of CTE, synthetic polymers (polyglycerol sebacate, polyethylene glycol, polyglycolic acid, poly-l-lactide, polyvinyl alcohol, polycaprolactone, polyurethanes and poly(N-isopropylacrylamide)) have been proven to exhibit suitable biodegradable and mechanical properties. Despite the fact that they show the required biocompatible behaviour, most synthetic polymers exhibit poor cell attachment capability. These synthetic polymers are mostly hydrophobic and lack cell recognition sites, limiting their application. Therefore, biofunctionalization of these biomaterials to enhance cell attachment and cell material interaction is being widely investigated. There are numerous approaches for functionalizing a material, which can be classified as mechanical, physical, chemical and biological. In this review, recent studies reported in the literature to functionalize scaffolds in the context of CTE, are discussed. Surface, morphological, chemical and biological modifications are introduced and the results of novel promising strategies and techniques are discussed.

  1. Biological adaptations for functional features of language in the face of cultural evolution.

    Science.gov (United States)

    Christiansen, Morten H; Reali, Florencia; Chater, Nick

    2011-04-01

    Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

  2. A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology.

    Science.gov (United States)

    Carbonell-Ballestero, Max; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard; Macía, Javier; Rodríguez-Caso, Carlos

    2014-12-16

    Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses-the so-called transfer function-and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.

  3. Substrate chemistry influences the morphology and biological function of adsorbed extracellular matrix assemblies.

    Science.gov (United States)

    Sherratt, Michael J; Bax, Daniel V; Chaudhry, Shazia S; Hodson, Nigel; Lu, Jian R; Saravanapavan, Priya; Kielty, Cay M

    2005-12-01

    In addition to mediating cell signalling events, native extracellular matrix (ECM) assemblies interact with other ECM components, act as reservoirs for soluble signalling molecules and perform structural roles. The potential of native ECM assemblies in the manufacture of biomimetic materials has not been fully exploited due, in part, to the effects of substrate interactions on their morphology. We have previously demonstrated that the ECM components, fibrillin and type VI collagen microfibrils, exhibit substrate dependent morphologies on chemically and topographically variable heterogeneous surfaces. Using both cleaning and coating approaches on silicon wafers and glass coverslips we have produced chemically homogeneous, topographically similar substrates which cover a large amphiphilic range. Extremes of substrate amphiphilicity induced morphological changes in periodicity, curvature and lateral spreading which may mask binding sites or disrupt domain structure. Biological functionality, as assayed by the ability to support cell spreading, was significantly reduced for fibrillin microfibrils adsorbed on highly hydrophilic substrates (contact angle 20.7 degrees) compared with less hydrophilic (contact angle 38.3 degrees) and hydrophobic (contact angle 92.8 degrees) substrates. With an appropriate choice of surface chemistry, multifunctional ECM assemblies retain their native morphology and biological functionality.

  4. Biology of bone and how it orchestrates the form and function of the skeleton

    Science.gov (United States)

    Sommerfeldt, D. W.; Rubin, C. T.

    2001-01-01

    The principal role of the skeleton is to provide structural support for the body. While the skeleton also serves as the body's mineral reservoir, the mineralized structure is the very basis of posture, opposes muscular contraction resulting in motion, withstands functional load bearing, and protects internal organs. Although the mass and morphology of the skeleton is defined, to some extent, by genetic determinants, it is the tissue's ability to remodel--the local resorption and formation of bone--which is responsible for achieving this intricate balance between competing responsibilities. The aim of this review is to address bone's form-function relationship, beginning with extensive research in the musculoskeletal disciplines, and focusing on several recent cellular and molecular discoveries which help understand the complex interdependence of bone cells, growth factors, physical stimuli, metabolic demands, and structural responsibilities. With a clinical and spine-oriented audience in mind, the principles of bone cell and molecular biology and physiology are presented, and an attempt has been made to incorporate epidemiologic data and therapeutic implications. Bone research remains interdisciplinary by nature, and a deeper understanding of bone biology will ultimately lead to advances in the treatment of diseases and injuries to bone itself.

  5. Structural characteristics and biological functions of the HIV-1 gp120 V3 region

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Recent studies demonstrate that the V3 loop of HIV-1 gp120 plays an important role in the attachment of HIV-1 to the target cells. Several amino acids in this domain are involved in the interaction of gp120 with the co-receptors. The V3 loop elicits one of the earliest antiviral antibody responses in HIV-1 infection and has been identified as the principal neutralizing determinant (PND). A subset of antibodies to V3 loop show a broad range of neutralizing activity. Unfortunately, this loop undergoes broad mutation and is one of the hypervariable regions. Mutations of some amino acids in this PND could affect syncytium formation, virus infectivity and neutralization. Knowing the structural characteristics and biological functions of the V3 region could help us to understand mechanism of HIV infection and to develop new strategy against HIV-1. In this review, the structural characteristics, variation and biological functions of the V3 loop as well as immunological responses to the V3 loop are discussed.

  6. The biology of cancer testis antigens: putative function, regulation and therapeutic potential.

    Science.gov (United States)

    Fratta, Elisabetta; Coral, Sandra; Covre, Alessia; Parisi, Giulia; Colizzi, Francesca; Danielli, Riccardo; Nicolay, Hugues Jean Marie; Sigalotti, Luca; Maio, Michele

    2011-04-01

    Cancer testis antigens (CTA) are a large family of tumor-associated antigens expressed in human tumors of different histological origin, but not in normal tissues except for testis and placenta. This tumor-restricted pattern of expression, together with their strong in vivo immunogenicity, identified CTA as ideal targets for tumor-specific immunotherapeutic approaches, and prompted the development of several clinical trials of CTA-based vaccine therapy. Driven by this practical clinical interest, a more detailed characterization of CTA biology has been recently undertaken. So far, at least 70 families of CTA, globally accounting for about 140 members, have been identified. Most of these CTA are expressed during spermatogenesis, but their function is still largely unknown. Epigenetic events, particularly DNA methylation, appear to be the primary mechanism regulating CTA expression in both normal and transformed cells, as well as in cancer stem cells. In view of the growing interest in CTA biology, the aim of this review is to provide the most recent information on their expression, regulation and function, together with a brief summary of the major clinical trials involving CTA as therapeutic agents. The pharmacologic modulation of CTA expression profiles on neoplastic cells by DNA hypomethylating drugs will also be discussed as a feasible approach to design new combination therapies potentially able to improve the clinical efficacy of currently adopted CTA-based immunotherapeutic regimens in cancer patients.

  7. [Construction of 3D tissue-like structure using functional magnetite nanoparticles].

    Science.gov (United States)

    Ito, Akira; Honda, Hiroyuki; Kamihira, Masamichi

    2008-01-01

    Magnetic nanoparticles for medical applications have been developed by many researchers. Since these nanoparticles have unique magnetic features not present in other materials, they can be applied to special medical techniques. Magnetite cationic liposomes (MCLs), one group of the cationic magnetic particles, can be used as carriers to introduce magnetite nanoparticles into target cells since their positively charged surface interacts with the negatively charged cell surface. Magnetite nanoparticles conjugated with antibodies (antibody-conjugated magnetoliposomes, AMLs) are applicable to introduce magnetite nanoparticles specifically into target cells, even when target cells coexist with other kinds of cells. Since the cells labeled with magnetite nanoparticles could be manipulated using magnets, we applied this technique to tissue engineering and termed it ;magnetic force-based tissue engineering (Mag-TE)'. Both magnetic force and functionalized magnetite nanoparticles were used in a process of tissue engineering: construction of multilayered cell sheet-like structures and tubular structures. Thus, the applications of these functionalized magnetite nanoparticles with their unique features will further improve tissue engineering techniques.

  8. Construction of a fucoidan/laminin functional multilayer to direction vascular cell fate and promotion hemocompatibility

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Changrong; Wang, Yan; Su, Hong; Yang, Ping; Huang, Nan [Key Laboratory of Advanced Materials Technology of Ministry of Education, Department of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China); Maitz, Manfred F. [Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Dresden 01069 (Germany); Zhao, Anshan [Key Laboratory of Advanced Materials Technology of Ministry of Education, Department of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China)

    2016-07-01

    Surface biofunctional modification of cardiovascular stents is a versatile approach to reduce the adverse effects after implantation. In this work, a novel multifunctional coating was fabricated by coimmobilization of the sulfated polysaccharide of brown algae fucoidan and laminin to biomimic the vascular intimal conditions in order to support rapid endothelialization, prevent restenosis and improve hemocompatibility. The surface properties of the coating such as hydrophilicity, bonding density of biomolecules and stability were evaluated and optimized. According to the biocompatibility tests, the fucoidan/laminin multilayer coated surface displayed less platelet adhesion with favorable anticoagulant property. In addition, the fucoidan/laminin complex showed function to selectively regulate vascular cells growth behavior. The proliferation of endothelial cells (ECs) on the fucoidan/laminin biofunctional coating was significantly promoted. For the smooth muscle cells (SMCs), inhibitory effects on cell adhesion and proliferation were observed. In conclusion, the fucoidan/laminin biofunctional coating was successfully fabricated with desirable anticoagulant and endothelialization properties which show a promising application in the vascular devices such as vascular stents or grafts surface modification. - Highlights: • Construction of fucoidan/laminin functional multilayer to biomimic the basement membrane of vascular • The fucoidan/laminin complex demonstrates anti-coagulation property. • The fucoidan/laminin complex can selectively regulate EC and SMC growth behavior to prevent restenosis.

  9. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  10. A biological model for construction of meaning to serve as an interface between an intelligent system and its environments

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, W.J. [Univ of California, Berkeley, CA (United States)

    1996-12-31

    There are two main levels of neural function to be modeled with appropriate state variables and operations. Microscopic activity is seen in the fraction of the variance of single neuron pulse trains (>99.9%) that is largely random and uncorrelated with pulse trains of other neurons in the neuropil. Macroscopic activity is revealed in the >0.1% of the total variance of each neuron that is covariant with all other neurons in neuropil comprising a population. It is observed in dendritic potentials recorded as surface EEGs. The {open_quotes}spontaneous{close_quotes} background activity of neuropil at both levels arises from mutual excitation within a population of excitatory neurons. Its governing point attractor is set by the macroscopic state, which acts as an order parameter to regulate the contributing neurons. The point attractor manifests a homogeneous field of white noise, which can be modeled by a continuous time state variable for pulse density. Neuropil comprises both excitatory and inhibitory neurons Their interactions at the macroscopic level give oscillations, manifesting a limit cycle attractor. Multiple areas of neuropil comprising a sensory system interact. Due to their incommensurate characteristic frequencies and the long axonal delays between them, the system maintains a global chaotic attractor having multiple wings, one for each discriminable class of stimuli. Access to each wing is by stimulus- induced state transitions, causing construction of macroscopic chaotic patterns, that are carried to targets of cortical transmission by axon tracts. AM patterns of the carrier are extracted by the targets by spatiotemporal integration, thereby retrieving the covariance comprising the chaotic signal. In digital models, noise serves to stabilize the chaotic attractors. An example will be given of the model operating as an interface between the environment and a pattern classifier, which learns to form its own feature detectors.

  11. Lead Coolant Test Facility Technical and Functional Requirements, Conceptual Design, Cost and Construction Schedule

    Energy Technology Data Exchange (ETDEWEB)

    Soli T. Khericha

    2006-09-01

    This report presents preliminary technical and functional requirements (T&FR), thermal hydraulic design and cost estimate for a lead coolant test facility. The purpose of this small scale facility is to simulate lead coolant fast reactor (LFR) coolant flow in an open lattice geometry core using seven electrical rods and liquid lead or lead-bismuth eutectic. Based on review of current world lead or lead-bismuth test facilities and research need listed in the Generation IV Roadmap, five broad areas of requirements of basis are identified: Develop and Demonstrate Prototype Lead/Lead-Bismuth Liquid Metal Flow Loop Develop and Demonstrate Feasibility of Submerged Heat Exchanger Develop and Demonstrate Open-lattice Flow in Electrically Heated Core Develop and Demonstrate Chemistry Control Demonstrate Safe Operation and Provision for Future Testing. These five broad areas are divided into twenty-one (21) specific requirements ranging from coolant temperature to design lifetime. An overview of project engineering requirements, design requirements, QA and environmental requirements are also presented. The purpose of this T&FRs is to focus the lead fast reactor community domestically on the requirements for the next unique state of the art test facility. The facility thermal hydraulic design is based on the maximum simulated core power using seven electrical heater rods of 420 kW; average linear heat generation rate of 300 W/cm. The core inlet temperature for liquid lead or Pb/Bi eutectic is 420oC. The design includes approximately seventy-five data measurements such as pressure, temperature, and flow rates. The preliminary estimated cost of construction of the facility is $3.7M. It is also estimated that the facility will require two years to be constructed and ready for operation.

  12. How biological soil crusts became recognized as a functional unit: a selective history

    Science.gov (United States)

    Lange, Otto L.; Belnap, Jayne

    2016-01-01

    It is surprising that despite the world-wide distribution and general importance of biological soil crusts (biocrusts), scientific recognition and functional analysis of these communities is a relatively young field of science. In this chapter, we sketch the historical lines that led to the recognition of biocrusts as a community with important ecosystem functions. The idea of biocrusts as a functional ecological community has come from two main scientific branches: botany and soil science. For centuries, botanists have long recognized that multiple organisms colonize the soil surface in the open and often dry areas occurring between vascular plants. Much later, after the initial taxonomic and phyto-sociological descriptions were made, soil scientists and agronomists observed that these surface organisms interacted with soils in ways that changed the soil structure. In the 1970’s, research on these communities as ecological units that played an important functional role in drylands began in earnest, and these studies have continued to this day. Here, we trace the history of these studies from the distant past until 1990, when biocrusts became well-known to scientists and the public.

  13. Construction of heteroduplex DNA and in vitro model for functional analysis of mismatch repair

    Institute of Scientific and Technical Information of China (English)

    WANG Yi; Clark Alan; WANG Jiaxun; SUN Menghong; SHI Daren

    2004-01-01

    Functional deficiency of mismatch repair (MMR) system is one of the mechanisms of tumorigenesis. With the development of the investigation and the requirement from the clinical diagnosis and treatment it is necessary to build up a method to evaluate the functional status of the whole MMR system in the concerned tumors. The original ssDNA and dsDNA from wild type (wt) bacteriophage M13mp2 and its three derivates with mutation points in the lacZα Gene have been used to construct two kinds of heteroduplex DNA molecules. One named del(2) has two bases deleted in the negative strand, the other has a G·G mismatch base pair in the negative strand too. Introducing this heteroduplex DNA into E. Coli NR9162 (mutS-) without the MMR ability on the indicator plate with x-gal and IPTG, there are three kinds of plaques, mixture plaque as the characteristic phenotype of heteroduplex DNA, blue and clear plaques. If the cell extract is mismatch repair competent the percentage of the mixture plaque will decrease after incubation with these heteroduplex DNA, the repair efficiency is expressed in percentage as 100× (1 minus the ratio of percentages of mixture plaque obtained from the extract-treated sample and untreated samples), which can imply the functional status of MMR system of certain samples. After large T-antigen-dependent SV-40 DNA replication assay cell extract from TK6, a human lymphoblastoid B-cell lymphoma cell line with MMR ability, and Lovo, a human colonic carcinoma cell line with MMR deficiency have incubated with these heteroduplex DNA. The repair efficiency of TK6 to del(2) is more than 60%, to G·G is more than 50%. The Lovo efficiency to del(2) is less than 10%, to G·G is less than 20%. Therefore, in this in vitro model used for functional analysis of mismatch repair of heteroduplex DNA as the repair target, TK6 can serve as the control for MMR proficiency and Lovo as the control for MMR deficiency. Using this model the tumor tissue from a case of hereditary

  14. Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).

    Science.gov (United States)

    Warshel, Arieh

    2014-09-15

    A detailed understanding of the action of biological molecules is a pre-requisite for rational advances in health sciences and related fields. Here, the challenge is to move from available structural information to a clear understanding of the underlying function of the system. In light of the complexity of macromolecular complexes, it is essential to use computer simulations to describe how the molecular forces are related to a given function. However, using a full and reliable quantum mechanical representation of large molecular systems has been practically impossible. The solution to this (and related) problems has emerged from the realization that large systems can be spatially divided into a region where the quantum mechanical description is essential (e.g. a region where bonds are being broken), with the remainder of the system being represented on a simpler level by empirical force fields. This idea has been particularly effective in the development of the combined quantum mechanics/molecular mechanics (QM/MM) models. Here, the coupling between the electrostatic effects of the quantum and classical subsystems has been a key to the advances in describing the functions of enzymes and other biological molecules. The same idea of representing complex systems in different resolutions in both time and length scales has been found to be very useful in modeling the action of complex systems. In such cases, starting with coarse grained (CG) representations that were originally found to be very useful in simulating protein folding, and augmenting them with a focus on electrostatic energies, has led to models that are particularly effective in probing the action of molecular machines. The same multiscale idea is likely to play a major role in modeling of even more complex systems, including cells and collections of cells.

  15. [The biological reaction of inflammation, methylglyoxal of blood plasma, functional and structural alterations in elastic type arteries at the early stage of hypertension disease].

    Science.gov (United States)

    Titov, V N; Dmitriev, V A; Oshchepkov, E V; Balakhonova, T V; Tripoten', M I; Shiriaeva, Iu K

    2012-08-01

    The article deals with studying of the relationship between biologic reaction of inflammation with glycosylation reaction and content of methylglyoxal in blood serum. The positive correlation between pulse wave velocity and content of methylglyoxal, C-reactive protein in intercellular medium and malleolar brachial index value was established. This data matches the experimental results concerning involvement of biological reaction of inflammation into structural changes of elastic type arteries under hypertension disease, formation of arteries' rigidity and increase of pulse wave velocity. The arterial blood pressure is a biological reaction of hydrodynamic pressure which is used in vivo by several biological functions: biological function of homeostasis, function of endoecology, biological function of adaptation and function of locomotion. The biological reaction of hydrodynamic (hydraulic) pressure is a mode of compensation of derangement of several biological functions which results in the very high rate of hypertension disease in population. As a matter of fact, hypertension disease is a syndrome of lingering pathological compensation by higher arterial blood pressure of the biological functions derangements occurring in the distal section at the level of paracrine cenoses of cells. The arterial blood pressure is a kind of in vivo integral indicator of deranged metabolism. The essential hypertension disease pathogenically is a result of the derangement of three biological functions: biological function of homeostasis, biological function of trophology - nutrition (biological reaction of external feeding - exotrophia) and biological function of endoecology. In case of "littering" of intercellular medium in vivo with nonspecific endogenic flogogens a phylogenetically earlier activation of biological reactions of excretion, inflammation and hydrodynamic arterial blood pressure occur. In case of derangement of biological function of homeostasis, decreasing of

  16. Sufficient Condition for Monotonicity in Constructing the Distribution Function With Bernoulli Scheme

    Directory of Open Access Journals (Sweden)

    Vedenyapin Aleksandr Dmitrievich

    2015-11-01

    Full Text Available This paper is the construction of the distribution function using the Bernoulli scheme, and is also designed to correct some of the mistakes that were made in the article [2]. Namely, a function built in [2] need not be monotonous, and some formulas need to be adjusted. The idea of building as well as in [2], is based on the model of Cox-Ross-Rubinstein "binary market". The essence of the model was to divide time into N steps, and assuming that the price of an asset at each step can move either up to a certain value with probability p, or down also by some certain value with probability q = 1 - p. Prices in step N can take only a finite number of values. "Success" or "failure" was the changing price for some fixed value in the model of Cox-Ross-Rubinstein. Here as a "success" or "failure" at every step we consider the affiliation of changing the index value to the section [r, S] either to the interval [I, r. Further a function P(r was introduced, which at any step gives us the probability of "success". The maximum index value increase for the all period of time [T, 2T] will be equal nS, and the maximum possible reduction will be equal nI. Then let x ∈ [nI, nS]. This segment will reflect every possible total variation that we can get at the end of a period of time [T, 2T]. The further introduced inequality k ≥ (x - nI/(S - I gives us the minimum number of successes that needed for total changing could be in the section [x, nS] if was n - k reductions with the index value to I. Then was introduced the function r(x, kmin which is defined on the interval (nI, nS] and provided us some assurance that the total index changing could be in the section [x, nS] if successful interval is [r(x, kmin, S] and the amount of success is satisfying to our inequality. The probability of k "successes" and n - k "failures" is calculated according to the formula of Bernoulli, where the probability of "success" is determined by the function P(r, and r is determined

  17. Functional evaluation of artificial skeletal muscle tissue constructs fabricated by a magnetic force-based tissue engineering technique.

    Science.gov (United States)

    Yamamoto, Yasunori; Ito, Akira; Fujita, Hideaki; Nagamori, Eiji; Kawabe, Yoshinori; Kamihira, Masamichi

    2011-01-01

    Skeletal muscle tissue engineering is currently applied in a variety of research fields, including regenerative medicine, drug screening, and bioactuator development, all of which require the fabrication of biomimic and functional skeletal muscle tissues. In the present study, magnetite cationic liposomes were used to magnetically label C2C12 myoblast cells for the construction of three-dimensional artificial skeletal muscle tissues by an applied magnetic force. Skeletal muscle functions, such as biochemical and contractile properties, were evaluated for the artificial tissue constructs. Histological studies revealed that elongated and multinucleated myotubes were observed within the tissue. Expression of muscle-specific markers, such as myogenin, myosin heavy chain and tropomyosin, were detected in the tissue constructs by western blot analysis. Further, creatine kinase activity increased during differentiation. In response to electric pulses, the artificial tissue constructs contracted to generate a physical force (the maximum twitch force, 33.2 μN [1.06 mN/mm2]). Rheobase and chronaxie of the tissue were determined as 4.45 V and 0.72 ms, respectively. These results indicate that the artificial skeletal muscle tissue constructs fabricated in this study were physiologically functional and the data obtained for the evaluation of their functional properties may provide useful information for future skeletal muscle tissue engineering studies.

  18. Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation.

    Directory of Open Access Journals (Sweden)

    Xia Wang

    Full Text Available Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ~100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase-LacI expression system was used to replace the σ(54-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ~42% of the nitrogenase activity of the σ(54-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology.

  19. Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation.

    Science.gov (United States)

    Wang, Xia; Yang, Jian-Guo; Chen, Li; Wang, Ji-Long; Cheng, Qi; Dixon, Ray; Wang, Yi-Ping

    2013-01-01

    Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ~100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase-LacI expression system was used to replace the σ(54)-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ~42% of the nitrogenase activity of the σ(54)-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology.

  20. A Model of Functional Integration and Conflict: The Case of Purchasing-Production in a Construction Company

    DEFF Research Database (Denmark)

    Ellegaard, Chris; Koch, Christian

    2014-01-01

    -depth interviewing of managers in the production and purchasing functions of a construction company, as well as by its suppliers. Findings – Given low functional integration, antagonistic reasoning within each function and resultant conflicting behaviors are allowed to develop in a negative cycle, escalating...... the conflict between purchasing and production. This process leads to the creation of two opposing functional sourcing models that serve as blueprints for behavior. Research limitations/implications – The single case methodology was chosen to maximize depth and detail and form an ideal foundation for theory...... the constructs of integration, group reasoning, and conflict, thereby generating knowledge on conflict development processes in cross-functional interfaces. Furthermore, the article contributes by uncovering the difficulties associated with implementing spend consolidation, a prevailing sourcing strategy....

  1. Species composition,distribution patterns and ecological functions of biological soil crusts in the Gurbantunggut Desert

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    As one of the most important biological factors that maintain the stability of the largest fixed and semi-fixed desert in China,the Gurbantunggut Desert,the biological soil crusts (BSCs) develop well and play critical ecological roles in the desert ecosystem. In this paper,we briefly summarize our research findings since 2002 including species composition,distribution pattern and ecological functions of BSCs in the desert. Our results indicate abundant species diversity of BSCs in the Gurbantunggut Desert in comparison to other deserts in China. At the scales of sand dune or whole desert,the distribution patterns of BSCs are location-specific. The existence of BSCs in this desert could:(1) accelerate the formation of desert soil and the weathering of minerals; (2) accumulate organic matter in surface soil through related species in soil crusts; (3) enhance the abilities of sand surface to resist wind erosion; (4) influence seed germination of vascular plants; and (5) enhance the production of dew deposition on sandy soil surface.

  2. The role of ontologies in biological and biomedical research: a functional perspective.

    Science.gov (United States)

    Hoehndorf, Robert; Schofield, Paul N; Gkoutos, Georgios V

    2015-11-01

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  3. Identification of distinct biological functions for four 3′-5′ RNA polymerases

    Science.gov (United States)

    Long, Yicheng; Abad, Maria G.; Olson, Erik D.; Carrillo, Elisabeth Y.; Jackman, Jane E.

    2016-01-01

    The superfamily of 3′-5′ polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNAHis guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNAHis maturation reaction, which is distinct from the tRNAHis maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5′-editing in vivo and in vitro, establishing template-dependent 3′-5′ polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3′-5′ polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3′-5′ polymerases in eukaryotes. PMID:27484477

  4. Identification of distinct biological functions for four 3'-5' RNA polymerases.

    Science.gov (United States)

    Long, Yicheng; Abad, Maria G; Olson, Erik D; Carrillo, Elisabeth Y; Jackman, Jane E

    2016-09-30

    The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNA(His) maturation reaction, which is distinct from the tRNA(His) maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5'-editing in vivo and in vitro, establishing template-dependent 3'-5' polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3'-5' polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3'-5' polymerases in eukaryotes.

  5. The role of ontologies in biological and biomedical research: a functional perspective

    KAUST Repository

    Hoehndorf, Robert

    2015-04-10

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  6. Acceleration of cardiovascular-biological age by amphetamine exposure is a power function of chronological age

    Science.gov (United States)

    Norman, Amanda; Hulse, Gary Kenneth

    2017-01-01

    Background Amphetamine abuse is becoming more widespread internationally. The possibility that its many cardiovascular complications are associated with a prematurely aged cardiovascular system, and indeed biological organism systemically, has not been addressed. Methods Radial arterial pulse tonometry was performed using the SphygmoCor system (Sydney). 55 amphetamine exposed patients were compared with 107 tobacco smokers, 483 non-smokers and 68 methadone patients (total=713 patients) from 2006 to 2011. A cardiovascular-biological age (VA) was determined. Results The age of the patient groups was 30.03±0.51–40.45±1.15 years. This was controlled for with linear regression. The sex ratio was the same in all groups. 94% of amphetamine exposed patients had used amphetamine in the previous week. When the (log) VA was regressed against the chronological age (CA) and a substance-type group in both cross-sectional and longitudinal models, models quadratic in CA were superior to linear models (both pamphetamine exposure persisted after adjustment for all known cardiovascular risk factors (pamphetamines is associated with an advancement of cardiovascular-organismal age both over age and over time, and is robust to adjustment. That this is associated with power functions of age implies a feed-forward positively reinforcing exacerbation of the underlying ageing process. PMID:28243315

  7. The relationship between the connecting peptide of recombined single chain insulin and its biological function

    Institute of Scientific and Technical Information of China (English)

    黄一丁; 梁镇和; 冯佑民

    2001-01-01

    To investigate the relationship between the biological activity of recombined single chain insulin and the length of the connecting peptide, we designed and prepared three single chain insulin molecules, namely, PIP, [A]5PIP and [A]10PIP, by site-directed mutagenesis, in which B30 and A1 were linked through dipeptide A-K, heptapeptide A-A-A-A-A-A-K, and dodecapeptide A-A-A-A-A-A-A-A-A-A-A-K, respectively. Their receptor binding capacities were 0.14%, 14.3% and 11.1% of that of insulin respectively and their in vivo biological activities were in consistence with their receptor binding capacity; whereas their growth promoting activities were 17%, 116.3% and 38% of that of insulin. These results suggested the following conclusions. (i) The recombined single chain insulin could also possess the same metabolic and mitogenic function as insulin. (ii) The receptor binding capacity of recombined single chain insulin to insulin receptor was closely related to the length and amino acid composition of the connecting peptide and could change from 0 to 100% of insulin depending on the different connecting peptides. This result further illustrated the necessity of B chain C-terminus swaying away from A chain N-terminus when insulin binds to its receptor. (iii) The mitogenic activity of recombined single chain insulin also depended on the length and the amino acid composition of the connecting peptide and was higher than its metabolic activity.

  8. A construction of the Schr\\"odinger Functional for M\\"obius Domain Wall Fermions

    CERN Document Server

    Murakami, Yuko

    2014-01-01

    We construct the Schr\\"odinger Functional (SF) setup for the M\\"obius domain wall fermions (MDWF). The method is an extension of the method proposed by Takeda for the standard domain wall fermion. In order to fulfill the requirement that the lattice Dirac operator with the SF boundary obeys the L\\"uscher's universality argument: the lattice chiral fermion with the SF boundary condition breaks the chiral symmetry at the temporal boundary, we impose the parity symmetry with respect to the fifth-direction on the MDWF operator. This additional symmetry restricts the choice of the parameter of the MDWF so that the optimal parameter from the Zolotarev optimal approximation cannot be applied. We introduce a modified parameter set having the fifth-dimensional parity symmetry. We investigate the MDWF with the SF boundary by observing eigenvalues of the Hermitian operator and the Ginsparg-Wilson relation violation at the tree-level. We compare the computational cost with that of the standard DWF with the SF scheme.

  9. Organizational bases of creation and functioning of the integrated structures in the investment in construction sphere

    Directory of Open Access Journals (Sweden)

    Subbotin Artem Sergeevich

    2014-04-01

    Full Text Available Integration is one of the results of the world industrial and economic processes globalization. Integration of production and commercial units and formation of modern structures of corporate level are one of current trends of development of the organization and management, both science, and practice. Formation and development of integrated structures became an important modern phenomenon in the organization of corporate level. Integration processes in organizations to large extend influence the relation of competitive strengths on the market and as a result the competitive ability of its objects. It is accepted to distinguish vertically and horizontally integrated structures. The use of the integrated structures allows providing steady development of investment and construction activity within state-private partnership, and thanks to its flexible structure it is capable to react to changes of external and internal factors quickly and adequately. Moreover, it is necessary to point out the possibility of using the cluster model in the process of describing functioning of integrated structures.

  10. THE FUNCTIONAL EFFECTIVENESS OF A CELL-ENGINEERED CONSTRUCT FOR THE REGENERATION OF ARTICULAR CARTILAGE

    Directory of Open Access Journals (Sweden)

    V. I. Sevastianov

    2015-01-01

    Full Text Available The aim of this study is an analysis of the functional effectiveness of a biomedical cell product consisting of a biopolymer microheterogeneous collagen-containing hydrogel (BMCH, human adipose-derived mesenchymal stromal cells (hADMSCs, and chondrogenic induction medium in the regeneration of articular cartilage. Materials and methods. The test model of the adjuvant arthritis was used (female Soviet Chinchilla rabbits with the further development into osteoarthrosis (OA combined with the clinical, biochemical, radiological, and histochemical trials. Results. On Day 92 of the OA model it has been found that the intra-articular introduction of a BMCH with hADMSCs into the left knee joint (n = 3 30 days after the OA modeling, as opposed to the right joint (negative control, n = 3, stimulates the regenerative processes of the cartilaginous tissue structure characterized by the formation of chondrocyte «columns», the emergence of isogenic groups in the intracellular matrix and the regeneration of its structure. Upon the intra-articular introduction of a BMCH (n = 3 such effects are markedly less pronounced. Conclusions. A significant regenerative potential of a cell-engineered construct of human articular tissue (CEC ATh has been proven. It is possible to presume that biostimulating properties of CEC ATh are due to the activating effect of a biomedical cell product on the stem cell migration processes from the surrounding tissue into the injured area with their subsequent differentiation. 

  11. Positive Psychological Functioning: evidence for a new construct and its measurement

    Directory of Open Access Journals (Sweden)

    Mª Dolores Merino

    2015-01-01

    Full Text Available In 2007, the Institute of Happiness conducted one of the most ambitious studies ever done on this subject in Spain. Many different variables were measured: socio-demographics and psychological, (the latter through new instruments and all were applied to a representative sample of 3000 participants of the Spanish population. Study 1 of this research used that database. The objective of this Study was to understand how key psychological resources are organized (Autonomy, Resilience, Self-Esteem, Purpose in life, Enjoyment, Optimism, Curiosity, Creativity, Humor, Environmental mastery and Vitality. The purpose of Study 2 was to replicate the results of Study 1 and to test the psychometrical properties of the new scales used in Study 1, but using a sample of 130 college students. This research proves that key psychological resources are interconnected, forming a second order construct we call Positive Psychological Functioning (PPF, and, it develops a new Spanish scale to assess it. This measure is formed with 11 subscales each containing three items. This scale structure allows a general and a specific assessment of PPF and, in consequence, of human psychological well-being.

  12. Blind polarization demultiplexing by constructing a cost function for coherent optical PDM-OFDM.

    Science.gov (United States)

    Yu, Zhenming; Chen, Minghua; Chen, Hongwei; Yi, Xingwen; Yang, Sigang; Xie, Shizhong

    2015-07-13

    We propose a training symbols-free polarization demultiplexing method by constructing a cost function (CCF-PDM) for coherent optical PDM-OFDM. This method is applicable for high-speed, wide-bandwidth OFDM signals, different subcarrier modulation formats and long-haul transmission. It shows comparable performance with that of conventional method but without overhead and converges fast. Since the neighboring subcarriers experience similar polarization effects, we set the initial matrix parameters by the neighboring subcarrier to reduce the number of iteration for the gradient algorithm and prevent swapping the data of the two orthogonal polarizations. We verify this method in experiment by transmitting 66.6-Gb/s PDM-OFDM signal with 4QAM subcarrier modulation over 5440 km SSMF and 133.3-Gb/s PDM-OFDM signal with 16QAM subcarrier modulation over 960 km SSMF respectively. We compare its performance with that of training symbols. We also analyze the convergence speed of this method.

  13. Restoration of voice function by using biological feedback in laryngeal and hypopharyngeal carcinoma patients

    Science.gov (United States)

    Choinzonov, E. L.; Balatskaya, L. N.; Chizhevskaya, S. Yu.; Meshcheryakov, R. V.; Kostyuchenko, E. Yu.; Ivanova, T. A.

    2016-08-01

    The aim of the research is to develop and introduce a new technique of post-laryngectomy voice rehabilitation of laryngeal and hypopharyngeal carcinoma patients. The study involves comparing and analyzing 82 cases of voice function restoration by using biological feedback based on mathematical modeling of voice production. The advantage of the modern technology-based method in comparison with the conventional one is proved. Restoration of voice function using biofeedback allows taking into account patient's abilities, adjusting parameters of voice trainings, and controlling their efficiency in real-time mode. The data obtained indicate that the new method contributes to the rapid inclusion of self-regulation mechanisms of the body and results in the overall success rate of voice rehabilitation in totally laryngectomized patients reaching 92%, which reduces the rehabilitation period to 18 days, compared to 86% and 38 days in the control group, respectively. Restoration of disturbed functions after successful treatment is an important task of rehabilitation and is crucial in terms of the quality of cancer patients' lives. To assess life quality of laryngeal cancer patients, the EORTC Quality of Life Core Questionnaire (QLQ-C30), and head and neck module (QLQ-H&N35) were used. The analyzed results proved that the technique of biofeedback voice restoration significantly improves the quality of life of laryngectomized patients. It allows reducing the number of disabled people, restoring patients' ability to work-related activities, and significantly improving social adaptation of these patients.

  14. Distinguishing Pattern Formation Phenotypes: Applying Minkowski Functionals to Cell Biology Systems

    Science.gov (United States)

    Rericha, Erin; Guven, Can; Parent, Carole; Losert, Wolfgang

    2011-03-01

    Spatial Clustering of proteins within cells or cells themselves frequently occur in cell biology systems. However quantifying the underlying order and determining the regulators of these cluster patterns have proved difficult due to the inherent high noise levels in the systems. For instance the patterns formed by wild type and cyclic-AMP regulatory mutant Dictyostelium cells are visually distinctive, yet the large error bars in measurements of the fractal number, area, Euler number, eccentricity, and wavelength making it difficult to quantitatively distinguish between the patterns. We apply a spatial analysis technique based on Minkowski functionals and develop metrics which clearly separate wild type and mutant cell lines into distinct categories. Having such a metric facilitated the development of a computational model for cellular aggregation and its regulators. Supported by NIH-NGHS Nanotechnology (R01GM085574) and the Burroughs Wellcome Fund.

  15. The universality and biological significance of signal molecules with intracellular-extracellular compatible functions

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Generally,cell signal molecules are classified into the extracellular signal molecules (the first messengers) and the intracellular signal ones (the second messengers).Cyclic adenosine monophosphate (cAMP),calcium ions and calmodulin (CaM) are the traditional intracellular messengers,but they are also present in extracellular matrix (ECM).Some of them have been discovered to act as the first messengers through cell surface receptors.Other second messengers,such as cyclic guanosine monophosphate (cGMP),cyclic adenosine diphosphate ribose (cADPR) and annexin,are also found existing outside animal and plant cells.The existence of these messengers with intracellular-extracellular compatible functions in cells may be a regular biological phenomenon.These compatible messengers might be the communication factors between intracellular and extracellular regions or among the cell populations,and are also important in regulating cell development procedure.

  16. Function of parotid gland following irradiation and its relation to biological parameters

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, T. (Tohoku Univ., Sendai, Japan); Yamamoto, M.; Takeda, M.

    1980-09-01

    The function of the parotid gland in the mouse (synthesis and secretion of ..cap alpha..-amylase) following X irradiation was analyzed in relation to the parameters of surviving acinar cell fraction, DNA or protein content, and wet weight of the gland. Both synthesis and secretion of amylase in parotid were essentially unchanged when mice were irradiated with a dose of up to 3000 rad. When mice were irradiated and then given a proliferative stimulus of isoproterenol, latent lethal damage in the acinar cell population was expressed and resulted in cell degeneration in a dose-dependent manner. The mean value of amylase activity per gland in similarly treated parotids was, however, totally unaffected. The relationship between amylase activity per gland and the other biological parameters was analyzed by regression analysis. The results indicate that amylase activity per surviving acinar cell increased proportionately to compensate for the loss of acinar cells.

  17. The Evolution of Human Basophil Biology from Neglect towards Understanding of Their Immune Functions

    Science.gov (United States)

    Steiner, Markus; Huber, Sara; Harrer, Andrea

    2016-01-01

    Being discovered long ago basophils have been neglected for more than a century. During the past decade evidence emerged that basophils share features of innate and adaptive immunity. Nowadays, basophils are best known for their striking effector role in the allergic reaction. They hence have been used for establishing new diagnostic tests and therapeutic approaches and for characterizing natural and recombinant allergens as well as hypoallergens, which display lower or diminished IgE-binding activity. However, it was a long way from discovery in 1879 until identification of their function in hypersensitivity reactions, including adverse drug reactions. Starting with a historical background, this review highlights the modern view on basophil biology. PMID:28078302

  18. N-Hexyl-4-aminobutyl glycosides for investigating structures and biological functions of carbohydrates.

    Science.gov (United States)

    Suzuki, Katsuhiko; Tobe, Akifumi; Adachi, Shin; Daikoku, Shusaku; Hasegawa, Yasuko; Shioiri, Yuki; Kobayashi, Mariko; Kanie, Osamu

    2009-11-21

    The potential applications of N-hexyl-4-aminobutyl glycosides in the mass spectrometric investigation of glycan structure and in the investigation of glycan functions were studied. Under collision-induced dissociation (CID) conditions, sodiated glycosides carrying N-hexyl-4-aminobutyl groups effectively produced a hemiacetal species (C-ions), which is important in mass-spectrometry-based structural investigation. The usefulness of N-hexyl-4-aminobutyl glycosides in biological analysis was also confirmed by obtaining a binding constant for the binding of dipyrrometheneboron difluoride C3-labeled N-hexyl-4-aminobutyl beta-lactoside with an Erythrina cristagalli lectin, and by visualizing cellular organelles using a more hydrophobic BODIPY-labeled compound.

  19. Perspectives in the biological function and the technological application of polygalacturonases.

    Science.gov (United States)

    Lang, C; Dörnenburg, H

    2000-04-01

    Polygalacturonases (PG) have evolved in the past years from a pectinase "simply" being used for food processing to an important parameter in plant-fungal interaction. PG-inhibiting proteins (PGIP) that are synthesised in plants as a specific response to PGs of pathogenic fungi, have become a focus as a possible target in resistance breeding, and PGIPs are also a concern as an inhibiting factor in food processing. Plant PGs have been identified as a major factor in fruit ripening, and PG-deficient transgenic plants have been bred. Mainly fungal PGs are used in industrial processes for juice clarification and the range of enzymes is being extended through new recombinant and non-recombinant fungal strains. Finally, novel fields of application can be envisaged for PGs in the production of oligogalacturonides as functional food components. Here we aim to highlight the various fields where PGs are encountered and where they are of biological or technological importance.

  20. Stereoelectronic effects dictate molecular conformation and biological function of heterocyclic amides.

    Science.gov (United States)

    Reid, Robert C; Yau, Mei-Kwan; Singh, Ranee; Lim, Junxian; Fairlie, David P

    2014-08-27

    Heterocycles adjacent to amides can have important influences on molecular conformation due to stereoelectronic effects exerted by the heteroatom. This was shown for imidazole- and thiazole-amides by comparing low energy conformations (ab initio MP2 and DFT calculations), charge distribution, dipole moments, and known crystal structures which support a general principle. Switching a heteroatom from nitrogen to sulfur altered the amide conformation, producing different three-dimensional electrostatic surfaces. Differences were attributed to different dipole and orbital alignments and spectacularly translated into opposing agonist vs antagonist functions in modulating a G-protein coupled receptor for inflammatory protein complement C3a on human macrophages. Influences of the heteroatom were confirmed by locking the amide conformation using fused bicyclic rings. These findings show that stereoelectronic effects of heterocycles modulate molecular conformation and can impart strikingly different biological properties.

  1. Optimization of Two-species Whole-cell Immobilization System Constructed with Marine-derived Fungi and Its Biological Degradation Ability

    Institute of Scientific and Technical Information of China (English)

    陈慧英; 王明霞; 沈煜斌; 姚善泾

    2014-01-01

    Mycelia pellet formed spontaneously in the process of cultivation was exploited as a biological carrier for whole-cell immobilization due to its unique structural characteristic. An innovative two-species whole-cell im-mobilization system was achieved by inoculating the marine-derived fungus Pestalotiopsis sp. J63 spores into cul-ture medium containing another fungus Penicillium janthinellum P1 pre-grown mycelia pellets for 2 days without any pretreatment. In order to evaluate the biological degradation capacity of this novel constructed immobilization system, the immobilized pellets were applied to treat paper mill effluent and decolorize dye Azure B. The use of the constructed immobilization system in the effluent resulted in successful and rapid biodegradation of numerous in-soluble fine fibers. The optimum conditions of immobilized procedure for maximum biodegradation capacity were determined using orthogonal design with biomass of P1 pellets 10 g (wet mass), concentration of J63 spore 2×109 ml-1, and immobilization time 2 d. The results demonstrate that immobilized pellets have more than 99%biodegra-dation capacity in a ten-hour treatment process. The kinetics of biodegradation fits the Michaelis-Menten equation well. Besides, the decolorization capability of immobilized pellets is more superior than that of P1 mycelia pellets. Overall, the present study offers a simple and reproducible way to construct a two-species whole-cell immobiliza-tion system for sewage treatment.

  2. Teacher-student co-construction processes in biology: Strategies for developing mental models in large group discussions

    Science.gov (United States)

    Nunez Oviedo, Maria Cecilia

    The aim of this study was to describe co-construction processes in large group discussions. Co-construction, as used here, is a process by which the teacher and the students work together to construct and evaluate mental models of a target concept. Data were collected for an in-depth case study of a single teacher instructing middle school students with an innovative curriculum on human respiration. Data came from transcripts of video taped lessons, drawings, and pre- and post-test scores. Quantitative and qualitative analyses were conducted. In the quantitative analysis, differences in gains between one and two standard deviations in size were found between the pre- and post-test scores indicating that the students increased their understanding about human respiration. In the qualitative analysis, a generative exploratory method followed by a convergent coded method was conducted to examine teacher-student interaction patterns. The aim of this part was to determine how learning occurred by attempting to connect dialogue patterns with underlying cognitive processes. The main outcome of the study is a hypothesized model containing four layers of nested teaching strategies. Listed from large to small time scales these are: the Macro Cycle, the Co-construction Modes, the Micro Cycle, and the Teaching Tactics. The most intensive analysis focused on identifying and articulating the Co-construction Modes---Accretion Mode, Disconfirmation Mode, Modification Mode, Evolution Mode, and Competition Mode---and their relations to the other levels of the model. These modes can either describe the construction and evaluation of individual model elements or of entire models giving a total of ten modes. The frequency of these co-construction modes was then determined by coding, twenty-six hours of transcripts. The most frequent modes were the Accretion Mode and the Disconfirmation Mode. The teacher's and the students' contributions to the co-construction process were also examined

  3. Design and construction of a first-generation high-throughput integrated molecular biology platform for production of optimized synthetic genes and improved industrial strains

    Science.gov (United States)

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

  4. Arterial Input Function Placement for Accurate CT Perfusion Map Construction in Acute Stroke

    Science.gov (United States)

    Ferreira, Rafael M.; Lev, Michael H.; Goldmakher, Gregory V.; Kamalian, Shahmir; Schaefer, Pamela W.; Furie, Karen L.; Gonzalez, R. Gilberto; Sanelli, Pina C.

    2013-01-01

    OBJECTIVE The objective of our study was to evaluate the effect of varying arterial input function (AIF) placement on the qualitative and quantitative CT perfusion parameters. MATERIALS AND METHODS Retrospective analysis of CT perfusion data was performed on 14 acute stroke patients with a proximal middle cerebral artery (MCA) clot. Cerebral blood flow (CBF), cerebral blood volume (CBV), and mean transit time (MTT) maps were constructed using a systematic method by varying only the AIF placement in four positions relative to the MCA clot including proximal and distal to the clot in the ipsilateral and contralateral hemispheres. Two postprocessing software programs were used to evaluate the effect of AIF placement on perfusion parameters using a delay-insensitive deconvolution method compared with a standard deconvolution method. RESULTS One hundred sixty-eight CT perfusion maps were constructed for each software package. Both software programs generated a mean CBF at the infarct core of < 12 mL/100 g/min and a mean CBV of < 2 mL/100 g for AIF placement proximal to the clot in the ipsilateral hemisphere and proximal and distal to the clot in the contralateral hemisphere. For AIF placement distal to the clot in the ipsilateral hemisphere, the mean CBF significantly increased to 17.3 mL/100 g/min with delay-insensitive software and to 19.4 mL/100 g/min with standard software (p < 0.05). The mean MTT was significantly decreased for this AIF position. Furthermore, this AIF position yielded qualitatively different parametric maps, being most pronounced with MTT and CBF. Overall, CBV was least affected by AIF location. CONCLUSION For postprocessing of accurate quantitative CT perfusion maps, laterality of the AIF location is less important than avoiding AIF placement distal to the clot as detected on CT angiography. This pitfall is less severe with deconvolution-based software programs using a delay-insensitive technique than with those using a standard deconvolution

  5. Organic Composition and Morphology of Sea Spray Aerosols as a Function of Biological Life during IMPACTS

    Science.gov (United States)

    Pham, D.; Moffet, R.; Fraund, M. W.; O'Brien, R.; Laskina, O.; Prather, K. A.; Grassian, V. H.; Beall, C.; Wang, X.; Forestieri, S.; Cappa, C. D.

    2015-12-01

    Aerosols influence climate by directly reflecting or absorbing sunlight, or indirectly by affecting clouds. A major source of aerosols is from oceanic wave breaking. Due to their complexity, the effects of marine aerosol on climate are uncertain. To provide more detailed measurements of the chemical composition of marine aerosols, Scanning Transmission X-Ray Microscopy coupled with Near Edge X-Ray Absorption Fine Structure (SXTM-NEXAFS) was used to give spatially resolved molecular information for carbon and oxygen. Application of STXM/NEXAFS to particles collected during a mesocosm study using a unique wave channel facility to generate aerosols shows that the organic volume fraction of aerosols at the aerodynamic diameter size range of 0.18-0.32 μm are a direct function of the biological activity in the sea water. Aerosol organic volume fraction increased from 0.32 for particles generated from seawater containing low biolife to 0.49 and 0.40 for particles produced during phytoplankton blooms. However, the organic volume fraction of aerosols at the aerodynamic diameter size range of 0.56-1 μm did not change with biological activity. Measurements also show that different types of organics can concentrate into aerosols depending on the enzyme activity expressed at the time. Enhanced spectral signatures for aliphatic hydrocarbons were observed during the first phytoplankton bloom compared to a second phytoplankton bloom occurring directly thereafter. The decreased signature of aliphatic organics in the second phytoplankton bloom was correlated with increased lipase activity from heterobacteria. Organic aggregates having similar morphology also differ in composition from their carbon spectra from the two blooms. For July 17, organic aggregates were much richer in hydrocarbons, which showed a remarkably intense C-H absorbance and a broad C-C absorbance. Organic aggregates observed for July 26-27, did not have the C-H and C-C signatures, but contained more polar

  6. Investigational study on construction of the physical function database; Shintai kino data base no kochiku ni kansuru chosa kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-03-01

    An investigational study was carried out on construction of the physical function database which can supply data useful for planning, design and production when companies provide products and barrier-free environment for the aged society. Up to now, the final image of database was studied as to the visual function. In addition, this study is aimed at constructing the physical function database. In the literature survey, basic data on physical characteristics of the aged which have lain scattered were collected and systematically sorted in relation to the exercise function in order to make an analysis of the data and measuring technology in terms of reliability, importance, and applied values. In the survey of corporate needs, an examination of concrete needs for the exercise function and auditory function was made for general companies and companies related to the medical and welfare apparatus field. As to the visual function, a study was conducted on selection of new items for visual measurement and measuring methods. In the study of the database structure, a pilot database was constructed and subjects were extracted. 529 refs., 57 figs., 15 tabs.

  7. [The hyperiricosuria as an indicator of derangement of biologic functions of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension].

    Science.gov (United States)

    Titov, V N; Oshchepkova, E V; Dmitriev, V A; Gushchina, O V; Shiriaeva, Iu K; Iashin, A Ia

    2012-04-01

    During millions years in all animals allantoine (oxidized by uricase uric acid) was catabolite of purines and ascorbic acid was an acceptor of active forms of oxygen. The proximal tubules of nephron reabsorbed the trace amounts of uric acid Then during phylogenesis the primates had a mutation of ascorbic acid gen minus. Later on occurred a second spontaneous mutation and uricase gen minus and uric acid became catabolites of purines. In absence of ascorbic acid synthesis ions of urates became a major capturers of active forms of oxygen and all uric acid as before underwent the reabsorption. Later the carriers were formed which began in epithelium of proximal tubules to secrete all uric acid into urine. At every incident of "littering" of intercellular medium with endogenic flogogens (impairment of biologic function of endoecology) under compensatory development of biologic reaction of inflammation the need in inactivation of active forms of oxygen increases. Hence later on in phylogenesis one more stage was formed--post secretory reabsorption of uric acid In the biologic reaction of inflammation epithelium of proximal tubules initiates retentional hyperiricosuria. The general antioxidant activity of human blood plasma in 60% is presented by urates' ions. The excretion of uric acid includes 4 stages: filtration, full reabsorption, secretion and post secretory reabsorption. In phylogenesis these stages formed in sequence. The mild hyperiricosuria is most frequently considered as a non-specific indicator of activation of biologic reaction of inflammation. The productive hyperiricosuria develops more infrequently under surplus of meat food and cytolysis syndrome (intensification of cell loss in vivo). Under concentration of uric acid more than 400 mkmol/l part of urates circulates in intercellular medium in the form of crystals. The microcrystals of uric acid (biologic "litter") initiate the syndrome of systemic inflammatory response as an endogenic flogogen

  8. Construction of shRNA of Fulminant Hepatitis Related Gene mfgl2 and Investigation of Its Biological Effects in vitro

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This study was designed to explore the RNA interference technique in inhibition of the expression of the mouse fibrinogen like protein 2 (mfgl2), which has been reported to be involved in the development a variety of diseases including fulminant viral hepatitis. A plasmid named p-mfgl2shRNA,complementary to the sequence of mfgl2 was constructed, while another short hairpin RNA (shRNA)which was a mutated form of the mfgl2shRNA sequences was used as a control. A plasmid named pEGFP-mfgl2 expressing the mfgl2-EGFP fusion protein was also constructed for the screening of the effect of p-mfgl2shRNA on mfgl2 expression. By cotransfection of p-mfgl2shRNA and pEGFP-mfgl2 or pcDNA3.1-mfgl2 expression construct into CHO cells or HeLa cells, the inhibition of mfgl2 expression by mfgl2shRNA was analyzed by direct observation through fluorescent microscopy, FACS, RT-PCR and immunohistochemistry staining. The experiments showed the significant inhibitory effect of p-mfgl2shRNA on mfgl2 expression at 48h post-transfection in both CHO and Hela cell lines with the inhibitory efficiency as high as 80.1%. The study demonstrated that the construct of p-mfgl2shRNA successfully interfered with the mfgl2 expression in vitro.

  9. Construction, Expression and In Vitro Biological Behaviors of Ig scFv Fragment in Patients with Chronic B Cell Leukemia

    Institute of Scientific and Technical Information of China (English)

    ZHU Lijuan; LIAO Wenjun; ZHU Huifen; LEI Ping; WANG Zhihua; SHAO Jingfang; ZHANG Yue; SHEN Guanxin

    2006-01-01

    The expression vector of SmIg scFv fragment was constructed in patient with B cell chronic lymphocyte leukemia (B-CLL) and expressed in E. coli to obtain scFv fragment, and the effect of the protein on the proliferation of stimulated peripheral blood mononuclear cells (PBMC) was investigated in vitro. Two pairs of primers were designed, and variable region genes of light chain and heavy chain were amplified by PCR respectively from the pGEM-T vectors previously constructed in our laboratory which containing light chain gene or Fd fragment of heavy chain gene. The PCR product was digested, purified and inserted into pHEN2 vector to construct the soluble expression vector pHEN2-scFv. After the induction by IPTG, the scFv protein was identified by SDSPAGE electrophoresis and purified by Ni-NTA-Chromatography. MTT was used to determine the effect of purified protein on the proliferation of stimulated PBMC in vitro. Plasmid PCR and restriction enzyme digestion of pHEN2-scFv revealed the pHEN2-scFv vector was constructed successfully. Id-scFv protein was expressed in positive clone after induced by IPTG. SDS-PAGE analysis showed that the relative molecular weight of fusion protein was about 30 kD (1 kD=0.9921 ku),which was consistent with the theoretically predicted value. Proliferation of PBMC could be induced by purified Id-scFv. It was suggested that the expression vector of SmIg scFv fragment was constructed successfully, and scFv protein was expressed and secreted from E. coli, which could induce proliferation of PBMC. This may lay an experimental foundation for further research of IdHSP complex vaccine for B-CLL.

  10. Construction, Expression and in vitro Biological Effects of Idiotype Ig Fab Fragment of B-Chronic Lymphocytic Leukemia

    Institute of Scientific and Technical Information of China (English)

    Feng WANG; Ping LEI; Ping HU; Lijuan ZHU; Huifeng ZHU; Yue ZHANG; Jing YANG; Guanxin SHEN

    2008-01-01

    Summary: The purpose of this study was to construct expression vectors of idiotype (Id) Smlg in patients with B-chronic lymphocytic leukemia and to express them in E.coli to obtain recombinant Id,and to investigate the effect of the protein on the proliferation and secretion of IL-2 and IFN-γ of stimulated peripheral blood mononuclear cells (PBMC) in vitro. Light chain gene and Fd fragment of heavy chain gene were inserted into fd-tet-DOG2 vector to construct fd-tet-DOG2-Fab. Fab gene was further cloned into expression vector pHEN2 to construct the soluble expression vector pHEN2-Fab. After induction by IPTG, Fab protein was purified by Ni-NTA-chromatography. MTT was used to determine the effects of purified protein on the proliferation of stimulated PBMC in vitro and the concentrations of IL-2 and IFN-γ in the culture supernatants were detected by ELISA. The results showed that recombinant pHEN2-Fab expression vector was constructed successfully. Fab protein was expressed in positive clone after induced by 1PTG and two specific bands at 24-25 kD position were observed by SDS-PAGE electrophoresis. Proliferation of PBMC could be induced by purified Fab and the concentrations of IL-2 and IFN-γ, in culture supernatants were increased significantly after induction. It was suggested that the expression vector of SmIg Fab fragment was constructed successfully, and expressed and secreted from E. Coli. The Fab protein could induce proliferation of PBMC and promote secretion of IL-2 and IFN-γ.

  11. Mimicking/extracting structure and functions of natural products: synthetic approaches that address unexplored needs in chemical biology.

    Science.gov (United States)

    Hirai, Go

    2015-04-01

    Natural products are often attractive and challenging targets for synthetic chemists, and many have interesting biological activities. However, synthetic chemists need to be more than simply suppliers of compounds to biologists. Therefore, we have been seeking ways to actively apply organic synthetic methods to chemical biology studies of natural products and their activities. In this personal review, I would like to introduce our work on the development of new biologically active compounds inspired by, or extracted from, the structures of natural products, focusing on enhancement of functional activity and specificity and overcoming various drawbacks of the parent natural products.

  12. Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function

    Energy Technology Data Exchange (ETDEWEB)

    Alfano, Robert R.; Yang, Yuanlong

    2003-09-02

    Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

  13. SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function.

    Science.gov (United States)

    Tomer, Raju; Lovett-Barron, Matthew; Kauvar, Isaac; Andalman, Aaron; Burns, Vanessa M; Sankaran, Sethuraman; Grosenick, Logan; Broxton, Michael; Yang, Samuel; Deisseroth, Karl

    2015-12-17

    The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca(2+) imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function.

  14. Biology of Bone Tissue: Structure, Function, and Factors That Influence Bone Cells.

    Science.gov (United States)

    Florencio-Silva, Rinaldo; Sasso, Gisela Rodrigues da Silva; Sasso-Cerri, Estela; Simões, Manuel Jesus; Cerri, Paulo Sérgio

    2015-01-01

    Bone tissue is continuously remodeled through the concerted actions of bone cells, which include bone resorption by osteoclasts and bone formation by osteoblasts, whereas osteocytes act as mechanosensors and orchestrators of the bone remodeling process. This process is under the control of local (e.g., growth factors and cytokines) and systemic (e.g., calcitonin and estrogens) factors that all together contribute for bone homeostasis. An imbalance between bone resorption and formation can result in bone diseases including osteoporosis. Recently, it has been recognized that, during bone remodeling, there are an intricate communication among bone cells. For instance, the coupling from bone resorption to bone formation is achieved by interaction between osteoclasts and osteoblasts. Moreover, osteocytes produce factors that influence osteoblast and osteoclast activities, whereas osteocyte apoptosis is followed by osteoclastic bone resorption. The increasing knowledge about the structure and functions of bone cells contributed to a better understanding of bone biology. It has been suggested that there is a complex communication between bone cells and other organs, indicating the dynamic nature of bone tissue. In this review, we discuss the current data about the structure and functions of bone cells and the factors that influence bone remodeling.

  15. Catalytic enantioselective construction of quaternary stereocenters: assembly of key building blocks for the synthesis of biologically active molecules.

    Science.gov (United States)

    Liu, Yiyang; Han, Seo-Jung; Liu, Wen-Bo; Stoltz, Brian M

    2015-03-17

    The ever-present demand for drugs with better efficacy and fewer side effects continually motivates scientists to explore the vast chemical space. Traditionally, medicinal chemists have focused much attention on achiral or so-called "flat" molecules. More recently, attention has shifted toward molecules with stereogenic centers since their three-dimensional structures represent a much larger fraction of the chemical space and have a number of superior properties compared with flat aromatic compounds. Quaternary stereocenters, in particular, add greatly to the three-dimensionality and novelty of the molecule. Nevertheless, synthetic challenges in building quaternary stereocenters have largely prevented their implementation in drug discovery. The lack of effective and broadly general methods for enantioselective formation of quaternary stereocenters in simple molecular scaffolds has prompted us to investigate new chemistry and develop innovative tools and solutions. In this Account, we describe three approaches to constructing quaternary stereocenters: nucleophilic substitution of 3-halooxindoles, conjugate addition of boronic acids to cyclic enones, and allylic alkylation of enolates. In the first approach, malonic ester nucleophiles attack electrophilic 3-halooxindoles, mediated by a copper(II)-bisoxazoline catalyst. A variety of oxindoles containing a benzylic quaternary stereocenter can be accessed through this method. However, it is only applicable to the specialized 3,3-disubstituted oxindole system. To access benzylic quaternary stereocenters in a more general context, we turned our attention to the enantioselective conjugate addition of carbon nucleophiles to α,β-unsaturated carbonyl acceptors. We discovered that in the presence of catalytic palladium-pyridinooxazoline complex, arylboronic acids add smoothly to β-substituted cyclic enones to furnish ketones with a β-benzylic quaternary stereocenter in high yields and enantioselectivities. The reaction is

  16. Fantasy Orientation Constructs and Related Executive Function Development in Preschool: Developmental Benefits to Executive Functions by Being a Fantasy-Oriented Child

    Science.gov (United States)

    Pierucci, Jillian M.; O'Brien, Christopher T.; McInnis, Melissa A.; Gilpin, Ansley Tullos; Barber, Angela B.

    2014-01-01

    This study explored unique constructs of fantasy orientation and whether there are developmental benefits for fantasy-oriented children. By age 3, children begin developing executive functions, with some children exhibiting high fantasy orientation in their cognitions and behaviors. Preschoolers ("n" = 106) completed fantasy orientation…

  17. Decreased functional diversity and biological pest control in conventional compared to organic crop fields.

    Science.gov (United States)

    Krauss, Jochen; Gallenberger, Iris; Steffan-Dewenter, Ingolf

    2011-01-01

    Organic farming is one of the most successful agri-environmental schemes, as humans benefit from high quality food, farmers from higher prices for their products and it often successfully protects biodiversity. However there is little knowledge if organic farming also increases ecosystem services like pest control. We assessed 30 triticale fields (15 organic vs. 15 conventional) and recorded vascular plants, pollinators, aphids and their predators. Further, five conventional fields which were treated with insecticides were compared with 10 non-treated conventional fields. Organic fields had five times higher plant species richness and about twenty times higher pollinator species richness compared to conventional fields. Abundance of pollinators was even more than one-hundred times higher on organic fields. In contrast, the abundance of cereal aphids was five times lower in organic fields, while predator abundances were three times higher and predator-prey ratios twenty times higher in organic fields, indicating a significantly higher potential for biological pest control in organic fields. Insecticide treatment in conventional fields had only a short-term effect on aphid densities while later in the season aphid abundances were even higher and predator abundances lower in treated compared to untreated conventional fields. Our data indicate that insecticide treatment kept aphid predators at low abundances throughout the season, thereby significantly reducing top-down control of aphid populations. Plant and pollinator species richness as well as predator abundances and predator-prey ratios were higher at field edges compared to field centres, highlighting the importance of field edges for ecosystem services. In conclusion organic farming increases biodiversity, including important functional groups like plants, pollinators and predators which enhance natural pest control. Preventative insecticide application in conventional fields has only short-term effects on aphid

  18. Pegylation of fibronectin and its functional domains: Effect on stability and biological activity

    Science.gov (United States)

    Zhang, Chen

    Delayed wound healing in many chronic wounds has been linked to the lack of extracellular matrix (ECM) support and the degradation of fibronectin (FN) by an abnormally high protease level. The ECM provides physical and chemical cues that direct tissue growth and development while FN is a key ECM protein that attracts and binds different molecules and cells. The goal of my study is creating an ECM analogue based on a composite of polyethylene glycol (PEG) hydrogels and FN binding domains and stabilizing FN against proteolytic degradation by conjugating it to PEG. The work presented here shows a two-prong approach by which the problem of ECM degradation and deficiency chronic wound healing can be addressed. The first approach for addressing ECM deficiency is through a scaffold design methodology. The novelty of the scaffold approach is that it uses the cell-binding domains of FN instead of the often-used RGD peptide. I demonstrate that a PEG hydrogel with the cell-binding domain produces a more robust biological response in cells than a PEG hydrogel with the RGD peptide. I also demonstrate that varying different functional domains of FN can be used to controllably stimulate multiple biological responses. The second approach demonstrates a method by which FN, a key ECM protein, is stabilized against proteolytic degradation without perturbing its activity. These studies of creating PEG-FN conjugates are the first of their kind. Collectively, the data that I present in this thesis will lead to novel therapeutic methods for treating chronic wounds.

  19. Construction of biological control strain of Trichoderma viride and study of their ability to induce plant disease resistance

    Institute of Scientific and Technical Information of China (English)

    LIU Shi-wang; GUO Ze-jian

    2004-01-01

    @@ Plant diseases heavily affct plant growth and crop yield even in modern agriculture. Control its difficult because pathogens mutate frequently, and this leads in frequent breaking of disease resistance in commercial cultivars. The excessive application of chemical pesticides is not only producing pesticideresistant pathogens, but it is harming the environment threatening the health of human beings.Therefore, the use of biological control agents (BCA) may provide an environmental friendly alternative to chemicals for plant disease control. Hypersensitive response (HR) and systemic acquired resistance (SAR) are the typical expressions of plant defense reactions. Once SAR is established,, the plants exhibits a broad-spectrum of disease resistance against pathogen attack. Researchers have identified elicitor proteins, such as elicitins and harpins, which activate plant defense reactions. It would be useful to explore the possibility of using biological control agents to induce a status of SAR in crop plants.

  20. Metalloproteinases: A parade of functions in matrix biology and an outlook for the future.

    Science.gov (United States)

    Apte, Suneel S; Parks, William C

    2015-01-01

    This issue of Matrix Biology is devoted to exploring how metalloproteinases - here inclusive of related families of extracellular proteinases - act on extracellular matrix (ECM) proteins to influence an astonishing diversity of biological systems and diseases. Since their discovery in the 1960's, matrix metalloproteinases (MMPs) have oft and widely been considered as the principal mediators of ECM destruction. However, as becomes clear from several articles in this issue, MMPs affect processes that both promote and limit ECM assembly, structure, and quantity. Furthermore, it has become increasingly apparent that ECM proteolysis is neither the exclusive function of MMPs nor their only sphere of influence. Thus, other enzymes may be important participants in ECM proteolysis, and indeed they are. The ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type 1 repeat) proteinases, BMP/tolloid proteases, and meprins have all emerged as major mechanisms of ECM proteolysis. An aggregate view of proteolysis as an exquisitely specific and crucial post-translational modification of secreted proteins emerges from these reviews. The cumulative evidence strongly suggests that although some MMPs can and do cleave ECM components, notably fibrillar collagens, the majority of these proteinases are not key physiological participants in morphogenesis nor in control of matrix metabolism in homeostasis or disease. In contrast, deficiency of ADAMTS proteases leads to a remarkable array of morphogenetic defects and connective tissue disorders consistent with a specialized role in turnover of the embryonic provisional ECM and in ECM assembly. Astacin-related proteases emerge into crucial positions in ECM assembly and turnover, although they also have numerous roles related to morphogen and growth factor regulation. To further turn the traditional view on its head, it is clear that many MMPs are key participants in many, diverse immune and inflammation processes

  1. Recent advances in alveolar biology: evolution and function of alveolar proteins.

    Science.gov (United States)

    Orgeig, Sandra; Hiemstra, Pieter S; Veldhuizen, Edwin J A; Casals, Cristina; Clark, Howard W; Haczku, Angela; Knudsen, Lars; Possmayer, Fred

    2010-08-31

    This review is focused on the evolution and function of alveolar proteins. The lung faces physical and environmental challenges, due to changing pressures/volumes and foreign pathogens, respectively. The pulmonary surfactant system is integral in protecting the lung from these challenges via two groups of surfactant proteins - the small molecular weight hydrophobic SPs, SP-B and -C, that regulate interfacial adsorption of the lipids, and the large hydrophilic SPs, SP-A and -D, which are surfactant collectins capable of inhibiting foreign pathogens. Further aiding pulmonary host defence are non-surfactant collectins and antimicrobial peptides that are expressed across the biological kingdoms. Linking to the first symposium session, which emphasised molecular structure and biophysical function of surfactant lipids and proteins, this review begins with a discussion of the role of temperature and hydrostatic pressure in shaping the evolution of SP-C in mammals. Transitioning to the role of the alveolus in innate host defence we discuss the structure, function and regulation of antimicrobial peptides, the defensins and cathelicidins. We describe the recent discovery of novel avian collectins and provide evidence for their role in preventing influenza infection. This is followed by discussions of the roles of SP-A and SP-D in mediating host defence at the alveolar surface and in mediating inflammation and the allergic response of the airways. Finally we discuss the use of animal models of lung disease including knockouts to develop an understanding of the role of these proteins in initiating and/or perpetuating disease with the aim of developing new therapeutic strategies.

  2. Modeling injury rates as a function of industrialized versus on-site construction techniques.

    Science.gov (United States)

    Rubio-Romero, J C; Suárez-Cebador, M; Abad, Jesús

    2014-05-01

    It is often predicted that the industrialization of building activities will lead to a reduction of accident rates in the construction sector, particularly as a result of switching activities from building sites to factories. However, to date no scientific research has provided objective quantitative results to back up this claim. The aim of this paper is to evaluate how industrialization affects the accident rate in different industrialized building systems in Spain. Our results revealed that the industrialized steel modular system presents the lowest accident rate, while the highest accident rate was recorded in the construction method with cast-in-place concrete. The lightweight construction system also presents a high accident rate. Accordingly, industrialized building systems cannot claim to be safer than traditional ones. The different types of "on-site work" seem to be the main variable which would explain the accident rates recorded in industrialized construction systems.

  3. Properties of Healthcare Teaming Networks as a Function of Network Construction Algorithms

    CERN Document Server

    Zand, Martin S; Farooq, Samir A; Fucile, Christopher; Ghoshal, Grourab; White, Robert J; Quill, Caroline M; Rosenberg, Alexander; Serrano, Hugo; Chafi, Hassan; Boudreau, Timothy

    2016-01-01

    Network models of healthcare systems can be used to examine how providers collaborate, communicate, refer patients to each other. Most healthcare service network models have been constructed from patient claims data, using billing claims to link patients with providers. The data sets can be quite large, making standard methods for network construction computationally challenging and thus requiring the use of alternate construction algorithms. While these alternate methods have seen increasing use in generating healthcare networks, there is little to no literature comparing the differences in the structural properties of the generated networks. To address this issue, we compared the properties of healthcare networks constructed using different algorithms and the 2013 Medicare Part B outpatient claims data. Three different algorithms were compared: binning, sliding frame, and trace-route. Unipartite networks linking either providers or healthcare organizations by shared patients were built using each method. We...

  4. Performance of digester decant system with biological filter followed by constructed wetland and solar reactor in the treatment of domestic sewage

    Directory of Open Access Journals (Sweden)

    Delfran Batista dos Santos

    2012-08-01

    Full Text Available This study aimed to analyze the performance of digester decant system with biological filter followed by constructed wetland and solar reactor in the treatment of domestic sewage from Milagres rural community in Apodi-RN. The treatment system was monitored for the period of October and November 2010, 48 days after planting Pennisetum purpureum Schumach. Samples of domestic sewage were collected at different stages of treatment, in four replications on time, to determine physicochemical and microbiological characteristics about the system performance. The results indicated significant removal of turbidity, biochemical oxygen demand, chemical oxygen demand, total solids, suspended solids, phosphorus and oil and grease using the set digester decant with biological filter, followed by constructed wetland and solar reactor; the association of average solar radiation of 28.73 MJ m-2 d-1, effluent depth of 0.10 m on reactor and time of sun exposure of 12 hours provided removal of fecal coliform up to 99.99% of domestic sewage in Apodi, RN, the treated effluent met microbiological standard of the Brazilian guidelines for agricultural use with restrictions.

  5. The Biological Function of the Prion Protein: A Cell Surface Scaffold of Signaling Modules

    Science.gov (United States)

    Linden, Rafael

    2017-01-01

    The prion glycoprotein (PrPC) is mostly located at the cell surface, tethered to the plasma membrane through a glycosyl-phosphatydil inositol (GPI) anchor. Misfolding of PrPC is associated with the transmissible spongiform encephalopathies (TSEs), whereas its normal conformer serves as a receptor for oligomers of the β-amyloid peptide, which play a major role in the pathogenesis of Alzheimer’s Disease (AD). PrPC is highly expressed in both the nervous and immune systems, as well as in other organs, but its functions are controversial. Extensive experimental work disclosed multiple physiological roles of PrPC at the molecular, cellular and systemic levels, affecting the homeostasis of copper, neuroprotection, stem cell renewal and memory mechanisms, among others. Often each such process has been heralded as the bona fide function of PrPC, despite restricted attention paid to a selected phenotypic trait, associated with either modulation of gene expression or to the engagement of PrPC with a single ligand. In contrast, the GPI-anchored prion protein was shown to bind several extracellular and transmembrane ligands, which are required to endow that protein with the ability to play various roles in transmembrane signal transduction. In addition, differing sets of those ligands are available in cell type- and context-dependent scenarios. To account for such properties, we proposed that PrPC serves as a dynamic platform for the assembly of signaling modules at the cell surface, with widespread consequences for both physiology and behavior. The current review advances the hypothesis that the biological function of the prion protein is that of a cell surface scaffold protein, based on the striking similarities of its functional properties with those of scaffold proteins involved in the organization of intracellular signal transduction pathways. Those properties are: the ability to recruit spatially restricted sets of binding molecules involved in specific signaling

  6. Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets.

    Science.gov (United States)

    Bassel, George W; Glaab, Enrico; Marquez, Julietta; Holdsworth, Michael J; Bacardit, Jaume

    2011-09-01

    The meta-analysis of large-scale postgenomics data sets within public databases promises to provide important novel biological knowledge. Statistical approaches including correlation analyses in coexpression studies of gene expression have emerged as tools to elucidate gene function using these data sets. Here, we present a powerful and novel alternative methodology to computationally identify functional relationships between genes from microarray data sets using rule-based machine learning. This approach, termed "coprediction," is based on the collective ability of groups of genes co-occurring within rules to accurately predict the developmental outcome of a biological system. We demonstrate the utility of coprediction as a powerful analytical tool using publicly available microarray data generated exclusively from Arabidopsis thaliana seeds to compute a functional gene interaction network, termed Seed Co-Prediction Network (SCoPNet). SCoPNet predicts functional associations between genes acting in the same developmental and signal transduction pathways irrespective of the similarity in their respective gene expression patterns. Using SCoPNet, we identified four novel regulators of seed germination (ALTERED SEED GERMINATION5, 6, 7, and 8), and predicted interactions at the level of transcript abundance between these novel and previously described factors influencing Arabidopsis seed germination. An online Web tool to query SCoPNet has been developed as a community resource to dissect seed biology and is available at http://www.vseed.nottingham.ac.uk/.

  7. Object-based attentional modulation of biological motion processing: spatiotemporal dynamics using functional magnetic resonance imaging and electroencephalography.

    Science.gov (United States)

    Safford, Ashley S; Hussey, Elizabeth A; Parasuraman, Raja; Thompson, James C

    2010-07-07

    Although it is well documented that the ability to perceive biological motion is mediated by the lateral temporal cortex, whether and when neural activity in this brain region is modulated by attention is unknown. In particular, it is unclear whether the processing of biological motion requires attention or whether such stimuli are processed preattentively. Here, we used functional magnetic resonance imaging, high-density electroencephalography, and cortically constrained source estimation methods to investigate the spatiotemporal effects of attention on the processing of biological motion. Directing attention to tool motion in overlapping movies of biological motion and tool motion suppressed the blood oxygenation level-dependent (BOLD) response of the right superior temporal sulcus (STS)/middle temporal gyrus (MTG), while directing attention to biological motion suppressed the BOLD response of the left inferior temporal sulcus (ITS)/MTG. Similarly, category-based modulation of the cortical current source density estimates from the right STS/MTG and left ITS was observed beginning at approximately 450 ms following stimulus onset. Our results indicate that the cortical processing of biological motion is strongly modulated by attention. These findings argue against preattentive processing of biological motion in the presence of stimuli that compete for attention. Our findings also suggest that the attention-based segregation of motion category-specific responses only emerges relatively late (several hundred milliseconds) in processing.

  8. Construction of Control Lyapunov Functions for a Class of Nonlinear Systems%一类非线性系统控制Lyapunov函数的构造

    Institute of Scientific and Technical Information of China (English)

    蔡秀珊; 韩正之; 汪晓东

    2006-01-01

    The construction of control Lyapunov functions for a class of nonlinear systems is considered. We develop a method by which a control Lyapunov function for the feedback linearizable part can be constructed systematically via Lyapunov equation. Moreover, by a control Lyapunov function of the feedback linearizable part and a Lyapunov function of the zero dynamics, a control Lyapunov function for the overall nonlinear system is established.

  9. Carbohydrate/glycan-binding specificity of legume lectins in respect to their proposed biological functions

    Directory of Open Access Journals (Sweden)

    Márcio Viana Ramos

    2000-01-01

    Full Text Available The lectins, proteins which specifically recognize carbohydrate moieties, have been extensively studied in many biochemical and structural aspects in order to establish the molecular basis of this non-catalytic event. On the other hand, their clinical and agricultural potentials have been growing fast. Although lectins, mainly those from legume plants, had been investigated for biological properties, studies about the physiological functions of lectins are scarce in literature. Therefore, despite the accumulated data on lectins (as proteins, the role played by these signalizing molecules is poorly discussed. In the light of our accumulated results on legume lectins, specially those obtained from plants belonging to the Diocleinae sub-tribe and available data in literature, we discuss here the main hypothesis of their functions according to their carbohydrate/glycan-binding specificity.As lectinas, proteinas que especificamente reconhecem estruturas que contém carboidratos, têm sido extensivamente estudadas em muitos aspectos bioquímicos e estruturais, objetivando estabelecer as bases moleculares deste evento não-catalítico. Por outro lado, os potenciais clínicos e agriculturais destas proteínas têm crescido rapidamente. Embora as lectinas, principalmente aquelas de legumes tenham sido bastante investigadas em suas propriedades biológicas, estudos sobre as funcões fisiológicas de lectinas são escassos na literatura. Além disto, a despeito da quantidade de dados acumulados sobre lectinas (como proteínas, o papel desempenhado por estas moléculas de sinalização é pobremente discutido. Valendo-se de nossos estudos sobre lectinas de leguminosas, principalmente da sub-tribo Diocleinae, e outros dados presentes na literatura, discutimos aqui, as principais hipóteses de suas funções com base na especificidade por carboidratos e glicanos complexos.

  10. Unexpected functional similarities between gatekeeper tumour suppressor genes and proto-oncogenes revealed by systems biology.

    Science.gov (United States)

    Zhao, Yongzhong; Epstein, Richard J

    2011-05-01

    Familial tumor suppressor genes comprise two subgroups: caretaker genes (CTs) that repair DNA, and gatekeeper genes (GKs) that trigger cell death. Since GKs may also induce cell cycle delay and thus enhance cell survival by facilitating DNA repair, we hypothesized that the prosurvival phenotype of GKs could be selected during cancer progression, and we used a multivariable systems biology approach to test this. We performed multidimensional data analysis, non-negative matrix factorization and logistic regression to compare the features of GKs with those of their putative antagonists, the proto-oncogenes (POs), as well as with control groups of CTs and functionally unrelated congenital heart disease genes (HDs). GKs and POs closely resemble each other, but not CTs or HDs, in terms of gene structure (P<0.001), expression level and breadth (P<0.01), DNA methylation signature (P<0.001) and evolutionary rate (P<0.001). The similar selection pressures and epigenetic trajectories of GKs and POs so implied suggest a common functional attribute that is strongly negatively selected-that is, a shared phenotype that enhances cell survival. The counterintuitive finding of similar evolutionary pressures affecting GKs and POs raises an intriguing possibility: namely, that cancer microevolution is accelerated by an epistatic cascade in which upstream suppressor gene defects subvert the normal bifunctionality of wild-type GKs by constitutively shifting the phenotype away from apoptosis towards survival. If correct, this interpretation would explain the hitherto unexplained phenomenon of frequent wild-type GK (for example, p53) overexpression in tumors.

  11. Construction of a tissue engineered intervertebral disc with high biological activity using an allogeneic intervertebral disc supplemented with transfected nucleus pulposus cells expressing exogenous dopamine beta-hydroxylase.

    Science.gov (United States)

    Bai, M; Wang, Y H; Yin, H P; Li, S W

    2015-09-09

    This study addressed the in vitro construction and biological activity of tissue engineered intervertebral discs with exogenous human dopamine beta-hydroxylase (DBH) nucleus pulposus cells. pSNAV2.0-DBH expression plasmids were utilized to enhance the survival rates of intervertebral disc tissue cells. Various concentrations of transfected nucleus pulposus cells were injected into the discs, and DBH mRNA expression was determined using polymerase chain reaction amplification. Polysaccharide content and total collagen protein content in the engineered disc nucleus pulposus tissue were determined. The visible fluorescence intensities of the 1 x 10(5) and 1 x 10(6) groups vs the 1 x 10(4) group were significantly increased (P 0.05) at 7 days after injection. DBH mRNA expression could be detected in the all but the EGFP control group at 14 days culture. No significant difference was observed in the protein content between the 1 x 10(4) and the control groups at various times, while the protein content was significantly higher in the 1 x 10(5) vs the control and the 1 x 10(4) groups at 7-, 14-, and 21-day cultures. These results demonstrate that a tissue engineered intervertebral disc with high biological activity can be constructed by utilizing allogeneic intervertebral discs stored in liquid nitrogen and a 1 x 10(5) transfected nucleus pulposus cell complex with in vitro culture for 14 days. This model can be used in animal experiments to study the biological activity of the engineered discs.

  12. Construction and Application of Harmful Biology Database System of Cassava%木薯有害生物数据库的构建与应用

    Institute of Scientific and Technical Information of China (English)

    时涛; 李超萍; 范志伟; 程汉亭; 黄贵修

    2011-01-01

    Based on recent study progress of diseases, pests (mites)and weeds on cassava, a database system was constructed with relative information and pictures to meet the the quick search of cassava harmful biology information. The database, including disease, pests (mites)and weeds sub -libraries, provides multi -query mode consisted of sub-library query, general query and quick query. The principles of open and standardization were undertaken in the construction of the database, which was helpful in keeping collecting and improving all kinds of cassaca harmful biology information. The database could also supply supporting data for further development of a harmful biology information platform on early warning and monitoring, risk assessment, remote identification and diagnoses.%以危害木薯生产的病害、虫(螨)害和草害为研究对象,根据国内外相关研究进展,经过系统整理和有序化存储,构建了图文并茂的数据库系统,实现了基于Web的木薯有害生物相关信息的快速查询.数据库包括木薯病害、木薯虫(螨)害和木薯草害3个子库,提供子库查询、综合查询、快速查询等多种查询方式.数据库的构建遵循开放、标准化的原则,有利于不断收集和完善木薯有害生物各类信息,并为进一步建设有害生物预警监测、风险评估、远程识别与诊断等信息平台提供支撑数据.

  13. Improved normal tissue sparing in head and neck radiotherapy using biological cost function based-IMRT.

    Science.gov (United States)

    Anderson, N; Lawford, C; Khoo, V; Rolfo, M; Joon, D L; Wada, M

    2011-12-01

    Intensity-modulated radiotherapy (IMRT) has reduced the impact of acute and late toxicities associated with head and neck radiotherapy. Treatment planning system (TPS) advances in biological cost function based optimization (BBO) and improved segmentation techniques have increased organ at risk (OAR) sparing compared to conventional dose-based optimization (DBO). A planning study was undertaken to compare OAR avoidance in DBO and BBO treatment planning. Simultaneous integrated boost treatment plans were produced for 10 head and neck patients using both planning systems. Plans were compared for tar get coverage and OAR avoidance. Comparisons were made using the BBO TPS Monte Carlo dose engine to eliminate differences due to inherent algorithms. Target coverage (V95%) was maintained for both solutions. BBO produced lower OAR doses, with statistically significant improvement to left (12.3%, p = 0.005) and right parotid mean dose (16.9%, p = 0.004), larynx V50_Gy (71.0%, p = 0.005), spinal cord (21.9%, p < 0.001) and brain stem dose maximums (31.5%, p = 0.002). This study observed improved OAR avoidance with BBO planning. Further investigations will be undertaken to review any clinical benefit of this improved planned dosimetry.

  14. Melanocyte biology and function with reference to oral melanin hyperpigmentation in HIV-seropositive subjects.

    Science.gov (United States)

    Feller, Liviu; Chandran, Rakesh; Kramer, Beverley; Khammissa, Razia A G; Altini, Mario; Lemmer, Johan

    2014-09-01

    The color of normal skin and of oral mucosa is not determined by the number of melanocytes in the epithelium but rather by their melanogenic activity. Pigmented biopolymers or melanins are synthesized in melanosomes. Tyrosinase is the critical enzyme in the biosynthesis of both brown/black eumelanin and yellow/red pheomelanin. The number of the melanosomes within the melanocytes, the type of melanin within the melanosomes, and the efficacy of the transfer of melanosomes from the melanocytes to the neighboring keratinocytes all play an important role in tissue pigmentation. Melanin production is regulated by locally produced factors including proopiomelanocortin and its derivative peptides, particularly alpha-melanocyte-stimulating hormone (α-MSH), melanocortin 1 receptor (MC1R), adrenergic and cholinergic agents, growth factors, cytokines, and nitric oxide. Both eumelanin and pheomelanin can be produced by the same melanocytes, and the proportion of the two melanin types is influenced by the degree of functional activity of the α-MSH/MC1R intracellular pathway. The cause of HIV oral melanosis is not fully understood but may be associated with HIV-induced cytokine dysregulation, with the medications commonly prescribed to HIV-seropositive persons, and with adrenocortical dysfunction, which is not uncommon in HIV-seropositive subjects with AIDS. The purpose of this article is to discuss some aspects of melanocyte biology and HIV-associated oral melanin hyperpigmentation.

  15. Functional and biological diversity of foliar spectra in tree canopies throughout the Andes to Amazon region.

    Science.gov (United States)

    Asner, Gregory P; Martin, Roberta E; Carranza-Jiménez, Loreli; Sinca, Felipe; Tupayachi, Raul; Anderson, Christopher B; Martinez, Paola

    2014-10-01

    Spectral properties of foliage express fundamental chemical interactions of canopies with solar radiation. However, the degree to which leaf spectra track chemical traits across environmental gradients in tropical forests is unknown. We analyzed leaf reflectance and transmittance spectra in 2567 tropical canopy trees comprising 1449 species in 17 forests along a 3400-m elevation and soil fertility gradient from the Amazonian lowlands to the Andean treeline. We developed quantitative links between 21 leaf traits and 400-2500-nm spectra, and developed classifications of tree taxa based on spectral traits. Our results reveal enormous inter-specific variation in spectral and chemical traits among canopy trees of the western Amazon. Chemical traits mediating primary production were tightly linked to elevational changes in foliar spectral signatures. By contrast, defense compounds and rock-derived nutrients tracked foliar spectral variation with changing soil fertility in the lowlands. Despite the effects of abiotic filtering on mean foliar spectral properties of tree communities, the spectra were dominated by phylogeny within any given community, and spectroscopy accurately classified 85-93% of Amazonian tree species. Our findings quantify how tropical tree canopies interact with sunlight, and indicate how to measure the functional and biological diversity of forests with spectroscopy.

  16. Expression of a Magnaporthe grisea Elicitor and Its Biological Function in Activating Resistance in Rice

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The expression of a protein elicitor from Magnaporthe griesea and its biological function in activating resistance in rice (Oryza sativa L) were reported. The gene of elicitor was expressed in Escherichia coli cells and produced a His6-fusion protein with 42 kD apparent molecular weight on SDS-PAGE. The purified protein could induce the resistance to blast disease, with the control efficiency of 46.47% and 36.41% at the 14th day and the 21st day after blast inoculation, respectively.After treatment with the expressed protein, the phenylalanine ammonia-lyase (PAL) and peroxidase (POD) activities were promoted in rice plants, meanwhile, the transcription levels of STKM, FAD, PBZ1 and PR1 genes were increased in rice plants. Moreover, after comparing the profile of total rice leaf proteins on two-dimensional eiectrophoresis gel, about 14proteins were found to be increased in expression level after the expressed protein treatment. All the results indicated that the expressed protein could act as an elicitor to trigger the resistance in rice.

  17. Gene-based GWAS and biological pathway analysis of the resilience of executive functioning.

    Science.gov (United States)

    Mukherjee, Shubhabrata; Kim, Sungeun; Ramanan, Vijay K; Gibbons, Laura E; Nho, Kwangsik; Glymour, M Maria; Ertekin-Taner, Nilüfer; Montine, Thomas J; Saykin, Andrew J; Crane, Paul K

    2014-03-01

    Resilience in executive functioning (EF) is characterized by high EF measured by neuropsychological test performance despite structural brain damage from neurodegenerative conditions. We previously reported single nucleotide polymorphism (SNP) genome-wide association study (GWAS) results for EF resilience. Here, we report gene- and pathway-based analyses of the same resilience phenotype, using an optimal SNP-set (Sequence) Kernel Association Test (SKAT) for gene-based analyses (conservative threshold for genome-wide significance = 0.05/18,123 = 2.8 × 10(-6)) and the gene-set enrichment package GSA-SNP for biological pathway analyses (False discovery rate (FDR) resilience (p = 1.33 × 10(-7)). Genetic pathways involved with dendritic/neuron spine, presynaptic membrane, postsynaptic density, etc., were enriched with association to EF resilience. Although replication of these results is necessary, our findings indicate the potential value of gene- and pathway-based analyses in research on determinants of cognitive resilience.

  18. The biology and functional morphology of Macoma biota (Bivalvia: Tellinidae: Macominae

    Directory of Open Access Journals (Sweden)

    Pedro Ribeiro Piffer

    2011-06-01

    Full Text Available Macoma biota Arruda & Domaneschi, 2005, is a recently described species known only from the intertidal zone of Praia da Cidade, Caraguatatuba Bay, in the state of São Paulo, southeastern Brazil. The main purpose of the present paper is to describe the biology of M. biota, beginning with a detailed analysis of its anatomy and functional morphology and how these attributes are correlated with its habitat and life history. The morphology of the organs in the pallial cavity and their sorting devices indicate that this species has efficient mechanisms to process large amounts of particles that enter this cavity via the inhalant current. M. biota can rapidly select the material suitable for ingestion and direct the undesired excess to the rejection mantle tracts. These characteristics along with the siphon's behavior and the digestive tract configuration reveal that this species can be classified primarily as a deposit feeder, like other species of the genus; however, it can also behave as a suspension feeder, depending on the environmental conditions.

  19. Biological functions of glycosyltransferase genes involved in O-fucose glycan synthesis.

    Science.gov (United States)

    Okajima, Tetsuya; Matsuura, Aiko; Matsuda, Tsukasa

    2008-07-01

    Rare types of glycosylation often occur in a domain-specific manner and are involved in specific biological processes. Well-known examples of such modification are O-linked fucose (O-fucose) and O-linked glucose (O-glucose) glycans on epidermal growth factor (EGF) domains. In particular, O-fucose glycans are reported to regulate the functions of EGF domain-containing proteins such as urinary-type plasminogen activator and Notch receptors. Two glycosyltransferases catalyze the initiation and elongation of O-fucose glycans. The initiation process is catalyzed by O-fucosyltransferase 1, which is essential for Notch signalling in both Drosophila and mice. O-fucosyltransferase 1 can affect the folding, ligand interaction and endocytosis of Notch receptors, and both the glycosyltransferase and non-catalytic activities of O-fucosyltransferase 1 have been reported. The elongation of O-fucose monosaccharide is catalyzed by Fringe-related genes, which differentially modulate the interaction between Notch and two classes of ligands, namely, Delta and Serrate/Jagged. In this article, we have reviewed the recent reports addressing the distinctive features of the glycosyltransferases and O-glycans present on the EGF domains.

  20. Mechanically robust, rapidly actuating, and biologically functionalized macroporous poly(N-isopropylacrylamide)/silk hybrid hydrogels.

    Science.gov (United States)

    Gil, Eun Seok; Park, Sang-Hyug; Tien, Lee W; Trimmer, Barry; Hudson, Samuel M; Kaplan, David L

    2010-10-05

    A route toward mechanically robust, rapidly actuating, and biologically functionalized polymeric actuators using macroporous soft materials is described. The materials were prepared by combining silk protein and a synthetic polymer (poly(N-isopropylacrylamide) (PNIAPPm)) to form interpenetrating network materials and macroporous structures by freeze-drying, with hundreds of micrometer diameter pores and exploiting the features of both polymers related to dynamic materials and structures. The chemically cross-linked PNIPAAm networks provided stimuli-responsive features, while the silk interpenetrating network formed by inducing protein β-sheet crystallinity in situ for physical cross-links provided material robustness, improved expansion force, and enzymatic degradability. The macroporous hybrid hydrogels showed enhanced thermal-responsive properties in comparison to pure PNIPAAm hydrogels, nonporous silk/PNIPAAm hybrid hydrogels, and previously reported macroporous PNIPAAm hydrogels. These new systems reach near equilibrium sizes in shrunken/swollen states in less than 1 min, with the structural features providing improved actuation rates and stable oscillatory properties due to the macroporous transport and the mechanically robust silk network. Confocal images of the hydrated hydrogels around the lower critical solution temperature (LCST) revealed macropores that could be used to track changes in the real time morphology upon thermal stimulus. The material system transformed from a macroporous to a nonporous structure upon enzymatic degradation. To extend the utility of the system, an affinity platform for a switchable or tunable system was developed by immobilizing biotin and avidin on the macropore surfaces.

  1. Soft robotic arm inspired by the octopus: I. From biological functions to artificial requirements.

    Science.gov (United States)

    Margheri, L; Laschi, C; Mazzolai, B

    2012-06-01

    Octopuses are molluscs that belong to the group Cephalopoda. They lack joints and rigid links, and as a result, their arms possess virtually limitless freedom of movement. These flexible appendages exhibit peculiar biomechanical features such as stiffness control, compliance, and high flexibility and dexterity. Studying the capabilities of the octopus arm is a complex task that presents a challenge for both biologists and roboticists, the latter of whom draw inspiration from the octopus in designing novel technologies within soft robotics. With this idea in mind, in this study, we used new, purposively developed methods of analysing the octopus arm in vivo to create new biologically inspired design concepts. Our measurements showed that the octopus arm can elongate by 70% in tandem with a 23% diameter reduction and exhibits an average pulling force of 40 N. The arm also exhibited a 20% mean shortening at a rate of 17.1 mm s(-1) and a longitudinal stiffening rate as high as 2 N (mm s)(-1). Using histology and ultrasounds, we investigated the functional morphology of the internal tissues, including the sinusoidal arrangement of the nerve cord and the local insertion points of the longitudinal and transverse muscle fibres. The resulting information was used to create novel design principles and specifications that can in turn be used in developing a new soft robotic arm.

  2. Structural changes in PVDF fibers due to electrospinning and its effect on biological function.

    Science.gov (United States)

    Damaraju, Sita M; Wu, Siliang; Jaffe, Michael; Arinzeh, Treena Livingston

    2013-08-01

    Polyvinylidine fluoride (PVDF) is being investigated as a potential scaffold for bone tissue engineering because of its proven biocompatibility and piezoelectric property, wherein it can generate electrical activity when mechanically deformed. In this study, PVDF scaffolds were prepared by electrospinning using different voltages (12-30 kV), evaluated for the presence of the piezoelectric β-crystal phase and its effect on biological function. Electrospun PVDF was compared with unprocessed/raw PVDF, films and melt-spun fibers for the presence of the piezoelectric β-phase using differential scanning calorimetry, Fourier transform infrared spectroscopy and x-ray diffraction. The osteogenic differentiation of human mesenchymal stem cells (MSCs) was evaluated on scaffolds electrospun at 12 and 25 kV (PVDF-12 kV and PVDF-25 kV, respectively) and compared to tissue culture polystyrene (TCP). Electrospinning PVDF resulted in the formation of the piezoelectric β-phase with the highest β-phase fraction of 72% for electrospun PVDF at 25 kV. MSCs cultured on both the scaffolds were well attached as indicated by a spread morphology. Cells on PVDF-25 kV scaffolds had the greatest alkaline phosphatase activity and early mineralization by day 10 as compared to TCP and PVDF-12 kV. The results demonstrate the potential for the use of PVDF scaffolds for bone tissue engineering applications.

  3. Molecular mechanism and biological function of miRNA-155 and its target genes on endometriosis

    Institute of Scientific and Technical Information of China (English)

    Na Ji; Li Zhao; Xin Feng; Li-Mei Luo; Ting Liang; Chen-Yu Zhuang; Li-Hua Zhang

    2015-01-01

    Objective:To explore molecular mechanism and biological function of miR-155 and its target genes on endometriosis.Methods: The expression of miR-155 in Ems patient and healthy control were assayed by RT-PCR. After miR-155 mimic and inhibitor were transfected into Ems endometrial cells for 48 h, the viability of cell was detected by MTT assay. Transwell migration and invasion assay were used to detect cell migration and invasion. The expression of cell apoptotic protein Bax and Bcl-2, matrix metalloproteinase (MMP 2) and MMP 9 were assayed by western blot.Results: The expression of miR-155 in Ems patient was more than that in the health control (P<0.01). After miR-155 mimic and inhibitor were transfected into Ems endometrial cells for 48 h, miR-155 over-expression could increase cell viability, and promoted cell migration and invasion, which was related to down-regulation of Bax along with up-regulation of Bcl-2, MMP 2 and MMP 9.Conclusion:These results suggested miR-155 lower expression inhibit endometrial cell proliferation and migration of the Ems.

  4. Synthetic biology for therapeutic applications.

    Science.gov (United States)

    Abil, Zhanar; Xiong, Xiong; Zhao, Huimin

    2015-02-02

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders.

  5. CONSTRUCTING AAV-TGFβ1 AND COMPARISING ITS BIOLOGICAL EFFECTS ON PROTEOGLYCAN SYNTHESIS OF NUCLEUS PULPOUS CELLS WITH AV-TGFβ1

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective To construct adeno-associated virus express system for TGFβ1 (AAV-TGFβ1) and compare its biological effects on proteoglycan synthesis of the rabbit lumbar disc nucleus pulpous (NP) cells with adenovirus (Ad) express system for TGFβ1 (AV-TGFβ1). Methods TGFβ1 gene was obtained by polymerase chain reactions (PCR). The upstream of TGFβ1 contained restriction enzyme site of EcoR Ⅰ, and the restriction enzyme site of Sal Ⅰ was at the downstream of TGFβ1. Using the multiple cloning sites (MCS) in plasmid AAV and the corresponding contained restriction enzyme site in PCR product of TGFβ1, TGFβ1 gene was subcloned into AAV. The recombinant plasmid AAV-TGFβ1 was detected by restriction enzyme digestion and DNA sequencing. Then, AAV-TGFβ1 virus was packaged and TGFβ1 expression mediated by AAV was detected by immunofluence analysis in H293 cells. AAV transfection rate to NP cells was evaluated with AAV-PEGF. After NP cells were respectively transfected by AAV-TGFβ1 virus and AV-TGFβ1 virus, proteoglycan synthesis was detected and compared by using Antonopulos methods. Results DNA sequencing revealed that the PCR-amplified TGFβ1 gene was consistent with NCBI Gene Bank. The recombinant plasmid was proved to be constructed successfully by restriction enzyme digestion. AAV could be transfected into NP cells and mediate an efficient expression of TGFβ1 protein. AV-TGFβ1 virus could quickly enhance the proteoglycan synthesis of the NP cells, but its biological effect was transient. AAV-TGFβ1 virus could enhance stably proteoglycan synthesis. Conclusion AAV-TGFβ1 virus was successful constructed and enhanced stably proteoglycan synthesis of NP cells.

  6. Construction of uricase-overproducing strains of Hansenula polymorpha and its application as biological recognition element in microbial urate biosensor

    Directory of Open Access Journals (Sweden)

    Schuhmann Wolfgang

    2011-05-01

    Full Text Available Abstract Background The detection and quantification of uric acid in human physiological fluids is of great importance in the diagnosis and therapy of patients suffering from a range of disorders associated with altered purine metabolism, most notably gout and hyperuricaemia. The fabrication of cheap and reliable urate-selective amperometric biosensors is a challenging task. Results A urate-selective microbial biosensor was developed using cells of the recombinant thermotolerant methylotrophic yeast Hansenula polymorpha as biorecognition element. The construction of uricase (UOX producing yeast by over-expression of the uricase gene of H. polymorpha is described. Following a preliminary screening of the transformants with increased UOX activity in permeabilized yeast cells the optimal cultivation conditions for maximal UOX yield namely a 40-fold increase in UOX activity were determined. The UOX producing cells were coupled to horseradish peroxidase and immobilized on graphite electrodes by physical entrapment behind a dialysis membrane. A high urate selectivity with a detection limit of about 8 μM was found. Conclusion A strain of H. polymorpha overproducing UOX was constructed. A cheap urate selective microbial biosensor was developed.

  7. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    Science.gov (United States)

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  8. 肠出血性大肠杆菌O157∶H7Ⅲ型分泌系统效应蛋白NleF基因敲除菌株的构建及其生物学功能初探%Construction and preliminary study of biological functions of O157∶H7 typeⅢsecre-tion system effector NleF gene knockout mutant

    Institute of Scientific and Technical Information of China (English)

    徐婷婷; 宋婷; 周围; 戴红梅; 岳俊杰; 梁龙

    2015-01-01

    目的:构建肠出血性大肠杆菌(enterohemorrhagic Escherichia coli,EHEC)O157∶H7 T3SS效应蛋白NleF敲除菌株和回复菌株,研究其对细菌生长和细胞死亡的影响。方法利用λ-Red同源重组的方法构建nleF基因敲除菌株ΔnleF;将pET-24a(+)-NleF重组质粒导入敲除菌感受态细胞中构建回复菌株ΔnleF/NleF。将野生株、敲除株和回复株分别用LB和DMEM(10%FBS)培养,每隔1 h测定D600,绘制生长曲线;分别用3种菌株感染HeLa细胞,用细胞毒性试剂盒检测上清中乳酸脱氢酶( LDH)的释放量,计算细胞毒性。结果成功构建NleF敲除菌株ΔnleF和回复菌株ΔnleF/NleF;野生株、敲除株和回复株三者的生长速率无明显差异;与野生株相比,ΔnleF感染HeLa细胞后,细胞毒性增加,ΔnleF/NleF感染后HeLa细胞毒性与野生株相当。结论 EHEC O157∶H7 T3SS 效应蛋白NleF对细菌的生长无明显影响,但可能抑制由细菌感染引起的宿主细胞死亡。%Objective To construct Escherichia coli O157∶H7 T3SS effector NleF gene knockout mutant and its com-plementary strain, and probe its effects on bacterial growth and cell death .Methods T3SS Effector NleF gene knockout mutant ΔnleF was constructed with λ-Red homologous recombination .Complementary strain ΔnleF/NleF was constructed by transferring pET-24a(+)-NleF into ΔnleF competent cells.Wild type,ΔnleF and ΔnleF/NleF were cultured in LB and DMEM(10%FBS) respectively,D600 was measured every hour , and the growth curve was drawn .HeLa cells were infected with three kinds of strains , the supernatant of LDH release was detected with cytotoxicity detection kit ,and the cytotoxicity was calculated .Results ΔnleF and ΔnleF/NleF were constructed .The growth rates of wild type , ΔnleF and ΔnleF/NleF was not significantly different .Wild type O157 infection induced cell death .Cytotoxicity was increased as much in ΔnleF in

  9. Short term recovery of soil biological functions in a new vineyard cultivated in organic farming

    Science.gov (United States)

    Costantini, Edoardo; Agnelli, Alessandro; Fabiani, Arturo; Gagnarli, Elena; Mocali, Stefano; Priori, Simone; Simoni, Sauro; Valboa, Giuseppe

    2014-05-01

    soil biological classes). Physical soil characteristics remained unchanged after the first year from the earthworks and did not change under grass cover. Chemical analysis only indicated a significant effect of earthworks. Over the 2010-2013 period, the new vineyard showed a slight increase of TOC and total N contents; as compared to the old vineyard, it averaged lower TOC and total N, and higher CaCO3 contents, suggesting still evolving equilibrium conditions. Microarthropod analysis showed significant different abundances and communities' structures both by management system and by year, increasing where the land use pressure was reduced by permanent grass cover and along with the aging of vineyard. Though the euedaphic forms, well adapted to soil life, were always rare. Microbiological analysis showed a different structure of eubacterial communities and a lower microbial activity in the new vineyard, especially during 2010-2012. In contrast, significant differences were not observed between the two vineyards in 2013, and grass cover effect was controversial. To sum up, the consequence of deep earthworks on chemical and biological properties were still evident after four years from planting and more time was needed to recover soil functions. Permanent grass cover did not always show a consistent positive effect.

  10. Single Fluorescent Molecules as Nano-Illuminators for Biological Structure and Function

    Science.gov (United States)

    Moerner, W. E.

    2011-03-01

    Since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. {62}, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. For example, the shape of single filaments in a living cell can be extracted simply by allowing a single molecule to move through the filament (PNAS {103}, 10929 (2006)). The addition of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (super-resolution) and a new array of acronyms (PALM, STORM, F-PALM etc.) and advances have appeared. We have used the native blinking and switching of a common yellow-emitting variant of green fluorescent protein (EYFP) reported more than a decade ago (Nature {388}, 355 (1997)) to achieve sub-40 nm super-resolution imaging of several protein structures in the bacterium Caulobacter crescentus: the quasi-helix of the actin-like protein MreB (Nat. Meth. {5}, 947 (2008)), the cellular distribution of the DNA binding protein HU (submitted), and the recently discovered division spindle composed of ParA filaments (Nat. Cell Biol. {12}, 791 (2010)). Even with these advances, better emitters would provide more photons and improved resolution, and a new photoactivatable small-molecule emitter has recently been synthesized and targeted to specific structures in living cells to provide super-resolution images (JACS {132}, 15099 (2010)). Finally, a new optical method for extracting three-dimensional position information based on

  11. Budget-limited thermal biology: Design, construction and performance of a large, walk-in style temperature-controlled chamber.

    Science.gov (United States)

    Martinez, Eloy; Agosta, Salvatore J

    2016-05-01

    We describe a partial redesign of the conventional air-conditioning system and apply it to the construction of a relatively large (1.87m(3) air mass), walk-in style temperature-controlled chamber (TCC) using parts easily obtained in most countries. We conducted several tests to demonstrate the performance of the TCC. Across the physiologically relevant range of 5-37°C, the TCC took 26.5-50.0min to reach the desired set point temperature. Once at set point, temperature inside the chamber was controlled with an accuracy of ±1.0°C. User-entry effects on deviations from and return times to set point temperature were minimal. Overall, performance of the TCC was sufficient to make precise physiological measurements of insect metabolic rate while controlling assay temperature. Major advantages of the TCC include its simplicity, flexibility, and low cost.

  12. Rapid DNA Library Construction for Functional Genomic and Metagenomic Screening▿ †

    OpenAIRE

    2007-01-01

    A rapid protocol was developed for constructing plasmid libraries from small quantities of genomic/metagenomic DNA. The technique utilizes linker amplification with topoisomerase cloning and allows for inducible transcription in Escherichia coli. As proof of principle, several anti-Bacillus lysins were cloned from bacteriophage genomes and an aerolysin was cloned from a metagenomic sample.

  13. The multi-functional cleanroom of TNO Building and Construction Research at Delft (NL)

    NARCIS (Netherlands)

    Ham, P.J.

    1996-01-01

    For studies in rooms in which dust-free air is important, the department of Indoor Environment, Building Physics and Systems of TNO Building and Construction Research has access to a multifunctional cleanroom annex operating theatre (OP). On the ICCCS-symposium in Zürich 1990 TNO Building and Constr

  14. Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes.

    Science.gov (United States)

    Ufarté, Lisa; Bozonnet, Sophie; Laville, Elisabeth; Cecchini, Davide A; Pizzut-Serin, Sandra; Jacquiod, Samuel; Demanèche, Sandrine; Simonet, Pascal; Franqueville, Laure; Veronese, Gabrielle Potocki

    2016-01-01

    Activity-based metagenomics is one of the most efficient approaches to boost the discovery of novel biocatalysts from the huge reservoir of uncultivated bacteria. In this chapter, we describe a highly generic procedure of metagenomic library construction and high-throughput screening for carbohydrate-active enzymes. Applicable to any bacterial ecosystem, it enables the swift identification of functional enzymes that are highly efficient, alone or acting in synergy, to break down polysaccharides and oligosaccharides.

  15. Biological oscillations for learning walking coordination: dynamic recurrent neural network functionally models physiological central pattern generator.

    Science.gov (United States)

    Hoellinger, Thomas; Petieau, Mathieu; Duvinage, Matthieu; Castermans, Thierry; Seetharaman, Karthik; Cebolla, Ana-Maria; Bengoetxea, Ana; Ivanenko, Yuri; Dan, Bernard; Cheron, Guy

    2013-01-01

    The existence of dedicated neuronal modules such as those organized in the cerebral cortex, thalamus, basal ganglia, cerebellum, or spinal cord raises the question of how these functional modules are coordinated for appropriate motor behavior. Study of human locomotion offers an interesting field for addressing this central question. The coordination of the elevation of the 3 leg segments under a planar covariation rule (Borghese et al., 1996) was recently modeled (Barliya et al., 2009) by phase-adjusted simple oscillators shedding new light on the understanding of the central pattern generator (CPG) processing relevant oscillation signals. We describe the use of a dynamic recurrent neural network (DRNN) mimicking the natural oscillatory behavior of human locomotion for reproducing the planar covariation rule in both legs at different walking speeds. Neural network learning was based on sinusoid signals integrating frequency and amplitude features of the first three harmonics of the sagittal elevation angles of the thigh, shank, and foot of each lower limb. We verified the biological plausibility of the neural networks. Best results were obtained with oscillations extracted from the first three harmonics in comparison to oscillations outside the harmonic frequency peaks. Physiological replication steadily increased with the number of neuronal units from 1 to 80, where similarity index reached 0.99. Analysis of synaptic weighting showed that the proportion of inhibitory connections consistently increased with the number of neuronal units in the DRNN. This emerging property in the artificial neural networks resonates with recent advances in neurophysiology of inhibitory neurons that are involved in central nervous system oscillatory activities. The main message of this study is that this type of DRNN may offer a useful model of physiological central pattern generator for gaining insights in basic research and developing clinical applications.

  16. Biological oscillations for learning walking coordination: dynamic recurrent neural network functionally models physiological central pattern generator

    Directory of Open Access Journals (Sweden)

    Thomas eHoellinger

    2013-05-01

    Full Text Available The existence of dedicated neuronal modules such as those organized in the cerebral cortex, thalamus, basal ganglia, cerebellum or spinal cord raises the question of how these functional modules are coordinated for appropriate motor behavior. Study of human locomotion offers an interesting field for addressing this central question. The coordination of the elevation of the 3 leg segments under a planar covariation rule (Borghese et al., 1996 was recently modeled (Barliya et al., 2009 by phase-adjusted simple oscillators shedding new light on the understanding of the central pattern generator processing relevant oscillation signals. We describe the use of a dynamic recurrent neural network (DRNN mimicking the natural oscillatory behavior of human locomotion for reproducing the planar covariation rule in both legs at different walking speeds. Neural network learning was based on sinusoid signals integrating frequency and amplitude features of the first three harmonics of the sagittal elevation angles of the thigh, shank and foot of each lower limb. We verified the biological plausibility of the neural networks. Best results were obtained with oscillations extracted from the first three harmonics in comparison to oscillations outside the harmonic frequency peaks. Physiological replication steadily increased with the number of neuronal units from 1 to 80, where similarity index reached 0.99. Analysis of synaptic weighting showed that the proportion of inhibitory connections consistently increased with the number of neuronal units in the DRNN. This emerging property in the artificial neural networks resonates with recent advances in neurophysiology of inhibitory neurons that are involved in central nervous system oscillatory activities. The main message of this study is that this type of DRNN may offer a useful model of physiological central pattern generator for gaining insights in basic research and developing clinical applications.

  17. Interaction of hepatitis B virus with tumor suppressor gene p53: its significance and biological function

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The mechanism of the interaction of hepatitis B virus (HBV) with tumor suppressor p53 and its role in the hepatocarcinogenesis have been studied by PCR-directed sequencing, gel shift assays and in situ ultraviolet cross-linking assay. The biological function of the interaction of HBV with p53 gene was investigated by co-transfection of chloramphenicol acetyltransferase (CAT) reporter gene, p53 and HBV DNA, and quantitative PCR. Among the 16 primary hepatocellular carcinoma (PHC) samples, 13 were HBV-DNA positive,10 HBxAg positive and 9 p53 protein positive. The p53 gene point mutation was found in 5 samples, one of which had a G to T substitution located at codon 249. After analyzing the HBV genome by a computer program, a p53 response element binding sequence was found in HBV genome at upstream of enhancer I, from 1047 to 1059 nucleotides. This sequence could specifically bind to p53 protein, increase p53 protein accumulation in the PHC cells and stimulate the transactivating activity of p53 and HBV replication .The results also revealed that HBxAg could combine with p53 protein to form a complex in the cells and enhance CAT expression. Immunocytochemical staining showed that p53 protein complex was located in the cytoplasm and the process of p53 entry to nuclei was, in part, blocked. From our results, we conclude that the mutation of p53 gene at codon 249 is infrequent in HBV-associated PHC, the DNA-protein binding between HBV and p53, and the protein-protein binding between HBxAg and p53 might lead to the reduction or inactivation of p53 protein, which in turn resulting in HBV-associated hepatocarcinogenesis.

  18. Biological function of hpsh4590 localized in the plasticity zone of Helicobacter pylori.

    Science.gov (United States)

    Gu, Yu-feng; Li, Yu; Song, Yu; Chang, Xin; Qu, Ye-Min; Wang, Ming-Yi; Gao, Xiao-Zhong

    2016-04-01

    The aim of this study was to determine the biological function of hpsh4590 in Helicobacter pylori. After Hpsh4590 was expressed using a prokaryotic expression system, the cytotoxic effects and IL-8 production of Hpsh4590 were analyzed by co-culturing with GES-1 cells. Meanwhile, the antibody of rHpsh4590, produced by immunizing rabbit, was used for localization and protein interaction studies. Hpsh4590 fusion protein was expressed successfully in Escherichia coli Rosetta (DE3), and the polyclonal antibody was produced at high titers. The MTT assay showed that the inhibition ratio of GES-1 cells cultured with 0.1 μg/mL rHpsh4590 (3.02% ± 0.02%) was significantly lower than that of 20 μg/mL rHpsh4590 (57.57% ± 0.03%, p < 0.01), while DAPI staining showed the cytotoxic effects of rHpsh4590 for GES-1 cells. The up-regulation of cleaved caspase-3 and cleaved PARP was observed after GES-1 cells co-cultured with rHpsh4590 by Western blot. Co-culturing of GES-1 cells with rHpsh0459 (20 μg/mL) led to significant production of IL-8 at 12 h(1097.74 ± 212.37 pg/mL) and 24 h (1379.55 ± 209.58 pg/mL) then at 6 h(134.68 ± 14.64 pg/mL, p < 0.01). These observations suggest that the cytotoxicity of Hpsh4590 occurred in a concentration dependent manner, which is related with IL-8 secretion from gastric mucosal epithelial cells. Hpsh4590 was found localized in the membrane and the periplasm of H. pylori, interacted with zinc finger protein and methionine ABC transporter ATP-binding protein, and potentially regulates DNA uptake or transfer.

  19. Rapidly restoring biological soil crusts and ecosystem functions in a severely disturbed desert ecosystem.

    Science.gov (United States)

    Chiquoine, Lindsay P; Abella, Scott R; Bowker, Matthew A

    2016-06-01

    Restoring biological soil crusts (biocrusts) in degraded drylands can contribute to recovery of ecosystem functions that have global implications, including erosion resistance and nutrient cycling. To examine techniques for restoring biocrusts, we conducted a replicated, factorial experiment on recently abandoned road surfaces by applying biocrust inoculation (salvaged and stored dry for two years), salvaged topsoil, an abiotic soil amendment (wood shavings), and planting of a dominant perennial shrub (Ambrosia dumosa). Eighteen months after treatments, we measured biocrust abundance and species composition, soil chlorophyll a content and fertility, and soil resistance to erosion. Biocrust addition significantly accelerated biocrust recovery on disturbed soils, including increasing lichen and moss cover and cyanobacteria colonization. Compared to undisturbed controls, inoculated plots had similar lichen and moss composition, recovered 43% of total cyanobacteria density, had similar soil chlorophyll content, and exhibited recovery of soil fertility and soil stability. Inoculation was the only treatment that generated lichen and moss cover. Topsoil application resulted in partial recovery of the cyanobacteria community and soil properties. Compared to untreated disturbed plots, topsoil application without inoculum increased cyanobacteria density by 186% and moderately improved soil chlorophyll and ammonium content and soil stability. Topsoil application produced 22% and 51% of the cyanobacteria density g⁻¹ soil compared to undisturbed and inoculated plots, respectively. Plots not treated with either topsoil or inoculum had significantly lower cyanobacteria density, soil chlorophyll and ammonium concentrations, and significantly higher soil nitrate concentration. Wood shavings and Ambrosia had no influence on biocrust lichen and moss species recovery but did affect cyanobacteria composition and soil fertility. Inoculation of severely disturbed soil with native

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

    Science.gov (United States)

    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

  1. Synergistic Synthetic Biology: Units in Concert.

    Science.gov (United States)

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

  2. Impacts of multiple stressors on ecosystem function: Leaf decomposition in constructed urban wetlands.

    Science.gov (United States)

    Mackintosh, Teresa J; Davis, Jenny A; Thompson, Ross M

    2016-01-01

    The impact of stormwater on stream biota is well documented, but less is known about the impacts on ecosystem processes, such as the breakdown of organic matter. This study sought to establish whether the degree of urbanisation affected rates of leaf-litter breakdown within constructed wetlands. A litter bag method was used to ascertain rate of decomposition along a gradient of urbanisation (total imperviousness, TI), in constructed wetlands in western and south-eastern Melbourne. A significant positive relationship between TI and breakdown rate was found in the south-eastern wetlands. The significant reduction in rate of invertebrate-mediated breakdown with increasing concentration of certain metals was consistent with other studies. However, overall there was an increase in rate of breakdown. Studies have shown that the effects of heavy metals can be negated if nutrient levels are high. Our results suggest that other parameters besides exposure to contaminants are likely to affect leaf litter breakdown.

  3. Virtual Agonist-antagonist Mechanisms Produce Biological Muscle-like Functions: An Application for Robot Joint Control

    DEFF Research Database (Denmark)

    Xiong, Xiaofeng; Wörgötter, Florentin; Manoonpong, Poramate

    2014-01-01

    or torque sensing systems; thereby capable of implementing the model on small legged robots driven by, e.g., standard servo motors. Thus, the VAAM minimizes hardware and reduces system complexity. From this point of view, the model opens up another way of simulating muscle behaviors on artificial machines......Purpose – Biological muscles of animals have a surprising variety of functions, i.e., struts, springs, and brakes. According to this, the purpose of this paper is to apply virtual agonist-antagonist mechanisms to robot joint control allowing for muscle-like functions and variably compliant joint......, variably compliant joint motions can be produced without mechanically bulky and complex mechanisms or complex force/toque sensing at each joint. Moreover, through tuning the damping coefficient of the VAAM, the functions of the VAAM are comparable to biological muscles. Originality/value – The model (i...

  4. Construction of convex solutions for the second type of Feigenbaum’s functional equations

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper, convex solutions for the second type of Feigenbaum’s equation f (x) = λ1 f (f (λx)), 0 < λ < 1, f (0) = 1, 0 f (x) 1, x ∈ [0, 1] are investigated. Using constructive methods, we discuss the existence and uniqueness of continuous convex solutions, C1-convex solutions and C2-convex solutions of the above equation.

  5. Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Christer; Sun, Chuanxin; Ghebramedhin, Haile; Hoglund, Anna-Stina; Jansson, Christer

    2008-01-15

    Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN technology in studies on starch branching enzyme activities in barley leaves. We also comment on the mechanism for ODN uptake in plant cells. Antisense ODNs are short (12-25 nt-long) stretches of single-stranded ODNs that hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. They are naturally occurring in both prokaryotes and eukaryotes where they partake in gene regulation and defense against viral infection. The mechanisms for antisense ODN inhibition are not fully understood but it is generally considered that the ODN either sterically interferes with translation or promotes transcript degradation by RNase H activation. The earliest indication of the usefulness of antisense ODN technology for the purposes of molecular biology and medical therapy was the demonstration in 1978 that synthetic ODNs complementary to Raos sarcoma virus could inhibit virus replication in tissue cultures of chick embryo fibroblasts. Since then the antisense ODN technology has been widely used in animal sciences and as an important emerging therapeutic approach in clinical medicine. However, antisense ODN inhibition has been an under-exploited strategy for plant tissues, although the prospects for plant cells in suspension cultures to take up single-stranded ODNs was reported over a decade ago. In 2001, two reports from Malho and coworker demonstrated the use of cationic-complexed antisense ODNs to suppress expression of genes encoding pollen

  6. Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Christer; Sun, Chuanxin; Ghebramedhin, Haile; Hoglund, Anna-Stina; Jansson, Christer

    2008-01-15

    Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN technology in studies on starch branching enzyme activities in barley leaves. We also comment on the mechanism for ODN uptake in plant cells. Antisense ODNs are short (12-25 nt-long) stretches of single-stranded ODNs that hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. They are naturally occurring in both prokaryotes and eukaryotes where they partake in gene regulation and defense against viral infection. The mechanisms for antisense ODN inhibition are not fully understood but it is generally considered that the ODN either sterically interferes with translation or promotes transcript degradation by RNase H activation. The earliest indication of the usefulness of antisense ODN technology for the purposes of molecular biology and medical therapy was the demonstration in 1978 that synthetic ODNs complementary to Raos sarcoma virus could inhibit virus replication in tissue cultures of chick embryo fibroblasts. Since then the antisense ODN technology has been widely used in animal sciences and as an important emerging therapeutic approach in clinical medicine. However, antisense ODN inhibition has been an under-exploited strategy for plant tissues, although the prospects for plant cells in suspension cultures to take up single-stranded ODNs was reported over a decade ago. In 2001, two reports from Malho and coworker demonstrated the use of cationic-complexed antisense ODNs to suppress expression of genes encoding pollen

  7. On the construction of cryptographically strong Boolean functions with desirable trade-off

    Institute of Scientific and Technical Information of China (English)

    REN Kui; PARK Jaemin; KIM Kwangjo

    2005-01-01

    This paper proposes a practical algorithm for systematically generating strong Boolean functions (f:GF(2)n→GF(2))with cryptographic meaning. This algorithm takes bent function as input and directly outputs the resulted Boolean function in terms of truth table sequence. This algorithm was used to develop two classes of balanced Boolean functions, one of which has very good cryptographic properties: nl(f)=22k-1-2k+2k-2 (n=2k), with the sum-of-squares avalanche characteristic off satisfying σf=24k+23k+2+23k+23k-2 and the absolute avalanche characteristic of △f satisfying △f=2k+1. This is the best result up to now compared to existing ones. Instead of bent sequences, starting from random Boolean functions was also tested in the algorithm. Experimental results showed that starting from bent sequences is highly superior to starting from random Boolean functions.

  8. A Functional Model for Teaching Osmosis-Diffusion to Biology Students

    Science.gov (United States)

    Olsen, Richard W.; Petry, Douglas E.

    1976-01-01

    Described is a maternal-fetal model, operated by the student, to teach osmosis-diffusion to biology students. Included are materials needed, assembly instructions, and student operating procedures. (SL)

  9. Synthesis, characterization and functionalization of silicon nanoparticle based hybrid nanomaterials for photovoltaic and biological applications

    Science.gov (United States)

    Xu, Zejing

    Silicon nanoparticles are attractive candidates for biological, photovoltaic and energy storage applications due to their size dependent optoelectronic properties. These include tunable light emission, high brightness, and stability against photo-bleaching relative to organic dyes (see Chapter 1). The preparation and characterization of silicon nanoparticle based hybrid nanomaterials and their relevance to photovoltaic and biological applications are described. The surface-passivated silicon nanoparticles were produced in one step from the reactive high-energy ball milling (RHEBM) of silicon wafers with various organic ligands. The surface structure and optical properties of the passivated silicon nanoparticles were systematically characterized. Fast approaches for purifying and at the same time size separating the silicon nanoparticles using a gravity GPC column were developed. The hydrodynamic diameter and size distribution of these size-separated silicon nanoparticles were determined using GPC and Diffusion Ordered NMR Spectroscopy (DOSY) as fast, reliable alternative approaches to TEM. Water soluble silicon nanoparticles were synthesized by grafting PEG polymers onto functionalized silicon nanoparticles with distal alkyne or azide moieties. The surface-functionalized silicon nanoparticles were produced from the reactive high-energy ball milling (RHEBM) of silicon wafers with a mixture of either 5-chloro-1-pentyne in 1-pentyne or 1,7 octadiyne in 1-hexyne to afford air and water stable chloroalkyl or alkynyl terminated nanoparticles, respectively. Nanoparticles with the ω-chloroalkyl substituents were easily converted to ω-azidoalkyl groups through the reaction of the silicon nanoparticles with sodium azide in DMF. The azido terminated nanoparticles were then grafted with monoalkynyl-PEG polymers using a copper catalyzed alkyne-azide cycloaddition (CuAAC) reaction to afford core-shell silicon nanoparticles with a covalently attached PEG shell. Covalently

  10. Molecular Clone, Expression, and Prediction of Construction and Function to Key Genes of Interleukin Family of Porcine

    Institute of Scientific and Technical Information of China (English)

    JING Zhi-zhong; DOU Yong-xi; LUO Qi-hui; CHEN Guo-hua; MENG Xue-lian; ZHENG Ya-dong; LUO Xue-nong; CAI Xue-peng

    2007-01-01

    This research was to clone, express, and analyze the structure and function of major molecules of porcine interleukin family. Genes of porcine interleukin family were cloned by RT-PCR from stimulated porcine PBMC by LPS and PHA, and then expressed in E. coli, and the structure and function of these molecules were predicted by ExPASY. The results showed that genes of IL-4, IL-6, and IL-18 were successfully cloned and expressed. Furthermore, the expression products of recombinant IL-4 and IL-6 both have multiple biological activities. By analyzing these genes with the NCBI/GenBank data, the homologies of the nucleotide acid sequence are 99.25, 99.21, and 100%, respectively, and have great species differences when compared with other animal species. The results of the prediction showed that all these molecules contain several phosphorylation, glycosylation, protein kinase, and signal transduction bonding sites in secondary structure, and all are compact globularity protein in space configuration. These characteristics of structure are the basis for their multiple biological functions. The genes, structure and function of key molecular of porcine interleukin family were successfully cloned, expressed, and analyzed in this paper.

  11. Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.

    Science.gov (United States)

    Chen, Z; Lönnberg, T; Lahesmaa, R

    2013-08-01

    Current knowledge of helper T cell differentiation largely relies on data generated from mouse studies. To develop therapeutical strategies combating human diseases, understanding the molecular mechanisms how human naïve T cells differentiate to functionally distinct T helper (Th) subsets as well as studies on human differentiated Th cell subsets is particularly valuable. Systems biology approaches provide a holistic view of the processes of T helper differentiation, enable discovery of new factors and pathways involved and generation of new hypotheses to be tested to improve our understanding of human Th cell differentiation and immune-mediated diseases. Here, we summarize studies where high-throughput systems biology approaches have been exploited to human primary T cells. These studies reveal new factors and signalling pathways influencing T cell differentiation towards distinct subsets, important for immune regulation. Such information provides new insights into T cell biology and into targeting immune system for therapeutic interventions.

  12. [THE FUNCTIONAL CONSTITUENT OF A BIOLOGICAL COMPONENT IN PROGRAMS FOR TRAINING SPECIALISTS IN THE AREA OF PARASITOLOGY FOR ACCREDITATION].

    Science.gov (United States)

    Dovgalev, A S; Astanina, S Yu; Andreeva, N D

    2015-01-01

    The paper considers the functional aspects of a biological component in programs for training specialists in the area of Parasitology for accreditation within the current enactments, including those on modernization of public health and additional professional education. The working program of the module "Fundamental Disciplines" has been used as an example to outline approaches to molding a medical parasitologist's capacity and readiness to solve professional tasks on the basis of knowledge of fundamental disciplines: biology, immunology, and medical geography. Education fundamentalization is shown to suggest more unsupervised work of a learner in the teaching process. The fundamental constituent of a biological component of the 'programs for training learners in the specialty of Parasitology for accreditation is shown in the interaction of all sections of this area with special and allied subjects.

  13. Construction and packaging of pseudotype retrovirus containing human N—ras cDNA antisense sequence and its biological effects on human hepatoma cells

    Institute of Scientific and Technical Information of China (English)

    JIALIBIN; WANGXIANG; 等

    1990-01-01

    N-ras is one of the transforming genes in human hepatic cancer cells.It has been found that N-ras was overexpressed at the mRNA and protein level in hepatoma cells.In order to explore the biological roles of N-ras in human hepatic carcinogenesis and the potential application in control of cancer cell growth,a preudotype retrovirus containing antisense sequence of human N-ras was constructed and packaged.A recombinant retrovirus vector containing antisense or sense sequences of N-ras cDNA was constructed by pZIP-NeoSV(X)1.The pseudotype virus was packaged ang rescued by transfection and infection in PA317 and ψ 2 helper cells.It has been demonstrated that the pseudotype retrovirus containing antisense N-ras sequence did inhibit the growth of human PLC/PRF/5 hepatoma cells accompanied with inhibition of p21 expression,while the retrovirus containing sense sequence had none.The pseudotype virus had no effect on human diploid fibroblasts.

  14. Analysis of the metabolic utilization of carbon sources and potential functional diversity of the bacterial community in lab-scale horizontal subsurface-flow constructed wetlands.

    Science.gov (United States)

    Deng, Huanhuan; Ge, Liyun; Xu, Tan; Zhang, Minghua; Wang, Xuedong; Zhang, Yalei; Peng, Hong

    2011-01-01

    Microorganisms are an integral part of the biogeochemical processes in wetlands. To improve the performance of constructed wetlands, it is very important to know the metabolic properties and functional diversity of the microbial communities. The purpose of this study is to analyze the metabolic properties and functional diversity of the microbial community in a horizontal subsurface-flow constructed wetland (CW) in a laboratory study through the sole-carbon-source utilization profiles using Biolog-ECO microplates. The technique has advantages over traditional cell culture techniques, such as molecular-level techniques-RNA amplification, which are time-consuming, expensive, and only applicable to the small number of species that may be cultured. This CW was designed to treat rural eutrophic water in China, using the plant L. This study showed that the metabolic activities of upper front substrate microorganisms (UF) were greater than those of the lower back substrate microorganisms (LB) in the CW. Integrated areas under average well color development (AWCD) curves of substrate microorganisms in the UF were 131.9, 4.8, and 99.3% higher than in the lower front part (LF), the upper back part (UB), and the LB part of the CW, respectively. Principal components analysis showed significant differences in both community structure and metabolic utilization of carbon sources between substrate microorganisms from different sampling sites. Carbon source utilization of polymers, carbohydrates, carboxylic acids, and amino acids was higher in UF than in LF, but that of amines and phenolic compounds was very similar in UF and LF. The richness, evenness, and diversity of upper substrate microbial communities were significantly higher than those of lower substrate. The LF substrate microbial communities had lower evenness than the other sampling plots, and the lowest richness of substrate microbial community was found in the LB part of the CW.

  15. Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea

    Science.gov (United States)

    Díaz-Pérez, Leopoldo; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D.; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María del Carmen

    2016-01-01

    This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea. PMID:27579575

  16. Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea.

    Science.gov (United States)

    Díaz-Pérez, Leopoldo; Rodríguez-Zaragoza, Fabián Alejandro; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María Del Carmen

    2016-01-01

    This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea.

  17. A Note on "On the Construction of Boolean Functions with Optimal Algebraic Immunity"

    CERN Document Server

    Li, Yuan; Kokichi, Futatsugi

    2011-01-01

    In this note, we go further on the "basis exchange" idea presented in \\cite{LiNa1} by using Mobious inversion. We show that the matrix $S_1(f)S_0(f)^{-1}$ has a nice form when $f$ is chosen to be the majority function, where $S_1(f)$ is the matrix with row vectors $\\upsilon_k(\\alpha)$ for all $\\alpha \\in 1_f$ and $S_0(f)=S_1(f\\oplus1)$. And an exact counting for Boolean functions with maximum algebraic immunity by exchanging one point in on-set with one point in off-set of the majority function is given. Furthermore, we present a necessary condition according to weight distribution for Boolean functions to achieve algebraic immunity not less than a given number.

  18. Adolescent Emotionality and Effortful Control : Core Latent Constructs and Links to Psychopathology and Functioning

    NARCIS (Netherlands)

    Snyder, Hannah R.; Gulley, Lauren D.; Bijttebier, Patricia; Hartman, Catharina A.; Oldehinkel, Albertine J.; Mezulis, Amy; Young, Jami F.; Hankin, Benjamin L.

    2015-01-01

    Temperament is associated with important outcomes in adolescence, including academic and interpersonal functioning and psychopathology. Rothbart's temperament model is among the most well-studied and supported approaches to adolescent temperament, and contains 3 main components: positive emotionalit

  19. Estimate of -Functionals and Modulus of Smoothness Constructed by Generalized Spherical Mean Operator

    Indian Academy of Sciences (India)

    M El Hamma; R Daher

    2014-05-01

    Using a generalized spherical mean operator, we define generalized modulus of smoothness in the space $L^2_k(\\mathbb{R}^d)$. Based on the Dunkl operator we define Sobolev-type space and -functionals. The main result of the paper is the proof of the equivalence theorem for a -functional and a modulus of smoothness for the Dunkl transform on $\\mathbb{R}^d$.

  20. Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region

    Science.gov (United States)

    Bowker, M.A.; Miller, M.E.; Belnap, J.; Sisk, T.D.; Johnson, N.C.

    2008-01-01

    Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r = 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands. ?? 2008 Society for Conservation Biology.

  1. From essential to persistent genes: a functional approach to constructing synthetic life.

    Science.gov (United States)

    Acevedo-Rocha, Carlos G; Fang, Gang; Schmidt, Markus; Ussery, David W; Danchin, Antoine

    2013-05-01

    A central undertaking in synthetic biology (SB) is the quest for the 'minimal genome'. However, 'minimal sets' of essential genes are strongly context-dependent and, in all prokaryotic genomes sequenced to date, not a single protein-coding gene is entirely conserved. Furthermore, a lack of consensus in the field as to what attributes make a gene truly essential adds another aspect of variation. Thus, a universal minimal genome remains elusive. Here, as an alternative to defining a minimal genome, we propose that the concept of gene persistence can be used to classify genes needed for robust long-term survival. Persistent genes, although not ubiquitous, are conserved in a majority of genomes, tend to be expressed at high levels, and are frequently located on the leading DNA strand. These criteria impose constraints on genome organization, and these are important considerations for engineering cells and for creating cellular life-like forms in SB.

  2. A review of construction and functionality of photogrammetric unmanned aerial vehicles

    Directory of Open Access Journals (Sweden)

    Paweł Burdziakowski

    2016-12-01

    Full Text Available A photogrammetry from an unmanned aerial vehicle (UAV can be understood as a new measurement tool. It introduces low-cost alternatives for a traditional aerial photogrammetry, combining terrestrial, aerial, and satellite photogrammetry techniques. This paper presents a photogrammetric UAV construction basics, a recommended platform analysis, and a review of commercially available components and systems’ elements designed for photogrammetric UAV purposes. As the results show, a motoglider can be recommended as a platform for a photogrammetric task, where the priority is to execute the maximum area coverage during one flight. That platform type is resistant to windy conditions and is able to execute long flight, opposite to multirotor platforms.[b]Keywords:[/b] photogrammetry, remote sensing, navigation, unmanned aerial vehicle, commercial of-the-shelf

  3. Unexpected properties of bandwidth choice when smoothing discrete data for constructing a functional data classifier

    KAUST Repository

    Carroll, Raymond J.

    2013-12-01

    The data functions that are studied in the course of functional data analysis are assembled from discrete data, and the level of smoothing that is used is generally that which is appropriate for accurate approximation of the conceptually smooth functions that were not actually observed. Existing literature shows that this approach is effective, and even optimal, when using functional data methods for prediction or hypothesis testing. However, in the present paper we show that this approach is not effective in classification problems. There a useful rule of thumb is that undersmoothing is often desirable, but there are several surprising qualifications to that approach. First, the effect of smoothing the training data can be more significant than that of smoothing the new data set to be classified; second, undersmoothing is not always the right approach, and in fact in some cases using a relatively large bandwidth can be more effective; and third, these perverse results are the consequence of very unusual properties of error rates, expressed as functions of smoothing parameters. For example, the orders of magnitude of optimal smoothing parameter choices depend on the signs and sizes of terms in an expansion of error rate, and those signs and sizes can vary dramatically from one setting to another, even for the same classifier.

  4. The hunt for original microbial enzymes: an initiatory review on the construction and functional screening of (metagenomic libraries

    Directory of Open Access Journals (Sweden)

    Martin, M.

    2016-01-01

    Full Text Available Introduction. Discovering novel enzymes is of interest in both applied and basic science. Microbial enzymes, which are incredibly diverse and easy to produce, are increasingly sought by diverse approaches. Literature. This review first distinguishes culture-based from culture-independent methods, detailing within each group the advantages and drawbacks of sequence- and function-based methods. It then discusses the main factors affecting the success of endeavors to identify novel enzymes through construction and functional screening of genomic or metagenomic libraries: the sampled environment, how DNA is extracted and processed, the vector used (plasmid, cosmid, fosmid, BAC, or shuttle vector, the host cell chosen from the available prokaryotic and eukaryotic ones and the main screening steps. Conclusions. Library construction and screening can be tricky and requires expertise. Combining different strategies, such as working with cultivable and non-cultivable organisms, using sequence- and function-based approaches, or performing multihost screenings, is probably the best way to identify novel and diverse enzymes from an environmental sample.

  5. The use of possessive constructions in English and Slovene and the reference-point function of prenominal possessors

    Directory of Open Access Journals (Sweden)

    Frančiška Lipovšek

    2002-12-01

    Full Text Available The paper presents the findings of the study concerning the use of prenominal and postnominal constructions in English and Slovene. The study has been based on the cognitive approach according to which the possesor functions as a reference point facilitating identification of the possessee. The term "identification value" has been used in the study to refer to the cluster of properties that render a nominal compatible with the reference-point function. The main factors contributing to the identification value of the possessor nominal are its "topicality" (i.e. mental accessibility and its "informativity" (i.e. ability to be an effective cue fot the identification of the relation between the possessor and the possessee. The findings of the study confirm that in both languages (i the pronominal possessor has the reference-point function by default, and that (ii the identification value of the possessor is the main factor determining the choice between the prenominal and the postnominal constructions.

  6. Functional impression and jaw registration: a single session procedure for the construction of complete dentures.

    Science.gov (United States)

    Utz, K-H; Müller, F; Kettner, N; Reppert, G; Koeck, B

    2004-06-01

    The conventional fabrication of complete dentures involves two separate clinical sessions for functional impression making and jaw registration. The presented method combines both procedures in one session. The aim of this study was to survey the three-dimensional tooth positions in complete dentures with reference to the ridges to establish arbitrary guideline values that could be used for the manufacturing of tooth-position analogue plastic rims on functional impression trays. New complete dentures were fabricated by supervised undergraduate students in the conventional manner for 104 edentulous patients. The position of the maxillary teeth was surveyed in the horizontal plane using the Schmuth 'vizor-measuring plate'. The vertical dimension of occlusion, represented as the distance between opposing ridge areas of the dentures in maximum intercuspation, was measured at different sites by means of a Gutowski gauge. The tooth positions on the dentures varied widely, e.g. the horizontal distances between the incisive papilla and the maxillary incisors was 7.1 +/- 2.3 (3-14) mm. The vertical dimension of occlusion, which is most important in the jaw registration, varied equally with an anterior inter-alveolar distance between 12 and 33 (20.4 +/- 4.0) mm. Arbitrary moulding of the tooth position-analogue plastic rims does not seems to be an ideal method of pre-shaping functional impression trays, because the individual anatomical variation is considerable. Alternatively, the horizontal and vertical tooth positions of functionally and aesthetically pleasing dentures should be measured to pre-shape the rims of functional impression trays in the maxillary and the mandibular jaw. Such trays are a valuable tool for functional impressions and an immediate preliminary jaw registration in the fabrication of new complete dentures. This method allows a first try-in of the full set-up in the third clinical visit without loosing precision.

  7. FUNCTION IN BIOLOGY: ETIOLOGICAL AND ORGANIZATIONAL PERSPECTIVES Función en Biología: perspectivas etiológicas y organizacionales

    Directory of Open Access Journals (Sweden)

    CHARBEL NIÑO EL-HANI

    Full Text Available In this paper, we argue for a taxonomy of approaches to function based on different epistemological perspectives assumed with regard to the treatment of this central concept in the life sciences. We distinguish between etiological and organizational perspectives on function, analyzing distinct theories: Wright's selectionist etiological approach and Godfrey-Smith's modern history theory of functions, in the case of the etiological perspective; and Cummins' functional analysis and Collier's interactivist approach to function, among organizational accounts. We explain differences and similarities between these theories and the broader perspectives on function, arguing for a particular way of understanding the consensus without unity in debates about function. While explaining the accounts of function, we also deal with the relationship between this concept and other important biological concepts, such as adaptation, selection, complexity, and autonomy. We also advance an argument for the limits and prospects of the explanatory role of function in evolution. By arguing that changes in functionality are always grounded on changes in systems' organization, we show that function can never explain the origins of traits. Nevertheless, it can explain the spread of traits in populations, but only when we are dealing with functionally novel traits. Finally, we stress that organizational accounts of function are needed to understand how new functions appear by means of changes in systems' organization.En este artículo, argumentamos a favor de una taxonomía de abordajes del concepto función basada en diferentes perspectivas epistemológicas de acuerdo al tratamiento de este concepto central en las ciencias de la vida. Distinguimos entre perspectivas etiológicas y organizacionales sobre la noción de función, analizando teorías distintas: la teoría etiológica seleccionista de Wright y la teoría de la historia moderna de Godfrey-Smith, en el caso de

  8. Discovering and validating biological hypotheses from coherent patterns in functional genomics data

    Energy Technology Data Exchange (ETDEWEB)

    Joachimiak, Marcin Pawel

    2008-08-12

    The area of transcriptomics analysis is among the more established in computational biology, having evolved in both technology and experimental design. Transcriptomics has a strong impetus to develop sophisticated computational methods due to the large amounts of available whole-genome datasets for many species and because of powerful applications in regulatory network reconstruction as well as elucidation and modeling of cellular transcriptional responses. While gene expression microarray data can be noisy and comparisons across experiments challenging, there are a number of sophisticated methods that aid in arriving at statistically and biologically significant conclusions. As such, computational transcriptomics analysis can provide guidance for analysis of results from newer experimental technologies. More recently, search methods have been developed to identify modules of genes, which exhibit coherent expression patterns in only a subset of experimental conditions. The latest advances in these methods allow to integrate multiple data types anddatasets, both experimental and computational, within a single statistical framework accounting for data confidence and relevance to specific biological questions. Such frameworks provide a unified environment for the exploration of specific biological hypothesis and for the discovery of coherent data patterns along with the evidence supporting them.

  9. Human embryonic stem cells : advancing biology and cardiogenesis towards functional applications l

    NARCIS (Netherlands)

    Braam, Stefan Robbert

    2010-01-01

    Human embryonic stem cells (hESC) hold great potential as a model for human development, disease pathology, drug discovery and safety pharmacology. All these applications will depend on comprehensive knowledge of their biology and control of their signaling mechanisms and fate choices. To begin to a

  10. Photoligation of self-assembled DNA constructs containing anthracene-functionalized 2'-amino-LNA monomers

    DEFF Research Database (Denmark)

    Pasternak, Karol; Pasternak, Anna; Gupta, Pankaj

    2011-01-01

    Efficient synthesis of a novel anthracene-functionalized 2'-amino-LNA phosphoramidite derivative is described together with its incorporation into oligodeoxynucleotides. Two DNA strands with the novel 2'-N-anthracenylmethyl-2'-amino-LNA monomers can be effectively cross-linked by photoligation...

  11. Collaborative Role Construction in a Conversation with Dementia: An Application of Systemic Functional Linguistics

    Science.gov (United States)

    Muller, Nicole; Wilson, Brent T.

    2008-01-01

    This study applies the tools provided by Systemic Functional Linguistics (SFL) to the description of patterns in a conversation between a person with dementia and a person without. It shows how, in the presence of, on the one hand, considerable communicative and cognitive deficits, and on the other, a collaborative interlocutor, a person with…

  12. Testing the Construct Validity of the Gambling Functional Assessment-Revised

    Science.gov (United States)

    Weatherly, Jeffrey N.; Miller, Joseph C.; Terrell, Heather K.

    2011-01-01

    An attempt was made to modify the Gambling Functional Assessment (GFA), which was proposed to identify four possible contingencies maintaining the respondent's gambling behavior. However, previous research found that it only identified two contingencies (i.e., positive vs. negative reinforcement), with some items cross-loading on both…

  13. The function-transferring model construction for X-ray digital radiographic system

    Science.gov (United States)

    Xiao, Wang; Yan, Han; Guo, Wenming

    2008-02-01

    This paper is aimed at presenting a renovated model-building method of transfer function for industrial X-ray digital radiography based on the amorphous silicon X-ray flat-panel detector. The system, known as point-spreading function (PSF), is composed of three parts: the system geometrical dispersion with a non-spot power source, the scintillating screen dispersion and the aperture sampling of the pixel detector. For the innovation purpose, we have first of all established a mathematical simulation of the PSF and the modulation transfer function (MTF) on the basis of analyzing the intensity distribution of X-ray penetration area in each part and by taking Gaussian functions as a mathematical equation for depicting the transfer behavior of each part of the system. And, then, we have worked out the approximately effective bandwidth of the system from its half-wave width. And, finally, by taking the digital radiography based on the flat-panel detector for sampling, the paper has provided a theoretical foundation for the industrial X-ray radiographic testing and measurement operation. In addition, the author has also estimated the validation of the model through experiments and proved that the method helps to make high resolutions of the diacritical tiniest details in the work-pieces, which has shown and will show its technical rationality, technical appropriateness and practical working value.

  14. Executive Function and Mathematics Achievement: Are Effects Construct- and Time-General or Specific?

    Science.gov (United States)

    Duncan, Robert; Nguyen, Tutrang; Miao, Alicia; McClelland, Megan; Bailey, Drew

    2016-01-01

    Executive function (EF) is considered a set of interrelated cognitive processes, including inhibitory control, working memory, and attentional shifting, that are connected to the development of the prefrontal cortex and contribute to children's problem solving skills and self regulatory behavior (Best & Miller, 2010; Garon, Bryson, &…

  15. Construction of New Electronic Density Functionals with Error Estimation Through Fitting

    DEFF Research Database (Denmark)

    Petzold, V.; Bligaard, T.; Jacobsen, K. W.

    2012-01-01

    We investigate the possibilities and limitations for the development of new electronic density functionals through large-scale fitting to databases of binding energies obtained experimentally or through high-quality calculations. We show that databases with up to a few hundred entries allow for up...

  16. Using logical functions for constructing non-linear analytical formulae in combinatorics and number theory

    OpenAIRE

    Chebrakov, Yu. V.

    2014-01-01

    In this paper we discuss techniques suitable for translating the verbal descriptions of computative algorithms into a set of mathematical formulae and demonstrate that logical functions can be used effectively in order to create non-linear analytical formulae, describing a set of combinatorial and number-theoretic computative algorithms.

  17. Tetrahedron-structured DNA and functional oligonucleotide for construction of an electrochemical DNA-based biosensor.

    Science.gov (United States)

    Bu, Nan-Nan; Tang, Chun-Xia; He, Xi-Wen; Yin, Xue-Bo

    2011-07-21

    Tetrahedron-structured DNA (ts-DNA) in combination with a functionalized oligonucleotide was used to develop a "turn-on" biosensor for Hg(2+) ions. The ts-DNA provided an improved sensitivity and was used to block the active sites.

  18. Constructing a Pragmatic Science of Learning and Instruction with Functional Contextualism

    Science.gov (United States)

    Fox, Eric J.

    2006-01-01

    Constructivism has been embraced by many in the field of instructional design and technology (IDT), but its advocates have struggled to move beyond theory to practice or to empirically demonstrate the effectiveness of their approach. As an alternative to constructivism, a new perspective emerging in psychology, known as functional contextualism,…

  19. Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

    Science.gov (United States)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

  20. Relationship between chemical composition and biological function of Pseudomonas aeruginosa lipopolysaccharide: effect on human neutrophil chemotaxis and oxidative burst

    DEFF Research Database (Denmark)

    Kharazmi, A; Fomsgaard, A; Conrad, R S;

    1991-01-01

    There are conflicting data on the effect of bacterial lipopolysaccharides (LPS) on the function of human neutrophils. The present study was designed to examine the relationship between chemical composition and the modulatory effect of LPS on human neutrophil function. LPS was extracted from five ...... composition of the LPS molecule may play an important role in biological activity of LPS.......There are conflicting data on the effect of bacterial lipopolysaccharides (LPS) on the function of human neutrophils. The present study was designed to examine the relationship between chemical composition and the modulatory effect of LPS on human neutrophil function. LPS was extracted from five...... no effect on neutrophil chemotaxis and a slight effect on chemiluminescence. The major differences in chemical composition of the LPS from these two strains are in the rhamnose and heptose content of the O side chain and in the alanine content of the core region. These data indicate that chemical...