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

Science.gov (United States)

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

2016-10-01

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, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous 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 diabetes (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. Copyright © 2016. Production and hosting by Elsevier Ltd.

Anatomic Mesenchymal Stem Cell-Based Engineered Cartilage Constructs for Biologic Total Joint Replacement

Science.gov (United States)

Saxena, Vishal; Kim, Minwook; Keah, Niobra M.; Neuwirth, Alexander L.; Stoeckl, Brendan D.; Bickard, Kevin; Restle, David J.; Salowe, Rebecca; Wang, Margaret Ye; Steinberg, David R.

2016-01-01

Cartilage has a poor healing response, and few viable options exist for repair of extensive damage. Hyaluronic acid (HA) hydrogels seeded with mesenchymal stem cells (MSCs) polymerized through UV crosslinking can generate functional tissue, but this crosslinking is not compatible with indirect rapid prototyping utilizing opaque anatomic molds. Methacrylate-modified polymers can also be chemically crosslinked in a cytocompatible manner using ammonium persulfate (APS) and N,N,N′,N′-tetramethylethylenediamine (TEMED). The objectives of this study were to (1) compare APS/TEMED crosslinking with UV crosslinking in terms of functional maturation of MSC-seeded HA hydrogels; (2) generate an anatomic mold of a complex joint surface through rapid prototyping; and (3) grow anatomic MSC-seeded HA hydrogel constructs using this alternative crosslinking method. Juvenile bovine MSCs were suspended in methacrylated HA (MeHA) and crosslinked either through UV polymerization or chemically with APS/TEMED to generate cylindrical constructs. Minipig porcine femoral heads were imaged using microCT, and anatomic negative molds were generated by three-dimensional printing using fused deposition modeling. Molded HA constructs were produced using the APS/TEMED method. All constructs were cultured for up to 12 weeks in a chemically defined medium supplemented with TGF-β3 and characterized by mechanical testing, biochemical assays, and histologic analysis. Both UV- and APS/TEMED-polymerized constructs showed increasing mechanical properties and robust proteoglycan and collagen deposition over time. At 12 weeks, APS/TEMED-polymerized constructs had higher equilibrium and dynamic moduli than UV-polymerized constructs, with no differences in proteoglycan or collagen content. Molded HA constructs retained their hemispherical shape in culture and demonstrated increasing mechanical properties and proteoglycan and collagen deposition, especially at the edges compared to the center of these

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.

The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

Science.gov (United States)

Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

2012-01-01

Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

On the origin of biological construction, with a focus on multicellularity.

Science.gov (United States)

van Gestel, Jordi; Tarnita, Corina E

2017-10-17

Biology is marked by a hierarchical organization: all life consists of cells; in some cases, these cells assemble into groups, such as endosymbionts or multicellular organisms; in turn, multicellular organisms sometimes assemble into yet other groups, such as primate societies or ant colonies. The construction of new organizational layers results from hierarchical evolutionary transitions, in which biological units (e.g., cells) form groups that evolve into new units of biological organization (e.g., multicellular organisms). Despite considerable advances, there is no bottom-up, dynamical account of how, starting from the solitary ancestor, the first groups originate and subsequently evolve the organizing principles that qualify them as new units. Guided by six central questions, we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions. These insights also provide a starting point for understanding the types of subsequent organizational complexity. The central research questions outlined here naturally link existing research programs on biological construction (e.g., on cooperation, multilevel selection, self-organization, and development) and thereby help integrate knowledge stemming from diverse fields of biology.

Automatic Construction of Java Programs from Functional Program Specifications

OpenAIRE

Md. Humayun Kabir

2015-01-01

This paper presents a novel approach to construct Java programs automatically from the input functional program specifications on natural numbers from the constructive proofs of the input specifications using an inductive theorem prover called Poiti'n. The construction of a Java program from the input functional program specification involves two phases. The theorem prover is used to construct a higher order functional (HOF) program from the input specification expressed as an existential the...

An algorithm for constructing Lyapunov functions

Directory of Open Access Journals (Sweden)

Sigurdur Freyr Hafstein

2007-08-01

Full Text Available In this monograph we develop an algorithm for constructing Lyapunov functions for arbitrary switched dynamical systems $dot{mathbf{x}} = mathbf{f}_sigma(t,mathbf{x}$, possessing a uniformly asymptotically stable equilibrium. Let $dot{mathbf{x}}=mathbf{f}_p(t,mathbf{x}$, $pinmathcal{P}$, be the collection of the ODEs, to which the switched system corresponds. The number of the vector fields $mathbf{f}_p$ on the right-hand side of the differential equation is assumed to be finite and we assume that their components $f_{p,i}$ are $mathcal{C}^2$ functions and that we can give some bounds, not necessarily close, on their second-order partial derivatives. The inputs of the algorithm are solely a finite number of the function values of the vector fields $mathbf{f}_p$ and these bounds. The domain of the Lyapunov function constructed by the algorithm is only limited by the size of the equilibrium's region of attraction. Note, that the concept of a Lyapunov function for the arbitrary switched system $dot{mathbf{x}} = mathbf{f}_sigma(t,mathbf{x}$ is equivalent to the concept of a common Lyapunov function for the systems $dot{mathbf{x}}=mathbf{f}_p(t,mathbf{x}$, $pinmathcal{P}$, and that if $mathcal{P}$ contains exactly one element, then the switched system is just a usual ODE $dot{mathbf{x}}=mathbf{f}(t,mathbf{x}$. We give numerous examples of Lyapunov functions constructed by our method at the end of this monograph.

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.

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.

Measuring coalition functioning: refining constructs through factor analysis.

Science.gov (United States)

Brown, Louis D; Feinberg, Mark E; Greenberg, Mark T

2012-08-01

Internal and external coalition functioning is an important predictor of coalition success that has been linked to perceived coalition effectiveness, coalition goal achievement, coalition ability to support evidence-based programs, and coalition sustainability. Understanding which aspects of coalition functioning best predict coalition success requires the development of valid measures of empirically unique coalition functioning constructs. The goal of the present study is to examine and refine the psychometric properties of coalition functioning constructs in the following six domains: leadership, interpersonal relationships, task focus, participation benefits/costs, sustainability planning, and community support. The authors used factor analysis to identify problematic items in our original measure and then piloted new items and scales to create a more robust, psychometrically sound, multidimensional measure of coalition functioning. Scales displayed good construct validity through correlations with other measures. Discussion considers the strengths and weaknesses of the refined instrument.

A Unifying Theory of Biological Function.

Science.gov (United States)

van Hateren, J H

2017-01-01

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological (or selected effects) theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness and normativity of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism's fitness, and modulates the organism's variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories.

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)

Hybrid printing of mechanically and biologically improved constructs for cartilage tissue engineering applications

International Nuclear Information System (INIS)

Xu Tao; Binder, Kyle W; Albanna, Mohammad Z; Dice, Dennis; Zhao Weixin; Yoo, James J; Atala, Anthony

2013-01-01

Bioprinting is an emerging technique used to fabricate viable, 3D tissue constructs through the precise deposition of cells and hydrogels in a layer-by-layer fashion. Despite the ability to mimic the native properties of tissue, printed 3D constructs that are composed of naturally-derived biomaterials still lack structural integrity and adequate mechanical properties for use in vivo, thus limiting their development for use in load-bearing tissue engineering applications, such as cartilage. Fabrication of viable constructs using a novel multi-head deposition system provides the ability to combine synthetic polymers, which have higher mechanical strength than natural materials, with the favorable environment for cell growth provided by traditional naturally-derived hydrogels. However, the complexity and high cost associated with constructing the required robotic system hamper the widespread application of this approach. Moreover, the scaffolds fabricated by these robotic systems often lack flexibility, which further restrict their applications. To address these limitations, advanced fabrication techniques are necessary to generate complex constructs with controlled architectures and adequate mechanical properties. In this study, we describe the construction of a hybrid inkjet printing/electrospinning system that can be used to fabricate viable tissues for cartilage tissue engineering applications. Electrospinning of polycaprolactone fibers was alternated with inkjet printing of rabbit elastic chondrocytes suspended in a fibrin–collagen hydrogel in order to fabricate a five-layer tissue construct of 1 mm thickness. The chondrocytes survived within the printed hybrid construct with more than 80% viability one week after printing. In addition, the cells proliferated and maintained their basic biological properties within the printed layered constructs. Furthermore, the fabricated constructs formed cartilage-like tissues both in vitro and in vivo as evidenced by the

An integrative approach to inferring biologically meaningful gene modules

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Wang Kai

2011-07-01

Full Text Available Abstract Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

Personal Constructions of Biological Concepts – The Repertory Grid Approach

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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.

Distinguishing between "function" and "effect" in genome biology.

Science.gov (United States)

Doolittle, W Ford; Brunet, Tyler D P; Linquist, Stefan; Gregory, T Ryan

2014-05-09

Much confusion in genome biology results from conflation of possible meanings of the word "function." We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions. Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Unifying Theory of Biological Function

NARCIS (Netherlands)

van Hateren, J. H.

2017-01-01

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological (or selected effects) theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms

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. PMID:25022769

Synergistic Synthetic Biology: Units in Concert

International Nuclear Information System (INIS)

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.

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.

A functional overview of conservation biological control

DEFF Research Database (Denmark)

Begg, Graham S; Cook, Samantha M; Dye, Richard

2017-01-01

Conservation biological control (CBC) is a sustainable approach to pest management that can contribute to a reduction in pesticide use as part of an Integrated Pest Management (IPM) strategy. CBC is based on the premise that countering habitat loss and environmental disturbance associated...... CBC prescriptions have proved elusive. To tackle this, we consolidate existing knowledge of CBC using a simple conceptual model that organises the functional elements of CBC into a common, unifying framework. We identify and integrate the key biological processes affecting natural enemies...... and their biological control function across local and regional scales, and consider the interactions, interdependencies and constraints that determine the outcome of CBC strategies. Conservation measures are often effective in supporting natural enemy populations but their success cannot be guaranteed; the greatest...

Uncovering Biological Network Function via Graphlet Degree Signatures

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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.

Numerical construction of 'optimal' nonoscillating amplitude and phase functions

International Nuclear Information System (INIS)

Matzkin, A.; Lombardi, M.

2002-01-01

A numerical recipe for the construction of nonoscillating amplitude and phase functions for potentials with a single minimum is given. We give different examples illustrating the recipe, showing the usefulness of the procedure for the construction of basis functions in bound-state scattering processes, such as those described by quantum defect theory. The resulting amplitude and accumulated phase functions are coined as 'optimal' nonoscillating (as a function of the space and energy variables) because they are the counterpart for the quantum problem of the classical action for the analog semiclassical problem

RAFT Nano-constructs: surfing to biological applications.

Science.gov (United States)

Boturyn, Didier; Defrancq, Eric; Dolphin, Gunnar T; Garcia, Julian; Labbe, Pierre; Renaudet, Olivier; Dumy, Pascal

2008-02-01

Biologically programmed molecular recognition provides the basis of all natural systems and supplies evolution-optimized functional materials from self-assembly of a limited number of molecular building blocks. Biomolecules such as peptides, nucleic acids and carbohydrates represent a diverse supply of structural building blocks for the chemist to design and fabricate new functional nanostructured architectures. In this context, we review here the chemistry we have developed to conjugate peptides with nucleic acids, carbohydrates, and organic molecules, as well as combinations thereof using a template-assembled approach. With this methodology, we have prepared new integrated functional systems exhibiting designed properties in the field of nanovectors, biosensors as well as controlled peptide self-assembly. Thus this molecular engineering approach allows for the rational design of systems with integrated tailor-made properties and paves the way to more elaborate applications by bottom-up design in the domain of nanobiosciences.

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.

Integrated pathway clusters with coherent biological themes for target prioritisation.

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Yi-An Chen

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

Radical C-H functionalization to construct heterocyclic compounds.

Science.gov (United States)

Yu, Jin-Tao; Pan, Changduo

2016-02-07

Heterocyclic compounds are widely present in natural products, pharmaceuticals and bioactive molecules. Thus, organic and pharmaceutical chemists have been making extensive efforts to construct those heterocyclic frameworks through developing versatile and efficient synthetic strategies. The direct C-H functionalization via the radical pathway has emerged as a promising and dramatic approach towards heterocycles with high atom- and step-economy. Heterocyclic compounds such as coumarins, furans, benzofurans, xanthones, benzothiazoles, indoles, indolines, oxindoles, quinolines, isoquinolines, quinoxaline, and phenanthridines have been successfully synthesized by C-H functionalization through the radical pathway. In this review, recent advances on radical C-H functionalization to construct heterocyclic compounds are highlighted with discussions.

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...

Function of dynamic models in systems biology: linking structure to behaviour.

Science.gov (United States)

Knüpfer, Christian; Beckstein, Clemens

2013-10-08

Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

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.

The biological function of consciousness

Directory of Open Access Journals (Sweden)

Brian eEarl

2014-08-01

Full Text Available 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., is 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.

Photoacoustic-Based Multimodal Nanoprobes: from Constructing to Biological Applications.

Science.gov (United States)

Gao, Duyang; Yuan, Zhen

2017-01-01

Multimodal nanoprobes have attracted intensive attentions since they can integrate various imaging modalities to obtain complementary merits of single modality. Meanwhile, recent interest in laser-induced photoacoustic imaging is rapidly growing due to its unique advantages in visualizing tissue structure and function with high spatial resolution and satisfactory imaging depth. In this review, we summarize multimodal nanoprobes involving photoacoustic imaging. In particular, we focus on the method to construct multimodal nanoprobes. We have divided the synthetic methods into two types. First, we call it "one for all" concept, which involves intrinsic properties of the element in a single particle. Second, "all in one" concept, which means integrating different functional blocks in one particle. Then, we simply introduce the applications of the multifunctional nanoprobes for in vivo imaging and imaging-guided tumor therapy. At last, we discuss the advantages and disadvantages of the present methods to construct the multimodal nanoprobes and share our viewpoints in this area.

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. © 2016 The Author(s).

Construction of functional linkage gene networks by data integration.

Science.gov (United States)

Linghu, Bolan; Franzosa, Eric A; Xia, Yu

2013-01-01

Networks of functional associations between genes have recently been successfully used for gene function and disease-related research. A typical approach for constructing such functional linkage gene networks (FLNs) is based on the integration of diverse high-throughput functional genomics datasets. Data integration is a nontrivial task due to the heterogeneous nature of the different data sources and their variable accuracy and completeness. The presence of correlations between data sources also adds another layer of complexity to the integration process. In this chapter we discuss an approach for constructing a human FLN from data integration and a subsequent application of the FLN to novel disease gene discovery. Similar approaches can be applied to nonhuman species and other discovery tasks.

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, (c) subject-auxiliary inversion, and (d) cross-linguistic linking generalizations between semantics and syntax.

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

Construction of new biological research facility for internal emitter and prospect

International Nuclear Information System (INIS)

Matsuoka, Osamu

1979-01-01

The construction of the new biological research facility for internal emitters is to start in 1979 in the National Institute of Radiological Sciences. The bodily harm of plutonium had been studied in 1965 for the first time in Japan, and mice and rats were tested as the experimental animals. The conceptual design of the biological research facility for internal emitters has been conducted from 1976 to 1978. The causes making the construction of this facility difficult are as follows: 1) the regulation concerning the handling of plutonium has no lower limit, and the animals administered with dosage of plutonium are not permitted to be kept outdoors, 2) the waste disposal of dead bodies and excrements of the animals is controlled very severely, 3) many animal breeders with the knowledge of radiation protection are needed for the special experiment, and 4) the budget is not sufficient for this experiment of handling plutonium. To resolve these problems, much efforts have been exerted on the test of breeding dogs and monkeys, the disposal of radioactive animal wastes, the treatment of urine of radioactive animals, the reduction of labor for breeding contaminated animals, and keeping of safety. The present situation of the researches on internal emitters in the USA, Germany, Britain, France and the Soviet Union is reviewed for reference. The outline of the new biological research facility for internal emitters is presented. The building has seven floors with the total area of about 13,000 m 2 , and comprises three controlled areas and no contamination laboratories. The future experiments, which are expected to be conducted after the completion of this facility, are the animal tests to evaluate the influence of fissile materials, especially plutonium, and the fundamental experiments to take out the radioactive nuclides accidentally taken into bodies. (Nakai, Y.)

Bioprinting of a functional vascularized mouse thyroid gland construct.

Science.gov (United States)

Bulanova, Elena A; Koudan, Elizaveta V; Degosserie, Jonathan; Heymans, Charlotte; Pereira, Frederico DAS; Parfenov, Vladislav A; Sun, Yi; Wang, Qi; Akhmedova, Suraya A; Sviridova, Irina K; Sergeeva, Natalia S; Frank, Georgy A; Khesuani, Yusef D; Pierreux, Christophe E; Mironov, Vladimir A

2017-08-18

Bioprinting can be defined as additive biofabrication of three-dimensional (3D) tissues and organ constructs using tissue spheroids, capable of self-assembly, as building blocks. The thyroid gland, a relatively simple endocrine organ, is suitable for testing the proposed bioprinting technology. Here we report the bioprinting of a functional vascularized mouse thyroid gland construct from embryonic tissue spheroids as a proof of concept. Based on the self-assembly principle, we generated thyroid tissue starting from thyroid spheroids (TS) and allantoic spheroids (AS) as a source of thyrocytes and endothelial cells (EC), respectively. Inspired by mathematical modeling of spheroid fusion, we used an original 3D bioprinter to print TS in close association with AS within a collagen hydrogel. During the culture, closely placed embryonic tissue spheroids fused into a single integral construct, EC from AS invaded and vascularized TS, and epithelial cells from the TS progressively formed follicles. In this experimental setting, we observed formation of a capillary network around follicular cells, as observed during in utero thyroid development when thyroid epithelium controls the recruitment, invasion and expansion of EC around follicles. To prove that EC from AS are responsible for vascularization of the thyroid gland construct, we depleted endogenous EC from TS before bioprinting. EC from AS completely revascularized depleted thyroid tissue. The cultured bioprinted construct was functional as it could normalize blood thyroxine levels and body temperature after grafting under the kidney capsule of hypothyroid mice. Bioprinting of functional vascularized mouse thyroid gland construct represents a further advance in bioprinting technology, exploring the self-assembling properties of tissue spheroids.

Construction of Green's functions for the Black-Scholes equation

Directory of Open Access Journals (Sweden)

Yuri A. Melnikov

2007-11-01

Full Text Available A technique is proposed for the construction of Green's functions for terminal-boundary value problems of the Black-Scholes equation. The technique permits an application to a variety of problems that vary by boundary conditions imposed. This is possible by extension of an approach that was earlier developed for partial differential equations in applied mechanics. The technique is based on the method of integral Laplace transform and the method of variation of parameters. It provides closed form analytic representations for the constructed Green's functions.

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/.

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

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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

Construction of Lyapunov Function for Dissipative Gyroscopic System

International Nuclear Information System (INIS)

Xu Wei; Ao Ping; Yuan Bo

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. (general)

Partly occupied Wannier functions: Construction and applications

DEFF Research Database (Denmark)

Thygesen, Kristian Sommer; Hansen, Lars Bruno; Jacobsen, Karsten Wedel

2005-01-01

We have developed a practical scheme to construct partly occupied, maximally localized Wannier functions (WFs) for a wide range of systems. We explain and demonstrate how the inclusion of selected unoccupied states in the definition of the WFs can improve both their localization and symmetry...

Towards biologically conformal radiation therapy (BCRT): Selective IMRT dose escalation under the guidance of spatial biology distribution

International Nuclear Information System (INIS)

Yang Yong; Xing Lei

2005-01-01

It is well known that the spatial biology distribution (e.g., clonogen density, radiosensitivity, tumor proliferation rate, functional importance) in most tumors and sensitive structures is heterogeneous. Recent progress in biological imaging is making the mapping of this distribution increasingly possible. The purpose of this work is to establish a theoretical framework to quantitatively incorporate the spatial biology data into intensity modulated radiation therapy (IMRT) inverse planning. In order to implement this, we first derive a general formula for determining the desired dose to each tumor voxel for a known biology distribution of the tumor based on a linear-quadratic model. The desired target dose distribution is then used as the prescription for inverse planning. An objective function with the voxel-dependent prescription is constructed with incorporation of the nonuniform dose prescription. The functional unit density distribution in a sensitive structure is also considered phenomenologically when constructing the objective function. Two cases with different hypothetical biology distributions are used to illustrate the new inverse planning formalism. For comparison, treatments with a few uniform dose prescriptions and a simultaneous integrated boost are also planned. The biological indices, tumor control probability (TCP) and normal tissue complication probability (NTCP), are calculated for both types of plans and the superiority of the proposed technique over the conventional dose escalation scheme is demonstrated. Our calculations revealed that it is technically feasible to produce deliberately nonuniform dose distributions with consideration of biological information. Compared with the conventional dose escalation schemes, the new technique is capable of generating biologically conformal IMRT plans that significantly improve the TCP while reducing or keeping the NTCPs at their current levels. Biologically conformal radiation therapy (BCRT

A Constructive Sharp Approach to Functional Quantization of Stochastic Processes

OpenAIRE

Junglen, Stefan; Luschgy, Harald

2010-01-01

We present a constructive approach to the functional quantization problem of stochastic processes, with an emphasis on Gaussian processes. The approach is constructive, since we reduce the infinite-dimensional functional quantization problem to a finite-dimensional quantization problem that can be solved numerically. Our approach achieves the sharp rate of the minimal quantization error and can be used to quantize the path space for Gaussian processes and also, for example, Lévy processes.

Lipid polymorphism and the functional roles of lipids in biological membranes

NARCIS (Netherlands)

Cullis, P.R.; Kruijff, B. de

1979-01-01

The reasons for the great variety of lipids found in biological membranes, and the relations between lipid composition and membrane function pose major unsolved problems in membrane biology. Perhaps the only major functional role of lipids which may be regarded as firmly established involves the

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.

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...

A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

Science.gov (United States)

Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

2017-11-01

The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach

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...

Construction of Nanowire Heterojunctions: Photonic Function-Oriented Nanoarchitectonics.

Science.gov (United States)

Li, Yong Jun; Yan, Yongli; Zhao, Yong Sheng; Yao, Jiannian

2016-02-10

Nanophotonics has received broad research interest because it may provide an alternative opportunity to overcome the fundamental limitations of electronic circuits. So far, diverse photonic functions, such as light generation, modulation, and detection, have been realized based on various nano-materials. The exact structural features of these material systems, including geometric characteristics, surface morphology, and material composition, play a key role in determining the photonic functions. Therefore, rational designs and constructions of materials on both morphological and componential levels, namely nanoarchitectonics, are indispensable for any photonic device with specific functionalities. Recently, a series of nanowire heterojunctions (NWHJs), which are usually made from two or more kinds of material compositions, were constructed for novel photonic applications based on various interactions between different materials at the junctions, for instance, energy transfer, exciton-plasmon coupling, or photon-plasmon coupling. A summary of these works is necessary to get a more comprehensive understanding of the relationship between photonic functions and architectonics of NWHJs, which will be instructive for designing novel photonic devices towards integrated circuits. Here, photonic function oriented nanoarchitectonics based on recent breakthroughs in nanophotonic devices are discussed, with emphasis on the design mechanisms, fabrication strategies, and excellent performances. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Explicit constructions of automorphic L-functions

CERN Document Server

Gelbart, Stephen; Rallis, Stephen

1987-01-01

The goal of this research monograph is to derive the analytic continuation and functional equation of the L-functions attached by R.P. Langlands to automorphic representations of reductive algebraic groups. The first part of the book (by Piatetski-Shapiro and Rallis) deals with L-functions for the simple classical groups; the second part (by Gelbart and Piatetski-Shapiro) deals with non-simple groups of the form G GL(n), with G a quasi-split reductive group of split rank n. The method of proof is to construct certain explicit zeta-integrals of Rankin-Selberg type which interpolate the relevant Langlands L-functions and can be analyzed via the theory of Eisenstein series and intertwining operators. This is the first time such an approach has been applied to such general classes of groups. The flavor of the local theory is decidedly representation theoretic, and the work should be of interest to researchers in group representation theory as well as number theory.

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.

Non-perturbative construction of the Luttinger-Ward functional

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M.Potthoff

2006-01-01

Full Text Available For a system of correlated electrons, the Luttinger-Ward functional provides a link between static thermodynamic quantities on the one hand and single-particle excitations on the other. The functional is useful in deriving several general properties of the system as well as in formulating the thermodynamically consistent approximations. Its original construction, however, is perturbative as it is based on the weak-coupling skeleton-diagram expansion. Here, it is shown that the Luttinger-Ward functional can be derived within a general functional-integral approach. This alternative and non-perturbative approach stresses the fact that the Luttinger-Ward functional is universal for a large class of models.

Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

Science.gov (United States)

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

Generative mechanistic explanation building in undergraduate molecular and cellular biology

Science.gov (United States)

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-09-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among scientists, we created and applied a theoretical framework to explore the strategies students use to construct explanations for 'novel' biological phenomena. Specifically, we explored how students navigated the multi-level nature of complex biological systems using generative mechanistic reasoning. Interviews were conducted with introductory and upper-division biology students at a large public university in the United States. Results of qualitative coding revealed key features of students' explanation building. Students used modular thinking to consider the functional subdivisions of the system, which they 'filled in' to varying degrees with mechanistic elements. They also hypothesised the involvement of mechanistic entities and instantiated abstract schema to adapt their explanations to unfamiliar biological contexts. Finally, we explored the flexible thinking that students used to hypothesise the impact of mutations on multi-leveled biological systems. Results revealed a number of ways that students drew mechanistic connections between molecules, functional modules (sets of molecules with an emergent function), cells, tissues, organisms and populations.

Molecular automata assembly: principles and simulation of bacterial membrane construction.

Science.gov (United States)

Lahoz-Beltra, R

1997-01-01

The motivation to understand the basic rules and principles governing molecular self-assembly may be relevant to explain in the context of molecular biology the self-organization and biological functions exhibited within cells. This paper presents a molecular automata model to simulate molecular self-assembly introducing the concept of molecular programming to simulate the biological function or operation performed by an assembled molecular state machine. The method is illustrated modelling Escherichia coli membrane construction including the assembly and operation of ATP synthase as well as the assembly of the bacterial flagellar motor. Flagellar motor operation was simulated using a different approach based on state machine definition used in virtual reality systems. The proposed methodology provides a modelling framework for simulation of biological functions performed by cellular components and other biological systems suitable to be modelled as molecular state machines.

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.

Construction of A Trial Function In The Variational Procedure of ...

African Journals Online (AJOL)

A form of variational method for calculating the ground state energy of a quantum mechanical system is considered. The method is based on a systematic construction of a trial variational function at each step of the calculation of the ground state energy. The construction involves introducing more variational parameters to ...

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.

On the construction of translationally invariant deformed wave functions

International Nuclear Information System (INIS)

Guardiola, R.

1975-01-01

Translationally invariant nuclear wave functions are constructed from deformed harmonic oscillator shell-model wave functions, with an exact projection of angular momentum quantum numbers. It is shown that the computation of matrix elements with the translationally invariant wave functions is as simple as the standard calculation, and formulae are obtained for (i) the potential energy, (ii) the kinetic energy and rms radius, and (iii) the charge form factor. (Auth.)

Bioinspiration: applying mechanical design to experimental biology.

Science.gov (United States)

Flammang, Brooke E; Porter, Marianne E

2011-07-01

The production of bioinspired and biomimetic constructs has fostered much collaboration between biologists and engineers, although the extent of biological accuracy employed in the designs produced has not always been a priority. Even the exact definitions of "bioinspired" and "biomimetic" differ among biologists, engineers, and industrial designers, leading to confusion regarding the level of integration and replication of biological principles and physiology. By any name, biologically-inspired mechanical constructs have become an increasingly important research tool in experimental biology, offering the opportunity to focus research by creating model organisms that can be easily manipulated to fill a desired parameter space of structural and functional repertoires. Innovative researchers with both biological and engineering backgrounds have found ways to use bioinspired models to explore the biomechanics of organisms from all kingdoms to answer a variety of different questions. Bringing together these biologists and engineers will hopefully result in an open discourse of techniques and fruitful collaborations for experimental and industrial endeavors.

Biological pathways and genetic mechanisms involved in social functioning.

Science.gov (United States)

Ordoñana, Juan R; Bartels, Meike; Boomsma, Dorret I; Cella, David; Mosing, Miriam; Oliveira, Joao R; Patrick, Donald L; Veenhoven, Ruut; Wagner, Gert G; Sprangers, Mirjam A G

2013-08-01

To describe the major findings in the literature regarding associations between biological and genetic factors and social functioning, paying special attention to: (1) heritability studies on social functioning and related concepts; (2) hypothesized biological pathways and genetic variants that could be involved in social functioning, and (3) the implications of these results for quality-of-life research. A search of Web of Science and PubMed databases was conducted using combinations of the following keywords: genetics, twins, heritability, social functioning, social adjustment, social interaction, and social dysfunction. Variability in the definitions and measures of social functioning was extensive. Moderate to high heritability was reported for social functioning and related concepts, including prosocial behavior, loneliness, and extraversion. Disorders characterized by impairments in social functioning also show substantial heritability. Genetic variants hypothesized to be involved in social functioning are related to the network of brain structures and processes that are known to affect social cognition and behavior. Better knowledge and understanding about the impact of genetic factors on social functioning is needed to help us to attain a more comprehensive view of health-related quality-of-life (HRQOL) and will ultimately enhance our ability to identify those patients who are vulnerable to poor social functioning.

On The Construction of Models for Electrical Conduction in Biological Tissues

International Nuclear Information System (INIS)

Gomez-Aguilar, F.; Bernal-Alvarado, J.; Cordova-Fraga, T.; Rosales-Garcia, J.; Guia-Calderon, M.

2010-01-01

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.

Biologic variability and correlation of platelet function testing in healthy dogs.

Science.gov (United States)

Blois, Shauna L; Lang, Sean T; Wood, R Darren; Monteith, Gabrielle

2015-12-01

Platelet function tests are influenced by biologic variability, including inter-individual (CVG ) and intra-individual (CVI ), as well as analytic (CVA ) variability. Variability in canine platelet function testing is unknown, but if excessive, would make it difficult to interpret serial results. Additionally, the correlation between platelet function tests is poor in people, but not well described in dogs. The aims were to: (1) identify the effect of variation in preanalytic factors (venipuncture, elapsed time until analysis) on platelet function tests; (2) calculate analytic and biologic variability of adenosine diphosphate (ADP) and arachidonic acid (AA)-induced thromboelastograph platelet mapping (TEG-PM), ADP-, AA-, and collagen-induced whole blood platelet aggregometry (WBA), and collagen/ADP and collagen/epinephrine platelet function analysis (PFA-CADP, PFA-CEPI); and (3) determine the correlation between these variables. In this prospective observational trial, platelet function was measured once every 7 days, for 4 consecutive weeks, in 9 healthy dogs. In addition, CBC, TEG-PM, WBA, and PFA were performed. Overall coefficients of variability ranged from 13.3% to 87.8% for the platelet function tests. Biologic variability was highest for AA-induced maximum amplitude generated during TEG-PM (MAAA; CVG = 95.3%, CVI = 60.8%). Use of population-based reference intervals (RI) was determined appropriate only for PFA-CADP (index of individuality = 10.7). There was poor correlation between most platelet function tests. Use of population-based RI appears inappropriate for most platelet function tests, and tests poorly correlate with one another. Future studies on biologic variability and correlation of platelet function tests should be performed in dogs with platelet dysfunction and those treated with antiplatelet therapy. © 2015 American Society for Veterinary Clinical Pathology.

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. Copyright © 2016 Elsevier Ltd. All rights reserved.

Posttraumatic Growth in Populations with Posttraumatic Stress Disorder-A Systematic Review on Growth-Related Psychological Constructs and Biological Variables.

Science.gov (United States)

Schubert, Christine F; Schmidt, Ulrike; Rosner, Rita

2016-11-01

Posttraumatic growth (PTG) and Posttraumatic Stress Disorder (PTSD) are possible consequences of trauma. PTG is supposed to emerge from cognitive processes and can have functional and dysfunctional aspects. This systematic review aims to identify and evaluate publications assessing PTG in adults diagnosed with PTSD in order to analyse the relationship between both constructs, how PTG is related to specific psychological variables and if there are biological variables linked to PTG. This extended review evaluates the quality of measures applied and is the first to study PTG only in populations meeting full PTSD criteria. In addition, the relationship between PTG and other relevant constructs, such as openness, optimism and social support, is explored. Our systematic literature search identified 140 studies of which 19 fulfilled our inclusion criteria; most of them used the Post-Traumatic Growth Inventory. Results indicate that trauma survivors with PTSD exhibit more PTG than those without PTSD and that PTG can be intensified during the therapeutic process whereat it is unclear whether PTG is a desirable outcome of PTSD therapy. Positive correlations between PTG and PTSD are reported. For diagnosed populations, we could not find strong evidence of a quadratic relationship between PTG and PTSD, although some studies support this hypothesis. Findings regarding the association of PTG with psychological variables are heterogeneous. Only one study focused on PTG as well as on biological variables (salivary cortisol) but did not discuss possible links between these two so far unconnected research fields in PTSD. Copyright © 2015 John Wiley & Sons, Ltd. Trauma survivors with PTSD develop more PTG than those without PTSD, it remains unclear whether PTSD and PTG are curvilinearly related. PTG can be enhanced through PTSD therapy, nevertheless one must not assume that PTG is a favorable treatment outcome since we do not know if the development of PTG during therapy promotes

Inverse problems in systems biology

International Nuclear Information System (INIS)

Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

2009-01-01

Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

Science.gov (United States)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

Science.gov (United States)

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

Linking structural features of protein complexes and biological function.

Science.gov (United States)

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

2015-09-01

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

Fibrin Gels Exhibit Improved Biological, Structural, and Mechanical Properties Compared with Collagen Gels in Cell-Based Tendon Tissue-Engineered Constructs

Science.gov (United States)

Dyment, Nathaniel A.; Lu, Yinhui; Rao, Marepalli; Shearn, Jason T.; Rowe, David W.; Kadler, Karl E.; Butler, David L.

2015-01-01

The prevalence of tendon and ligament injuries and inadequacies of current treatments is driving the need for alternative strategies such as tissue engineering. Fibrin and collagen biopolymers have been popular materials for creating tissue-engineered constructs (TECs), as they exhibit advantages of biocompatibility and flexibility in construct design. Unfortunately, a few studies have directly compared these materials for tendon and ligament applications. Therefore, this study aims at determining how collagen versus fibrin hydrogels affect the biological, structural, and mechanical properties of TECs during formation in vitro. Our findings show that tendon and ligament progenitor cells seeded in fibrin constructs exhibit improved tenogenic gene expression patterns compared with their collagen-based counterparts for approximately 14 days in culture. Fibrin-based constructs also exhibit improved cell-derived collagen alignment, increased linear modulus (2.2-fold greater) compared with collagen-based constructs. Cyclic tensile loading, which promotes the maturation of tendon constructs in a previous work, exhibits a material-dependent effect in this study. Fibrin constructs show trending reductions in mechanical, biological, and structural properties, whereas collagen constructs only show improved tenogenic expression in the presence of mechanical stimulation. These findings highlight that components of the mechanical stimulus (e.g., strain amplitude or time of initiation) need to be tailored to the material and cell type. Given the improvements in tenogenic expression, extracellular matrix organization, and material properties during static culture, in vitro findings presented here suggest that fibrin-based constructs may be a more suitable alternative to collagen-based constructs for tissue-engineered tendon/ligament repair. PMID:25266738

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

Science.gov (United States)

Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes; Yu, Hanry

2012-03-21

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. 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. 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.

The hydrological functioning of a constructed fen wetland watershed.

Science.gov (United States)

Ketcheson, Scott J; Price, Jonathan S; Sutton, Owen; Sutherland, George; Kessel, Eric; Petrone, Richard M

2017-12-15

Mine reclamation requires the reconstruction of entire landforms and drainage systems. The hydrological regime of reclaimed landscapes will be a manifestation of the processes operating within the individual landforms that comprise it. Hydrology is the most important process regulating wetland function and development, via strong controls on chemical and biotic processes. Accordingly, this research addresses the growing and immediate need to understand the hydrological processes that operate within reconstructed landscapes following resource extraction. In this study, the function of a constructed fen watershed (the Nikanotee Fen watershed) is evaluated for the first two years following construction (2013-2014) and is assessed and discussed within the context of the construction-level design. The system design was capable of sustaining wet conditions within the Nikanotee Fen during the snow-free period in 2013 and 2014, with persistent ponded water in some areas. Evapotranspiration dominated the water fluxes from the system. These losses were partially offset by groundwater discharge from the upland aquifer, which demonstrated strong hydrologic connectivity with the fen in spite of most construction materials having lower than targeted saturated hydraulic conductivities. However, the variable surface infiltration rates and thick placement of a soil-capping layer constrained recharge to the upland aquifer, which remained below designed water contents in much of the upland. These findings indicate that it is possible to engineer the landscape to accommodate the hydrological functions of a fen peatland following surface oil sands extraction. Future research priorities should include understanding the storage and release of water within coarse-grained reclaimed landforms as well as evaluating the relative importance of external water sources and internal water conservation mechanisms for the viability of fen ecosystems over the longer-term. Copyright © 2017 Elsevier B

Constructive definition of functional derivatives in density-functional theory

International Nuclear Information System (INIS)

Luo Ji

2006-01-01

It is shown that the functional derivatives in density-functional theory (DFT) can be explicitly defined within the domain of electron densities restricted by the electron number, and a constructive definition of such restricted derivatives is suggested. With this definition, Kohn-Sham (KS) equations can be established for an N-electron system without extending the functional domain and introducing a Lagrange multiplier. This may clarify some of the fundamental questions raised by Nesbet (1998 Phys. Rev. A 58 R12). The definition naturally leads to the fact that the KS effective potential is determined only to within an additive constant, thus the KS levels can shift freely and the relation between the highest occupied molecular orbital (HOMO) energy and the ionization potential of the system depends on the choice of the constant. On the other hand, if the domain of functionals is indeed extended beyond the electron number restriction, conclusions depend on whether the extended functionals have unrestricted derivatives or not. It is shown that the ensemble extension of DFT to open systems of mixed states (Perdew et al 1982 Phys. Rev. Lett. 49 1691) leads to an energy functional which has no unrestricted derivative at integer electron numbers. Hence after this extension, the relation between the HOMO energy and the ionization potential for an N-electron system is still uncertain. Besides, there are different extensions of the energy functional to a domain of densities unrestricted by the integer electron number, resulting in different unrestricted derivatives and electron systems with different chemical potentials. Even for the exact exchange-correlation potential, there is still an undetermined constant, whether it is a restricted or unrestricted derivative

Wave functions constructed from an invariant sum over histories satisfy constraints

International Nuclear Information System (INIS)

Halliwell, J.J.; Hartle, J.B.

1991-01-01

Invariance of classical equations of motion under a group parametrized by functions of time implies constraints between canonical coordinates and momenta. In the Dirac formulation of quantum mechanics, invariance is normally imposed by demanding that physical wave functions are annihilated by the operator versions of these constraints. In the sum-over-histories quantum mechanics, however, wave functions are specified, directly, by appropriate functional integrals. It therefore becomes an interesting question whether the wave functions so specified obey the operator constraints of the Dirac theory. In this paper, we show for a wide class of theories, including gauge theories, general relativity, and first-quantized string theories, that wave functions constructed from a sum over histories are, in fact, annihilated by the constraints provided that the sum over histories is constructed in a manner which respects the invariance generated by the constraints. By this we mean a sum over histories defined with an invariant action, invariant measure, and an invariant class of paths summed over

Biological sulfate removal from gypsum contaminated construction and demolition debris.

Science.gov (United States)

Kijjanapanich, Pimluck; Annachhatre, Ajit P; Esposito, Giovanni; van Hullebusch, Eric D; Lens, Piet N L

2013-12-15

Construction and demolition debris (CDD) contains high levels of sulfate that can cause detrimental environmental impacts when disposed without adequate treatment. In landfills, sulfate can be converted to hydrogen sulfide under anaerobic conditions. CDD can thus cause health impacts or odor problems to landfill employees and surrounding residents. Reduction of the sulfate content of CDD is an option to overcome these problems. This study aimed at developing a biological sulfate removal system to reduce the sulfate content of gypsum contaminated CDD in order to decrease the amount of solid waste, to improve the quality of CDD waste for recycling purposes and to recover sulfur from CDD. The treatment leached out the gypsum contained in CDD by water in a leaching column. The sulfate loaded leachate was then treated in a biological sulfate reducing Upflow Anaerobic Sludge Blanket (UASB) reactor to convert the sulfate to sulfide. The UASB reactor was operated at 23 ± 3 °C with a hydraulic retention time and upflow velocity of 15.5 h and 0.1 m h(-1), respectively while ethanol was added as electron donor at a final organic loading rate of 3.46 g COD L(-1) reactor d(-1). The CDD leachate had a pH of 8-9 and sulfate dissolution rates of 526.4 and 609.8 mg L(-1) d(-1) were achieved in CDD gypsum and CDD sand, respectively. Besides, it was observed that the gypsum dissolution was the rate limiting step for the biological treatment of CDD. The sulfate removal efficiency of the system stabilized at around 85%, enabling the reuse of the UASB effluent for the leaching step, proving the versatility of the bioreactor for practical applications. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

International Nuclear Information System (INIS)

Demirag, N

2014-01-01

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

Construction and Use of Recombinant Isogenic Cell Libraries in Functional Genomics

DEFF Research Database (Denmark)

Christiansen, Helle

  While nowadays robotics enable performing whole genome functional screens within a few days, the availability of suitable cellular systems to investigate the function or pathway of choice represents as a major bottleneck. In most applications, it is desirable to use cell lines with stably...... or inactivation of a gene of choice in a constitutive or tetracycline-inducible fashion. We also provide proof-of-principle that this technique can be used for the construction of double recombinant cell lines, which allows for analyses at advanced levels of complexity, e. g. by the construction of double...

Predictive value and construct validity of the work functioning screener-healthcare (WFS-H)

Science.gov (United States)

Boezeman, Edwin J.; Nieuwenhuijsen, Karen; Sluiter, Judith K.

2016-01-01

Objectives: To test the predictive value and convergent construct validity of a 6-item work functioning screener (WFS-H). Methods: Healthcare workers (249 nurses) completed a questionnaire containing the work functioning screener (WFS-H) and a work functioning instrument (NWFQ) measuring the following: cognitive aspects of task execution and general incidents, avoidance behavior, conflicts and irritation with colleagues, impaired contact with patients and their family, and level of energy and motivation. Productivity and mental health were also measured. Negative and positive predictive values, AUC values, and sensitivity and specificity were calculated to examine the predictive value of the screener. Correlation analysis was used to examine the construct validity. Results: The screener had good predictive value, since the results showed that a negative screener score is a strong indicator of work functioning not hindered by mental health problems (negative predictive values: 94%-98%; positive predictive values: 21%-36%; AUC:.64-.82; sensitivity: 42%-76%; and specificity 85%-87%). The screener has good construct validity due to moderate, but significant (pvalue and good construct validity. Its score offers occupational health professionals a helpful preliminary insight into the work functioning of healthcare workers. PMID:27010085

Predictive value and construct validity of the work functioning screener-healthcare (WFS-H).

Science.gov (United States)

Boezeman, Edwin J; Nieuwenhuijsen, Karen; Sluiter, Judith K

2016-05-25

To test the predictive value and convergent construct validity of a 6-item work functioning screener (WFS-H). Healthcare workers (249 nurses) completed a questionnaire containing the work functioning screener (WFS-H) and a work functioning instrument (NWFQ) measuring the following: cognitive aspects of task execution and general incidents, avoidance behavior, conflicts and irritation with colleagues, impaired contact with patients and their family, and level of energy and motivation. Productivity and mental health were also measured. Negative and positive predictive values, AUC values, and sensitivity and specificity were calculated to examine the predictive value of the screener. Correlation analysis was used to examine the construct validity. The screener had good predictive value, since the results showed that a negative screener score is a strong indicator of work functioning not hindered by mental health problems (negative predictive values: 94%-98%; positive predictive values: 21%-36%; AUC:.64-.82; sensitivity: 42%-76%; and specificity 85%-87%). The screener has good construct validity due to moderate, but significant (ppredictive value and good construct validity. Its score offers occupational health professionals a helpful preliminary insight into the work functioning of healthcare workers.

Method of construction of the Riemann function for a second-order hyperbolic equation

Science.gov (United States)

Aksenov, A. V.

2017-12-01

A linear hyperbolic equation of the second order in two independent variables is considered. The Riemann function of the adjoint equation is shown to be invariant with respect to the fundamental solutions transformation group. Symmetries and symmetries of fundamental solutions of the Euler-Poisson-Darboux equation are found. The Riemann function is constructed with the aid of fundamental solutions symmetries. Examples of the application of the algorithm for constructing Riemann function are given.

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

Science.gov (United States)

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

2015-12-15

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

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.

Chemically-functionalized microcantilevers for detection of chemical, biological and explosive material

Science.gov (United States)

Pinnaduwage, Lal A [Knoxville, TN; Thundat, Thomas G [Knoxville, TN; Brown, Gilbert M [Knoxville, TN; Hawk, John Eric [Olive Branch, MS; Boiadjiev, Vassil I [Knoxville, TN

2007-04-24

A chemically functionalized cantilever system has a cantilever coated on one side thereof with a reagent or biological species which binds to an analyte. The system is of particular value when the analyte is a toxic chemical biological warfare agent or an explosive.

Heavy water effects on the structure, functions and behavior of biological systems

International Nuclear Information System (INIS)

Buzgariu, Wanda; Caloianu, Maria; Moldovan, Lucia; Titescu, G.

2003-01-01

The H 2 O substitution for D 2 O either in environment or in the culture medium of the living systems generates changes in their main functions and composition. In this paper some of the heavy water effects in biological systems such as structural and functional changes were reviewed: normal cell architecture alterations, cell division and membrane functions disturbance, muscular contractility and the perturbations of biological oscillators such as circadian rhythm, heart rate, respiratory cycle, tidal and ultradian rhythm. (authors)

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

Directory of Open Access Journals (Sweden)

Lo Kenneth

2012-08-01

Full Text Available Abstract Background Inference about regulatory networks from high-throughput genomics data is of great interest in systems biology. We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge. Results We formulate network construction as a series of variable selection problems and use linear regression to model the data. Our method summarizes additional data sources with an informative prior probability distribution over candidate regression models. We extend the Bayesian model averaging (BMA variable selection method to select regulators in the regression framework. We summarize the external biological knowledge by an informative prior probability distribution over the candidate regression models. Conclusions We demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.

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

International Nuclear Information System (INIS)

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. (general)

A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

OpenAIRE

D'Onofrio, David J; An, Gary

2010-01-01

Abstract Background The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these pr...

Ultra-Fast Glyco-Coating of Non-Biological Surfaces

Directory of Open Access Journals (Sweden)

Eleanor Williams

2016-01-01

Full Text Available The ability to glycosylate surfaces has medical and diagnostic applications, but there is no technology currently recognized as being able to coat any surface without the need for prior chemical modification of the surface. Recently, a family of constructs called function-spacer-lipids (FSL has been used to glycosylate cells. Because it is known that lipid-based material can adsorb onto surfaces, we explored the potential and performance of cell-labelling FSL constructs to “glycosylate” non-biological surfaces. Using blood group A antigen as an indicator, the performance of a several variations of FSL constructs to modify a large variety of non-biological surfaces was evaluated. It was found the FSL constructs when optimised could in a few seconds glycosylate almost any non-biological surface including metals, glass, plastics, rubbers and other polymers. Although the FSL glycan coating was non-covalent, and therefore temporary, it was sufficiently robust with appropriate selection of spacer and surface that it could capture anti-glycan antibodies, immobilize cells (via antibody, and withstand incubation in serum and extensive buffer washing, making it suitable for diagnostic and research applications.

Construction of CRISPR Libraries for Functional Screening.

Science.gov (United States)

Carstens, Carsten P; Felts, Katherine A; Johns, Sarah E

2018-01-01

Identification of gene function has been aided by the ability to generate targeted gene knockouts or transcriptional repression using the CRISPR/CAS9 system. Using pooled libraries of guide RNA expression vectors that direct CAS9 to a specific genomic site allows identification of genes that are either enriched or depleted in response to a selection scheme, thus linking the affected gene to the chosen phenotype. The quality of the data generated by the screening is dependent on the quality of the guide RNA delivery library with regards to error rates and especially evenness of distribution of the guides. Here, we describe a method for constructing complex plasmid libraries based on pooled designed oligomers with high representation and tight distributions. The procedure allows construction of plasmid libraries of >60,000 members with a 95th/5th percentile ratio of less than 3.5.

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.

Synthetic Biology for Specialty Chemicals.

Science.gov (United States)

Markham, Kelly A; Alper, Hal S

2015-01-01

In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

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.

The biological effectiveness of antiproton irradiation

DEFF Research Database (Denmark)

Holzscheiter, Michael H.; Bassler, Niels; Agazaryan, Nzhde

2006-01-01

ever measurements of the biological effectiveness of antiprotons. Materials and methods: V79 cells were suspended in a semi-solid matrix and irradiated with 46.7 MeV antiprotons, 48 MeV protons, or 60Co c-rays. Clonogenic survival was determined as a function of depth along the particle beams. Dose...... and particle fluence response relationships were constructed from data in the plateau and Bragg peak regions of the beams and used to assess the biological effectiveness. Results: Due to uncertainties in antiproton dosimetry we defined a new term, called the biologically effective dose ratio (BEDR), which...... has a higher relative biological effectiveness (RBE). Conclusion: We have produced the first measurements of the biological consequences of antiproton irradiation. These data substantiate theoretical predictions of the biological effects of antiproton annihilation within the Bragg peak, and suggest...

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.

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

International Nuclear Information System (INIS)

Kijjanapanich, Pimluck; Do, Anh Tien; Annachhatre, Ajit P.; Esposito, Giovanni; Yeh, Daniel H.; Lens, Piet N.L.

2014-01-01

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 −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 −1 did not give any adverse effect on the sulfate removal efficiency of the IFB and GL-AnMBR systems

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

Unsupervised Learning and Pattern Recognition of Biological Data Structures with Density Functional Theory and Machine Learning.

Science.gov (United States)

Chen, Chien-Chang; Juan, Hung-Hui; Tsai, Meng-Yuan; Lu, Henry Horng-Shing

2018-01-11

By introducing the methods of machine learning into the density functional theory, we made a detour for the construction of the most probable density function, which can be estimated by learning relevant features from the system of interest. Using the properties of universal functional, the vital core of density functional theory, the most probable cluster numbers and the corresponding cluster boundaries in a studying system can be simultaneously and automatically determined and the plausibility is erected on the Hohenberg-Kohn theorems. For the method validation and pragmatic applications, interdisciplinary problems from physical to biological systems were enumerated. The amalgamation of uncharged atomic clusters validated the unsupervised searching process of the cluster numbers and the corresponding cluster boundaries were exhibited likewise. High accurate clustering results of the Fisher's iris dataset showed the feasibility and the flexibility of the proposed scheme. Brain tumor detections from low-dimensional magnetic resonance imaging datasets and segmentations of high-dimensional neural network imageries in the Brainbow system were also used to inspect the method practicality. The experimental results exhibit the successful connection between the physical theory and the machine learning methods and will benefit the clinical diagnoses.

Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology.

Science.gov (United States)

Schmidt, Markus; de Lorenzo, Víctor

2012-07-16

The plausible release of deeply engineered or even entirely synthetic/artificial microorganisms raises the issue of their intentional (e.g. bioremediation) or accidental interaction with the Environment. Containment systems designed in the 1980s-1990s for limiting the spread of genetically engineered bacteria and their recombinant traits are still applicable to contemporary Synthetic Biology constructs. Yet, the ease of DNA synthesis and the uncertainty on how non-natural properties and strains could interplay with the existing biological word poses yet again the challenge of designing safe and efficacious firewalls to curtail possible interactions. Such barriers may include xeno-nucleic acids (XNAs) instead of DNA as information-bearing molecules, rewriting the genetic code to make it non-understandable by the existing gene expression machineries, and/or making growth dependent on xenobiotic chemicals. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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

Marine Carotenoids: Biological Functions and Commercial Applications

Science.gov (United States)

Vílchez, Carlos; Forján, Eduardo; Cuaresma, María; Bédmar, Francisco; Garbayo, Inés; Vega, José M.

2011-01-01

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. PMID:21556162

Toward scalable parts families for predictable design of biological circuits.

Science.gov (United States)

Lucks, Julius B; Qi, Lei; Whitaker, Weston R; Arkin, Adam P

2008-12-01

Our current ability to engineer biological circuits is hindered by design cycles that are costly in terms of time and money, with constructs failing to operate as desired, or evolving away from the desired function once deployed. Synthetic biologists seek to understand biological design principles and use them to create technologies that increase the efficiency of the genetic engineering design cycle. Central to the approach is the creation of biological parts--encapsulated functions that can be composited together to create new pathways with predictable behaviors. We define five desirable characteristics of biological parts--independence, reliability, tunability, orthogonality and composability, and review studies of small natural and synthetic biological circuits that provide insights into each of these characteristics. We propose that the creation of appropriate sets of families of parts with these properties is a prerequisite for efficient, predictable engineering of new function in cells and will enable a large increase in the sophistication of genetic engineering applications.

DNA nanovehicles and the biological barriers

DEFF Research Database (Denmark)

Okholm, Anders Hauge; Kjems, Jørgen

2016-01-01

DNA is emerging as a smart material to construct nanovehicles for targeted drug delivery. The programmability of Watson-Crick base paring enables construction of defined and dynamic DNA nanostructures of almost arbitrary shape and DNA can readily be functionalized with a variety of molecular...... be overcome. Here, we highlight recent strategies for DNA nanostructures in drug delivery, DNA nanovehicles, to facilitate targeting and crossing of the biological barriers. In light of this, we discuss future solutions and challenges for DNA nanovehicles to unravel their great potential to facilitate...

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.

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

Synthesis of O-glycopeptides and construction of glycopeptide microarrays

DEFF Research Database (Denmark)

Blixt, Klas Ola; Cló, Emiliano

2013-01-01

O-glycosylation of proteins is an important modification which affects biological function and immunity. In this chapter, we provide protocols for efficient solid-phase O-glycopeptide synthesis (SPGPS) and protocols for the construction of glycopeptide microarray chips for screening applications....

Synthetic Biology of Cyanobacteria: Unique Challenges and Opportunities

Directory of Open Access Journals (Sweden)

Bertram M Berla

2013-08-01

Full Text Available Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria’s potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as ‘chassis’ strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a ‘green E. coli’. In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

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.

The functioning and behaviour of biological parents of children ...

African Journals Online (AJOL)

Parenting a child with ADHD may intensify parental stress through functional impairment notwithstanding the diagnosis of ADHD. Methods: Eighty-one biological parents of children diagnosed with attention-deficit/ hyperactivity disorder were screened using self-reporting measurements. ADHD self-report scale (ASRS-V 1.1) ...

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....

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.

Mechanical properties and structure-function relationships of human chondrocyte-seeded cartilage constructs after in vitro culture.

Science.gov (United States)

Middendorf, Jill M; Griffin, Darvin J; Shortkroff, Sonya; Dugopolski, Caroline; Kennedy, Stephen; Siemiatkoski, Joseph; Cohen, Itai; Bonassar, Lawrence J

2017-10-01

Autologous Chondrocyte Implantation (ACI) is a widely recognized method for the repair of focal cartilage defects. Despite the accepted use, problems with this technique still exist, including graft hypertrophy, damage to surrounding tissue by sutures, uneven cell distribution, and delamination. Modified ACI techniques overcome these challenges by seeding autologous chondrocytes onto a 3D scaffold and securing the graft into the defect. Many studies on these tissue engineered grafts have identified the compressive properties, but few have examined frictional and shear properties as suggested by FDA guidance. This study is the first to perform three mechanical tests (compressive, frictional, and shear) on human tissue engineered cartilage. The objective was to understand the complex mechanical behavior, function, and changes that occur with time in these constructs grown in vitro using compression, friction, and shear tests. Safranin-O histology and a DMMB assay both revealed increased sulfated glycosaminoglycan (sGAG) content in the scaffolds with increased maturity. Similarly, immunohistochemistry revealed increased lubricin localization on the construct surface. Confined compression and friction tests both revealed improved properties with increased construct maturity. Compressive properties correlated with the sGAG content, while improved friction coefficients were attributed to increased lubricin localization on the construct surfaces. In contrast, shear properties did not improve with increased culture time. This study suggests the various mechanical and biological properties of tissue engineered cartilage improve at different rates, indicating thorough mechanical evaluation of tissue engineered cartilage is critical to understanding the performance of repaired cartilage. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2298-2306, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

Science.gov (United States)

Ohno, Hirohisa; Saito, Hirohide

2016-01-01

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Metabolomics for functional genomics, systems biology, and biotechnology.

Science.gov (United States)

Saito, Kazuki; Matsuda, Fumio

2010-01-01

Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

Carbon nanotubes for biological and biomedical applications

International Nuclear Information System (INIS)

Yang Wenrong; Thordarson, Pall; Gooding, J Justin; Ringer, Simon P; Braet, Filip

2007-01-01

Ever since the discovery of carbon nanotubes, researchers have been exploring their potential in biological and biomedical applications. The recent expansion and availability of chemical modification and bio-functionalization methods have made it possible to generate a new class of bioactive carbon nanotubes which are conjugated with proteins, carbohydrates, or nucleic acids. The modification of a carbon nanotube on a molecular level using biological molecules is essentially an example of the 'bottom-up' fabrication principle of bionanotechnology. The availability of these biomodified carbon nanotube constructs opens up an entire new and exciting research direction in the field of chemical biology, finally aiming to target and to alter the cell's behaviour at the subcellular or molecular level. This review covers the latest advances of bio-functionalized carbon nanotubes with an emphasis on the development of functional biological nano-interfaces. Topics that are discussed herewith include methods for biomodification of carbon nanotubes, the development of hybrid systems of carbon nanotubes and biomolecules for bioelectronics, and carbon nanotubes as transporters for a specific delivery of peptides and/or genetic material to cells. All of these current research topics aim at translating these biotechnology modified nanotubes into potential novel therapeutic approaches. (topical review)

Synthetic Biology and Personalized Medicine

Science.gov (United States)

Jain, K.K.

2013-01-01

Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task. PMID:22907209

MicroRNA functional network in pancreatic cancer: From biology to ...

Indian Academy of Sciences (India)

[Wang J and Sen S 2011 MicroRNA functional network in pancreatic cancer: From biology to biomarkers of disease. ... growth factor type I receptor; INSR, insulin receptor; IPA, Ingenuity Pathway Analysis; IPMN, ..... Prostate cancer signalling.

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.

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.

Defining and detecting structural sensitivity in biological models: developing a new framework.

Science.gov (United States)

Adamson, M W; Morozov, A Yu

2014-12-01

When we construct mathematical models to represent biological systems, there is always uncertainty with regards to the model specification--whether with respect to the parameters or to the formulation of model functions. Sometimes choosing two different functions with close shapes in a model can result in substantially different model predictions: a phenomenon known in the literature as structural sensitivity, which is a significant obstacle to improving the predictive power of biological models. In this paper, we revisit the general definition of structural sensitivity, compare several more specific definitions and discuss their usefulness for the construction and analysis of biological models. Then we propose a general approach to reveal structural sensitivity with regards to certain system properties, which considers infinite-dimensional neighbourhoods of the model functions: a far more powerful technique than the conventional approach of varying parameters for a fixed functional form. In particular, we suggest a rigorous method to unearth sensitivity with respect to the local stability of systems' equilibrium points. We present a method for specifying the neighbourhood of a general unknown function with [Formula: see text] inflection points in terms of a finite number of local function properties, and provide a rigorous proof of its completeness. Using this powerful result, we implement our method to explore sensitivity in several well-known multicomponent ecological models and demonstrate the existence of structural sensitivity in these models. Finally, we argue that structural sensitivity is an important intrinsic property of biological models, and a direct consequence of the complexity of the underlying real systems.

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

Science.gov (United States)

Dirnbeck, Matthew R.

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

Designable DNA-binding domains enable construction of logic circuits in mammalian cells.

Science.gov (United States)

Gaber, Rok; Lebar, Tina; Majerle, Andreja; Šter, Branko; Dobnikar, Andrej; Benčina, Mojca; Jerala, Roman

2014-03-01

Electronic computer circuits consisting of a large number of connected logic gates of the same type, such as NOR, can be easily fabricated and can implement any logic function. In contrast, designed genetic circuits must employ orthogonal information mediators owing to free diffusion within the cell. Combinatorial diversity and orthogonality can be provided by designable DNA- binding domains. Here, we employed the transcription activator-like repressors to optimize the construction of orthogonal functionally complete NOR gates to construct logic circuits. We used transient transfection to implement all 16 two-input logic functions from combinations of the same type of NOR gates within mammalian cells. Additionally, we present a genetic logic circuit where one input is used to select between an AND and OR function to process the data input using the same circuit. This demonstrates the potential of designable modular transcription factors for the construction of complex biological information-processing devices.

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.

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

Directory of Open Access Journals (Sweden)

David Renfrew Haft

Full Text Available 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.

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

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.......e., VAAM) provides a way forward to emulate muscle-like functions that are comparable to those found in physiological experiments of biological muscles. Based on these muscle-like functions, the robotic joints can easily achieve variable compliance that does not require complex physical components...

Scavenger Receptor CD163 and Its Biological Functions

Directory of Open Access Journals (Sweden)

Gabriela Onofre

2009-01-01

Full Text Available CD163 is a member of scavenger receptor super family class B of the first subgroup. It is mapped to the region p13 on chromosome 12. Five different isoforms of CD163 have been described, which differ in the structure of their cytoplasmic domains and putative phosporylation sites. This scavenger receptor is selectively expressed on cells of monocytes and macrophages lineage exclusively. CD163 immunological function is essentially homeostatic. It also has other functions because participates in adhesion to endothelial cells, in tolerance induction and tissues regeneration. Other very important function of CD163 is the clearance of hemoglobin in its cell-free form and participation in anti-inflammation in its soluble form, exhibiting cytokine-like functions. We review the biological functions of CD163 which have been discovered until now. It seems apparent from this review that CD163 scavenger receptor can be used as biomarker in different diseases and as a valuable diagnostic parameter for prognosis of many diseases especially inflammatory disorders and sepsis.

Carotenoids from Marine Organisms: Biological Functions and Industrial Applications

Directory of Open Access Journals (Sweden)

Christian Galasso

2017-11-01

Full Text Available As is the case for terrestrial organisms, carotenoids represent the most common group of pigments in marine environments. They are generally biosynthesized by all autotrophic marine organisms, such as bacteria and archaea, algae and fungi. Some heterotrophic organisms also contain carotenoids probably accumulated from food or partly modified through metabolic reactions. These natural pigments are divided into two chemical classes: carotenes (such as lycopene and α- and β-carotene that are composed of hydrogen and carbon; xanthophylls (such as astaxanthin, fucoxanthin and lutein, which are constituted by hydrogen, carbon and oxygen. Carotenoids, as antioxidant compounds, assume a key role in the protection of cells. In fact, quenching of singlet oxygen, light capture and photosynthesis protection are the most relevant biological functions of carotenoids. The present review aims at describing (i the biological functions of carotenoids and their benefits for human health, (ii the most common carotenoids from marine organisms and (iii carotenoids having large success in pharmaceutical, nutraceutical and cosmeceutical industries, highlighting the scientific progress in marine species cultivation for natural pigments production.

Neurotrophin Propeptides: Biological Functions and Molecular Mechanisms.

Science.gov (United States)

Rafieva, Lola M; Gasanov, Eugene V

2016-01-01

Neurotrophins constitute a family of growth factors that play a key role in the regulation of the development and function of the central and peripheral nervous systems. A common feature of all the neurotrophins is their synthesis in cells as long precursors (pre-pro-neurotrophins) that contain an N-terminal signal peptide, a following propeptide and the mature neurotrophin. Although the signal peptide functions have been well studied, the role of neurotrophin propeptides is not so clear. Here, we briefly summarize the biochemistry of neurotrophin propeptides, including their role as folding-assistants for the mature factor and their role in processing and in secretion of neurotrophins. In the main part of the review we summarize our current state of knowledge of the biological activity of neurotrophin propeptides, their possible mechanisms of action, and their potential influence on the activity of the mature neurotrophins.

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

International Nuclear Information System (INIS)

Wu, Juan; Feng, Yuqin; Dai, Yanran; Cui, Naxin; Anderson, Bruce; Cheng, Shuiping

2016-01-01

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"−"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_P_S_I_I) 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 loads

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

[Research progress of mammalian synthetic biology in biomedical field].

Science.gov (United States)

Yang, Linfeng; Yin, Jianli; Wang, Meiyan; Ye, Haifeng

2017-03-25

Although still in its infant stage, synthetic biology has achieved remarkable development and progress during the past decade. Synthetic biology applies engineering principles to design and construct gene circuits uploaded into living cells or organisms to perform novel or improved functions, and it has been widely used in many fields. In this review, we describe the recent advances of mammalian synthetic biology for the treatment of diseases. We introduce common tools and design principles of synthetic gene circuits, and then we demonstrate open-loop gene circuits induced by different trigger molecules used in disease diagnosis and close-loop gene circuits used for biomedical applications. Finally, we discuss the perspectives and potential challenges of synthetic biology for clinical applications.

Creating biomaterials with spatially organized functionality.

Science.gov (United States)

Chow, Lesley W; Fischer, Jacob F

2016-05-01

Biomaterials for tissue engineering provide scaffolds to support cells and guide tissue regeneration. Despite significant advances in biomaterials design and fabrication techniques, engineered tissue constructs remain functionally inferior to native tissues. This is largely due to the inability to recreate the complex and dynamic hierarchical organization of the extracellular matrix components, which is intimately linked to a tissue's biological function. This review discusses current state-of-the-art strategies to control the spatial presentation of physical and biochemical cues within a biomaterial to recapitulate native tissue organization and function. © 2016 by the Society for Experimental Biology and Medicine.

Re-evaluating concepts of biological function in clinical medicine: towards a new naturalistic theory of disease.

Science.gov (United States)

Chin-Yee, Benjamin; Upshur, Ross E G

2017-08-01

Naturalistic theories of disease appeal to concepts of biological function, and use the notion of dysfunction as the basis of their definitions. Debates in the philosophy of biology demonstrate how attributing functions in organisms and establishing the function-dysfunction distinction is by no means straightforward. This problematization of functional ascription has undermined naturalistic theories and led some authors to abandon the concept of dysfunction, favoring instead definitions based in normative criteria or phenomenological approaches. Although this work has enhanced our understanding of disease and illness, we need not necessarily abandon naturalistic concepts of function and dysfunction in the disease debate. This article attempts to move towards a new naturalistic theory of disease that overcomes the limitations of previous definitions and offers advantages in the clinical setting. Our approach involves a re-evaluation of concepts of biological function employed by naturalistic theories. Drawing on recent insights from the philosophy of biology, we develop a contextual and evaluative account of function that is better suited to clinical medicine and remains consistent with contemporary naturalism. We also show how an updated naturalistic view shares important affinities with normativist and phenomenological positions, suggesting a possibility for consilience in the disease debate.

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

Science.gov (United States)

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

2017-07-03

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

The relationship between oral health status and biological and psychosocial function in the bedridden elderly.

Science.gov (United States)

Hanada, N; Tada, A

2001-01-01

The present study was conducted in order to determine what item of biological and psychosocial function is related to oral health status in the bedridden elderly. The subjects were 94 elderly individuals (30 males, 64 females) who had been admitted to a nursing home in Chiba city, Japan. We assessed the number of remaining teeth and the number of functional teeth as oral health status variables. Biological and psychosocial function levels were determined using the functional independence measure method developed by the State University of New York at Buffalo. More than 70% of subjects had less than ten remaining teeth. Almost all subjects needed prosthesis treatment. More than 50% of subjects had 27 or less functional teeth. Mann-Whitney U-test and logistic regression models showed that 'expression' was concerned with the number of remaining teeth and 'bladder management', 'locomotion', 'transfers' were related to the number of functional teeth. These data suggest close relation between oral health status and biological and psychosocial function levels in the bedridden elderly.

Construction of integrable model Kohn-Sham potentials by analysis of the structure of functional derivatives

International Nuclear Information System (INIS)

Gaiduk, Alex P.; Staroverov, Viktor N.

2011-01-01

A directly approximated exchange-correlation potential should, by construction, be a functional derivative of some density functional in order to avoid unphysical results. Using generalized gradient approximations (GGAs) as an example, we show that functional derivatives of explicit density functionals have a very rigid inner structure, the knowledge of which allows one to build the entire functional derivative from a small part. Based on this analysis, we develop a method for direct construction of integrable Kohn-Sham potentials. As an illustration, we transform the model potential of van Leeuwen and Baerends (which is not a functional derivative) into a semilocal exchange potential that has a parent GGA, yields accurate energies, and is free from the artifacts inherent in existing semilocal potential approximations.

PREFACE: Nanobiology: from physics and engineering to biology

Science.gov (United States)

Nussinov, Ruth; Alemán, Carlos

2006-03-01

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

Paul Langerhans: a prilgrim "traveling" from functional histology to marine biology.

Science.gov (United States)

Raica, Marius; Cimpean, Anca Maria

2017-06-01

The nineteenth century was the time of a real revolution in science and medicine. A lot of seminal discoveries in medicine and biology were done in this time, and many of them were coincident with the introduction of the compound microscope by Hermann van Deijl and the standard histological technique by Paul Ehrlich. The main tissue types and individual cells were characterized and originally classified more than hundred years ago, although less attention was paid to their basic functions. This was mainly due to the modality of tissue specimen processing that allowed particularly detailed descriptive studies. Even so, we can notice some attempts to correlate the structure with the function. The German scientist Paul Langerhans, well-known for the discovery of Langerhans islets of the pancreas and Langerhans cells from the epidermis, tried to change the conventional fate of morphological studies introducing in his works functional hypothesis based on traditional microscopic observations even from the beginning of his scientific career. Paul Langerhans was a complex personality of the second half of the nineteenth century, not only in medicine, but also in other fields of biology. In the present review, presented is the life and research activity of Paul Langerhans, not only because of the importance of his discoveries, but also for perspectives that were opened by these findings in unexpected fields of medicine and biology.

Parallel keyed hash function construction based on chaotic maps

International Nuclear Information System (INIS)

Xiao Di; Liao Xiaofeng; Deng Shaojiang

2008-01-01

Recently, a variety of chaos-based hash functions have been proposed. Nevertheless, none of them works efficiently in parallel computing environment. In this Letter, an algorithm for parallel keyed hash function construction is proposed, whose structure can ensure the uniform sensitivity of hash value to the message. By means of the mechanism of both changeable-parameter and self-synchronization, the keystream establishes a close relation with the algorithm key, the content and the order of each message block. The entire message is modulated into the chaotic iteration orbit, and the coarse-graining trajectory is extracted as the hash value. Theoretical analysis and computer simulation indicate that the proposed algorithm can satisfy the performance requirements of hash function. It is simple, efficient, practicable, and reliable. These properties make it a good choice for hash on parallel computing platform

Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

Science.gov (United States)

Barquilla, Manuel B.

2018-01-01

This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and

Progress in the biological function of alpha-enolase

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Hong Ji

2016-03-01

Full Text Available Alpha-enolase (ENO1, also known as 2-phospho-D-glycerate hydrolase, is a metalloenzyme that catalyzes the conversion of 2-phosphoglyceric acid to phosphoenolpyruvic acid in the glycolytic pathway. It is a multifunctional glycolytic enzyme involved in cellular stress, bacterial and fungal infections, autoantigen activities, the occurrence and metastasis of cancer, parasitic infections, and the growth, development and reproduction of organisms. This article mainly reviews the basic characteristics and biological functions of ENO1.

Facile Site-Directed Mutagenesis of Large Constructs Using Gibson Isothermal DNA Assembly.

Science.gov (United States)

Yonemoto, Isaac T; Weyman, Philip D

2017-01-01

Site-directed mutagenesis is a commonly used molecular biology technique to manipulate biological sequences, and is especially useful for studying sequence determinants of enzyme function or designing proteins with improved activity. We describe a strategy using Gibson Isothermal DNA Assembly to perform site-directed mutagenesis on large (>~20 kbp) constructs that are outside the effective range of standard techniques such as QuikChange II (Agilent Technologies), but more reliable than traditional cloning using restriction enzymes and ligation.

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

Science.gov (United States)

Kijjanapanich, Pimluck; Do, Anh Tien; Annachhatre, Ajit P; Esposito, Giovanni; Yeh, Daniel H; Lens, Piet N L

2014-03-30

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 15.5h. A high calcium concentration up to 1,000 mg L(-1) did not give any adverse effect on the sulfate removal efficiency of the IFB and GL-AnMBR systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Modeling dynamics of biological and chemical components of aquatic ecosystems

International Nuclear Information System (INIS)

Lassiter, R.R.

1975-05-01

To provide capability to model aquatic ecosystems or their subsystems as needed for particular research goals, a modeling strategy was developed. Submodels of several processes common to aquatic ecosystems were developed or adapted from previously existing ones. Included are submodels for photosynthesis as a function of light and depth, biological growth rates as a function of temperature, dynamic chemical equilibrium, feeding and growth, and various types of losses to biological populations. These submodels may be used as modules in the construction of models of subsystems or ecosystems. A preliminary model for the nitrogen cycle subsystem was developed using the modeling strategy and applicable submodels. (U.S.)

Biological markers for kidney injury and renal function in the intensive care unit

NARCIS (Netherlands)

Royakkers, A.A.N.M.

2014-01-01

The purpose of the investigations described in this thesis was to seek for answers to two relevant questions in ICUs in resource-rich settings, i.e., can new biological markers play a role in early recognition of AKI, and can new biological markers predict recovery of renal function in patients who

METHOD OF CONSTRUCTION OF GENETIC DATA CLUSTERS

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N. A. Novoselova

2016-01-01

Full Text Available The paper presents a method of construction of genetic data clusters (functional modules using the randomized matrices. To build the functional modules the selection and analysis of the eigenvalues of the gene profiles correlation matrix is performed. The principal components, corresponding to the eigenvalues, which are significantly different from those obtained for the randomly generated correlation matrix, are used for the analysis. Each selected principal component forms gene cluster. In a comparative experiment with the analogs the proposed method shows the advantage in allocating statistically significant different-sized clusters, the ability to filter non- informative genes and to extract the biologically interpretable functional modules matching the real data structure.

Building biological foundries for next-generation synthetic biology.

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Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

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

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.

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Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Uversky, Vladimir N; Obradovic, Zoran

2007-05-01

Identifying relationships between function, amino acid sequence, and protein structure represents a major challenge. In this study, we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from the Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins, and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our

The construction of an amino acid network for understanding protein structure and function.

Science.gov (United States)

Yan, Wenying; Zhou, Jianhong; Sun, Maomin; Chen, Jiajia; Hu, Guang; Shen, Bairong

2014-06-01

Amino acid networks (AANs) are undirected networks consisting of amino acid residues and their interactions in three-dimensional protein structures. The analysis of AANs provides novel insight into protein science, and several common amino acid network properties have revealed diverse classes of proteins. In this review, we first summarize methods for the construction and characterization of AANs. We then compare software tools for the construction and analysis of AANs. Finally, we review the application of AANs for understanding protein structure and function, including the identification of functional residues, the prediction of protein folding, analyzing protein stability and protein-protein interactions, and for understanding communication within and between proteins.

[Recent advances of synthetic biology for production of functional ingredients in Chinese materia medica].

Science.gov (United States)

Su, Xin-Yao; Xue, Jian-Ping; Wang, Cai-Xia

2016-11-01

The functional ingredients in Chinese materia medica are the main active substance for traditional Chinese medicine and most of them are secondary metabolites derivatives. Until now,the main method to obtain those functional ingredients is through direct extraction from the Chinese materia medica. However, the income is very low because of the high extraction costs and the decreased medicinal plants. Synthetic biology technology, as a new and microbial approach, can be able to carry out large-scale production of functional ingredients and greatly ease the shortage of traditional Chinese medicine ingredients. This review mainly focused on the recent advances in synthetic biology for the functional ingredients production. Copyright© by the Chinese Pharmaceutical Association.

Construction of Vibronic Diabatic Hamiltonian for Excited-State Electron and Energy Transfer Processes.

Science.gov (United States)

Xie, Yu; Jiang, Shengshi; Zheng, Jie; Lan, Zhenggang

2017-12-21

Photoinduced excited-state electron and energy transfer processes are crucial in biological photoharvesting systems and organic photovoltaic devices. We discuss the construction of a diabatic vibronic Hamiltonian for the proper treatment of these processes involving the projection approach acting on both electronic wave functions and vibrational modes. In the electronic part, the wave function projection approach is used to construct the diabatic Hamiltonian in which both local excited states and charge-transfer states are included on the same footing. For the vibrational degrees of freedom, the vibronic couplings in the diabatic Hamiltonian are obtained in the basis of the pseudonormal modes localized on each monomer site by applying delocalized-to-localized mode projection. This systematic approach allows us to construct the vibronic diabatic Hamiltonian in molecular aggregates.

Construction of renormalized coefficient functions of the Feynman diagrams by means of a computer

International Nuclear Information System (INIS)

Tarasov, O.V.

1978-01-01

An algorithm and short description of computer program, written in SCHOONSCHIP, are given. The program is assigned for construction of integrands of renormalized coefficient functions of the Feynman diagrams in scalar theories in the case of arbitrary subtraction point. For the given Feynman graph computer completely realizes the R-operation of Bogolubov-Parasjuk and gives the result as an integral over Feynman parameters. With the help of the program the time construction of the whole renormalized coefficient function is equal approximately 30 s on the CDC-6500 computer

Multiwire proportional chambers in the devices for molecular biology constructed at JINR

Energy Technology Data Exchange (ETDEWEB)

Anisimov, Y S; Chernenko, S P; Ivanov, A B; Peshekhonov, V D; Skvaril, J; Zanevsky, Y V [Joint Inst. for Nuclear Research, Dubna (USSR). Lab. of High Energy; Kheiker, D M [Joint Inst. for Nuclear Research, Dubna (USSR). Lab. of High Energy; AN SSSR, Moscow. Inst. Kristallografii)

1980-10-01

The automation of measuring processes in molecular biology is a current problem. In order to solve this problem, conventionally used methods should be changed for an up-to-date technique which allows the processes of data measurement and analysis to be automated. Toward this end two-coordinate proportional chambers (MWPCs) are coming widely into use. The use of MWPCs in devices for radiochromatography and x-ray diffractrometry is discussed in this paper. A new device consisting of proportional chambers has been constructed for an automated analysis of thin layer radiochromatograms. The device enables one to localize radioactive zones (labelled with /sup 3/H, /sup 14/C, /sup 32/P), to identify radionuclides and to measure their activities. The device has a high sensitivity (5 pCi for tritium), a small dead time, good space resolution (in the case of /sup 3/H zones spaced 1-2 mm apart are separated) and high reproducibility. For x-ray diffractometry of single crystals, a high counting rate device has been constructed on the basis of a MWPC with a total number of channels amounting to 350 x 200 = 70,000. The dead time of the device is about 0.6 ..mu..s which allows to detect 3 x 10/sup 5/ events/s at counting losses of no more than 20%. The quantum efficiency (Cu K..cap alpha..) is about 73%. The X and Y space resolution (fwhm) is equal to 1 mm and 1.7 mm, respectively.

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.

Computer-aided design of biological circuits using TinkerCell.

Science.gov (United States)

Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

2010-01-01

Synthetic biology is an engineering discipline that builds on modeling practices from systems biology and wet-lab techniques from genetic engineering. As synthetic biology advances, efficient procedures will be developed that will allow a synthetic biologist to design, analyze, and build biological networks. In this idealized pipeline, computer-aided design (CAD) is a necessary component. The role of a CAD application would be to allow efficient transition from a general design to a final product. TinkerCell is a design tool for serving this purpose in synthetic biology. In TinkerCell, users build biological networks using biological parts and modules. The network can be analyzed using one of several functions provided by TinkerCell or custom programs from third-party sources. Since best practices for modeling and constructing synthetic biology networks have not yet been established, TinkerCell is designed as a flexible and extensible application that can adjust itself to changes in the field. © 2010 Landes Bioscience

Biomarkers of Aging: From Function to Molecular Biology

Directory of Open Access Journals (Sweden)

Karl-Heinz Wagner

2016-06-01

Full Text Available 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.

Uniformly constructing combinatorial solutions, combining a rational function with hyperbolic or trigonometric functions, for the (2+1) dimensional Broer-Kaup-Kupershmidt equation

International Nuclear Information System (INIS)

Liu Qing; Wang Zihua

2010-01-01

According to two dependent rational solutions to a generalized Riccati equation together with the equation itself, a rational-exponent solution to a nonlinear partial differential equation can be constructed. By selecting different parameter values in the rational-exponent solution, many families of combinatorial solutions combined with a rational function such as hyperbolic functions or trigonometric functions, are rapidly derived. This method is applied to the Whitham-Broer-Kaup equation and a series of combinatorial solutions are obtained, showing that this method is a more concise and efficient approach and can uniformly construct many types of combined solutions to nonlinear partial differential equations.

The biological effectiveness of antiproton irradiation

International Nuclear Information System (INIS)

Holzscheiter, Michael H.; Bassler, Niels; Agazaryan, Nzhde; Beyer, Gerd; Blackmore, Ewart; DeMarco, John J.; Doser, Michael; Durand, Ralph E.; Hartley, Oliver; Iwamoto, Keisuke S.; Knudsen, Helge V.; Landua, Rolf; Maggiore, Carl; McBride, William H.; Moller, Soren Pape; Petersen, Jorgen; Skarsgard, Lloyd D.; Smathers, James B.; Solberg, Timothy D.; Uggerhoj, Ulrik I.; Vranjes, Sanja; Withers, H. Rodney; Wong, Michelle; Wouters, Bradly G.

2006-01-01

Background and purpose: Antiprotons travel through tissue in a manner similar to that for protons until they reach the end of their range where they annihilate and deposit additional energy. This makes them potentially interesting for radiotherapy. The aim of this study was to conduct the first ever measurements of the biological effectiveness of antiprotons. Materials and methods: V79 cells were suspended in a semi-solid matrix and irradiated with 46.7 MeV antiprotons, 48 MeV protons, or 6 Co γ-rays. Clonogenic survival was determined as a function of depth along the particle beams. Dose and particle fluence response relationships were constructed from data in the plateau and Bragg peak regions of the beams and used to assess the biological effectiveness. Results: Due to uncertainties in antiproton dosimetry we defined a new term, called the biologically effective dose ratio (BEDR), which compares the response in a minimally spread out Bragg peak (SOBP) to that in the plateau as a function of particle fluence. This value was ∼3.75 times larger for antiprotons than for protons. This increase arises due to the increased dose deposited in the Bragg peak by annihilation and because this dose has a higher relative biological effectiveness (RBE). Conclusion: We have produced the first measurements of the biological consequences of antiproton irradiation. These data substantiate theoretical predictions of the biological effects of antiproton annihilation within the Bragg peak, and suggest antiprotons warrant further investigation

Is synthetic biology mechanical biology?

Science.gov (United States)

Holm, Sune

2015-12-01

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

Automated quantitative assessment of proteins' biological function in protein knowledge bases.

Science.gov (United States)

Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

2008-01-01

Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

Directory of Open Access Journals (Sweden)

Gabriele Mayr

2008-01-01

Full Text Available Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Maria Simak

Full Text Available The great amount of gene expression data has brought a big challenge for the discovery of Gene Regulatory Network (GRN. For network reconstruction and the investigation of regulatory relations, it is desirable to ensure directness of links between genes on a map, infer their directionality and explore candidate biological functions from high-throughput transcriptomic data. To address these problems, we introduce a Boolean Function Network (BFN model based on techniques of hidden Markov model (HMM, likelihood ratio test and Boolean logic functions. BFN consists of two consecutive tests to establish links between pairs of genes and check their directness. We evaluate the performance of BFN through the application to S. cerevisiae time course data. BFN produces regulatory relations which show consistency with succession of cell cycle phases. Furthermore, it also improves sensitivity and specificity when compared with alternative methods of genetic network reverse engineering. Moreover, we demonstrate that BFN can provide proper resolution for GO enrichment of gene sets. Finally, the Boolean functions discovered by BFN can provide useful insights for the identification of control mechanisms of regulatory processes, which is the special advantage of the proposed approach. In combination with low computational complexity, BFN can serve as an efficient screening tool to reconstruct genes relations on the whole genome level. In addition, the BFN approach is also feasible to a wide range of time course datasets.

3D-printed biological organs: medical potential and patenting opportunity.

Science.gov (United States)

Yoo, Seung-Schik

2015-05-01

Three-dimensional (3D) bioprinting has emerged as a new disruptive technology that may address the ever-increasing demand for organ transplants. 3D bioprinting offers many technical features that allow for building functional biological tissue constructs by dispensing the individual or group of cells into specific locations along with various types of bio-scaffold materials and extracellular matrices, and thus, may provide flexibility needed for on-demand individualized construction of biological organs. Several key classes of 3D bioprinting techniques are reviewed, including potential medical and industrial applications. Several unanswered engineering components for the ultimate creation of printed biological organs are also discussed. The complicated nature of the human organs, in addition to the legal and ethical requirements for safe implantation into the human body, would require significant research and development to produce marketable bioprinted organs. This also suggests the possibility for further patenting and licensing opportunities from different sectors of the economy.

Teaching Cell Biology in Primary Schools

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Francele de Abreu Carlan

2014-01-01

Full Text Available Basic concepts of cell biology are essential for scientific literacy. However, because many aspects of cell theory and cell functioning are quite abstract, students experience difficulties understanding them. In this study, we investigated whether diverse teaching resources such as the use of replicas of Leeuwenhoek’s microscope, visualization of cells using an optical microscope, construction of three-dimensional cell models, and reading of a comic book about cells could mitigate the difficulties encountered when teaching cell biology to 8th-grade primary school students. The results suggest that these didactic activities improve students’ ability to learn concrete concepts about cell biology, such as the composition of living beings, growth, and cicatrization. Also, the development of skills was observed, as, for example, the notion of cell size. However, no significant improvements were observed in students’ ability to learn about abstract topics, such as the structures of subcellular organelles and their functions. These results suggest that many students in this age have not yet concluded Piaget’s concrete operational stage, indicating that the concepts required for the significant learning of abstract subjects need to be explored more thoroughly in the process of designing programs that introduce primary school students to cell biology.

Predicting Translation Initiation Rates for Designing Synthetic Biology

International Nuclear Information System (INIS)

Reeve, Benjamin; Hargest, Thomas; Gilbert, Charlie; Ellis, Tom

2014-01-01

In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process, models of prokaryotic protein production have been described. Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5′-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels. In this review, three currently available translation rate calculators developed for synthetic biology are considered, with limitations and possible future progress discussed.

Single amino acid substitution in important hemoglobinopathies does not disturb molecular function and biological process

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Viroj Wiwanitkit

2008-06-01

Full Text Available Viroj WiwanitkitDepartment of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandAbstract: Hemoglobin is an important protein found in the red cells of many animals. In humans, the hemoglobin is mainly distributed in the red blood cell. Single amino acid substitution is the main pathogenesis of most hemoglobin disorders. Here, the author used a new gene ontology technology to predict the molecular function and biological process of four important hemoglobin disorders with single substitution. The four studied important abnormal hemoglobins (Hb with single substitution included Hb S, Hb E, Hb C, and Hb J-Baltimore. Using the GoFigure server, the molecular function and biological process in normal and abnormal hemoglobins was predicted. Compared with normal hemoglobin, all studied abnormal hemoglobins had the same function and biological process. This indicated that the overall function of oxygen transportation is not disturbed in the studied hemoglobin disorders. Clinical findings of oxygen depletion in abnormal hemoglobin should therefore be due to the other processes rather than genomics, proteomics, and expression levels.Keywords: hemoglobin, amino acid, substitution, function

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...

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.

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.

Constructing a one-way hash function based on the unified chaotic system

International Nuclear Information System (INIS)

Long Min; Peng Fei; Chen Guanrong

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. (general)

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

International Nuclear Information System (INIS)

Vaughan, D.

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

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.

Constructs for the expression of repeating triple-helical protein domains

International Nuclear Information System (INIS)

Peng, Yong Y; Werkmeister, Jerome A; Vaughan, Paul R; Ramshaw, John A M

2009-01-01

The development of novel scaffolds will be an important aspect in future success of tissue engineering. Scaffolds will preferably contain information that directs the cellular content of constructs so that the new tissue that is formed is closely aligned in structure, composition and function to the target natural tissue. One way of approaching this will be the development of novel protein-based constructs that contain one or more repeats of functional elements derived from various proteins. In the present case, we describe a strategy to make synthetic, recombinant triple-helical constructs that contain repeat segments of biologically relevant domains. Copies of a DNA fragment prepared by PCR from human type III collagen have been inserted in a co-linear contiguous fashion into the yeast expression vector YEpFlag-1, using sequential addition between selected restriction sites. Constructs containing 1, 2 and 3 repeats were designed to maintain the (Gly-X-Y) repeat, which is essential for the formation of an extended triple helix. All constructs gave expressed protein, with the best being the 3-repeat construct which was readily secreted. This material had the expected composition and N-terminal sequence. Incubation of the product at low temperature led to triple-helix formation, shown by reaction with a conformation dependent monoclonal antibody.

Constructs for the expression of repeating triple-helical protein domains

Energy Technology Data Exchange (ETDEWEB)

Peng, Yong Y; Werkmeister, Jerome A; Vaughan, Paul R; Ramshaw, John A M, E-mail: jerome.werkmeister@csiro.a [CSIRO Molecular and Health Technologies, Bag 10, Clayton South, VIC 3169 (Australia)

2009-02-15

The development of novel scaffolds will be an important aspect in future success of tissue engineering. Scaffolds will preferably contain information that directs the cellular content of constructs so that the new tissue that is formed is closely aligned in structure, composition and function to the target natural tissue. One way of approaching this will be the development of novel protein-based constructs that contain one or more repeats of functional elements derived from various proteins. In the present case, we describe a strategy to make synthetic, recombinant triple-helical constructs that contain repeat segments of biologically relevant domains. Copies of a DNA fragment prepared by PCR from human type III collagen have been inserted in a co-linear contiguous fashion into the yeast expression vector YEpFlag-1, using sequential addition between selected restriction sites. Constructs containing 1, 2 and 3 repeats were designed to maintain the (Gly-X-Y) repeat, which is essential for the formation of an extended triple helix. All constructs gave expressed protein, with the best being the 3-repeat construct which was readily secreted. This material had the expected composition and N-terminal sequence. Incubation of the product at low temperature led to triple-helix formation, shown by reaction with a conformation dependent monoclonal antibody.

Enhanced Matrix Power Function for Cryptographic Primitive Construction

Directory of Open Access Journals (Sweden)

Eligijus Sakalauskas

2018-02-01

Full Text Available A new enhanced matrix power function (MPF is presented for the construction of cryptographic primitives. According to the definition in previously published papers, an MPF is an action of two matrices powering some base matrix on the left and right. The MPF inversion equations, corresponding to the MPF problem, are derived and have some structural similarity with classical multivariate quadratic (MQ problem equations. Unlike the MQ problem, the MPF problem seems to be more complicated, since its equations are not defined over the field, but are represented as left–right action of two matrices defined over the infinite near-semiring on the matrix defined over the certain infinite, additive, noncommuting semigroup. The main results are the following: (1 the proposition of infinite, nonsymmetric, and noncommuting algebraic structures for the construction of the enhanced MPF, satisfying associativity conditions, which are necessary for cryptographic applications; (2 the proof that MPF inversion is polynomially equivalent to the solution of a certain kind of generalized multivariate quadratic (MQ problem which can be reckoned as hard; (3 the estimation of the effectiveness of direct MPF value computation; and (4 the presentation of preliminary security analysis, the determination of the security parameter, and specification of its secure value. These results allow us to make a conjecture that enhanced MPF can be a candidate one-way function (OWF, since the effective (polynomial-time inversion algorithm for it is not yet known. An example of the application of the proposed MPF for the Key Agreement Protocol (KAP is presented. Since the direct MPF value is computed effectively, the proposed MPF is suitable for the realization of cryptographic protocols in devices with restricted computation resources.

Intestinal Vaginoplasty Revisited: A Review of Surgical Techniques, Complications, and Sexual Function

NARCIS (Netherlands)

Bouman, M.B.; van Zeijl, M.C.T.; Buncamper, M.E.; Meijerink, W.J.H.J.; van Bodegraven, A.A.; Mullender, M.G.

2014-01-01

Introduction: Vaginal (re)construction is essential for the psychological well-being of biological women with a dysfunctional vagina and male-to-female transgender women. However, the preferred method for vagina (re)construction with respect to functional as well as aesthetic outcomes is debated.

Event-based text mining for biology and functional genomics

Science.gov (United States)

Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

2015-01-01

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. PMID:24907365

Exploitation of complex network topology for link prediction in biological interactomes

KAUST Repository

Alanis Lobato, Gregorio

2014-06-01

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

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.

Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins with Long Disordered Regions

Science.gov (United States)

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Uversky, Vladimir N.; Obradovic, Zoran

2008-01-01

Identifying relationships between function, amino acid sequence and protein structure represents a major challenge. In this study we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical

Molecular tools for the construction of peptide-based materials.

Science.gov (United States)

Ramakers, B E I; van Hest, J C M; Löwik, D W P M

2014-04-21

Proteins and peptides are fundamental components of living systems where they play crucial roles at both functional and structural level. The versatile biological properties of these molecules make them interesting building blocks for the construction of bio-active and biocompatible materials. A variety of molecular tools can be used to fashion the peptides necessary for the assembly of these materials. In this tutorial review we shall describe five of the main techniques, namely solid phase peptide synthesis, native chemical ligation, Staudinger ligation, NCA polymerisation, and genetic engineering, that have been used to great effect for the construction of a host of peptide-based materials.

The cell engineering construction and function evaluation of multi-layer biochip dialyzer.

Science.gov (United States)

Zhu, Wen; Li, Jiwei; Liu, Jianfeng

2013-10-01

We report the fabrication and function evaluation of multi-layer biochip dialyzer. Such device may potentially be applied to the wearable hemodialysis systems. By merging the advantages of microfluidic chip technology with cell engineering, both functions of glomerular filtration and renal tubule physiological activity are integrated in the same device. This device is designed into a laminated structure, in which the chip number of the superimposed layer can be arbitrarily tailored in accordance with the requirements of dialysis capacity. We propose that such structure can overcome the obstacles of large size and detached structure of the traditional hollow fiber dialyzer. To construct this multilayer biochips dialyzer, two types of dialyzer device with two-layered and six-layered chips are assembled, respectively. Cell adhesion and proliferation on three different dialysis membrane materials under static and dynamic conditions are investigated and compared. The filtration capability, re-absorption function and excrete ammonia function of the resulting multi-layer biochip dialyzer are evaluated. The results reveal that the constructed device can perform higher filtration efficiency and also play a role of renal tubule. This methodology may be useful in developing "scaling down" artificial kidneys that can act as wearable or even implantable hemodialysis systems.

Investigations on construction material and construction concepts in order to obtain dose-reducing effects in the dismantling of the biological shield of a 1300 MWe-PWR

International Nuclear Information System (INIS)

Bittner, A.; Jungwirth, D.; Knell, M.; Schnitzler, L.

1984-04-01

Numerical values of neutron fluxes, activations, dose rates etc. as a function of characteristic values of materials required for optimization purposes to reduce the radiation effect of the biological shield of a PWR are not available. Design concepts are presented for biological shields of PWRs made of concrete with respect to both the most suitable application of materials and the design principles aiming at reduced radiation exposure as compared to present designs during entering, waste disposal and ultimate storage. To evaluate the present-state design the above values have been calculated. Suggested alternative designs are biological shields with selective material application, built from precast elements with or without boron carbide layer arranged in front of it. (orig./HP) [de

A functional approach to emotion in autonomous systems.

Science.gov (United States)

Sanz, Ricardo; Hernández, Carlos; Gómez, Jaime; Hernando, Adolfo

2010-01-01

The construction of fully effective systems seems to pass through the proper exploitation of goal-centric self-evaluative capabilities that let the system teleologically self-manage. Emotions seem to provide this kind of functionality to biological systems and hence the interest in emotion for function sustainment in artificial systems performing in changing and uncertain environments; far beyond the media hullabaloo of displaying human-like emotion-laden faces in robots. This chapter provides a brief analysis of the scientific theories of emotion and presents an engineering approach for developing technology for robust autonomy by implementing functionality inspired in that of biological emotions.

GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms.

Science.gov (United States)

Wang, Jia-Hong; Zhao, Ling-Feng; Lin, Pei; Su, Xiao-Rong; Chen, Shi-Jun; Huang, Li-Qiang; Wang, Hua-Feng; Zhang, Hai; Hu, Zhen-Fu; Yao, Kai-Tai; Huang, Zhong-Xi

2014-09-01

Identifying biological functions and molecular networks in a gene list and how the genes may relate to various topics is of considerable value to biomedical researchers. Here, we present a web-based text-mining server, GenCLiP 2.0, which can analyze human genes with enriched keywords and molecular interactions. Compared with other similar tools, GenCLiP 2.0 offers two unique features: (i) analysis of gene functions with free terms (i.e. any terms in the literature) generated by literature mining or provided by the user and (ii) accurate identification and integration of comprehensive molecular interactions from Medline abstracts, to construct molecular networks and subnetworks related to the free terms. http://ci.smu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

Science.gov (United States)

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

The functional biology of human milk oligosaccharides.

Science.gov (United States)

Bode, Lars

2015-11-01

Human milk oligosaccharides (HMOs) are a group of complex sugars that are highly abundant in human milk, but currently not present in infant formula. More than a hundred different HMOs have been identified so far. The amount and composition of HMOs are highly variable between women, and each structurally defined HMO might have a distinct functionality. HMOs are not digested by the infant and serve as metabolic substrates for select microbes, contributing to shape the infant gut microbiome. HMOs act as soluble decoy receptors that block the attachment of viral, bacterial or protozoan parasite pathogens to epithelial cell surface sugars, which may help prevent infectious diseases in the gut and also the respiratory and urinary tracts. HMOs are also antimicrobials that act as bacteriostatic or bacteriocidal agents. In addition, HMOs alter host epithelial and immune cell responses with potential benefits for the neonate. The article reviews current knowledge as well as future challenges and opportunities related to the functional biology of HMOs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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. © 2015 Wiley Periodicals, Inc.

Constructive Approaches for Understanding the Origin of Self-Replication and Evolution

Directory of Open Access Journals (Sweden)

Norikazu Ichihashi

2016-07-01

Full Text Available The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules. Using this approach, we are able to employ design principles to reproduce life-specific functions, and the knowledge gained through the reproduction process provides clues as to their origins. In this mini-review, we introduce recent insights gained using this approach, and propose important future directions for advancing our understanding of the origins of life.

Wireless Biological Electronic Sensors.

Science.gov (United States)

Cui, Yue

2017-10-09

The development of wireless biological electronic sensors could open up significant advances for both fundamental studies and practical applications in a variety of areas, including medical diagnosis, environmental monitoring, and defense applications. One of the major challenges in the development of wireless bioelectronic sensors is the successful integration of biosensing units and wireless signal transducers. In recent years, there are a few types of wireless communication systems that have been integrated with biosensing systems to construct wireless bioelectronic sensors. To successfully construct wireless biological electronic sensors, there are several interesting questions: What types of biosensing transducers can be used in wireless bioelectronic sensors? What types of wireless systems can be integrated with biosensing transducers to construct wireless bioelectronic sensors? How are the electrical sensing signals generated and transmitted? This review will highlight the early attempts to address these questions in the development of wireless biological electronic sensors.

Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

KAUST Repository

Wang, Wei; Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

2017-01-01

bioengineering applications and rational drug design. Constructing Markov State Models (MSMs) based on large-scale molecular dynamics simulations has emerged as a powerful approach to model functional conformational changes of the biomolecular system

Diffraction Techniques in Structural Biology

Science.gov (United States)

Egli, Martin

2016-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:27248784

Design of synthetic biological logic circuits based on evolutionary algorithm.

Science.gov (United States)

Chuang, Chia-Hua; Lin, Chun-Liang; Chang, Yen-Chang; Jennawasin, Tanagorn; Chen, Po-Kuei

2013-08-01

The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology. In this study, a real-structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis-regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting optimal design of these logic gates and circuits are established via the RSGA. The in silico computer-based modelling technology has been verified showing its great advantages in the purpose.

Synthetic biology approaches to engineer T cells.

Science.gov (United States)

Wu, Chia-Yung; Rupp, Levi J; Roybal, Kole T; Lim, Wendell A

2015-08-01

There is rapidly growing interest in learning how to engineer immune cells, such as T lymphocytes, because of the potential of these engineered cells to be used for therapeutic applications such as the recognition and killing of cancer cells. At the same time, our knowhow and capability to logically engineer cellular behavior is growing rapidly with the development of synthetic biology. Here we describe how synthetic biology approaches are being used to rationally alter the behavior of T cells to optimize them for therapeutic functions. We also describe future developments that will be important in order to construct safe and precise T cell therapeutics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of Physical Exercise on Cognitive Functioning and Wellbeing: Biological and Psychological Benefits

Directory of Open Access Journals (Sweden)

Laura Mandolesi

2018-04-01

Full Text Available Much evidence shows that physical exercise (PE is a strong gene modulator that induces structural and functional changes in the brain, determining enormous benefit on both cognitive functioning and wellbeing. PE is also a protective factor for neurodegeneration. However, it is unclear if such protection is granted through modifications to the biological mechanisms underlying neurodegeneration or through better compensation against attacks. This concise review addresses the biological and psychological positive effects of PE describing the results obtained on brain plasticity and epigenetic mechanisms in animal and human studies, in order to clarify how to maximize the positive effects of PE while avoiding negative consequences, as in the case of exercise addiction.

Development of a construct-based risk assessment framework for genetic engineered crops.

Science.gov (United States)

Beker, M P; Boari, P; Burachik, M; Cuadrado, V; Junco, M; Lede, S; Lema, M A; Lewi, D; Maggi, A; Meoniz, I; Noé, G; Roca, C; Robredo, C; Rubinstein, C; Vicien, C; Whelan, A

2016-10-01

Experience gained in the risk assessment (RA) of genetically engineered (GE) crops since their first experimental introductions in the early nineties, has increased the level of familiarity with these breeding methodologies and has motivated several agencies and expert groups worldwide to revisit the scientific criteria underlying the RA process. Along these lines, the need to engage in a scientific discussion for the case of GE crops transformed with similar constructs was recently identified in Argentina. In response to this need, the Argentine branch of the International Life Sciences Institute (ILSI Argentina) convened a tripartite working group to discuss a science-based evaluation approach for transformation events developed with genetic constructs which are identical or similar to those used in previously evaluated or approved GE crops. This discussion considered new transformation events within the same or different species and covered both environmental and food safety aspects. A construct similarity concept was defined, considering the biological function of the introduced genes. Factors like environmental and dietary exposure, familiarity with both the crop and the trait as well as the crop biology, were identified as key to inform a construct-based RA process.

Measuring personality functioning in older adults: construct validity of the Severity Indices of Personality Functioning - Short Form (SIPP-SF).

Science.gov (United States)

Rossi, Gina; Debast, Inge; van Alphen, S P J

2017-07-01

The dimensional personality disorders model in the Diagnostic and Statistical Manual (DSM)-5 section III conceptually differentiates impaired personality functioning (criterion A) from the presence of pathological traits (criterion B). This study is the first to specifically address the measurement of criterion A in older adults. Moreover, the convergent/divergent validity of criterion A and criterion B will be compared in younger and older age groups. The Severity Indices of Personality Functioning - Short Form (SIPP-SF) was administered in older (N = 171) and younger adults (N = 210). The factorial structure was analyzed with exploratory structural equation modeling. Differences in convergent/divergent validity between personality functioning (SIPP-SF) and pathological traits (Personality Inventory for DSM-5; Dimensional Assessment of Personality Pathology-Basic Questionnaire) were examined across age groups. Identity Integration, Relational Capacities, Responsibility, Self-Control, and Social Concordance were corroborated as higher order domains. Although the SIPP-SF domains measured unique variation, some high correlations with pathological traits referred to overlapping constructs. Moreover, in older adults, personality functioning was more strongly related to Psychoticism, Disinhibition, Antagonism and Dissocial Behavior compared to younger adults. The SIPP-SF construct validity was demonstrated in terms of a structure of five higher order domains of personality functioning. The instrument is promising as a possible measure of impaired personality functioning in older adults. As such, it is a useful clinical tool to follow up effects of therapy on levels of personality functioning. Moreover, traits were associated with different degrees of personality functioning across age groups.

[Differential gene expression profile in ischemic myocardium of Wistar rats with acute myocardial infarction: the study on gene construction, identification and function].

Science.gov (United States)

Guo, Chun Yu; Yin, Hui Jun; Jiang, Yue Rong; Xue, Mei; Zhang, Lu; Shi, Da Zhuo

2008-06-18

To construct the differential genes expressed profile in the ischemic myocardium tissue reduced from acute myocardial infarction(AMI), and determine the biological functions of target genes. AMI model was generated by ligation of the left anterior descending coronary artery in Wistar rats. Total RNA was extracted from the normal and the ischemic heart tissues under the ligation point 7 days after the operation. Differential gene expression profiles of the two samples were constructed using Long Serial Analysis of Gene Expression(LongSAGE). Real time fluorescence quantitative PCR was used to verify gene expression profile and to identify the expression of 2 functional genes. The activities of enzymes from functional genes were determined by histochemistry. A total of 15,966 tags were screened from the normal and the ischemic LongSAGE maps. The similarities of the sequences were compared using the BLAST algebra in NCBI and 7,665 novel tags were found. In the ischemic tissue 142 genes were significantly changed compared with those in the normal tissue (Ppathways of oxidation and phosphorylation, ATP synthesis and glycolysis. The partial genes identified by LongSAGE were confirmed using real time fluorescence quantitative PCR. Two genes related to energy metabolism, COX5a and ATP5e, were screened and quantified. Expression of two functional genes down-regulated at their mRNA levels and the activities of correlative functional enzymes decreased compared with those in the normal tissue. AMI causes a series of changes in gene expression, in which the abnormal expression of genes related to energy metabolism could be one of the molecular mechanisms of AMI. The intervention of the expressions of COX5a and ATP5e may be a new target for AMI therapy.

A sampling approach to constructing Lyapunov functions for nonlinear continuous–time systems

NARCIS (Netherlands)

Bobiti, R.V.; Lazar, M.

2016-01-01

The problem of constructing a Lyapunov function for continuous-time nonlinear dynamical systems is tackled in this paper via a sampling-based approach. The main idea of the sampling-based method is to verify a Lyapunov-type inequality for a finite number of points (known state vectors) in the

AFM imaging of functionalized carbon nanotubes on biological membranes

International Nuclear Information System (INIS)

Lamprecht, C; Danzberger, J; Rangl, M; Gruber, H J; Hinterdorfer, P; Kienberger, F; Ebner, A; Liashkovich, I; Neves, V; Heister, E; Coley, H M; McFadden, J; Flahaut, E

2009-01-01

Multifunctional carbon nanotubes are promising for biomedical applications as their nano-size, together with their physical stability, gives access into the cell and various cellular compartments including the nucleus. However, the direct and label-free detection of carbon nanotube uptake into cells is a challenging task. The atomic force microscope (AFM) is capable of resolving details of cellular surfaces at the nanometer scale and thus allows following of the docking of carbon nanotubes to biological membranes. Here we present topographical AFM images of non-covalently functionalized single walled (SWNT) and double walled carbon nanotubes (DWNT) immobilized on different biological membranes, such as plasma membranes and nuclear envelopes, as well as on a monolayer of avidin molecules. We were able to visualize DWNT on the nuclear membrane while at the same time resolving individual nuclear pore complexes. Furthermore, we succeeded in localizing individual SWNT at the border of incubated cells and in identifying bundles of DWNT on cell surfaces by AFM imaging.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

Science.gov (United States)

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

Design and construction of synthetic microbial consortia in China

Directory of Open Access Journals (Sweden)

Ming-Zhu Ding

2016-12-01

Full Text Available The rapid development of synthetic biology enables the design, construction and optimization of synthetic microbial consortia to achieve specific functions. In China, the “973” project-“Design and Construction of Microbial Consortia” was funded by the National Basic Research Program of China in January 2014. It was proposed to address the fundamental challenges in engineering natural microbial consortia and reconstructing microbial consortia to meet industrial demands. In this review, we will introduce this “973” project, including the significance of microbial consortia, the fundamental scientific issues, the recent research progresses, and some case studies about synthetic microbial consortia in the past two and a half years.

Recellularization of rat liver: An in vitro model for assessing human drug metabolism and liver biology.

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Matthew J Robertson

Full Text Available Liver-like organoids that recapitulate the complex functions of the whole liver by combining cells, scaffolds, and mechanical or chemical cues are becoming important models for studying liver biology and drug metabolism. The advantages of growing cells in three-dimensional constructs include enhanced cell-cell and cell-extracellular matrix interactions and preserved cellular phenotype including, prevention of de-differentiation. In the current study, biomimetic liver constructs were made via perfusion decellularization of rat liver, with the goal of maintaining the native composition and structure of the extracellular matrix. We optimized our decellularization process to produce liver scaffolds in which immunogenic residual DNA was removed but glycosaminoglycans were maintained. When the constructs were recellularized with rat or human liver cells, the cells remained viable, capable of proliferation, and functional for 28 days. Specifically, the cells continued to express cytochrome P450 genes and maintained their ability to metabolize a model drug, midazolam. Microarray analysis showed an upregulation of genes involved in liver regeneration and fibrosis. In conclusion, these liver constructs have the potential to be used as test beds for studying liver biology and drug metabolism.

Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments.

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Lee, Kyung-Ho; Kim, Dong-Myung

2013-11-01

Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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...... workers: demolition workers, insulators, carpenters and a control group of hospital porters aged 35-60 years answered a questionnaire and performed spirometry. Results were tested statistically for differences between occupational groups, and all analyses were adjusted for smoking status, age and body.......7 (95% CI 1.3-5.5) and for insulators compared to carpenters was 1.8 (95% CI 0.8-3.9). Demolition workers had significantly lower odds compared to all other groups for forced vital capacity construction workers...

Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer.

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Li, Yongsheng; Chen, Juan; Zhang, Jinwen; Wang, Zishan; Shao, Tingting; Jiang, Chunjie; Xu, Juan; Li, Xia

2015-09-22

Long non-coding RNAs (lncRNAs) play key roles in diverse biological processes. Moreover, the development and progression of cancer often involves the combined actions of several lncRNAs. Here we propose a multi-step method for constructing lncRNA-lncRNA functional synergistic networks (LFSNs) through co-regulation of functional modules having three features: common coexpressed genes of lncRNA pairs, enrichment in the same functional category and close proximity within protein interaction networks. Applied to three cancers, we constructed cancer-specific LFSNs and found that they exhibit a scale free and modular architecture. In addition, cancer-associated lncRNAs tend to be hubs and are enriched within modules. Although there is little synergistic pairing of lncRNAs across cancers, lncRNA pairs involved in the same cancer hallmarks by regulating same or different biological processes. Finally, we identify prognostic biomarkers within cancer lncRNA expression datasets using modules derived from LFSNs. In summary, this proof-of-principle study indicates synergistic lncRNA pairs can be identified through integrative analysis of genome-wide expression data sets and functional information.

Biological activity of lactoferrin-functionalized biomimetic hydroxyapatite nanocrystals

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Nocerino N

2014-03-01

Full Text Available Nunzia Nocerino,1 Andrea Fulgione,1 Marco Iannaccone,1 Laura Tomasetta,1 Flora Ianniello,1 Francesca Martora,1 Marco Lelli,2 Norberto Roveri,2 Federico Capuano,3 Rosanna Capparelli1 1Department of Agriculture Special Biotechnology Center Federico II, CeBIOTEC Biotechnology, University of Naples Federico II, Naples, 2Department of Chemistry, G Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, 3Department of Food Inspection IZS ME, Naples, Italy Abstract: The emergence of bacterial strains resistant to antibiotics is a general public health problem. Progress in developing new molecules with antimicrobial properties has been made. In this study, we evaluated the biological activity of a hybrid nanocomposite composed of synthetic biomimetic hydroxyapatite surface-functionalized by lactoferrin (LF-HA. We evaluated the antimicrobial, anti-inflammatory, and antioxidant properties of LF-HA and found that the composite was active against both Gram-positive and Gram-negative bacteria, and that it modulated proinflammatory and anti-inflammatory responses and enhanced antioxidant properties as compared with LF alone. These results indicate the possibility of using LF-HA as an antimicrobial system and biomimetic hydroxyapatite as a candidate for innovative biomedical applications. Keywords: lactoferrin, hydroxyapatite nanocrystals, biomimetism, biological activity, drug delivery

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

DEFF Research Database (Denmark)

Knudsen, Lars Ramkilde; Preneel, Bart

2002-01-01

constructions based on block ciphers such as the Data Encryption Standard (DES), where the key size is slightly smaller than the block size; IDEA, where the key size is twice the block size; Advanced Encryption Standard (AES), with a variable key size; and to MD4-like hash functions. Under reasonable...

Construction and operation of biogas plants. Bau und Betrieb von Biogasanlagen

Energy Technology Data Exchange (ETDEWEB)

Koenig, F. von

1985-01-01

Biogas utilisation in agriculture has increased considerably as a consequence of the energy crisis. So far, energy production was the most important aspect, and the high-quality natural fertilizer offered by the fermentation residues was commonly neglected. This fertilizer is an effective substitute for commercial fertilizers and thus contributes to the reduction of environmental pollution. The book discusses the chemical and biological mechanisms, the criteria of selection for plants and materials, optimum gas production techniques, uses of the product gas, and the advantages and properties of the biofertilizer produced. Planning procedures, design, construction, function and performance of several biogas production plants now in operation are described. Hints are given for do-it-yourself construction, as are cost-benefit calculations and decision aids for construction.

Modified glycogen as construction material for functional biomimetic microfibers.

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Rabyk, Mariia; Hruby, Martin; Vetrik, Miroslav; Kucka, Jan; Proks, Vladimir; Parizek, Martin; Konefal, Rafal; Krist, Pavel; Chvatil, David; Bacakova, Lucie; Slouf, Miroslav; Stepanek, Petr

2016-11-05

We describe a conceptually new, microfibrous, biodegradable functional material prepared from a modified storage polysaccharide also present in humans (glycogen) showing strong potential as direct-contact dressing/interface material for wound healing. Double bonds were introduced into glycogen via allylation and were further exploited for crosslinking of the microfibers. Triple bonds were introduced by propargylation and served for further click functionalization of the microfibers with bioactive peptide. A simple solvent-free method allowing the preparation of thick layers was used to produce microfibers (diameter ca 2μm) from allylated and/or propargylated glycogen. Crosslinking of the samples was performed by microtron beta-irradiation, and the irradiation dose was optimized to 2kGy. The results from biological testing showed that these highly porous, hydrophilic, readily functionalizable materials were completely nontoxic to cells growing in their presence. The fibers were gradually degraded in the presence of cells. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthetic biology meets tissue engineering.

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Davies, Jamie A; Cachat, Elise

2016-06-15

Classical tissue engineering is aimed mainly at producing anatomically and physiologically realistic replacements for normal human tissues. It is done either by encouraging cellular colonization of manufactured matrices or cellular recolonization of decellularized natural extracellular matrices from donor organs, or by allowing cells to self-organize into organs as they do during fetal life. For repair of normal bodies, this will be adequate but there are reasons for making unusual, non-evolved tissues (repair of unusual bodies, interface to electromechanical prostheses, incorporating living cells into life-support machines). Synthetic biology is aimed mainly at engineering cells so that they can perform custom functions: applying synthetic biological approaches to tissue engineering may be one way of engineering custom structures. In this article, we outline the 'embryological cycle' of patterning, differentiation and morphogenesis and review progress that has been made in constructing synthetic biological systems to reproduce these processes in new ways. The state-of-the-art remains a long way from making truly synthetic tissues, but there are now at least foundations for future work. © 2016 Authors; published by Portland Press Limited.

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

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Hughes, Stephen R; Butt, Tauseef R; Bartolett, Scott; Riedmuller, Steven B; Farrelly, Philip

2011-08-01

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. High-throughput integrated robotic molecular biology platforms that have the capacity to rapidly clone and express heterologous gene open reading frames in bacteria and yeast and to screen large numbers of expressed proteins for optimized function are an important technology for improving microbial strains for biofuel production. The process involves the production of full-length complementary DNA libraries as a source of plasmid-based clones to express the desired proteins in active form for determination of their functions. Proteins that were identified by high-throughput screening as having desired characteristics are overexpressed in microbes to enable them to perform functions that will allow more cost-effective and sustainable production of biofuels. Because the plasmid libraries are composed of several thousand unique genes, automation of the process is essential. This review describes the design and implementation of an automated integrated programmable robotic workcell capable of producing complementary DNA libraries, colony picking, isolating plasmid DNA, transforming yeast and bacteria, expressing protein, and performing appropriate functional assays. These operations will allow tailoring microbial strains to use renewable feedstocks for production of biofuels, bioderived chemicals, fertilizers, and other coproducts for profitable and sustainable biorefineries. Published by Elsevier Inc.

Clinical history and biologic age predicted falls better than objective functional tests.

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Gerdhem, Paul; Ringsberg, Karin A M; Akesson, Kristina; Obrant, Karl J

2005-03-01

Fall risk assessment is important because the consequences, such as a fracture, may be devastating. The objective of this study was to find the test or tests that best predicted falls in a population-based sample of elderly women. The fall-predictive ability of a questionnaire, a subjective estimate of biologic age and objective functional tests (gait, balance [Romberg and sway test], thigh muscle strength, and visual acuity) were compared in 984 randomly selected women, all 75 years of age. A recalled fall was the most important predictor for future falls. Only recalled falls and intake of psycho-active drugs independently predicted future falls. Women with at least five of the most important fall predictors (previous falls, conditions affecting the balance, tendency to fall, intake of psychoactive medication, inability to stand on one leg, high biologic age) had an odds ratio of 11.27 (95% confidence interval 4.61-27.60) for a fall (sensitivity 70%, specificity 79%). The more time-consuming objective functional tests were of limited importance for fall prediction. A simple clinical history, the inability to stand on one leg, and a subjective estimate of biologic age were more important as part of the fall risk assessment.

Complex heterogeneous tissue constructs containing multiple cell types prepared by inkjet printing technology.

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Xu, Tao; Zhao, Weixin; Zhu, Jian-Ming; Albanna, Mohammad Z; Yoo, James J; Atala, Anthony

2013-01-01

This study was designed to develop a versatile method for fabricating complex and heterogeneous three-dimensional (3D) tissue constructs using simultaneous ink-jetting of multiple cell types. Human amniotic fluid-derived stem cells (hAFSCs), canine smooth muscle cells (dSMCs), and bovine aortic endothelial cells (bECs), were separately mixed with ionic cross-linker calcium chloride (CaCl(2)), loaded into separate ink cartridges and printed using a modified thermal inkjet printer. The three cell types were delivered layer-by-layer to pre-determined locations in a sodium alginate-collagen composite located in a chamber under the printer. The reaction between CaCl(2) and sodium alginate resulted in a rapid formation of a solid composite gel and the printed cells were anchored in designated areas within the gel. The printing process was repeated for several cycles leading to a complex 3D multi-cell hybrid construct. The biological functions of the 3D printed constructs were evaluated in vitro and in vivo. Each of the printed cell types maintained their viability and normal proliferation rates, phenotypic expression, and physiological functions within the heterogeneous constructs. The bioprinted constructs were able to survive and mature into functional tissues with adequate vascularization in vivo. These findings demonstrate the feasibility of fabricating complex heterogeneous tissue constructs containing multiple cell types using inkjet printing technology. Copyright © 2012 Elsevier Ltd. All rights reserved.

The functional and biological properties of whey proteins: prospects for the development of functional foods

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H. J. T. KORHONEN

2008-12-01

Full Text Available Advances in processing technologies and the accumulation of scientific data on the functional and biological properties of whey components have contributed to the growing commercial valuation of cheese whey over the last decade. New membrane separation and chromatographic techniques have made it possible to fractionate and enrich various components of whey more efficiently than before. The specific properties of these components can now be examined in greater detail and new applications developed accordingly. The utilisation of cheese whey is evolving into a new industry producing a multitude of purified ingredients for numerous purposes. The most significant areas of R&D related to whey proteins include functional foods, the rheological properties of foodstuffs, and biopharmaceuticals.

Additive Manufacturing of Biomedical Constructs with Biomimetic Structural Organizations.

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Li, Xiao; He, Jiankang; Zhang, Weijie; Jiang, Nan; Li, Dichen

2016-11-09

Additive manufacturing (AM), sometimes called three-dimensional (3D) printing, has attracted a lot of research interest and is presenting unprecedented opportunities in biomedical fields, because this technology enables the fabrication of biomedical constructs with great freedom and in high precision. An important strategy in AM of biomedical constructs is to mimic the structural organizations of natural biological organisms. This can be done by directly depositing cells and biomaterials, depositing biomaterial structures before seeding cells, or fabricating molds before casting biomaterials and cells. This review organizes the research advances of AM-based biomimetic biomedical constructs into three major directions: 3D constructs that mimic tubular and branched networks of vasculatures; 3D constructs that contains gradient interfaces between different tissues; and 3D constructs that have different cells positioned to create multicellular systems. Other recent advances are also highlighted, regarding the applications of AM for organs-on-chips, AM-based micro/nanostructures, and functional nanomaterials. Under this theme, multiple aspects of AM including imaging/characterization, material selection, design, and printing techniques are discussed. The outlook at the end of this review points out several possible research directions for the future.

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.

A Model-Based Approach to Constructing Music Similarity Functions

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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.

A Model-Based Approach to Constructing Music Similarity Functions

Science.gov (United States)

West, Kris; Lamere, Paul

2006-12-01

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.

Constructing phylogenetic trees using interacting pathways.

Science.gov (United States)

Wan, Peng; Che, Dongsheng

2013-01-01

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships.

Viability of Bioprinted Cellular Constructs Using a Three Dispenser Cartesian Printer.

Science.gov (United States)

Dennis, Sarah Grace; Trusk, Thomas; Richards, Dylan; Jia, Jia; Tan, Yu; Mei, Ying; Fann, Stephen; Markwald, Roger; Yost, Michael

2015-09-22

Tissue engineering has centralized its focus on the construction of replacements for non-functional or damaged tissue. The utilization of three-dimensional bioprinting in tissue engineering has generated new methods for the printing of cells and matrix to fabricate biomimetic tissue constructs. The solid freeform fabrication (SFF) method developed for three-dimensional bioprinting uses an additive manufacturing approach by depositing droplets of cells and hydrogels in a layer-by-layer fashion. Bioprinting fabrication is dependent on the specific placement of biological materials into three-dimensional architectures, and the printed constructs should closely mimic the complex organization of cells and extracellular matrices in native tissue. This paper highlights the use of the Palmetto Printer, a Cartesian bioprinter, as well as the process of producing spatially organized, viable constructs while simultaneously allowing control of environmental factors. This methodology utilizes computer-aided design and computer-aided manufacturing to produce these specific and complex geometries. Finally, this approach allows for the reproducible production of fabricated constructs optimized by controllable printing parameters.

Presence of transient hydronephrosis immediately after surgery has a limited influence on renal function 1 year after ileal neobladder construction.

Science.gov (United States)

Narita, Takuma; Hatakeyama, Shingo; Koie, Takuya; Hosogoe, Shogo; Matsumoto, Teppei; Soma, Osamu; Yamamoto, Hayato; Yoneyama, Tohru; Tobisawa, Yuki; Yoneyama, Takahiro; Hashimoto, Yasuhiro; Ohyama, Chikara

2017-08-31

Urinary tract obstruction and postoperative hydronephrosis are risk factor for renal function deterioration after orthotopic ileal neobladder construction. However, reports of relationship between transient hydronephrosis and renal function are limited. We assess the influence of postoperative transient hydronephrosis on renal function in patients with orthotopic ileal neobladder construction. Between January 2006 and June 2013, we performed radical cystectomy in 164 patients, and 101 received orthotopic ileal neobladder construction. This study included data available from 64 patients with 128 renal units who were enrolled retrospectively. The hydronephrosis grade of each renal unit scored 0-4. The patients were divided into 4 groups according to the grade of hydronephrosis: control, low, intermediate, and high. The grade of postoperative hydronephrosis was compared with renal function 1 month and 1 year after surgery. There were no significant differences in renal function before surgery between groups. One month after surgery, the presence of hydronephrosis was significantly associated with decreased renal function. However, 1 year after urinary diversion hydronephrosis grades were improved significantly, and renal function was comparable between groups. Postoperative hydronephrosis at 1 month had no significant influence on renal function 1 year after ileal neobladder construction. Limitations include retrospective design, short follow-up periods, and a sample composition. The presence of transient hydronephrosis immediately after surgery may have limited influence on renal function 1 year after ileal neobladder construction.

Effect of biological factors during functional scintigraphy of the heart

Energy Technology Data Exchange (ETDEWEB)

Breuel, H P; Emrich, D; Luig, H [Goettingen Univ. (F.R. Germany). Abt. fuer Nuklearmedizin

1976-07-01

The parameters relating to functional scintigraphy of the heart (average circulation time, peak time) depend not only on the method (injection technique, radiopharmaceutical), but also on biological factors. Failure to take these into consideration may result in an erroneous interpretation of the findings. Circulation time in normal children aged 6 to 14 years, as determined by isotope methods is significantly shorter than in normal adults. Patients with compensated heart disease, as well trained athletes, show significant increase in all portions of the circulation time, when compared with normals of similar ages. This indicates that deviation in the haemodynamics of the circulation as shown by functional scintigraphy, can only be interpreted in the light of clinical findings.

Tongue and Taste Organ Biology and Function: Homeostasis Maintained by Hedgehog Signaling.

Science.gov (United States)

Mistretta, Charlotte M; Kumari, Archana

2017-02-10

The tongue is an elaborate complex of heterogeneous tissues with taste organs of diverse embryonic origins. The lingual taste organs are papillae, composed of an epithelium that includes specialized taste buds, the basal lamina, and a lamina propria core with matrix molecules, fibroblasts, nerves, and vessels. Because taste organs are dynamic in cell biology and sensory function, homeostasis requires tight regulation in specific compartments or niches. Recently, the Hedgehog (Hh) pathway has emerged as an essential regulator that maintains lingual taste papillae, taste bud and progenitor cell proliferation and differentiation, and neurophysiological function. Activating or suppressing Hh signaling, with genetic models or pharmacological agents used in cancer treatments, disrupts taste papilla and taste bud integrity and can eliminate responses from taste nerves to chemical stimuli but not to touch or temperature. Understanding Hh regulation of taste organ homeostasis contributes knowledge about the basic biology underlying taste disruptions in patients treated with Hh pathway inhibitors.

PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance.

Science.gov (United States)

van Oers, Johanna M M; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Hou, Harry; Sellers, Rani S; Modrich, Paul; Scharff, Matthew D; Edelmann, Winfried

2010-07-27

The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2-/- mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression.

Functions of MicroRNAs in Cardiovascular Biology and Disease

Science.gov (United States)

Hata, Akiko

2015-01-01

In 1993, lin-4 was discovered as a critical modulator of temporal development in Caenorhabditis elegans and, most notably, as the first in the class of small, single-stranded noncoding RNAs now defined as microRNAs (miRNAs). Another eight years elapsed before miRNA expression was detected in mammalian cells. Since then, explosive advancements in the field of miRNA biology have elucidated the basic mechanism of miRNA biogenesis, regulation, and gene-regulatory function. The discovery of this new class of small RNAs has augmented the complexity of gene-regulatory programs as well as the understanding of developmental and pathological processes in the cardiovascular system. Indeed, the contributions of miRNAs in cardiovascular development and function have been widely explored, revealing the extensive role of these small regulatory RNAs in cardiovascular physiology. PMID:23157557

Niche construction game cancer cells play.

Science.gov (United States)

Bergman, Aviv; Gligorijevic, Bojana

2015-10-01

Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

Niche construction game cancer cells play

Science.gov (United States)

Bergman, Aviv; Gligorijevic, Bojana

2015-10-01

Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

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...... at 366nm in various types of DNA constructs. Successful application of three differently functionalized 2'-amino-LNA monomers in self-assembled higher ordered structures for simultaneous cross-linking and monitoring of assembly formation is furthermore demonstrated....

Synthetic biology and its alternatives. Descartes, Kant and the idea of engineering biological machines.

Science.gov (United States)

Kogge, Werner; Richter, Michael

2013-06-01

The engineering-based approach of synthetic biology is characterized by an assumption that 'engineering by design' enables the construction of 'living machines'. These 'machines', as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes's and Kant's thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology's engineering paradigm. Copyright © 2013 Elsevier Ltd. All rights reserved.

Issues in Biological Shape Modelling

DEFF Research Database (Denmark)

Hilger, Klaus Baggesen

This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape or appear......This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape...

A program code generator for multiphysics biological simulation using markup languages.

Science.gov (United States)

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Adipose-Derived Cell Construct Stabilizes Heart Function and Increases Microvascular Perfusion in an Established Infarct

Science.gov (United States)

Nguyen, Quang T.; Touroo, Jeremy S.; Aird, Allison L.; Chang, Raymond C.; Ng, Chin K.; Hoying, James B.; Williams, Stuart K.

2013-01-01

We have previously shown that myocardial infarction (MI) immediately treated with an epicardial construct containing stromal vascular fraction (SVF) from adipose tissue preserved microvascular function and left ventricle contractile mechanisms. In order to evaluate a more clinically relevant condition, we investigated the cardiac recovery potential of an SVF construct implanted onto an established infarct. SVF cells were isolated from rat adipose tissue, plated on Vicryl, and cultured for 14 days. Fischer-344 rats were separated into MI groups: (a) 6-week MI (MI), (b) 6-week MI treated with an SVF construct at 2 weeks (MI SVF), (c) 6-week MI with Vicryl construct at 2 weeks (MI Vicryl), and (d) MI 2wk (time point of intervention). Emax, an indicator of systolic performance and contractile function, was lower in the MI and MI Vicryl versus MI SVF. Positron emission tomography imaging (18F-fluorodeoxyglucose) revealed a decreased percentage of relative infarct volume in the MI SVF versus MI and MI Vicryl. Total vessel count and percentage of perfusion assessed via immunohistochemistry were both increased in the infarct region of MI SVF versus MI and MI Vicryl. Overall cardiac function, percentage of relative infarct, and percentage of perfusion were similar between MI SVF and MI 2wk; however, total vessel count increased after SVF treatment. These data suggest that SVF treatment of an established infarct stabilizes the heart at the time point of intervention by preventing a worsening of cardiac performance and infarcted volume, and is associated with increased microvessel perfusion in the area of established infarct. PMID:24106337

Characteristics of microbial community functional structure of a biological coking wastewater treatment system.

Science.gov (United States)

Joshi, Dev Raj; Zhang, Yu; Zhang, Hong; Gao, Yingxin; Yang, Min

2018-01-01

Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina HiSeq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run (500days) bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, GeoChip 5.0 detected almost all key functional gene (average 61,940 genes) categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2diox; one ring2,3diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina HiSeq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes- nbzA (nitro-aromatics), tdnB (aniline), and scnABC (thiocyanate) were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, HiSeq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants; hence it will be useful in optimization strategies for biological treatment of coking wastewater. Copyright © 2017. Published by Elsevier B.V.

Constructed Wetlands

Science.gov (United States)

these systems can improve water quality, engineers and scientists construct systems that replicate the functions of natural wetlands. Constructed wetlands are treatment systems that use natural processes

Contemporary issues in evolutionary biology

Indian Academy of Sciences (India)

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

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.

Hash function construction using weighted complex dynamical networks

International Nuclear Information System (INIS)

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. (general)

The Hadamard construction of Green's functions on a curved space-time: physics and explicit rigorous results

International Nuclear Information System (INIS)

John, R.W.

1987-01-01

First, in connection with their construction due to Hadamard, the mathematical and physical meaning of covariant Green's functions in relativistic gravitational fields - according to Einstein: on curved space-time - is discussed. Then, in the case of a general static spherically symmetric space-time the construction equations for a scalar Green's function are cast into symmetry-adapted form providing a convenient starting point for an explicit calculation of the Hadamard building elements. In applying the obtained basic scheme to a special one-parameter family of model metrics one succeeds in advancing to the explicit exact calculation of tail-term coefficients of a massless Green's function which are simultaneously coefficients in the Schwinger-De Witt expansion of the Feynman propagator for the corresponding massive Klein-Gordon equation on curved space-time. (author)

Biofabrication to build the biology-device interface

International Nuclear Information System (INIS)

Liu Yi; Kim, Eunkyoung; Culver, James N; Bentley, William E; Payne, Gregory F; Ghodssi, Reza; Rubloff, Gary W

2010-01-01

The last century witnessed spectacular advances in both microelectronics and biotechnology yet there was little synergy between the two. A challenge to their integration is that biological and electronic systems are constructed using divergent fabrication paradigms. Biology fabricates bottom-up with labile components, while microelectronic devices are fabricated top-down using methods that are 'bio-incompatible'. Biofabrication-the use of biological materials and mechanisms for construction-offers the opportunity to span these fabrication paradigms by providing convergent approaches for building the bio-device interface. Integral to biofabrication are stimuli-responsive materials (e.g. film-forming polysaccharides) that allow directed assembly under near physiological conditions in response to device-imposed signals. Biomolecular engineering, through recombinant technology, allows biological components to be endowed with information for assembly (e.g. encoded in a protein's amino acid sequence). Finally, self-assembly and enzymatic assembly provide the mechanisms for construction over a hierarchy of length scales. Here, we review recent advances in the use of biofabrication to build the bio-device interface. We anticipate that the biofabrication toolbox will expand over the next decade as more researchers enlist the unique construction capabilities of biology. Further, we look forward to observing the application of this toolbox to create devices that can better diagnose disease, detect pathogens and discover drugs. Finally, we expect that biofabrication will enable the effective interfacing of biology with electronics to create implantable devices for personalized and regenerative medicine. (topical review)

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.

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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Construction of energy loss function for low-energy electrons in helium

Energy Technology Data Exchange (ETDEWEB)

Dayashankar, [Bhabha Atomic Research Centre, Bombay (India). Div. of Radiation Protection

1976-02-01

The energy loss function for electrons in the energy range from 50 eV to 1 keV in helium gas has been constructed by considering separately the energy loss in overcoming the ionization threshold, the loss manifested as kinetic energy of secondary electrons and the loss in the discrete state excitations. This has been done by utilizing recent measurements of Opal et al. on the energy spectrum of secondary electrons and incorporating the experimental data on cross sections for twenty-four excited states. The present results of the energy loss function are in good agreement with the Bethe formula for energies above 500 eV. For lower energies, where the Bethe formula is not applicable, the present results should be particularly useful.

The technique of the modified hamiltonian for construction of the spin-projected wave function

International Nuclear Information System (INIS)

Tsaune, A.Ya.; Glushkov, V.N.

1991-01-01

A method is suggested to construct the wave function, which is an eigenfunction for operator S 2 . A combination of Lowdin's projection operators and the method of taking into account the orthogonality conditions in variational problems previously developed by the authors is used for determination of the spin-current wave functions component. It is shown that the suggested method gives better results for the energies that the traditional restricted Hartee-Fock scheme

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.

The Ethics of Synthetic Biology

DEFF Research Database (Denmark)

Christiansen, Andreas

The dissertation analyses and discusses a number of ethical issues that have been raised in connection with the development of synthetic biology. Synthetic biology is a set of new techniques for DNA-level design and construction of living beings with useful properties. The dissertation especially...

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

Science.gov (United States)

Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

Directory of Open Access Journals (Sweden)

Matthias Christen

Full Text Available Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

[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

Utility function under decision theory: A construction arbitration application

Science.gov (United States)

Alozn, Ahmad E.; Galadari, Abdulla

2017-08-01

While a wide range of dispute resolution mechanisms exist, practitioners favor legally binding ones such as litigation and arbitration. Since initiating a litigation or arbitration case against a business partner may dissolve the business relationship between them, predicting the arbitrator's decision becomes valuable to the arbitrating parties. This paper proposes a construction-specific utility framework for the arbitrating party through decision theory, and based on expected utility theory. The proposed framework preserves the industry practicality and most importantly, considers direct short-term factors and indirect long-term factors as well. It is suggested that the arbitrating parties' utility functions could be then used to identify equilibrium points among them when interact via game theory principles, which would serve the purpose of predicting the arbitration outcome.

Synthetic biology era: Improving antibiotic's world.

Science.gov (United States)

Guzmán-Trampe, Silvia; Ceapa, Corina D; Manzo-Ruiz, Monserrat; Sánchez, Sergio

2017-06-15

The emergence of antibiotic-resistant pathogen microorganisms is problematic in the context of the current spectrum of available medication. The poor specificity and the high toxicity of some available molecules have made imperative the search for new strategies to improve the specificity and to pursue the discovery of novel compounds with increased bioactivity. Using living cells as platforms, synthetic biology has counteracted this problem by offering novel pathways to create synthetic systems with improved and desired functions. Among many other biotechnological approaches, the advances in synthetic biology have made it possible to design and construct novel biological systems in order to look for new drugs with increased bioactivity. Advancements have also been made in the redesigning of RNA and DNA molecules in order to engineer antibiotic clusters for antibiotic overexpression. As for the production of these antibacterial compounds, yeasts and filamentous fungi as well as gene therapy are utilized to enhance protein solubility. Specific delivery is achieved by creating chimeras using plant genes into bacterial hosts. Some of these synthetic systems are currently in clinical trials, proving the proficiency of synthetic biology in terms of both pharmacological activities as well as an increase in the biosafety of treatments. It is possible that we may just be seeing the tip of the iceberg, and synthetic biology applications will overpass expectations beyond our present knowledge. Copyright © 2017. Published by Elsevier Inc.

FUNCTION IN BIOLOGY: ETIOLOGICAL AND ORGANIZATIONAL PERSPECTIVES

Directory of Open Access Journals (Sweden)

Charbel Niño El-Hani

2009-10-01

Full Text Available 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’ organization. KEYWORDS: Function; Teleology; Explanation; Etiology; Organization.   RESUMEN. En este artículo, argumentamos a favor de una taxonomía de abordajes sobre función basada en diferentes perspectivas epistemológicas a cerca del tratamiento de este concepto central en las ciencias de la vida. Distinguimos entre perspectivas etiológicas y organizacionales sobre función, analizando dos teorías distintas

Wigner functions for noncommutative quantum mechanics: A group representation based construction

Energy Technology Data Exchange (ETDEWEB)

Chowdhury, S. Hasibul Hassan, E-mail: shhchowdhury@gmail.com [Chern Institute of Mathematics, Nankai University, Tianjin 300071 (China); Department of Mathematics and Statistics, Concordia University, Montréal, Québec H3G 1M8 (Canada); Ali, S. Twareque, E-mail: twareque.ali@concordia.ca [Department of Mathematics and Statistics, Concordia University, Montréal, Québec H3G 1M8 (Canada)

2015-12-15

This paper is devoted to the construction and analysis of the Wigner functions for noncommutative quantum mechanics, their marginal distributions, and star-products, following a technique developed earlier, viz, using the unitary irreducible representations of the group G{sub NC}, which is the three fold central extension of the Abelian group of ℝ{sup 4}. These representations have been exhaustively studied in earlier papers. The group G{sub NC} is identified with the kinematical symmetry group of noncommutative quantum mechanics of a system with two degrees of freedom. The Wigner functions studied here reflect different levels of non-commutativity—both the operators of position and those of momentum not commuting, the position operators not commuting and finally, the case of standard quantum mechanics, obeying the canonical commutation relations only.

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.

The construction of control chart for PM10 functional data

Science.gov (United States)

Shaadan, Norshahida; Jemain, Abdul Aziz; Deni, Sayang Mohd

2014-06-01

In this paper, a statistical procedure to construct a control chart for monitoring air quality (PM10) using functional data is proposed. A set of daily indices that represent the daily PM10 curves were obtained using Functional Principal Component Analysis (FPCA). By means of an iterative charting procedure, a reference data set that represented a stable PM10 process was obtained. The data were then used as a reference for monitoring future data. The application of the procedure was conducted using seven-year (2004-2010) period of recorded data from the Klang air quality monitoring station located in the Klang Valley region of Peninsular Malaysia. The study showed that the control chart provided a useful visualization tool for monitoring air quality and was capable in detecting abnormality in the process system. As in the case of Klang station, the results showed that with reference to 2004-2008, the air quality (PM10) in 2010 was better than that in 2009.

Reports on construction experience of Monju, 1

International Nuclear Information System (INIS)

Nagahiro, Yoshihiko; Okuma, Nobutaka; Jin, Satoru; Odo, Toshihiro; Wachi, Eiji.

1991-01-01

Following are a part of results obtained through the design and fabrication works of Monju construction; (1) strengthening-ring, attached to the large-diameter containment vessel as a countermeasure for the buckling stress induced by the outer pressure, were effective also on the seismic design, (2) design and evaluation methods have been established for the ferro-concrete structure under the condition of high temperature in case of the sodium leakage accidents, and reduced scale models were confirmed to be very useful to make arrangements for execution of the complex structure, (3) steel-plate-concrete structures which are applied to Monju biological shielding wall have been confirmed to attain the high precision of the construction and the reduction of the period required for the installation works, and (4) an optimum design was obtained for the lining system with the functions required in case of the sodium leakage accidents by using a combination of three types of liners. (author)

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...... and laboratory experiments. Krill biomass was highest in the middle fjord and inner fjord, whereas no krill was found offshore. The dominating species Thysanoessa raschii revealed a type III functional response when fed with the diatom Thalassiosira weissflogii. At food saturation, T. raschii exhibited a daily...... 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...

PreproVIP-derived peptides in the human female genital tract: expression and biological function

DEFF Research Database (Denmark)

Bredkjoer, H E; Palle, C; Ekblad, E

1997-01-01

The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination with immunohistoc......The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination...... with immunohistochemistry were used. The effect of preproVIP 22-79, preproVIP 111-122 and preproVIP 156-170 on genital smooth muscle activity in the Fallopian tube was investigated in vitro and compared to that of VIP. All the preproVIP-derived peptides were expressed throughout the genital tract in neuronal elements...

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.

Using biological indices to classify schizophrenia and other psychotic patients.

Science.gov (United States)

Sponheim, S R; Iacono, W G; Thuras, P D; Beiser, M

2001-07-01

Although classification of mental disorders using more than clinical description would be desirable, there is scant evidence that available laboratory tests (i.e. biological indices) would provide more valid classifications than current diagnostic systems (e.g. DSM-IV). We used cluster analysis of four biological variables to classify 163 psychotic patients and 83 nonpsychiatric comparison subjects. Analyses revealed a three-cluster solution with the first cluster reflecting electrodermal deviance, the second cluster representing nondeviant biological function, and the third cluster reflecting increased nailfold plexus visibility and ocular motor dysfunction. To assess the construct validity of proband clusters we examined ocular motor performance in 156 first-degree relatives as a function of proband cluster membership. First-degree relatives of third cluster probands exhibited worse ocular motor performance than relatives of other cluster probands. Additionally, better classification sensitivity and specificity were obtained for the relatives when they were grouped by proband cluster than by proband DSM-IV diagnosis. When a single proband characteristic (i.e. eyetracking performance) was used to group relatives, classification sensitivity and specificity failed to significantly increase over grouping by proband DSM-IV diagnosis. Multivariate biologically defined clusters may offer an advantage over DSM-IV classification when examining nosology and etiology of psychotic disorders.

Biological effects of simple changes in functionality on rhodium metalloinsertors

Science.gov (United States)

Weidmann, Alyson G.; Komor, Alexis C.; Barton, Jacqueline K.

2013-01-01

DNA mismatch repair (MMR) is crucial to ensuring the fidelity of the genome. The inability to correct single base mismatches leads to elevated mutation rates and carcinogenesis. Using metalloinsertors–bulky metal complexes that bind with high specificity to mismatched sites in the DNA duplex–our laboratory has adopted a new chemotherapeutic strategy through the selective targeting of MMR-deficient cells, that is, those that have a propensity for cancerous transformation. Rhodium metalloinsertors display inhibitory effects selectively in cells that are deficient in the MMR machinery, consistent with this strategy. However, a highly sensitive structure–function relationship is emerging with the development of new complexes that highlights the importance of subcellular localization. We have found that small structural modifications, for example a hydroxyl versus a methyl functional group, can yield profound differences in biological function. Despite similar binding affinities and selectivities for DNA mismatches, only one metalloinsertor shows selective inhibition of cellular proliferation in MMR-deficient versus -proficient cells. Studies of whole-cell, nuclear and mitochondrial uptake reveal that this selectivity depends upon targeting DNA mismatches in the cell nucleus. PMID:23776288

A Synthetic Biology Project - Developing a single-molecule device for screening drug-target interactions.

Science.gov (United States)

Firman, Keith; Evans, Luke; Youell, James

2012-07-16

This review describes a European-funded project in the area of Synthetic Biology. The project seeks to demonstrate the application of engineering techniques and methodologies to the design and construction of a biosensor for detecting drug-target interactions at the single-molecule level. Production of the proteins required for the system followed the principle of previously described "bioparts" concepts (a system where a database of biological parts - promoters, genes, terminators, linking tags and cleavage sequences - is used to construct novel gene assemblies) and cassette-type assembly of gene expression systems (the concept of linking different "bioparts" to produce functional "cassettes"), but problems were quickly identified with these approaches. DNA substrates for the device were also constructed using a cassette-system. Finally, micro-engineering was used to build a magnetoresistive Magnetic Tweezer device for detection of single molecule DNA modifying enzymes (motors), while the possibility of constructing a Hall Effect version of this device was explored. The device is currently being used to study helicases from Plasmodium as potential targets for anti-malarial drugs, but we also suggest other potential uses for the device. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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...

Structure, function, and behaviour of computational models in systems biology.

Science.gov (United States)

Knüpfer, Christian; Beckstein, Clemens; Dittrich, Peter; Le Novère, Nicolas

2013-05-31

Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such "bio-models" necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. We present a conceptual framework - the meaning facets - which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model's components (structure), the meaning of the model's intended use (function), and the meaning of the model's dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research.

TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions.

Science.gov (United States)

Martínez-Reyes, Inmaculada; Diebold, Lauren P; Kong, Hyewon; Schieber, Michael; Huang, He; Hensley, Christopher T; Mehta, Manan M; Wang, Tianyuan; Santos, Janine H; Woychik, Richard; Dufour, Eric; Spelbrink, Johannes N; Weinberg, Samuel E; Zhao, Yingming; DeBerardinis, Ralph J; Chandel, Navdeep S

2016-01-21

Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation. Copyright © 2016 Elsevier Inc. All rights reserved.

On Segal-Wilson's construction for the τ-functions of the constrained KP hierarchies

International Nuclear Information System (INIS)

Zhang You-jin.

1994-06-01

In this letter we study the constrained KP hierachies by employing Segal-Wilson's theory on the τ-functions of the KP hierarchy. We first describe the elements of the Grassmannian which correspond to solutions of the constrained KP hierarchy, and then we show how to construct its rational and soliton solutions from these elements of the Grassmannian. (author). 10 refs

Bioprinting scale-up tissue and organ constructs for transplantation.

Science.gov (United States)

Ozbolat, Ibrahim T

2015-07-01

Bioprinting is an emerging field that is having a revolutionary impact on the medical sciences. It offers great precision for the spatial placement of cells, proteins, genes, drugs, and biologically active particles to better guide tissue generation and formation. This emerging biotechnology appears to be promising for advancing tissue engineering toward functional tissue and organ fabrication for transplantation, drug testing, research investigations, and cancer or disease modeling, and has recently attracted growing interest worldwide among researchers and the general public. In this Opinion, I highlight possibilities for the bioprinting scale-up of functional tissue and organ constructs for transplantation and provide the reader with alternative approaches, their limitations, and promising directions for new research prospects. Copyright © 2015 Elsevier Ltd. All rights reserved.

Role of soil biology and soil functions in relation to land use intensity.

Science.gov (United States)

Bondi, Giulia; Wall, David; Bacher, Matthias; Emmet-Booth, Jeremy; Graça, Jessica; Marongiu, Irene; Creamer, Rachel

2017-04-01

The delivery of the ecosystem's functions is predominantly controlled by soil biology. The biology found in a gram of soil contains more than ten thousand individual species of bacteria and fungi (Torsvik et al., 1990). Understanding the role and the requirements of these organisms is essential for the protection and the sustainable use of soils. Soil biology represents the engine of all the processes occurring in the soil and it supports the ecosystem services such as: 1) nutrient mineralisation 2) plant production 3) water purification and regulation and 4) carbon cycling and storage. During the last years land management type and intensity have been identified as major drivers for microbial performance in soil. For this reason land management needs to be appropriately studied to understand the role of soil biology within this complex interplay of functions. We aimed to study whether and how land management drives soil biological processes and related functions. To reach this objective we built a land use intensity index (LUI) able to quantify the impact of the common farming practices carried out in Irish grassland soils. The LUI is derived from a detailed farmer questionnaire on grassland management practices at 38 farms distributed in the five major agro-climatic regions of Ireland defined by Holden and Brereton (2004). Soils were classified based on their drainage status according to the Irish Soil Information System by Creamer et al. (2014). This detailed questionnaire is then summarised into 3 management intensity components: (i) intensity of Fertilisation (Fi), (ii) frequency of Mowing (Mi) and (iii) intensity of Livestock Grazing (Gi). Sites were sampled to assess the impact of land management intensity on microbial community structure and enzyme behaviour in relation to nitrogen, phosphorus and carbon cycling. Preliminary results for enzymes linked to C and N cycles showed higher activity in relation to low grazing pressure (low Gi). Enzymes linked to P

Facile construction of structurally diverse thiazolidinedione-derived compounds via divergent stereoselective cascade organocatalysis and their biological exploratory studies.

Science.gov (United States)

Zhang, Yongqiang; Wang, Shengzheng; Wu, Shanchao; Zhu, Shiping; Dong, Guoqiang; Miao, Zhenyuan; Yao, Jianzhong; Zhang, Wannian; Sheng, Chunquan; Wang, Wei

2013-06-10

In this article, we present a new approach by merging two powerful synthetic tactics, divergent synthesis and cascade organocatalysis, to create a divergent cascade organocatalysis strategy for the facile construction of new "privileged" substructure-based DOS (pDOS) library. As demonstrated, notably 5 distinct molecular architectures are produced facilely from readily available simple synthons thiazolidinedione and its analogues and α,β-unsaturated aldehydes in 1-3 steps with the powerful strategy. The beauty of the chemistry is highlighted by the efficient formation of structurally new and diverse products from structurally close reactants under the similar reaction conditions. Notably, structurally diverse spiro-thiazolidinediones and -rhodanines are produced from organocatalytic enantioselective 3-component Michael-Michael-aldol cascade reactions of respective thiazolidinediones and rhodanines with enals. Nevertheless, under the similar reaction conditions, reactions of isorhodanine via a Michael-cyclization cascade lead to structurally different fused thiopyranoid scaffolds. This strategy significantly minimizes time- and cost-consuming synthetic works. Furthermore, these molecules possess high structural complexity and functional, stereochemical, and skeletal diversity with similarity to natural scaffolds. In the preliminary biological studies of these molecules, compounds 4f, 8a, and 10a exhibit inhibitory activity against the human breast cancer cells, while compounds 8a, 9a, and 9b display good antifungal activities against Candida albicans and Cryptococcus neoformans. Notably, their structures are different from clinically used triazole antifungal drugs. Therefore, they could serve as good lead compounds for the development of new generation of antifungal agents.

Microstructure, mechanical properties, and biological response to functionally graded HA coatings

International Nuclear Information System (INIS)

Rabiei, Afsaneh; Blalock, Travis; Thomas, Brent; Cuomo, Jerry; Yang, Y.; Ong, Joo

2007-01-01

Hydroxyapatite (HA) [Ca 10 (PO 4 ) 6 (OH) 2 ] is the primary mineral content, representing 43% by weight, of bone. Applying a thin layer of HA, to the surface of a metal implant, can promote osseointegration and increase the mechanical stability of the implant. In this study, a biocompatible coating comprising an HA film with functionally graded crystallinity is being deposited on a heated substrate in an Ion Beam Assisted Deposition (IBAD) system. The microstructure of the film was studied using Transmission Electron Microscopy techniques. Finally, initial cell adhesion and cell differentiation on the coating was evaluated using ATCC CRL 1486 human embryonic palatal mesenchymal cell, an osteoblast precursor cell line. The results have shown superior mechanical properties and biological response to the functionally graded HA film

The path to next generation biofuels: successes and challenges in the era of synthetic biology

Science.gov (United States)

2010-01-01

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels. PMID:20089184

3D Bioprinting of Artificial Tissues: Construction of Biomimetic Microstructures.

Science.gov (United States)

Luo, Yongxiang; Lin, Xin; Huang, Peng

2018-04-24

It is promising that artificial tissues/organs for clinical application can be produced via 3D bioprinting of living cells and biomaterials. The construction of microstructures biomimicking native tissues is crucially important to create artificial tissues with biological functions. For instance, the fabrication of vessel-like networks to supply cells with initial nutrient and oxygen, and the arrangement of multiple types of cells for creating lamellar/complex tissues through 3D bioprinting are widely reported. The current advances in 3D bioprinting of artificial tissues from the view of construction of biomimetic microstructures, especially the fabrication of lamellar, vascular, and complex structures are summarized. In the end, the conclusion and perspective of 3D bioprinting for clinical applications are elaborated. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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…

Pectin: cell biology and prospects for functional analysis.

Science.gov (United States)

Willats, W G; McCartney, L; Mackie, W; Knox, J P

2001-09-01

Pectin is a major component of primary cell walls of all land plants and encompasses a range of galacturonic acid-rich polysaccharides. Three major pectic polysaccharides (homogalacturonan, rhamnogalacturonan-I and rhamnogalacturonan-II) are thought to occur in all primary cell walls. This review surveys what is known about the structure and function of these pectin domains. The high degree of structural complexity and heterogeneity of the pectic matrix is produced both during biosynthesis in the endomembrane system and as a result of the action of an array of wall-based pectin-modifying enzymes. Recent developments in analytical techniques and in the generation of anti-pectin probes have begun to place the structural complexity of pectin in cell biological and developmental contexts. The in muro de-methyl-esterification of homogalacturonan by pectin methyl esterases is emerging as a key process for the local modulation of matrix properties. Rhamnogalacturonan-I comprises a highly diverse population of spatially and developmentally regulated polymers, whereas rhamnogalacturonan-II appears to be a highly conserved and stable pectic domain. Current knowledge of biosynthetic enzymes, plant and microbial pectinases and the interactions of pectin with other cell wall components and the impact of molecular genetic approaches are reviewed in terms of the functional analysis of pectic polysaccharides in plant growth and development.

Undergraduate Students’ Difficulties in Reading and Constructing Phylogenetic Tree

Science.gov (United States)

Sa'adah, S.; Tapilouw, F. S.; Hidayat, T.

2017-02-01

Representation is a very important communication tool to communicate scientific concepts. Biologists produce phylogenetic representation to express their understanding of evolutionary relationships. The phylogenetic tree is visual representation depict a hypothesis about the evolutionary relationship and widely used in the biological sciences. Phylogenetic tree currently growing for many disciplines in biology. Consequently, learning about phylogenetic tree become an important part of biological education and an interesting area for biology education research. However, research showed many students often struggle with interpreting the information that phylogenetic trees depict. The purpose of this study was to investigate undergraduate students’ difficulties in reading and constructing a phylogenetic tree. The method of this study is a descriptive method. In this study, we used questionnaires, interviews, multiple choice and open-ended questions, reflective journals and observations. The findings showed students experiencing difficulties, especially in constructing a phylogenetic tree. The students’ responds indicated that main reasons for difficulties in constructing a phylogenetic tree are difficult to placing taxa in a phylogenetic tree based on the data provided so that the phylogenetic tree constructed does not describe the actual evolutionary relationship (incorrect relatedness). Students also have difficulties in determining the sister group, character synapomorphy, autapomorphy from data provided (character table) and comparing among phylogenetic tree. According to them building the phylogenetic tree is more difficult than reading the phylogenetic tree. Finding this studies provide information to undergraduate instructor and students to overcome learning difficulties of reading and constructing phylogenetic tree.

BioNSi: A Discrete Biological Network Simulator Tool.

Science.gov (United States)

Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

2016-08-05

Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.

Models for synthetic biology.

Science.gov (United States)

Kaznessis, Yiannis N

2007-11-06

Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal.

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.

The use of constructed wetlands in the treatment of acid mine drainage

International Nuclear Information System (INIS)

Perry, A.; Kleinmann, R.L.P.

1991-01-01

US government regulations require that all effluents from industrial operations, including mining, meet certain water quality standards. Constructed wetlands have proven to be useful in helping to attain those standards. Application of this biotechnology to mine water drainage can reduce water treatment costs and improve water quality in streams and rivers adversely affected by acidic mine water drainage from abandoned mines. Over 400 constructed wetland water treatment systems have been built on mined lands largely as a result of research by the US Bureau of Mines. Wetlands are passive biological treatment systems that are relatively inexpensive to construct and require minimal maintenance. Chemical treatment costs are reduced sufficiently to repay the cost of construction in less than a year. The mine waste water is typically treated in a series of excavated ponds that resemble small marsh areas. The ponds are engineered to facilitate bacterial oxidation of iron. Ideally, the water then flows through a composted organic substrate supporting a population of sulphate-reducing bacteria which raises the pH. Constructed wetlands in the USA are described - their history, functions, construction methodologies, applicabilities, limitations and costs. (author). 26 refs, 2 figs

The use of constructed wetlands in the treatment of acid mine drainage

Energy Technology Data Exchange (ETDEWEB)

Perry, A [Department of the Interior, Washington, DC (United States). Bureau of Mines; Kleinmann, R L.P. [Department of the Interior, Pittsburgh, PA (United States). Bureau of Mines

1991-08-01

US government regulations require that all effluents from industrial operations, including mining, meet certain water quality standards. Constructed wetlands have proven to be useful in helping to attain those standards. Application of this biotechnology to mine water drainage can reduce water treatment costs and improve water quality in streams and rivers adversely affected by acidic mine water drainage from abandoned mines. Over 400 constructed wetland water treatment systems have been built on mined lands largely as a result of research by the US Bureau of Mines. Wetlands are passive biological treatment systems that are relatively inexpensive to construct and require minimal maintenance. Chemical treatment costs are reduced sufficiently to repay the cost of construction in less than a year. The mine waste water is typically treated in a series of excavated ponds that resemble small marsh areas. The ponds are engineered to facilitate bacterial oxidation of iron. Ideally, the water then flows through a composted organic substrate supporting a population of sulphate-reducing bacteria which raises the pH. Constructed wetlands in the USA are described - their history, functions, construction methodologies, applicabilities, limitations and costs. (author). 26 refs, 2 figs.

A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

Science.gov (United States)

2010-01-01

Background The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Methods Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Results Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological

A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA.

Science.gov (United States)

D'Onofrio, David J; An, Gary

2010-01-21

The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological systems do not have an

A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

Directory of Open Access Journals (Sweden)

D'Onofrio David J

2010-01-01

Full Text Available Abstract Background The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Methods Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1 orthogonal uniqueness, (2 low level formatting, (3 high level formatting and (4 translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Results Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT during high level formatting of the computer hard drive and the subsequent loading of an operating

[Mandible function in taking construction bite for activator].

Science.gov (United States)

Irie, M

1989-06-01

Functional effects of construction bite for activator (Andresen type) especially on lateral pterygoid muscle, as well as the positional changes of the mandible, hyoid bone and surface EMGs from bilateral anterior temporal (TA) and masseter (MM) muscle, were studied on the electric force scale, MKG, EMG and cephalometric radiographs in 14 subjects with anterior cross bite in mixed dentition. The cephalometric radiographs were taken at the start of each patient's treatment. One was taken with the mandible in the intercuspal position and one was also taken with the activator in the mouth at the overjet improvement. The activator patients were divided into two groups because of differences in the direction of movement of the hyoid bone in the FH plane. In group O (7 patients), the movement of the hyoid bone was at an oblique angle to the FH plane, while in group D (7 patients) the movement ot the hyoid bone with nearly direct below angle to FH plane. The patients were further divided into three types because of differences in the distance between the hyoid bone and mental spine, and combined with the groups OA (3 patients), OB (2 patients), OC (2 patients), DA (5 patients), DB (2 patients) and DC (Naught). The results obtained were as follows: The forces for the construction bite for groups O and D were 2.71 Kg and 2.72 kg, respectively. Type OC required significantly heavier force. (p less than 0.05) In the condylar test, O group was significantly smaller at the start of treatment, but not after overjet improvement. Type OA and OB were also significantly smaller at the start of treatment. (p less than 0.05) Velocity of opening for group D was significantly (p less than 0.05) faster at the start of treatment, but not after that. There was no significant difference in EMGs between the groups, with activator in the mouse D group much increased as it EMGs. The EMGs M/T ratio for both groups was approximately 100% at the start of treatment for overjet improvement. In cases

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

Science.gov (United States)

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

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

2014-01-01

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. PMID:24739808

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.

Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

International Nuclear Information System (INIS)

Upadhyayula, Venkata K.K.

2012-01-01

Highlights: ► Smart sensors are needed for detection of chemical and biological threat agents. ► Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. ► Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. ► Functionalized GNPs support multiple analytical methods for sensing threat agents. ► Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad range of threat agents, including radioactive substances, explosive compounds, chemical warfare agents, biotoxins, and

Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

Energy Technology Data Exchange (ETDEWEB)

Upadhyayula, Venkata K.K., E-mail: Upadhyayula.Venkata@epa.gov [Oak Ridge Institute of Science and Education (ORISE), MC-100-44, PO Box 117, Oak Ridge, TN 37831 (United States)

2012-02-17

Highlights: Black-Right-Pointing-Pointer Smart sensors are needed for detection of chemical and biological threat agents. Black-Right-Pointing-Pointer Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. Black-Right-Pointing-Pointer Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. Black-Right-Pointing-Pointer Functionalized GNPs support multiple analytical methods for sensing threat agents. Black-Right-Pointing-Pointer Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad

Biological response to purification and acid functionalization of carbon nanotubes

Science.gov (United States)

Figarol, Agathe; Pourchez, Jérémie; Boudard, Delphine; Forest, Valérie; Tulliani, Jean-Marc; Lecompte, Jean-Pierre; Cottier, Michèle; Bernache-Assollant, Didier; Grosseau, Philippe

2014-07-01

Acid functionalization has been considered as an easy way to enhance the dispersion and biodegradation of carbon nanotubes (CNT). However, inconsistencies between toxicity studies of acid functionalized CNT remain unexplained. This could be due to a joint effect of the main physicochemical modifications resulting from an acid functionalization: addition of surface acid groups and purification from catalytic metallic impurities. In this study, the impact on CNT biotoxicity of these two physiochemical features was assessed separately. The in vitro biological response of RAW 264.7 macrophages was evaluated after exposure to 15-240 µg mL-1 of two types of multi-walled CNT. For each type of CNT (small: 20 nm diameter, and big: 90 nm diameter), three different surface chemical properties were studied (total of six CNT samples): pristine, acid functionalized and desorbed. Desorbed CNT were purified by the acid functionalization but presented a very low amount of surface acid groups due to a thermal treatment under vacuum. A Janus effect of acid functionalization with two opposite impacts is highlighted. The CNT purification decreased the overall toxicity, while the surface acid groups intensified it when present at a specific threshold. These acid groups especially amplified the pro-inflammatory response. The threshold mechanism which seemed to regulate the impact of acid groups should be further studied to determine its value and potential link to the other physicochemical state of the CNT. The results suggest that, for a safer-design approach, the benefit-risk balance of an acid functionalization has to be considered, depending on the CNT primary state of purification. Further research should be conducted in this direction.

The necessity of a theory of biology for tissue engineering: metabolism-repair systems.

Science.gov (United States)

Ganguli, Suman; Hunt, C Anthony

2004-01-01

Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.

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.

The use of the dicentric assay for biological dosimetry for radiation accidents in Bulgaria.

Science.gov (United States)

Hadjidekova, Valeria; Hristova, Rositsa; Ainsbury, Elizabeth A; Atanasova, Petya; Popova, Ljubomira; Staynova, Albena

2010-02-01

This paper details the construction of a 137Cs gamma calibration curve that has been established for dicentric assay and the testing and validation of the curve through biological dosimetry in three situations of suspected workplace overexposure that arose accidentally or through negligence or lack of appropriate safety measures. The three situations were: (1) suspected 137Cs contamination in a factory air supply; (2) suspected exposure to an industrial 192Ir source; and (3) accidental exposure of construction workers to radiation from a 60Co radiotherapy source in a hospital medical physics department. From a total of 24 potentially-exposed subjects, only one worker was found to have a statistically significant dose (0.16 Gy, 95% confidence intervals 0.02-0.43 Gy). In all other cases, the main function of the biological dosimetry was to reassure the subjects that any dose received was low.

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

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?...

Direct 3D bioprinting of perfusable vascular constructs using a blend bioink.

Science.gov (United States)

Jia, Weitao; Gungor-Ozkerim, P Selcan; Zhang, Yu Shrike; Yue, Kan; Zhu, Kai; Liu, Wanjun; Pi, Qingment; Byambaa, Batzaya; Dokmeci, Mehmet Remzi; Shin, Su Ryon; Khademhosseini, Ali

2016-11-01

Despite the significant technological advancement in tissue engineering, challenges still exist towards the development of complex and fully functional tissue constructs that mimic their natural counterparts. To address these challenges, bioprinting has emerged as an enabling technology to create highly organized three-dimensional (3D) vascular networks within engineered tissue constructs to promote the transport of oxygen, nutrients, and waste products, which can hardly be realized using conventional microfabrication techniques. Here, we report the development of a versatile 3D bioprinting strategy that employs biomimetic biomaterials and an advanced extrusion system to deposit perfusable vascular structures with highly ordered arrangements in a single-step process. In particular, a specially designed cell-responsive bioink consisting of gelatin methacryloyl (GelMA), sodium alginate, and 4-arm poly(ethylene glycol)-tetra-acrylate (PEGTA) was used in combination with a multilayered coaxial extrusion system to achieve direct 3D bioprinting. This blend bioink could be first ionically crosslinked by calcium ions followed by covalent photocrosslinking of GelMA and PEGTA to form stable constructs. The rheological properties of the bioink and the mechanical strengths of the resulting constructs were tuned by the introduction of PEGTA, which facilitated the precise deposition of complex multilayered 3D perfusable hollow tubes. This blend bioink also displayed favorable biological characteristics that supported the spreading and proliferation of encapsulated endothelial and stem cells in the bioprinted constructs, leading to the formation of biologically relevant, highly organized, perfusable vessels. These characteristics make this novel 3D bioprinting technique superior to conventional microfabrication or sacrificial templating approaches for fabrication of the perfusable vasculature. We envision that our advanced bioprinting technology and bioink formulation may also

Particles matter: Transformation of suspended particles in constructed wetlands

NARCIS (Netherlands)

Mulling, B.T.M.

2013-01-01

This thesis shows that constructed wetlands transform suspended particles in (treated) municipal wastewater through selective precipitation in ponds, biological filtering by plankton communities and physical and biological retention in reed beds. These processes effectively remove faecal indicator

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

Construction and pilot assessment of the Lower Limb Function Assessment Scale.

Science.gov (United States)

Allart, Etienne; Paquereau, Julie; Rogeau, Caroline; Daveluy, Walter; Kozlowski, Odile; Rousseaux, Marc

2014-01-01

Stroke often leads to upright standing and walking impairments. Clinical assessments do not sufficiently address ecological aspects and the patient's subjective evaluation of function. To perform a pilot assessment of the psychometric properties of the Lower Limb-Function Assessment Scale (LL-FAS). The LL-FAS includes 30 items assessing the patient's perception (in a questionnaire) and the examiner's perception (in a practical test) of upright standing and walking impairments and their impact on activities of daily living. We analyzed the LL-FAS's reliability, construct validity, internal consistency, predictive validity and feasibility. Thirty-five stroke patients were included. The scale's mean ± SD completion time was 25 ± 6 min. Intra-observer reliability was good to excellent (intraclass correlation coefficients (ICC >0.82). Interobserver reliability was moderate (0.67 0.9) and predictive validity were excellent. The LL-FAS showed fair psychometric properties in this pilot study and may be of value for evaluating post-stroke lower limb impairment.

The role of cysteine residues in the sulphate transporter, SHST1: construction of a functional cysteine-less transporter.

Science.gov (United States)

Howitt, Susan M

2005-05-20

We investigated the role of cysteine residues in the sulphate transporter, SHST1, with the aim of generating a functional cysteine-less variant. SHST1 contains five cysteine residues and none was essential for function. However, replacement of C421 resulted in a reduction in transport activity. Sulphate transport by C205 mutants was dependent on the size of the residue at this position. Alanine at position 205 resulted in a complete loss of function whereas leucine resulted in a 3-fold increase in sulphate transport relative to wild type SHST1. C205 is located in a putative intracellular loop and our results suggest that this loop may be important for sulphate transport. By replacing C205 with leucine and the other four cysteine residues with alanine, we constructed a cysteine-less variant of SHST1 that has transport characteristics indistinguishable from wild type. This construct will be useful for further structure and function studies of SHST1.

Molecular biology of mycoplasmas: from the minimum cell concept to the artificial cell.

Science.gov (United States)

Cordova, Caio M M; Hoeltgebaum, Daniela L; Machado, Laís D P N; Santos, Larissa Dos

2016-01-01

Mycoplasmas are a large group of bacteria, sorted into different genera in the Mollicutes class, whose main characteristic in common, besides the small genome, is the absence of cell wall. They are considered cellular and molecular biology study models. We present an updated review of the molecular biology of these model microorganisms and the development of replicative vectors for the transformation of mycoplasmas. Synthetic biology studies inspired by these pioneering works became possible and won the attention of the mainstream media. For the first time, an artificial genome was synthesized (a minimal genome produced from consensus sequences obtained from mycoplasmas). For the first time, a functional artificial cell has been constructed by introducing a genome completely synthesized within a cell envelope of a mycoplasma obtained by transformation techniques. Therefore, this article offers an updated insight to the state of the art of these peculiar organisms' molecular biology.

Cumulative exposure to dust and gases as determinants of lung function decline in tunnel construction workers.

Science.gov (United States)

Bakke, B; Ulvestad, B; Stewart, P; Eduard, W

2004-03-01

To study the relation between lung function decrease and cumulative exposure to dust and gases in tunnel construction workers. A total of 651 male construction workers (drill and blast workers, tunnel concrete workers, shotcreting operators, and tunnel boring machine workers) were followed up by spirometric measurements in 1989-2002 for an average of six years. Outdoor concrete workers, foremen, and engineers served as a low exposed referent population. The between worker component of variability was considerably reduced within the job groups compared to the whole population, suggesting that the workers within job groups had similar exposure levels. The annual decrease in FEV1 in low-exposed non-smoking workers was 21 ml and 24 ml in low-exposed ever smokers. The annual decrease in FEV1 in tunnel construction workers was 20-31 ml higher than the low exposed workers depending on job group for both non-smokers and ever smokers. After adjustment for age and observation time, cumulative exposure to nitrogen dioxide showed the strongest association with a decrease in FEV1 in both non-smokers, and ever smokers. Cumulative exposure to nitrogen dioxide appeared to be a major risk factor for lung function decreases in these tunnel construction workers, although other agents may have contributed to the observed effect. Contact with blasting fumes should be avoided, diesel exhaust emissions should be reduced, and respiratory devices should be used to protect workers against dust and nitrogen dioxide exposure.

Biologic and synthetic skin substitutes: An overview.

Science.gov (United States)

Halim, Ahmad Sukari; Khoo, Teng Lye; Mohd Yussof, Shah Jumaat

2010-09-01

The current trend of burn wound care has shifted to more holistic approach of improvement in the long-term form and function of the healed burn wounds and quality of life. This has demanded the emergence of various skin substitutes in the management of acute burn injury as well as post burn reconstructions. Skin substitutes have important roles in the treatment of deep dermal and full thickness wounds of various aetiologies. At present, there is no ideal substitute in the market. Skin substitutes can be divided into two main classes, namely, biological and synthetic substitutes. The biological skin substitutes have a more intact extracellular matrix structure, while the synthetic skin substitutes can be synthesised on demand and can be modulated for specific purposes. Each class has its advantages and disadvantages. The biological skin substitutes may allow the construction of a more natural new dermis and allow excellent re-epithelialisation characteristics due to the presence of a basement membrane. Synthetic skin substitutes demonstrate the advantages of increase control over scaffold composition. The ultimate goal is to achieve an ideal skin substitute that provides an effective and scar-free wound healing.

Biologic and synthetic skin substitutes: An overview

Directory of Open Access Journals (Sweden)

Halim Ahmad

2010-10-01

Full Text Available The current trend of burn wound care has shifted to more holistic approach of improvement in the long-term form and function of the healed burn wounds and quality of life. This has demanded the emergence of various skin substitutes in the management of acute burn injury as well as post burn reconstructions. Skin substitutes have important roles in the treatment of deep dermal and full thickness wounds of various aetiologies. At present, there is no ideal substitute in the market. Skin substitutes can be divided into two main classes, namely, biological and synthetic substitutes. The biological skin substitutes have a more intact extracellular matrix structure, while the synthetic skin substitutes can be synthesised on demand and can be modulated for specific purposes. Each class has its advantages and disadvantages. The biological skin substitutes may allow the construction of a more natural new dermis and allow excellent re-epithelialisation characteristics due to the presence of a basement membrane. Synthetic skin substitutes demonstrate the advantages of increase control over scaffold composition. The ultimate goal is to achieve an ideal skin substitute that provides an effective and scar-free wound healing.

Environmental and biological monitoring of occupational exposure to polynuclear aromatic hydrocarbons during highway pavement construction in Italy.

Science.gov (United States)

Fostinelli, Jacopo; Madeo, Egidio; Toraldo, Emanuele; Sarnico, Michela; Luzzana, Giorgio; Tomasi, Cesare; De Palma, Giuseppe

2018-06-09

We performed a cross-sectional study with the main aim of evaluating occupational exposure to polycyclic aromatic hydrocarbons (PAHs) in workers involved in the pavement construction of a new highway in Northern Italy, where modified bitumen was used as binder for Hot Mix Asphalt. We applied a combined approach of air and biological monitoring. Both the aerosol and vapour phases of bitumen were collected applying the NIOSH 5506 method. The 16 PAHs listed as high priority by EPA were determined by HPLC-UV. End-of-shift urine samples were collected from 144 workers to determine 1-hydroxypyrene (1-OHP) and 2-naphthol (2-NAP) concentrations after enzyme digestion and HPLC-UV analysis. Socio-demographic and lifestyle information was collected by a questionnaire. Paving workers were actually exposed to PAHs, including carcinogenic compounds, that were measurable only in the aerosol phase. Higher exposure as well as dose levels were measured for the paver group. Biological monitoring confirmed that 1-OHP was less affected by smoking habits as compared to 2-NAP and showed a higher association with occupational exposure. Carcinogenic PAH compounds were detectable only in the aerosol phase and this must be taken into account in the adoption of preventive measures. Biomonitoring supported the superiority of 1-OHP as compared to 2-NAP in assessing the internal dose in such workers. Copyright © 2018. Published by Elsevier B.V.

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

OpenAIRE

Mi, Huaiyu; Guo, Nan; Kejariwal, Anish; Thomas, Paul D.

2006-01-01

PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles. Since 2005, there have been three main improvements to PANTHER. First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information. Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distri...

Treatment of wastewater with the constructed wetland

International Nuclear Information System (INIS)

Fernandez, R.; Olivares, S.

2003-01-01

Constructed wetland is an environmental sound, actual and economic solution for the treatment of wastewater. The use of these constructed wetlands increased in the last few years, principally in developed countries. However there is not much information about the performance of these biological systems in tropical and subtropical climates. In these review the state of art of these technology is given, and also the advantage of the use of the constructed wetland for the wastewater treatment in our country

Updating biological bases of social behavior.

Science.gov (United States)

O'Connor, Thomas G

2014-09-01

This month's collation of papers deals with social behaviors that operationalize key constructs in fields covered by the journal, including attachment theory and parenting; emotional regulation; psychopathology of several forms; general and specific cognitive abilities. Notably, many examples are offered of how these social behaviors link with biology. That is an obvious and important direction for clinical research insofar as it helps to erase a perceptual chasm and artificial duality between 'behavior' and 'biology'. But, although it must be the case that social behavior has biological connections of one sort or other, identifying reliable connections with practical application has proved to be a non-trivial challenge. In particular, the challenge seems to be in measuring social behavior meaningfully enough that it could be expected to have a biological pulse, and in measuring biological markers systematically enough that emergent-downstream effects would surface. Associations are not especially uncommon, but it has been a frustrating task in constructing a practically broad model from a bricolage of scattered and disconnected parts and findings in the literature. Several reports in this issue offer contrasts that may help move along this line of study. © 2014 Association for Child and Adolescent Mental Health.

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

into cross-functional conflict. Facing a conflicting functional relationship, managers must resort to conflict resolution methods, instead of attempting to integrate, as several integrative devices are not appropriate in conflicting interfaces. Originality/value – The proposed model contributes by connecting......Purpose – The purpose of this article is to generate theory on how functional integration and conflict interrelate by studying the interface between production and purchasing. Design/methodology/approach – An interpretive single case research methodology is adopted. The authors rely on in......-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...

Structure and function in biology

International Nuclear Information System (INIS)

Hirs, C.H.W.

1976-01-01

A summary is given of the history of the developments of structural chemistry in biology beginning with the work of the bacteriologist Ehrlich leading to a comprehensive examination of the influence of size and configuration on the interaction between specific antibodies and side-chain determinants. Recent developments include the recognition of a higher order of specificity in the interaction of proteins with one another

Designing synthetic biology.

Science.gov (United States)

Agapakis, Christina M

2014-03-21

Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

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

Construction of a fuel demand function portraying inter-fuel substitution, a system dynamics approach

International Nuclear Information System (INIS)

Abada, Ibrahim; Briat, Vincent; Massol, Olivier

2011-04-01

Most of the recent numerical market equilibrium models of natural gas markets use imperfect competition assumptions. These models are typically embedded with an oversimplified representation of the demand side, usually a single-variable affine function, that does not capture any dynamic adjustment to past prices. To remedy this, we report an effort to construct an enhanced functional specification using the system dynamics-based model of Moxnes (1987, 1990). Thanks to a vintage representation of capital stock, this putty-clay model captures the effect of both past and current energy prices on fuel consumption. Using a re-calibrated version of this model, we first confirm the pertinence of this modeling framework to represent inter-fuel substitutions at different fuel prices in the industrial sector. Building on these findings, a dynamic functional specification of the demand function for natural gas is then proposed and calibrated. (authors)

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.

One-way Hash function construction based on the chaotic map with changeable-parameter

International Nuclear Information System (INIS)

Xiao Di; Liao Xiaofeng; Deng Shaojiang

2005-01-01

An algorithm for one-way Hash function construction based on the chaotic map with changeable-parameter is proposed in this paper. A piecewise linear chaotic map with changeable-parameter P is chosen, and cipher block chaining mode (CBC) is introduced to ensure that the parameter P in each iteration is dynamically decided by the last-time iteration value and the corresponding message bit in different positions. The final Hash value is obtained by means of the linear transform on the iteration sequence. Theoretical analysis and computer simulation indicate that our algorithm can satisfy all the performance requirements of Hash function in an efficient and flexible manner. It is practicable and reliable, with high potential to be adopted for E-commerce

One-way Hash function construction based on the chaotic map with changeable-parameter

Energy Technology Data Exchange (ETDEWEB)

Xiao Di [College of Computer Science and Engineering, Chongqing University, Chongqing 400044 (China) and College of Mechanical Engineering, Chongqing University, Chongqing 400044 (China)]. E-mail: xiaodi_cqu@hotmail.com; Liao Xiaofeng [College of Computer Science and Engineering, Chongqing University, Chongqing 400044 (China)]. E-mail: xfliao@cqu.edu.cn; Deng Shaojiang [College of Computer Science and Engineering, Chongqing University, Chongqing 400044 (China)

2005-04-01

An algorithm for one-way Hash function construction based on the chaotic map with changeable-parameter is proposed in this paper. A piecewise linear chaotic map with changeable-parameter P is chosen, and cipher block chaining mode (CBC) is introduced to ensure that the parameter P in each iteration is dynamically decided by the last-time iteration value and the corresponding message bit in different positions. The final Hash value is obtained by means of the linear transform on the iteration sequence. Theoretical analysis and computer simulation indicate that our algorithm can satisfy all the performance requirements of Hash function in an efficient and flexible manner. It is practicable and reliable, with high potential to be adopted for E-commerce.

Late-stage diversification of biologically active pyridazinones via a direct C-H functionalization strategy.

Science.gov (United States)

Li, Wei; Fan, Zhoulong; Geng, Kaijun; Xu, Youjun; Zhang, Ao

2015-01-14

Divergent C-H functionalization reactions (arylation, carboxylation, olefination, thiolation, acetoxylation, halogenation, naphthylation) using a pyridazinone moiety as an internal directing group were successfully established. This approach offers a late-stage, ortho-selective diversification of a biologically active pyridazinone scaffold. Seven series of novel pyridazinone analogues were synthesized conveniently as the synthetic precursors of potential sortase A (SrtA) inhibitors.

Neurobiomimetic constructs for intelligent unmanned systems and robotics

Science.gov (United States)

Braun, Jerome J.; Shah, Danelle C.; DeAngelus, Marianne A.

2014-06-01

This paper discusses a paradigm we refer to as neurobiomimetic, which involves emulations of brain neuroanatomy and neurobiology aspects and processes. Neurobiomimetic constructs include rudimentary and down-scaled computational representations of brain regions, sub-regions, and synaptic connectivity. Many different instances of neurobiomimetic constructs are possible, depending on various aspects such as the initial conditions of synaptic connectivity, number of neuron elements in regions, connectivity specifics, and more, and we refer to these instances as `animats'. While downscaled for computational feasibility, the animats are very large constructs; the animats implemented in this work contain over 47,000 neuron elements and over 720,000 synaptic connections. The paper outlines aspects of the animats implemented, spatial memory and learning cognitive task, the virtual-reality environment constructed to study the animat performing that task, and discussion of results. In a broad sense, we argue that the neurobiomimetic paradigm pursued in this work constitutes a particularly promising path to artificial cognition and intelligent unmanned systems. Biological brains readily cope with challenges of real-life tasks that consistently prove beyond even the most sophisticated algorithmic approaches known. At the cross-over point of neuroscience, cognitive science and computer science, paradigms such as the one pursued in this work aim to mimic the mechanisms of biological brains and as such, we argue, may lead to machines with abilities closer to those of biological species.

Marine biology, intertidal ecology, and a new place for biology.

Science.gov (United States)

Benson, Keith R

2015-01-01

At the present time, there is considerable interest for the physical setting of science, that is, its actual 'place' of practice. Among historians of biology, place has been considered to be a crucial component for the study of ecology. Other historians have noted the 'built' environments (laboratories) for the study of biology along the seashore, even referring to these places in terms more applicable to vacation sites. In this paper, I examine the place of intertidal ecology investigations, both in terms of the physical space and the built space. Part of the examination will investigate the aesthetic aspect of the Pacific Coast, part will evaluate the unique character of the intertidal zone, and part will consider the construction of natural laboratories and built laboratories as characteristic places for biology.

Conceptual Barriers to Progress Within Evolutionary Biology.

Science.gov (United States)

Laland, Kevin N; Odling-Smee, John; Feldman, Marcus W; Kendal, Jeremy

2009-08-01

In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, "niche construction". This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.

Synthetic biology: an emerging engineering discipline.

Science.gov (United States)

Cheng, Allen A; Lu, Timothy K

2012-01-01

Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.

Biological origins of color categorization

OpenAIRE

Skelton, Alice E.; Catchpole, Gemma; Abbott, Joshua T.; Bosten, Jenny M.; Franklin, Anna

2017-01-01

The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants’ categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mappe...

Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation

Directory of Open Access Journals (Sweden)

Jeffrey Rosenfeld

2016-03-01

Full Text Available Twenty one fully sequenced and well annotated insect genomes were used to construct genome content matrices for phylogenetic analysis and functional annotation of insect genomes. To examine the role of e-value cutoff in ortholog determination we used scaled e-value cutoffs and a single linkage clustering approach.. The present communication includes (1 a list of the genomes used to construct the genome content phylogenetic matrices, (2 a nexus file with the data matrices used in phylogenetic analysis, (3 a nexus file with the Newick trees generated by phylogenetic analysis, (4 an excel file listing the Core (CORE genes and Unique (UNI genes found in five insect groups, and (5 a figure showing a plot of consistency index (CI versus percent of unannotated genes that are apomorphies in the data set for gene losses and gains and bar plots of gains and losses for four consistency index (CI cutoffs.

Functional soil microbial diversity across Europe estimated by EEA, MicroResp and BIOLOG

DEFF Research Database (Denmark)

Winding, Anne; Rutgers, Michiel; Creamer, Rachel

consisting of 81 soil samples covering five Biogeograhical Zones and three land-uses in order to test the sensitivity, ease and cost of performance and biological significance of the data output. The techniques vary in how close they are to in situ functions; dependency on growth during incubation......Soil microorganisms are abundant and essential for the bio-geochemical processes of soil, soil quality and soil ecosystem services. All this is dependent on the actual functions the microbial communities are performing in the soil. Measuring soil respiration has for many years been the basis...... of estimating soil microbial activity. However, today several techniques are in use for determining microbial functional diversity and assessing soil biodiversity: Methods based on CO2 development by the microbes such as substrate induced respiration (SIR) on specific substrates have lead to the development...

Crafting the TALE: construction of a measure to assess the functions of autobiographical remembering.

Science.gov (United States)

Bluck, Susan; Alea, Nicole

2011-07-01

Theory suggests that autobiographical remembering serves several functions. This research builds on previous empirical efforts (Bluck, Alea, Habermas, & Rubin, 2005) with the aim of constructing a brief, valid measure of three functions of autobiographical memory. Participants (N=306) completed 28 theoretically derived items concerning the frequency with which they use autobiographical memory to serve a variety of functions. To examine convergent and discriminant validity, participants rated their tendency to think about and talk about the past, and measures of future time orientation, self-concept clarity, and trait personality. Confirmatory factor analysis of the function items resulted in a respecified model with 15 items in three factors. The newly developed Thinking about Life Experiences scale (TALE) shows good internal consistency as well as convergent validity for three subscales: Self-Continuity, Social-Bonding, and Directing-Behaviour. Analyses demonstrate factorial equivalence across age and gender groups. Potential use and limitations of the TALE are discussed.

Long-term symptomatic, functional, and work outcomes of carpal tunnel syndrome among construction workers.

Science.gov (United States)

Evanoff, Bradley; Gardner, Bethany T; Strickland, Jaime R; Buckner-Petty, Skye; Franzblau, Alfred; Dale, Ann Marie

2016-05-01

The long-term outcomes of carpal tunnel syndrome (CTS) including symptoms, functional status, work disability, and economic impact are unknown. We conducted a retrospective study of 234 active construction workers with medical claims for CTS and 249 workers without CTS claims; non-cases were matched on age, trade, and insurance eligibility. We conducted telephone interviews with cases and non-cases and collected administrative data on work hours. Compared to non-cases, CTS cases were more likely to report recurrent hand symptoms, decreased work productivity/quality, decreased performance of physical work demands, and greater functional limitations. Surgical cases showed larger improvements on multiple outcomes than non-surgical cases. Minimal differences in paid work hours were seen between cases and non-cases in the years preceding and following CTS claims. Persistent symptoms and functional impairments were present several years after CTS diagnosis. Long-term functional limitations shown by this and other studies indicate the need for improved prevention and treatment. © 2016 Wiley Periodicals, Inc.

From Never Born Proteins to Minimal Living Cells: two projects in synthetic biology.

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Luisi, Pier Luigi; Chiarabelli, Cristiano; Stano, Pasquale

2006-12-01

The Never Born Proteins (NBPs) and the Minimal Cell projects are two currently developed research lines belonging to the field of synthetic biology. The first deals with the investigation of structural and functional properties of de novo proteins with random sequences, selected and isolated using phage display methods. The minimal cell is the simplest cellular construct which displays living properties, such as self-maintenance, self-reproduction and evolvability. The semi-synthetic approach to minimal cells involves the use of extant genes and proteins in order to build a supramolecular construct based on lipid vesicles. Results and outlooks on these two research lines are shortly discussed, mainly focusing on their relevance to the origin of life studies.

CONSTRUCTION COST PREDICTION USING NEURAL NETWORKS

Directory of Open Access Journals (Sweden)

Smita K Magdum

2017-10-01

Full Text Available Construction cost prediction is important for construction firms to compete and grow in the industry. Accurate construction cost prediction in the early stage of project is important for project feasibility studies and successful completion. There are many factors that affect the cost prediction. This paper presents construction cost prediction as multiple regression model with cost of six materials as independent variables. The objective of this paper is to develop neural networks and multilayer perceptron based model for construction cost prediction. Different models of NN and MLP are developed with varying hidden layer size and hidden nodes. Four artificial neural network models and twelve multilayer perceptron models are compared. MLP and NN give better results than statistical regression method. As compared to NN, MLP works better on training dataset but fails on testing dataset. Five activation functions are tested to identify suitable function for the problem. ‘elu' transfer function gives better results than other transfer function.

Triazole: a unique building block for the construction of functional materials.

Science.gov (United States)

Juríček, Michal; Kouwer, Paul H J; Rowan, Alan E

2011-08-21

Over the past 50 years, numerous roads towards carbon-based materials have been explored, all of them being paved using mainly one functional group as the brick: acetylene. The acetylene group, or the carbon-carbon triple bond, is one of the oldest and simplest functional groups in chemistry, and although not present in any of the naturally occurring carbon allotropes, it is an essential tool to access their synthetic carbon-rich family. In general, two strategies towards the synthesis of π-conjugated carbon-rich structures can be employed: (a) either the acetylene group serves as a building block to access acetylene-derived structures or (b) it serves as a synthetic tool to provide other, usually benzenoid, structures. The recently discovered copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction, however, represents a new powerful alternative: it transforms the acetylene group into a five-membered heteroaromatic 1H-1,2,3-triazole (triazole) ring and this gives rise to new opportunities. Compared with all-carbon aromatic non-functional rings, the triazole ring possesses three nitrogen atoms and, thus, can serve as a ligand to coordinate metals, or as a hydrogen bond acceptor and donor. This Feature Article summarises examples of using the triazole ring to construct conjugation- and/or function-related heteroaromatic materials, such as tuneable multichromophoric covalent ensembles, macrocyclic receptors or responsive foldamers. These recent examples, which open a new sub-field within organic materials, started to appear only few years ago and represent "a few more bricks" on the road to carbon-rich functional materials. This journal is © The Royal Society of Chemistry 2011

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

Science.gov (United States)

Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2013-10-01

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

Treatment of Ligament Constructs with Exercise-conditioned Serum: A Translational Tissue Engineering Model.

Science.gov (United States)

Lee-Barthel, Ann; Baar, Keith; West, Daniel W D

2017-06-11

In vitro experiments are essential to understand biological mechanisms; however, the gap between monolayer tissue culture and human physiology is large, and translation of findings is often poor. Thus, there is ample opportunity for alternative experimental approaches. Here we present an approach in which human cells are isolated from human anterior cruciate ligament tissue remnants, expanded in culture, and used to form engineered ligaments. Exercise alters the biochemical milieu in the blood such that the function of many tissues, organs and bodily processes are improved. In this experiment, ligament construct culture media was supplemented with experimental human serum that has been 'conditioned' by exercise. Thus the intervention is more biologically relevant since an experimental tissue is exposed to the full endogenous biochemical milieu, including binding proteins and adjunct compounds that may be altered in tandem with the activity of an unknown agent of interest. After treatment, engineered ligaments can be analyzed for mechanical function, collagen content, morphology, and cellular biochemistry. Overall, there are four major advantages versus traditional monolayer culture and animal models, of the physiological model of ligament tissue that is presented here. First, ligament constructs are three-dimensional, allowing for mechanical properties (i.e., function) such as ultimate tensile stress, maximal tensile load, and modulus, to be quantified. Second, the enthesis, the interface between boney and sinew elements, can be examined in detail and within functional context. Third, preparing media with post-exercise serum allows for the effects of the exercise-induced biochemical milieu, which is responsible for the wide range of health benefits of exercise, to be investigated in an unbiased manner. Finally, this experimental model advances scientific research in a humane and ethical manner by replacing the use of animals, a core mandate of the National

On the construction of Wannier functions in topological insulators

DEFF Research Database (Denmark)

Cornean, Decebal Horia; Monaco, Domenico

2017-01-01

vanish, we provide an algorithm which constructs a “multi-step logarithm” that is employed to continuously deform the given family into a constant one, identically equal to the identity matrix. This algorithm leads to a constructive procedure to produce the composite Wannier bases mentioned above....

TinkerCell: modular CAD tool for synthetic biology

Science.gov (United States)

Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

2009-01-01

Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. Results An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API). TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at . Conclusion An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled and analyzed computationally. TinkerCell can readily

TinkerCell: modular CAD tool for synthetic biology

Directory of Open Access Journals (Sweden)

Bergmann Frank T

2009-10-01

Full Text Available Abstract Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. Results An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at http://www.tinkercell.com. Conclusion An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled

[Effects of ADAM28 on biological functions of human dental pulp stem cells].

Science.gov (United States)

Zhao, Zheng; Liu, Hong-chen; E, Ling-ling; Wang, Yi; Wang, Dong-sheng

2010-06-01

To investigate the effects of a disintegrin and metalloproteinase 28 (ADAM28) on proliferation, differentiation and apoptosis of human dental pulp stem cells (HDPSCs) and the possible mechanism. Firstly, HDPSCs were isolated and cultured in vitro and identified. ADAM28 eukaryotic expression plasmid was constructed via gene rebuilt technique and transfected into HDPSCs. Then MTT chromatometry, enzyme dynamics and flow cytometry (FCM) techniques were performed to detect the effects of ADAM28 on biological characteristics of HDPSCs. Immunocytochemical and image analysis techniques were used to determine the influence of ADAM28 on HDPSCs expressing dentin sialophosphoprotein (DSPP), bone sialoprotein (BSP) and osteopontin (OPN). Statistical significance was assessed by the Student-Newman-Keuls (SNK) test with SPSS 13.0 software package. ADAM28 eukaryotic plasmid was constructed and transfected into HDPSCs for 48 hours successfully. In ADAM28 eukaryotic plasmid group, proliferation activity and index of HDPSCs were lower than those of pcDNA3.1(+) group and untransfected group significantly.Alkaline phosphatase (ALP) secretion level and percentage of apoptotic cells went up remarkly. Significant difference was detected between eukaryotic plasmid group and other groups (P<0.05). The expression level of DSPP in HDPSCs elevated significantly (P<0.05). ADAM28 could inhibit HDPSCs proliferation, promote ALP secretion activity and DSPP expression in HDPSCs and induce HDPSCs apoptosis significantly.

Construction of human induced pluripotent stem cell-derived oriented bone matrix microstructure by using in vitro engineered anisotropic culture model.

Science.gov (United States)

Ozasa, Ryosuke; Matsugaki, Aira; Isobe, Yoshihiro; Saku, Taro; Yun, Hui-Suk; Nakano, Takayoshi

2018-02-01

Bone tissue has anisotropic microstructure based on collagen/biological apatite orientation, which plays essential roles in the mechanical and biological functions of bone. However, obtaining an appropriate anisotropic microstructure during the bone regeneration process remains a great challenging. A powerful strategy for the control of both differentiation and structural development of newly-formed bone is required in bone tissue engineering, in order to realize functional bone tissue regeneration. In this study, we developed a novel anisotropic culture model by combining human induced pluripotent stem cells (hiPSCs) and artificially-controlled oriented collagen scaffold. The oriented collagen scaffold allowed hiPSCs-derived osteoblast alignment and further construction of anisotropic bone matrix which mimics the bone tissue microstructure. To the best of our knowledge, this is the first report showing the construction of bone mimetic anisotropic bone matrix microstructure from hiPSCs. Moreover, we demonstrated for the first time that the hiPSCs-derived osteoblasts possess a high level of intact functionality to regulate cell alignment. © 2017 The Authors Journal of Biomedical Materials Research Part A Published by Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 360-369, 2018. © 2017 The Authors Journal of Biomedical Materials Research Part A Published by Wiley Periodicals, Inc.

The emerging molecular biology toolbox for the study of long noncoding RNA biology.

Science.gov (United States)

Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

2017-10-01

Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

A Tricky Trait: Applying the Fruits of the "Function Debate" in the Philosophy of Biology to the "Venom Debate" in the Science of Toxinology.

Science.gov (United States)

Jackson, Timothy N W; Fry, Bryan G

2016-09-07

The "function debate" in the philosophy of biology and the "venom debate" in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between "venomous" and "non-venomous" species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.

Perchlorate exposure and association with iron homeostasis and other biological functions among NHANES 2005-2008 subjects

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Perchlorate exposure and association with iron homeostasis and other biological functions among NHANES 2005-2008 subjects Schreinemachers DM, Ghio AJ, Cascio WE, Sobus JR. U.S. EPA, RTP, NC, USA Perchlorate (ClO4-), an environmental pollutant, is a known thyroid toxicant and...

Using Fourier transform IR spectroscopy to analyze biological materials

Science.gov (United States)

Baker, Matthew J; Trevisan, Júlio; Bassan, Paul; Bhargava, Rohit; Butler, Holly J; Dorling, Konrad M; Fielden, Peter R; Fogarty, Simon W; Fullwood, Nigel J; Heys, Kelly A; Hughes, Caryn; Lasch, Peter; Martin-Hirsch, Pierre L; Obinaju, Blessing; Sockalingum, Ganesh D; Sulé-Suso, Josep; Strong, Rebecca J; Walsh, Michael J; Wood, Bayden R; Gardner, Peter; Martin, Francis L

2015-01-01

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing. PMID:24992094

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.

AP1000 construction schedule

International Nuclear Information System (INIS)

Winters, J.W.

2001-01-01

Westinghouse performed this study as part of EPRI interest in advancing the use of computer aided processes to reduce the cost of nuclear power plants. EPRI believed that if one could relate appropriate portions of an advanced light water reactor plant model to activities in its construction sequence, and this relationship could be portrayed visually, then optimization of the construction sequence could be developed as never before. By seeing a 3-D representation of the plant at any point in its construction sequence, more informed decisions can be made on the feasibility or attractiveness of follow on or parallel steps in the sequence. The 3-D representation of construction as a function of time (4-D) could also increase the confidence of potential investors concerning the viability of the schedule and the plant ultimate cost. This study performed by Westinghouse confirmed that it is useful to be able to visualize a plant construction in 3-D as a function of time in order to optimize the sequence of construction activities. (author)

A variational approach to niche construction.

Science.gov (United States)

Constant, Axel; Ramstead, Maxwell J D; Veissière, Samuel P L; Campbell, John O; Friston, Karl J

2018-04-01

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. © 2018 The Authors.

Construction of the Cognitive Dimension of the Scientific Literacy in the Students through the Costa Rican Biological Sciences Olympics

Directory of Open Access Journals (Sweden)

Shirley Camacho-Vargas

2012-08-01

Full Text Available This research recognizes the cognitive contributions to the students participating in the Third Costa Rican Biological Sciences Olympics that will define the advancement and strengthening in the construction of its conceptual dimension in the scientific literacy.  This paper is based, mainly, on qualitative approach techniques (ethnographic design:  case study; however, some data are interpreted through quantitative methodologies (descriptive design with an explanatory and exploratory touch for the analysis of a sample of 54 high school students, finalists in the category A of the Olympics, through the use of tools such as a documentary study and a survey, in July 2009.  The information generated was analyzed using elements of inferential and descriptive statistics, figures and histograms.  It was proved that there is a better cognitive management in the topics assessed, an increase in the students’ academic performance as the tests are applied, a commitment for the academic update supported by the development of several tasks for previous preparation, curriculum contributions unprecedented based on our sample, a consent to optimize student’s knowledge about Biology, which will allow the application of scientific notions to diversify and renew the knowledge, according to what is established in the principles of scientific literacy.

Yeast 2.0-connecting the dots in the construction of the world's first functional synthetic eukaryotic genome.

Science.gov (United States)

Pretorius, I S; Boeke, J D

2018-06-01

Historians of the future may well describe 2018 as the year that the world's first functional synthetic eukaryotic genome became a reality. Without the benefit of hindsight, it might be hard to completely grasp the long-term significance of a breakthrough moment in the history of science like this. The role of synthetic biology in the imminent birth of a budding Saccharomyces cerevisiae yeast cell carrying 16 man-made chromosomes causes the world of science to teeter on the threshold of a future-defining scientific frontier. The genome-engineering tools and technologies currently being developed to produce the ultimate yeast genome will irreversibly connect the dots between our improved understanding of the fundamentals of a complex cell containing its DNA in a specialised nucleus and the application of bioengineered eukaryotes designed for advanced biomanufacturing of beneficial products. By joining up the dots between the findings and learnings from the international Synthetic Yeast Genome project (known as the Yeast 2.0 or Sc2.0 project) and concurrent advancements in biodesign tools and smart data-intensive technologies, a future world powered by a thriving bioeconomy seems realistic. This global project demonstrates how a collaborative network of dot connectors-driven by a tinkerer's indomitable curiosity to understand how things work inside a eukaryotic cell-are using cutting-edge biodesign concepts and synthetic biology tools to advance science and to positively frame human futures (i.e. improved quality of life) in a planetary context (i.e. a sustainable environment). Explorations such as this have a rich history of resulting in unexpected discoveries and unanticipated applications for the benefit of people and planet. However, we must learn from past explorations into controversial futuristic sciences and ensure that researchers at the forefront of an emerging science such as synthetic biology remain connected to all stakeholders' concerns about the

An Inexpensive Biophysics Laboratory Apparatus for Acquiring Pulmonary Function Data with Clinical Applications

Science.gov (United States)

Harkay, Gregory

2001-11-01

Interest on the part of the Physics Department at KSC in developing a computer interfaced lab with appeal to biology majors and a need to perform a clinical pulmonological study to fulfill a biology requirement led to the author's undergraduate research project in which a recording spirometer (typical cost: $15K) was constructed from readily available materials and a typical undergraduate lab computer interface. Simple components, including a basic photogate circuit, CPU fan, and PVC couplings were used to construct an instrument for measuring flow rates as a function of time. Pasco software was used to build an experiment in which data was collected and integration performed such that one could obtain accurate values for FEV1 (forced expiratory volume for one second) and FVC (forced vital capacity) and their ratio for a large sample of subjects. Results were compared to published norms and subjects with impaired respiratory mechanisms identified. This laboratory exercise is one with which biology students can clearly identify and would be a robust addition to the repertoire for a HS or college physics or biology teaching laboratory.

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

Science.gov (United States)

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

2016-02-01

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

From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

Directory of Open Access Journals (Sweden)

Ward Alister C

2007-10-01

Full Text Available Abstract Background Our understanding of the importance of transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and the consistency of transcriptional stress responses to different types of environmental stress. In this study, we used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. Results We identified a series of gene functions that were involved in all stress responses examined here, suggesting some common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes; the responses of individual genes varied greatly across different stress types. In response to heat exposure over five days, a total of 324 gene loci were differentially expressed. Many heat-responsive genes had functions associated with protein turnover, metabolism, and the response to oxidative stress. We were also able to identify groups of co-regulated genes, the genes within which shared similar functions. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. We have shown that different types of environmental stress induce expression changes in genes with similar gene functions, but that the responses of individual genes vary between stress types. The functions of heat

FMFinder: A Functional Module Detector for PPI Networks

Directory of Open Access Journals (Sweden)

M. Modi

2017-10-01

Full Text Available Bioinformatics is an integrated area of data mining, statistics and computational biology. Protein-Protein Interaction (PPI network is the most important biological process in living beings. In this network a protein module interacts with another module and so on, forming a large network of proteins. The same set of proteins which takes part in the organic courses of biological actions is detected through the Function Module Detection method. Clustering process when applied in PPI networks is made of proteins which are part of a larger communication network. As a result of this, we can define the limits for module detection as well as clarify the construction of a PPI network. For understating the bio-mechanism of various living beings, a detailed study of FMFinder detection by clustering process is called for.

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

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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

Function-Based Algorithms for Biological Sequences

Science.gov (United States)

Mohanty, Pragyan Sheela P.

2015-01-01

Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

DNA recognition by synthetic constructs.

Science.gov (United States)

Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L

2011-09-05

The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

characteristics, have allowed us to better understand the interactions between the benthic fauna and their environment at a functional level. We present the initial findings of work conducted under the auspices of the EU-funded project ‘BENTHIS’ which aims to improve our understanding of the impacts of trawling...... 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...

Nucleobases, nucleosides, and nucleotides: versatile biomolecules for generating functional nanomaterials.

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Pu, Fang; Ren, Jinsong; Qu, Xiaogang

2018-02-21

The incorporation of biomolecules into nanomaterials generates functional nanosystems with novel and advanced properties, presenting great potential for applications in various fields. Nucleobases, nucleosides and nucleotides, as building blocks of nucleic acids and biological coenzymes, constitute necessary components of the foundation of life. In recent years, as versatile biomolecules for the construction or regulation of functional nanomaterials, they have stimulated interest in researchers, due to their unique properties such as structural diversity, multiplex binding sites, self-assembly ability, stability, biocompatibility, and chirality. In this review, strategies for the synthesis of nanomaterials and the regulation of their morphologies and functions using nucleobases, nucleosides, and nucleotides as building blocks, templates or modulators are summarized alongside selected applications. The diverse applications range from sensing, bioimaging, and drug delivery to mimicking light-harvesting antenna, the construction of logic gates, and beyond. Furthermore, some perspectives and challenges in this emerging field are proposed. This review is directed toward the broader scientific community interested in biomolecule-based functional nanomaterials.

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

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Schmitz, L.

2016-01-01

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

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

Science.gov (United States)

Price, S A; Schmitz, L

2016-04-05

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

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.

The role of ontologies in biological and biomedical research: a functional perspective

KAUST Repository

Hoehndorf, Robert; Schofield, P. N.; Gkoutos, G. V.

2015-01-01

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.

Bio-templated CdSe quantum dots green synthesis in the functional protein, lysozyme, and biological activity investigation

International Nuclear Information System (INIS)

Wang, Qisui; Li, Song; Liu, Peng; Min, Xinmin

2012-01-01

Bifunctional fluorescence (CdSe Quantum Dots) – protein (Lysozyme) nanocomposites were synthesized at room temperature by a protein-directed, solution-phase, green-synthetic method. Fluorescence (FL) and absorption spectra showed that CdSe QDs were prepared successfully with Lyz. The average particle size and crystalline structure of QDs were investigated by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD), respectively. With attenuated total reflection-fourier transform infrared (ATR-FTIR) spectra and thermogravimetric (TG) analysis, it was confirmed that there is interaction between QDs and amide I, amide II groups in Lyz. FL polarization was measured and FL imaging was done to monitor whether QDs could be responsible for possible changes in the conformation and activity of Lyz. Interestingly, the results showed Lyz still retain the biological activity after formation of QDs, but the secondary structure of the Lyz was changed. And the advantage of this synthesis method is producing excellent fluorescent QDs with specifically biological function. -- Highlights: ► Lysozyme-directed green synthesis of CdSe quantum dots. ► Lysozyme still retain the biological activity after formation of CdSe. ► The method is the production of fluorescent QDs with highly specific and functions.

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

Science.gov (United States)

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

2012-12-01

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

From Extremophiles to Star Trek, The Use of Synthetic Biology in Astrobiology

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Rothschild, Lynn J.; Fujishima, Kosuke; Lima, Ivan Paulino; Gentry, Diana; Phan, Samson; Navarette, Jesica; Palmer, Jesse; Burnier, Andre

2012-01-01

Synthetic biology – the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes – has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as bio-mining, human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

Life cycle performances of log wood applied for soil bioengineering constructions

Science.gov (United States)

Kalny, Gerda; Strauss-Sieberth, Alexandra; Strauss, Alfred; Rauch, Hans Peter

2016-04-01

Nowadays there is a high demand on engineering solutions considering not only technical aspects but also ecological and aesthetic values. Soil bioengineering is a construction technique that uses biological components for hydraulic and civil engineering solutions. Soil bioengineering solutions are based on the application of living plants and other auxiliary materials including among others log wood. This kind of construction material supports the soil bioengineering system as long as the plants as living construction material overtake the stability function. Therefore it is important to know about the durability and the degradation process of the wooden logs to retain the integral performance of a soil bio engineering system. These aspects will be considered within the framework of the interdisciplinary research project „ELWIRA Plants, wood, steel and concrete - life cycle performances as construction materials". Therefore field investigations on soil bioengineering construction material, specifically European Larch wood logs, of different soil bioengineering structures at the river Wien have been conducted. The drilling resistance as a parameter for particular material characteristics of selected logs was measured and analysed. The drilling resistance was measured with a Rinntech Resistograph instrument at different positions of the wooden logs, all surrounded with three different backfills: Fully surrounded with air, with earth contact on one side and near the water surface in wet-dry conditions. The age of the used logs ranges from one year old up to 20 year old. Results show progress of the drilling resistance throughout the whole cross section as an indicator to assess soil bioengineering construction material. Logs surrounded by air showed a higher drilling resistance than logs with earth contact and the ones exposed to wet-dry conditions. Hence the functional capability of wooden logs were analysed and discussed in terms of different levels of degradation

Establishing Early Functional Perfusion and Structure in Tissue Engineered Cardiac Constructs.

Science.gov (United States)

Wang, Bo; Patnaik, Sourav S; Brazile, Bryn; Butler, J Ryan; Claude, Andrew; Zhang, Ge; Guan, Jianjun; Hong, Yi; Liao, Jun

2015-01-01

Myocardial infarction (MI) causes massive heart muscle death and remains a leading cause of death in the world. Cardiac tissue engineering aims to replace the infarcted tissues with functional engineered heart muscles or revitalize the infarcted heart by delivering cells, bioactive factors, and/or biomaterials. One major challenge of cardiac tissue engineering and regeneration is the establishment of functional perfusion and structure to achieve timely angiogenesis and effective vascularization, which are essential to the survival of thick implants and the integration of repaired tissue with host heart. In this paper, we review four major approaches to promoting angiogenesis and vascularization in cardiac tissue engineering and regeneration: delivery of pro-angiogenic factors/molecules, direct cell implantation/cell sheet grafting, fabrication of prevascularized cardiac constructs, and the use of bioreactors to promote angiogenesis and vascularization. We further provide a detailed review and discussion on the early perfusion design in nature-derived biomaterials, synthetic biodegradable polymers, tissue-derived acellular scaffolds/whole hearts, and hydrogel derived from extracellular matrix. A better understanding of the current approaches and their advantages, limitations, and hurdles could be useful for developing better materials for future clinical applications.

Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments

Directory of Open Access Journals (Sweden)

de Marco Ario

2008-07-01

Full Text Available Abstract Structural characterization of proteins used in biological experiments is largely neglected. In most publications, the information available is totally insufficient to judge the functionality of the proteins used and, therefore, the significance of identified protein-protein interactions (was the interaction specific or due to unspecific binding of misfolded protein regions? or reliability of kinetic and thermodynamic data (how much protein was in its native form?. As a consequence, the results of single experiments might not only become questionable, but the whole reliability of systems biology, built on these fundaments, would be weakened. The introduction of Minimal Information concerning purified proteins to add as metadata to the main body of a manuscript would render straightforward the assessment of their functional and structural qualities and, consequently, of results obtained using these proteins. Furthermore, accepted standards for protein annotation would simplify data comparison and exchange. This article has been envisaged as a proposal for aggregating scientists who share the opinion that the scientific community needs a platform for Minimum Information for Protein Functionality Evaluation (MIPFE.

Validation of systems biology derived molecular markers of renal donor organ status associated with long term allograft function.

Science.gov (United States)

Perco, Paul; Heinzel, Andreas; Leierer, Johannes; Schneeberger, Stefan; Bösmüller, Claudia; Oberhuber, Rupert; Wagner, Silvia; Engler, Franziska; Mayer, Gert

2018-05-03

Donor organ quality affects long term outcome after renal transplantation. A variety of prognostic molecular markers is available, yet their validity often remains undetermined. A network-based molecular model reflecting donor kidney status based on transcriptomics data and molecular features reported in scientific literature to be associated with chronic allograft nephropathy was created. Significantly enriched biological processes were identified and representative markers were selected. An independent kidney pre-implantation transcriptomics dataset of 76 organs was used to predict estimated glomerular filtration rate (eGFR) values twelve months after transplantation using available clinical data and marker expression values. The best-performing regression model solely based on the clinical parameters donor age, donor gender, and recipient gender explained 17% of variance in post-transplant eGFR values. The five molecular markers EGF, CD2BP2, RALBP1, SF3B1, and DDX19B representing key molecular processes of the constructed renal donor organ status molecular model in addition to the clinical parameters significantly improved model performance (p-value = 0.0007) explaining around 33% of the variability of eGFR values twelve months after transplantation. Collectively, molecular markers reflecting donor organ status significantly add to prediction of post-transplant renal function when added to the clinical parameters donor age and gender.

Predictable grammatical constructions

DEFF Research Database (Denmark)

Lucas, Sandra

2015-01-01

My aim in this paper is to provide evidence from diachronic linguistics for the view that some predictable units are entrenched in grammar and consequently in human cognition, in a way that makes them functionally and structurally equal to nonpredictable grammatical units, suggesting that these p......My aim in this paper is to provide evidence from diachronic linguistics for the view that some predictable units are entrenched in grammar and consequently in human cognition, in a way that makes them functionally and structurally equal to nonpredictable grammatical units, suggesting...... that these predictable units should be considered grammatical constructions on a par with the nonpredictable constructions. Frequency has usually been seen as the only possible argument speaking in favor of viewing some formally and semantically fully predictable units as grammatical constructions. However, this paper...... semantically and formally predictable. Despite this difference, [méllo INF], like the other future periphrases, seems to be highly entrenched in the cognition (and grammar) of Early Medieval Greek language users, and consequently a grammatical construction. The syntactic evidence speaking in favor of [méllo...

FY 1999 report on the results on analysis of protein functions; 1999 nendo tanpakushitsu kino kaiseki seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-03-01

This project is aimed at construction of the intellectual infrastructures for biotechnologies, in order to accelerate development of the Japanese technologies and activate their application to industries. Described herein are the FY 1999 results. These infrastructures are for functional analysis of protein which will be one of the key issues in genome analysis, and collection and analysis of biological information. This project includes a total of 9 research and development themes for four research categories: frequency analysis of gene expression (development of the gene expression profile database system for functional analysis of human genome, and analysis of the gene expression and protein functions by the ECA chip technology), function analysis by the biological model (high-performance analysis by the bio-project, database system for drug metabolizing enzymes, analysis of gene functions using mutant mice, and simple genome function analysis of murine individuals using the RNAi effect), protein expression (function validation of unknown human genes based on the useful biological model, and protein function analysis using multi-purpose destination vectors), and protein function prediction by the information science method. (NEDO)

Construction of U-gauge Green's functions of gauge theories with spontaneous symmetry breaking and Slavnov identities

International Nuclear Information System (INIS)

Flume, R.

1978-01-01

The unitary (U) gauge Green's functions of the U(1) and SU(2) Higgs-Kibble models are constructed applying a renormalized point transformation and a non-local gauge changing transformation to a manifestly renormalizable (R gauge) version of the respective theory. It is shown that the cancellation mechanism known as 'tree graph unitarity' rendering in tree graph approximation a smooth high energy behaviour of the U gauge Green's functions on mass shell can in a natural way be extended to all orders of perturbation theory. The conditions imposed by this 'generalized tree graph unitarity' on the renormalization programme are shown to be equivalent with the requirement of renormalized Slavnov identities for the R gauge Green's functions

BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.

Science.gov (United States)

Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; van der Lek, Adrian; Mevissen, Theo; Fluck, Juliane

2016-01-01

Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biological networks, represented in Biological Expression Language (BEL), as training and test data. BEL is an advanced knowledge representation format which has been designed to be both human readable and machine processable. The specific goal of track 4 was to evaluate text mining systems capable of automatically constructing BEL statements from given evidence text, and of retrieving evidence text for given BEL statements. Given the complexity of the task, we designed an evaluation methodology which gives credit to partially correct statements. We identified various levels of information expressed by BEL statements, such as entities, functions, relations, and introduced an evaluation framework which rewards systems capable of delivering useful BEL fragments at each of these levels. The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text. © The Author(s) 2016. Published by Oxford University Press.

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Predicting Protein Function via Semantic Integration of Multiple Networks.

Science.gov (United States)

Yu, Guoxian; Fu, Guangyuan; Wang, Jun; Zhu, Hailong

2016-01-01

Determining the biological functions of proteins is one of the key challenges in the post-genomic era. The rapidly accumulated large volumes of proteomic and genomic data drives to develop computational models for automatically predicting protein function in large scale. Recent approaches focus on integrating multiple heterogeneous data sources and they often get better results than methods that use single data source alone. In this paper, we investigate how to integrate multiple biological data sources with the biological knowledge, i.e., Gene Ontology (GO), for protein function prediction. We propose a method, called SimNet, to Semantically integrate multiple functional association Networks derived from heterogenous data sources. SimNet firstly utilizes GO annotations of proteins to capture the semantic similarity between proteins and introduces a semantic kernel based on the similarity. Next, SimNet constructs a composite network, obtained as a weighted summation of individual networks, and aligns the network with the kernel to get the weights assigned to individual networks. Then, it applies a network-based classifier on the composite network to predict protein function. Experiment results on heterogenous proteomic data sources of Yeast, Human, Mouse, and Fly show that, SimNet not only achieves better (or comparable) results than other related competitive approaches, but also takes much less time. The Matlab codes of SimNet are available at https://sites.google.com/site/guoxian85/simnet.

Variations in the Biological Functions of HIV-1 Clade C Envelope in a SHIV-Infected Rhesus Macaque during Disease Progression.

Directory of Open Access Journals (Sweden)

For Yue Tso

Full Text Available A better understanding of how the biological functions of the HIV-1 envelope (Env changes during disease progression may aid the design of an efficacious anti-HIV-1 vaccine. Although studies from patient had provided some insights on this issue, the differences in the study cohorts and methodology had make it difficult to reach a consensus of the variations in the HIV-1 Env functions during disease progression. To this end, an animal model that can be infected under controlled environment and reflect the disease course of HIV-1 infection in human will be beneficial. Such an animal model was previously demonstrated by the infection of macaque with SHIV, expressing HIV-1 clade C Env V1-V5 region. By using this model, we examined the changes in biological functions of Env in the infected animal over the entire disease course. Our data showed an increase in the neutralization resistance phenotype over time and coincided with the decrease in the net charges of the V1-V5 region. Infection of PBMC with provirus expressing various Env clones, isolated from the infected animal over time, showed a surprisingly better replicative fitness for viruses expressing the Env from early time point. Biotinylation and ELISA data also indicated a decrease of cell-surface-associated Env and virion-associated gp120 content with disease progression. This decrease did not affect the CD4-binding capability of Env, but were positively correlated with the decrease of Env fusion ability. Interestingly, some of these changes in biological functions reverted to the pre-AIDS level during advance AIDS. These data suggested a dynamic relationship between the Env V1-V5 region with the host immune pressure. The observed changes of biological functions in this setting might reflect and predict those occurring during natural disease progression in human.

Beyond Design: The Importance of Construction and Post-Construction Phases in Green Developments

Directory of Open Access Journals (Sweden)

Mark Hostetler

2010-04-01

Full Text Available Green developments are becoming a popular land use planning concept that attempts to accommodate growth while minimizing impacts on natural resources. Various policies encourage conservation designs that usually translate into the clustering of homes and the conservation of some percentage of open space. However, the success of a design is determined by what happens during the construction and post-construction phases of a subdivision project. These two phases are often ignored in land use planning and given only minimal attention by built environment professionals. As a result, green developments may not be functioning as originally intended. This essay discusses the importance of construction and post-construction and a way forward to create functional, sustainable communities. Construction activities and decisions, such as impacts from earthwork machines, improper protection of conserved open spaces and trees, the choice of plants used for yards and common areas, and the storage of construction material all can lead to severe impacts on natural areas both within and surrounding a development site. During post-construction, a variety of improper management practices by homeowners can compromise the sustainability of a development. Developers and associated environmental consultant teams could implement approaches that would engage contractors and residents, such as environmental construction covenants and the installment of a neighborhood, environmental education program. To increase the adoption of relevant construction and post-construction practices, appropriate policies need to be created. However, the shift will only occur once the planning and built environment community acknowledges that design is only the first step towards sustainability. Academic design studios and continuing education courses can help with this culture shift by including construction and post-construction considerations within their curriculum.

The development of peptide-based interfacial biomaterials for generating biological functionality on the surface of bioinert materials.

Science.gov (United States)

Meyers, Steven R; Khoo, Xiaojuan; Huang, Xin; Walsh, Elisabeth B; Grinstaff, Mark W; Kenan, Daniel J

2009-01-01

Biomaterials used in implants have traditionally been selected based on their mechanical properties, chemical stability, and biocompatibility. However, the durability and clinical efficacy of implantable biomedical devices remain limited in part due to the absence of appropriate biological interactions at the implant interface and the lack of integration into adjacent tissues. Herein, we describe a robust peptide-based coating technology capable of modifying the surface of existing biomaterials and medical devices through the non-covalent binding of modular biofunctional peptides. These peptides contain at least one material binding sequence and at least one biologically active sequence and thus are termed, "Interfacial Biomaterials" (IFBMs). IFBMs can simultaneously bind the biomaterial surface while endowing it with desired biological functionalities at the interface between the material and biological realms. We demonstrate the capabilities of model IFBMs to convert native polystyrene, a bioinert surface, into a bioactive surface that can support a range of cell activities. We further distinguish between simple cell attachment with insufficient integrin interactions, which in some cases can adversely impact downstream biology, versus biologically appropriate adhesion, cell spreading, and cell survival mediated by IFBMs. Moreover, we show that we can use the coating technology to create spatially resolved patterns of fluorophores and cells on substrates and that these patterns retain their borders in culture.

On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

Science.gov (United States)

Gomez-Ramirez, Jaime; Sanz, Ricardo

2013-09-01

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

VE of construction industry

Energy Technology Data Exchange (ETDEWEB)

NONE

1987-10-15

This book gives descriptions of basic of VE of construction industry including doing away with mannerism, necessity of cost reduction, management method of cost reduction, thinking of idea, target of VE, starting VE activity, technical method of VE of construction industry such as thinking of idea with brainstorming, function trade method, new brainstorming, MM method, morphology analysis and lateral thinking, cases of VE of construction industry.

VE of construction industry

International Nuclear Information System (INIS)

1987-10-01

This book gives descriptions of basic of VE of construction industry including doing away with mannerism, necessity of cost reduction, management method of cost reduction, thinking of idea, target of VE, starting VE activity, technical method of VE of construction industry such as thinking of idea with brainstorming, function trade method, new brainstorming, MM method, morphology analysis and lateral thinking, cases of VE of construction industry.

Construction of Anterior Hemi-Corneal Equivalents Using Nontransfected Human Corneal Cells and Transplantation in Dog Models.

Science.gov (United States)

Xu, Bin; Song, Zhan; Fan, Tingjun

2017-11-01

Tissue-engineered human anterior hemi-cornea (TE-aHC) is a promising equivalent for treating anterior lamellar keratopathy to surmount the severe shortage of donated corneas. This study was intended to construct a functional TE-aHC with nontransfected human corneal stromal (ntHCS) and epithelial (ntHCEP) cells using acellular porcine corneal stromata (aPCS) as a carrier scaffold, and evaluate its biological functions in a dog model. To construct a TE-aHC, ntHCS cells were injected into an aPCS scaffold and cultured for 3 days; then, ntHCEP cells were inoculated onto the Bowman's membrane of the scaffold and cultured for 5 days under air-liquid interface condition. After its morphology and histological structure were characterized, the constructed TE-aHC was transplanted into dog eyes via lamellar keratoplasty. The corneal transparency, thickness, intraocular pressure, epithelial integrity, and corneal regeneration were monitored in vivo, and the histological structure and histochemical property were examined ex vivo 360 days after surgery, respectively. The results showed that the constructed TE-aHC was highly transparent and composed of a corneal epithelium of 7-8 layer ntHCEP cells and a corneal stroma of regularly aligned collagen fibers and well-preserved glycosaminoglycans with sparsely distributed ntHCS cells, mimicking a normal anterior hemi-cornea (aHC). Moreover, both ntHCEP and ntHCS cells maintained positive expression of their marker and functional proteins. After transplantation into dog eyes, the constructed TE-aHC acted naturally in terms of morphology, structure and inherent property, and functioned well in maintaining corneal clarity, thickness, normal histological structure, and composition in dog models by reconstructing a normal aHC, which could be used as a promising aHC equivalent in corneal regenerative medicine and aHC disorder therapy. © 2017 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Synthetic biological networks

International Nuclear Information System (INIS)

Archer, Eric; Süel, Gürol M

2013-01-01

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

Multiscale modeling of emergent materials: biological and soft matter

DEFF Research Database (Denmark)

Murtola, Teemu; Bunker, Alex; Vattulainen, Ilpo

2009-01-01

In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the c......In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed...

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

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

2017-06-21

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

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Science.gov (United States)

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology

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Blount, Benjamin A.; Weenink, Tim; Vasylechko, Serge; Ellis, Tom

2012-01-01

Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex “multi-wire” logic functions. PMID:22442681

Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology.

Science.gov (United States)

Blount, Benjamin A; Weenink, Tim; Vasylechko, Serge; Ellis, Tom

2012-01-01

Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex "multi-wire" logic functions.

Precision control of recombinant gene transcription for CHO cell synthetic biology.

Science.gov (United States)

Brown, Adam J; James, David C

2016-01-01

The next generation of mammalian cell factories for biopharmaceutical production will be genetically engineered to possess both generic and product-specific manufacturing capabilities that may not exist naturally. Introduction of entirely new combinations of synthetic functions (e.g. novel metabolic or stress-response pathways), and retro-engineering of existing functional cell modules will drive disruptive change in cellular manufacturing performance. However, before we can apply the core concepts underpinning synthetic biology (design, build, test) to CHO cell engineering we must first develop practical and robust enabling technologies. Fundamentally, we will require the ability to precisely control the relative stoichiometry of numerous functional components we simultaneously introduce into the host cell factory. In this review we discuss how this can be achieved by design of engineered promoters that enable concerted control of recombinant gene transcription. We describe the specific mechanisms of transcriptional regulation that affect promoter function during bioproduction processes, and detail the highly-specific promoter design criteria that are required in the context of CHO cell engineering. The relative applicability of diverse promoter development strategies are discussed, including re-engineering of natural sequences, design of synthetic transcription factor-based systems, and construction of synthetic promoters. This review highlights the potential of promoter engineering to achieve precision transcriptional control for CHO cell synthetic biology. Copyright © 2015. Published by Elsevier Inc.

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.

Some problems of NPP construction base improvement

International Nuclear Information System (INIS)

Movchan, S.V.

1984-01-01

NPP construction bases are characterized by high cost of construction and large area. Duration of base construction makes up 3-4 years, labour contents for their erection constitute 600-900 thousand man-days. Delays in organizing functional base services essentially decelerate construction rates of the main NPP buildings. Maximum joining of separate buildings by their functional assignment and structural peculiarities, wide application of container buildings, partial utilization of permanent buildings of production centre for construction needs; transition to new organizational form of construction based on industrial production of buildings; production of volumetric structural-technological cells with mounted equipment manufactured at specialized plants, mounting NPP components with stock produced cells, consideration of the problem of large power centre creation are necessary for reduction of construction centres, area reduction of cost and duration of their construction

Construction of fast experimental reactor 'Joyo' from start of construction to criticality

International Nuclear Information System (INIS)

Sakata, Hajime

1977-01-01

The fast experimental reactor ''Joyo'' is a sodium-cooled, fast neutron reactor using mixed oxide of uranium and plutonium, the first in Japan. The purposes of its construction are to experience and solve the various technical problems expected in the constructions of the prototype reactor ''Monju'' and future practical reactors, and to use as the irradiation facility for developing the fuel and material for fast breeder reactors in Japan after the completion. The construction finished by the end of 1974, and the synthetic functional test was carried out for about two years thereafter. The whole installation was handed over to PNC on March 8, 1977. The reactor attained the criticality on April 24, 1977. The outline of the construction works is described. ''Guidance to the structural design of sodium machinery for Joyo'' was compiled, and the analysis was made according to it. Moreover, various inspection standards regarding welding, electrical machinery, fuel and others were made. The revision of the design for improving the safety and performance was made during the construction at all times. The synthetic functional test was carried out for about two years on 266 items, and subsequently, the criticality test was completed satisfactorily. (Kako, I.)

Understanding the Biological Roles of Pectins in Plants through Physiological and Functional Characterizations of Plant and Fungal Mutants

DEFF Research Database (Denmark)

Stranne, Maria

The plant cell wall is a dynamic structure and it is involved in regulating a number of physiological features of plants such as physical strength, growth, cell differentiation, intercellular communication, water movement and defense responses. Pectins constitute a major class of plant cell wall...... polysaccharides and consist of backbones rich in galacturonic acids, which are decorated with a range of functional groups including acetyl esters and arabinan sidechains. Although much effort has been made to uncover biological functions of pectins in plants and remarkable progresses have taken place, many...... aspects remain elusive. Studies described in this thesis aimed at gaining new insights into the biological roles of pectin acetylation and arabinosylation in the model plant Arabidopsis thaliana. The thesis consists of four chapters: physiological characterization of cell wall mutants affected in cell...

Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design.

Science.gov (United States)

Hu, Chelsea Y; Takahashi, Melissa K; Zhang, Yan; Lucks, Julius B

2018-05-22

RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal. Here we use cell-free transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR constructs. Using parameter sensitivity analysis, we design a simple set of experiments that allow us to accurately predict NAR function in TX-TL. We transfer successful network designs into Escherichia coli and show that our sRNA transcriptional network reduces both network response time and steady-state gene expression. This work broadens our ability to construct increasingly sophisticated RNA genetic networks with predictable function.

Fabrication, Characterization, and Biological Activity of Avermectin Nano-delivery Systems with Different Particle Sizes

Science.gov (United States)

Wang, Anqi; Wang, Yan; Sun, Changjiao; Wang, Chunxin; Cui, Bo; Zhao, Xiang; Zeng, Zhanghua; Yao, Junwei; Yang, Dongsheng; Liu, Guoqiang; Cui, Haixin

2018-01-01

Nano-delivery systems for the active ingredients of pesticides can improve the utilization rates of pesticides and prolong their control effects. This is due to the nanocarrier envelope and controlled release function. However, particles containing active ingredients in controlled release pesticide formulations are generally large and have wide size distributions. There have been limited studies about the effect of particle size on the controlled release properties and biological activities of pesticide delivery systems. In the current study, avermectin (Av) nano-delivery systems were constructed with different particle sizes and their performances were evaluated. The Av release rate in the nano-delivery system could be effectively controlled by changing the particle size. The biological activity increased with decreasing particle size. These results suggest that Av nano-delivery systems can significantly improve the controllable release, photostability, and biological activity, which will improve efficiency and reduce pesticide residues.

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

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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.

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.

Use of expression constructs to dissect the functional domains of the CHS/beige protein: identification of multiple phenotypes.

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Ward, Diane McVey; Shiflett, Shelly L; Huynh, Dinh; Vaughn, Michael B; Prestwich, Glenn; Kaplan, Jerry

2003-06-01

The Chediak-Higashi Syndrome (CHS) and the orthologous murine disorder beige are characterized at the cellular level by the presence of giant lysosomes. The CHS1/Beige protein is a 3787 amino acid protein of unknown function. To determine functional domains of the CHS1/Beige protein, we generated truncated constructs of the gene/protein. These truncated proteins were transiently expressed in Cos-7 or HeLa cells and their effect on membrane trafficking was examined. Beige is apparently a cytosolic protein, as are most transiently expressed truncated Beige constructs. Expression of the Beige construct FM (amino acids 1-2037) in wild-type cells led to enlarged lysosomes. Similarly, expression of a 5.5-kb region (amino acids 2035-3787) of the carboxyl terminal of Beige (22B) also resulted in enlarged lysosomes. Expression of FM solely affected lysosome size, whereas expression of 22B led to alterations in lysosome size, changes in the Golgi and eventually cell death. The two constructs could be used to further dissect phenotypes resulting from loss of the Beige protein. CHS or beigej fibroblasts show an absence of nuclear staining using a monoclonal antibody directed against phosphatidylinositol 4,5 bisphosphate [PtdIns(4,5) P2]. Transformation of beige j fibroblasts with a YAC containing the full-length Beige gene resulted in the normalization of lysosome size and nuclear PtdIns(4,5)P2 staining. Expression of the carboxyl dominant negative construct 22B led to loss of nuclear PtdIns(4,5)P2 staining. Expression of the FM dominant negative clone did not alter nuclear PtdIns(4,5) P2 localization. These results suggest that the Beige protein interacts with at least two different partners and that the Beige protein affects cellular events, such as nuclear PtdIns(4,5)P2 localization, in addition to lysosome size.

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.

Optimization of polysaccharides extraction from watermelon rinds: Structure, functional and biological activities.

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Romdhane, Molka Ben; Haddar, Anissa; Ghazala, Imen; Jeddou, Khawla Ben; Helbert, Claire Boisset; Ellouz-Chaabouni, Semia

2017-02-01

In the present work, optimization of hot water extraction, structural characteristics, functional properties, and biological activities of polysaccharides extracted from watermelon rinds (WMRP) were investigated. The physicochemical characteristics and the monosaccharide composition of these polysaccharides were then determined using chemical composition analysis, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and gas chromatography-flame ionization detection (GC-FID). SEM images showed that extracted polysaccharides had a rough surface with many cavities. GC-FID results proved that galactose was the dominant sugar in the extracted polysaccharides, followed by arabinose, glucose, galacturonic acid, rhamnose, mannose, xylose and traces of glucuronic acid. The findings revealed that WMRP displayed excellent antihypertensive and antioxidant activities. Those polysaccharides had also a protection effect against hydroxyl radical-induced DNA damage. Functional properties of extracted polysaccharides were also evaluated. WMRP showed good interfacial dose-dependent proprieties. Overall, the results suggested that WMRP presents a promising natural source of antioxidants and antihypertensive agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions

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Kohn, Kathryn P.; Underwood, Sonia M.; Cooper, Melanie M.

2018-01-01

While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively.…

Carcinogenesis: alterations in reciprocal interactions of normal functional structure of biologic systems.

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