WorldWideScience

Sample records for biological function analyses

  1. Biological aerosol warner and analyser

    Science.gov (United States)

    Schlemmer, Harry; Kürbitz, Gunther; Miethe, Peter; Spieweck, Michael

    2006-05-01

    The development of an integrated sensor device BiSAM (Biological Sampling and Analysing Module) is presented which is designed for rapid detection of aerosol or dust particles potentially loaded with biological warfare agents. All functional steps from aerosol collection via immuno analysis to display of results are fully automated. The core component of the sensor device is an ultra sensitive rapid analyser PBA (Portable Benchtop Analyser) based on a 3 dimensional immuno filtration column of large internal area, Poly HRP marker technology and kinetic optical detection. High sensitivity despite of the short measuring time, high chemical stability of the micro column and robustness against interferents make the PBA an ideal tool for fielded sensor devices. It is especially favourable to combine the PBA with a bio collector because virtually no sample preparation is necessary. Overall, the BiSAM device is capable to detect and identify living micro organisms (bacteria, spores, viruses) as well as toxins in a measuring cycle of typically half an hour duration. In each batch up to 12 different tests can be run in parallel together with positive and negative controls to keep the false alarm rate low.

  2. Preparation of biological samples for SIMS analyses

    International Nuclear Information System (INIS)

    Full text: For the first time at ANSTO, a program of SIMS analysis of biological samples was undertaken. This presentation will discuss how the wide variety of samples were prepared, and the methods used to gain useful information from SIMS analysis. Lack of matrix-matched standards made quantification difficult, but the strength of SIMS lies in the ability to detect a wide range of stable isotopes with good spatial resolution. This makes the technique suitable for studying organisms that archive signature elements in their structure. Samples such as bivalve shells and crocodile osteoderms were vacuum-impregnated in resin to a size suitable for the SIMS sample holder. Polishing was followed by a sputter coating with gold to alleviate charging of the sample during SIMS analysis. Some samples were introduced directly on the sample holder, either stuck to a glass slide or simply held in place with spring and backing plate. The only treatment in this case was gold coating and degassing in a vacuum pumping station. The porous nature of materials such as leaves and stromatolites requires a period of time under vacuum to remove gases which could interfere with the ultra high vacuum required for SIMS analysis. A calcite standard was used for comparison of oxygen isotopic ratios, but the only matrix-matched standard was available for metal analysis of coral skeletons. Otherwise, the calcium content of the material was assumed to be uniform and acted as an internal standard from which isotopic ratios of other elements could be determined. SIMS analysis of biological samples demonstrated that some matrices could reveal an archive of pollution histories. These samples require matrix-matched standards if the trends observed from analyses are to be quantified

  3. Functions in Biological Kind Classification

    Science.gov (United States)

    Lombrozo, Tania; Rehder, Bob

    2012-01-01

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

  4. The relativity of biological function.

    Science.gov (United States)

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

    2015-12-01

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

  5. Functional Analyses and Treatment of Precursor Behavior

    OpenAIRE

    Najdowski, Adel C; Wallace, Michele D; Ellsworth, Carrie L; MacAleese, Alicia N; Cleveland, Jackie M

    2008-01-01

    Functional analysis has been demonstrated to be an effective method to identify environmental variables that maintain problem behavior. However, there are cases when conducting functional analyses of severe problem behavior may be contraindicated. The current study applied functional analysis procedures to a class of behavior that preceded severe problem behavior (precursor behavior) and evaluated treatments based on the outcomes of the functional analyses of precursor behavior. Responding fo...

  6. Analyses of environmental and biological specimens by PIXE

    International Nuclear Information System (INIS)

    Analyses of environmental and biological specimens were carried out by PIXE. The yield of potassium (Kα line) is used as a standard for other elements. Environmental and biological samples studied here are standard polished glass beads (30/60 mesh), soil dust generated by studded tires, materials accumulated in a water supplying pipe, perfumes of China and Japan, ash, asbestos-dark, briquettes, synovial fluids, sex skin of a chimpanzee and so on. Concentrations of K, Ca, Fe and Zn in these biological samples are noticeable. (author)

  7. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Ihekwaba, Adoha

    2007-01-01

    A. Ihekwaba, R. Mardare. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems. Case study: NFkB system. In Proc. of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2...

  8. The biological function of consciousness

    Science.gov (United States)

    Earl, Brian

    2014-01-01

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

  9. Functional Aspects of Biological Networks

    Science.gov (United States)

    Sneppen, Kim

    2007-03-01

    We discuss biological networks with respect to 1) relative positioning and importance of high degree nodes, 2) function and signaling, 3) logic and dynamics of regulation. Visually the soft modularity of many real world networks can be characterized in terms of number of high and low degrees nodes positioned relative to each other in a landscape analogue with mountains (high-degree nodes) and valleys (low-degree nodes). In these terms biological networks looks like rugged landscapes with separated peaks, hub proteins, which each are roughly as essential as any of the individual proteins on the periphery of the hub. Within each sup-domain of a molecular network one can often identify dynamical feedback mechanisms that falls into combinations of positive and negative feedback circuits. We will illustrate this with examples taken from phage regulation and bacterial uptake and regulation of small molecules. In particular we find that a double negative regulation often are replaced by a single positive link in unrelated organisms with same functional requirements. Overall we argue that network topology primarily reflects functional constraints. References: S. Maslov and K. Sneppen. ``Computational architecture of the yeast regulatory network." Phys. Biol. 2:94 (2005) A. Trusina et al. ``Functional alignment of regulatory networks: A study of temerate phages". Plos Computational Biology 1:7 (2005). J.B. Axelsen et al. ``Degree Landscapes in Scale-Free Networks" physics/0512075 (2005). A. Trusina et al. ``Hierarchy and Anti-Hierarchy in Real and Scale Free networks." PRL 92:178702 (2004) S. Semsey et al. ``Genetic Regulation of Fluxes: Iron Homeostasis of Escherichia coli". (2006) q-bio.MN/0609042

  10. Comparing functional annotation analyses with Catmap

    Directory of Open Access Journals (Sweden)

    Krogh Morten

    2004-12-01

    Full Text Available Abstract Background Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restricted to a category score based on a cutoff in the ranked list and a significance calculation based on random gene permutations as null hypothesis. Results We analysed three publicly available data sets, in each of which samples were divided in two classes and genes ranked according to their correlation to class labels. We developed a program, Catmap (available for download at http://bioinfo.thep.lu.se/Catmap, to compare different scores and null hypotheses in gene category analysis, using Gene Ontology annotations for category definition. When a cutoff-based score was used, results depended strongly on the choice of cutoff, introducing an arbitrariness in the analysis. Comparing results using random gene permutations and random sample permutations, respectively, we found that the assigned significance of a category depended strongly on the choice of null hypothesis. Compared to sample label permutations, gene permutations gave much smaller p-values for large categories with many coexpressed genes. Conclusions In gene category analyses of ranked gene lists, a cutoff independent score is preferable. The choice of null hypothesis is very important; random gene permutations does not work well as an approximation to sample label permutations.

  11. Biological couplings: Function, characteristics and implementation mode

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

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

  12. Pegasys: software for executing and integrating analyses of biological sequences

    Directory of Open Access Journals (Sweden)

    Lett Drew

    2004-04-01

    Full Text Available Abstract Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

  13. Functional quantum biology in photosynthesis and magnetoreception

    CERN Document Server

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

    2012-01-01

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

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

    Science.gov (United States)

    Haave, Neil

    2012-01-01

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

  15. Structure and function in biology

    International Nuclear Information System (INIS)

    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

  16. Synthetic biology analysed tools for discussion and evaluation

    CERN Document Server

    2016-01-01

    Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic bi...

  17. Photosynthetic system as a biological functional element

    International Nuclear Information System (INIS)

    Photosynthetic apparatus of high plants and photosynthetic bacteria is essentially autonomic system in terms of genetics and structural -functional properties located in specific medium, a bio-membrane. Processes of light absorption and exciton migration in light harvesting antenna, separation and further transfer of charges in reaction centers have specific features, which may be used for application of these objects as key elements in construction of future biological functional elements. Progress in study and genetic modification of photosynthetic membranes achieved during the last decade opens great prospects in development biological functional elements and systems. The main characteristics of photosynthetic system for these purposes are: (i) energy conversion processes in the first light phase of the photosynthesis have very short periods, up to picoseconds, which indicates possibility of creation of ultrafast functional elements on their basis; (ii) characteristics sizes of photosynthetic units, 10-100 nm, and possibility to arrange regularly disposed elements in relevant membranes could be prospective point for creation of nano structures and on their basis relevant biologic functional elements; (iii) elements based on modified photosynthetic apparatus and bio-membranes might be efficiently created by methods of gene engineering and manipulation, that open huge opportunities for development of read biological functional systems. In the paper structural-functional properties and characteristics of high plants and purple photosynthetic bacteria, which may be useful for creation of future biological functional elements are considered. (author)

  18. Complex Analyses of Plankton Structure and Function

    Directory of Open Access Journals (Sweden)

    Karl E. Havens

    2001-01-01

    Full Text Available This paper critically evaluates some complex methods that have been used to characterize the structure and function of freshwater plankton communities. The focus is on methods related to plankton size structure and carbon transfer. The specific methods reviewed are 1 size spectrum analysis, 2 size-fractionated phytoplankton productivity, 3 size-fractionated zooplankton grazing, 4 plankton ecological transfer efficiency, and 5 grazer effects on phytoplankton community structure. Taken together, these methods can provide information on community ecological properties that are directly related to practical issues including water quality and fisheries productivity. However, caution is warranted since application without a complete understanding of assumptions and context of the manipulations could lead to erroneous conclusions. As an example, experimental studies involving the addition or removal of zooplankton, especially when coupled with nutrient addition treatments, could provide information on the degree of consumer vs. resource control of phytoplankton. Resource managers subsequently could use this information in developing effective measures for controlling nuisance algal biomass. However, the experiments must be done critically and with sufficient safeguards and other measurements to ensure that treatments (e.g., zooplankton exclosure by screening of water actually are successful and do not introduce other changes in the community (e.g., removal of large algae. In all of the methods described here, the investigator must take care when generalizing results and, in particular, carry out a sufficient number of replications to encompass both the major seasonal and spatial variation that occurs in the ecosystem.

  19. Metacognition: computation, biology and function.

    Science.gov (United States)

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

    2012-05-19

    Many complex systems maintain a self-referential check and balance. In animals, such reflective monitoring and control processes have been grouped under the rubric of metacognition. In this introductory article to a Theme Issue on metacognition, we review recent and rapidly progressing developments from neuroscience, cognitive psychology, computer science and philosophy of mind. While each of these areas is represented in detail by individual contributions to the volume, we take this opportunity to draw links between disciplines, and highlight areas where further integration is needed. Specifically, we cover the definition, measurement, neurobiology and possible functions of metacognition, and assess the relationship between metacognition and consciousness. We propose a framework in which level of representation, order of behaviour and access consciousness are orthogonal dimensions of the conceptual landscape. PMID:22492746

  20. Training Residential Staff to Conduct Trial-Based Functional Analyses

    Science.gov (United States)

    Lambert, Joseph M.; Bloom, Sarah E.; Kunnavatana, S. Shanun; Collins, Shawnee D.; Clay, Casey J.

    2013-01-01

    We taught 6 supervisors of a residential service provider for adults with developmental disabilities to train 9 house managers to conduct trial-based functional analyses. Effects of the training were evaluated with a nonconcurrent multiple baseline. Results suggest that house managers can be trained to conduct trial-based functional analyses with…

  1. Marine Carotenoids: Biological Functions and Commercial Applications

    OpenAIRE

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

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesised 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 wide range of commercial applications. Indeed, recent interest in the carotenoids has be...

  2. Chromatic alteration on marble surfaces analysed by molecular biology tools

    OpenAIRE

    Franco Palla; Elena Tartamella

    2007-01-01

    The patina represents a superficial natural alteration of the constituting matter of the work of art. It emerges from the natural and usual stabilization process that the materials of the surface undergo because of the interaction with outdoor agents characterizing the surrounding environment. Besides, it is not linked to an obvious phenomenon of degradation that can be noticed through the change in the original colour of the matter. This is what we intend when we talk about biological patina...

  3. Structure and Associated Biological Functions of Viroids.

    Science.gov (United States)

    Steger, Gerhard; Perreault, Jean-Pierre

    2016-01-01

    Mature viroids consist of a noncoding, covalently closed circular RNA that is able to autonomously infect respective host plants. Thus, they must utilize proteins of the host for most biological functions such as replication, processing, transport, and pathogenesis. Therefore, viroids can be regarded as minimal parasites of the host machinery. They have to present to the host machinery the appropriate signals based on either their sequence or their structure. Here, we summarize such sequence and structural features critical for the biological functions of viroids. PMID:26997592

  4. Trends and implications of biological analyses for agricultural operations

    Energy Technology Data Exchange (ETDEWEB)

    Ash, D.H.; Salladay, D.G.

    1994-10-01

    State and federal legislatures, regulatory agencies, the agricultural community, and the public at large have increasing concerns about groundwater contamination and other environmental issues. The U.S. Congress has requested all federal agencies working with agriculture to address these issues. Even with current pressures to {open_quotes}cut government spending,{close_quotes} public pressure prevails to clean up polluted sites and to prevent future contamination. Farmers, agrichemical dealers and producers, and related trade associations have voiced concern about regulations affecting their industries. Over the last three decades positive changes have evolved in the disposal or final resolution of agricultural wastes from indiscriminate disposal on land and in water, through regulated land filling and incineration to a point where biological treatment/remediation strategies are coming to the forefront. These biological strategies bring with them different requirements for analytical methods. In March of this year the Environmental Protection Agency (EPA) and ARA organized a work group which met in Cincinnati, Ohio, to discuss the bioremediation of pesticide-laden soil. This work group consisted of EPA researchers, regulators, and administrators; state ag-environmental technologists and program directors; ag-chemical producer, remediation program managers, university ag researchers, USDA researchers, and TVA technologists. Consensus was quickly obtained on the utter unaffordability of current chemical and thermal treatment schemes for agricultural wastes, contaminated soils, and rinsewaters. Consensus was also reached that conventional analytical methods are too expensive and complicated for use in the field demonstration/application of the bioremediation-type processes. Thus the group recommended and supported field agrichemical dealer demonstrations of landfarming and composting with an emphasis on the need to develop low cost, easy toxicological measurements.

  5. Inferring Biologically Relevant Models: Nested Canalyzing Functions

    CERN Document Server

    Hinkelmann, Franziska

    2010-01-01

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

  6. Chromatic alteration on marble surfaces analysed by molecular biology tools

    Directory of Open Access Journals (Sweden)

    Franco Palla

    2007-07-01

    Full Text Available The patina represents a superficial natural alteration of the constituting matter of the work of art. It emerges from the natural and usual stabilization process that the materials of the surface undergo because of the interaction with outdoor agents characterizing the surrounding environment. Besides, it is not linked to an obvious phenomenon of degradation that can be noticed through the change in the original colour of the matter. This is what we intend when we talk about biological patina usually generated by macro and/or micro-organic colonization (fungi, bacteria, alga which contributes to surface bio-deterioration and thus lead to the formation of orange, red or even brown and dark pigmented areas. The presence of chromatic alterations (rose-coloured areas, as a consequence of bacterial colonization, was most particularly pointed out in different sites, such as in the marble slabs on the facades of both the Cathedral of Siena (Duomo di Siena and the Certosa of Pavia. The present study shows an example of chromatic alteration of the surface of marble works due to bacterial colonization.

  7. Insights into the functional biology of schistosomes

    OpenAIRE

    Walker Anthony

    2011-01-01

    Abstract The need to discover new treatments for human schistosomiasis has been an important driver for molecular research on schistosomes, a major breakthrough being the publication of the Schistosoma mansoni and Schistosoma japonicum genomes in 2009. This 'Primer' considers recent advances in the understanding of schistosome biology by providing a snapshot of selected areas of contemporary functional schistosome research, including that on the genome, the tegument, cell signalling and devel...

  8. Imaging cellular and molecular biological functions

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-07-01

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

  9. 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...... feed on cells .10 mm. Meganyctiphanes norvegica show maximum predation on 800–1600 mm sized copepods, corresponding to a predator:prey size ratio of 17.0+2.2. Functional response experiments with M. norvegica follow a Holling type III functional response, both when feeding on diatoms and copepods, but...

  10. Uncovering Biological Network Function via Graphlet Degree Signatures

    Directory of Open Access Journals (Sweden)

    Nataša Pržulj

    2008-01-01

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

  11. Interpretation of differential item functioning analyses using external review

    DEFF Research Database (Denmark)

    Scott, Neil W; Fayers, Peter M; Aaronson, Neil K; Bottomley, Andrew; de Graeff, Alexander; Groenvold, Mogens; Gundy, Chad; Koller, Michael; Petersen, Morten A; Sprangers, Mirjam A G

    2010-01-01

    Differential item functioning (DIF) analyses are used to determine whether certain groups respond differently to a particular item of a test or questionnaire; however, these do not explain the reasons for observed response differences. Many studies have used external reviews of items, sometimes u...

  12. Biological functions of decorin in cancer

    Institute of Scientific and Technical Information of China (English)

    Xiu-Li Bi; Wancai Yang

    2013-01-01

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

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

    OpenAIRE

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

    2015-01-01

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

  14. DMPD: Structural and functional analyses of bacterial lipopolysaccharides. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 12106784 Structural and functional analyses of bacterial lipopolysaccharides. Carof...html) (.csml) Show Structural and functional analyses of bacterial lipopolysaccharides. PubmedID 12106784 Ti...tle Structural and functional analyses of bacterial lipopolysaccharides. Authors

  15. FUNCTIONAL ANALYSIS IN PUBLIC SCHOOLS: A SUMMARY OF 90 FUNCTIONAL ANALYSES

    OpenAIRE

    Mueller, Michael M; Nkosi, Ajamu; Hine, Jeffrey F

    2011-01-01

    Several review and epidemiological studies have been conducted over recent years to inform behavior analysts of functional analysis outcomes. None to date have closely examined demographic and clinical data for functional analyses conducted exclusively in public school settings. The current paper presents a data-based summary of 90 functional analyses conducted in public school settings from 2006 through 2009 for 69 students. Specifically, we present data on gender, age, race, diagnosis, topo...

  16. A real-time transfer function analyser program for PFR

    International Nuclear Information System (INIS)

    A transfer function analyser software package has been produced which is believed to constitute a significant advance over others reported in the literature. The main advantages of the system are its operating speed, especially at low frequencies, which is due to its use of part-cycle integration and its high degree of interactive operator control. The driving sine wave, the return signals and the computed vector diagrams are displayed on TV type visual display units. Data output is by means of an incremental graph plotter or an IBM typewriter. (author)

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

    Directory of Open Access Journals (Sweden)

    Powers TuShun R

    2012-06-01

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

  18. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

    Full Text Available Ceramide monohexosides (CMHs, cerebrosides are glycosphingolipids composed of a hydrophobic ceramide linked to one sugar unit. In fungal cells, CMHs are very conserved molecules consisting of a ceramide moiety containing 9-methyl-4,8-sphingadienine in amidic linkage to 2-hydroxyoctadecanoic or 2-hydroxyhexadecanoic acids, and a carbohydrate portion consisting of one residue of glucose or galactose. 9-Methyl 4,8-sphingadienine-containing ceramides are usually glycosylated to form fungal cerebrosides, but the recent description of a ceramide dihexoside (CDH presenting phytosphingosine in Magnaporthe grisea suggests the existence of alternative pathways of ceramide glycosylation in fungal cells. Along with their unique structural characteristics, fungal CMHs have a peculiar subcellular distribution and striking biological properties. In Pseudallescheria boydii, Candida albicans, Cryptococcus neoformans, Aspergillus nidulans, A. fumigatus, and Schizophyllum commune, CMHs are apparently involved in morphological transitions and fungal growth. The elucidation of structural and functional aspects of fungal cerebrosides may therefore contribute to the design of new antifungal agents inhibiting growth and differentiation of pathogenic species.

  19. Implementation of response function concept for spent fuel cask analyses

    International Nuclear Information System (INIS)

    Due to the uncertain schedule about the first disposal of the large quantity of spent nuclear fuel (SNF) accumulated at the US commercial nuclear power plants, and due to the wide range of burnups and cooling times of the SNF, it is urgent to develop a quick and realistic method for analyzing an interim-storage or shipping package of SNF. The existing method uses design-basis SNF, and it is unnecessarily conservative and therefore uneconomic. This paper demonstrates the use of response-function concept for shielding and criticality analysis for a commercial SNF shipping cask. A PC-based computer code is written for this purpose. The program allows users to perform accurate shielding and criticality analyses for any selected cask payload on real-time basis. The results are less conservative, but more realistic than that of the design-basis analyses. One must be noted, however, that the response function is cask-specific. Therefore, the concept is most beneficial to the major cask type which is to be repeatedly used for a large number of SNF shipments

  20. [Biodiversity and Function Analyses of BIOLAK Activated Sludge Metagenome].

    Science.gov (United States)

    Tian, Mei; Liu, Han-hu; Shen, Xin; Zhao, Fang-qing; Chen, Shuai; Yao, Yong-jia

    2015-05-01

    The BIOLAK is a multi-stage activated sludge process, which has been successfully promoted worldwide. However, the biological community and function of the BIOLAK activated sludge ( the core component in the process) have not been reported so far. In this study, taking Lianyungang Dapu Industrial Zone WWTP as an example, a large-scale metagenomic data (428 588 high-quality DNA sequences) of the BIOLAK activated sludge were obtained by means of a new generation of high-throughput sequencing technology. Amazing biodiversity was revealed in the BIOLAK activated sludge, which included 47 phyla, 872 genera and 1351 species. There were 33 phyla identified in the Bacteria domain (289 933 sequences). Proteohacteria was the most abundant phylum (62.54%), followed by Bacteroidetes (11.29%), Nitrospirae ( 5. 65%) and Planctomycetes (4.79%), suggesting that these groups played a key role in the BIOLAK wastewater treatment system. Among the 748 bacterial genera, Nitrospira (5.60%) was the most prevalent genus, which was a key group in the nitrogen cycle. Followed by Gemmatimonas (2.45%), which was an important genus in the biological phosphorus removal process. In Archaea domain (1019 sequences), three phyla and 39 genera were detected. In Eukaryota domain (1055 sequences), 60 genera and 10 phyla were identified, among which Ciliophora was the largest phylum (257 sequences). Meanwhile, 448 viral sequences were detected in the BIOLAK sludge metagenome, which were dominated by bacteriophages. The proportions of nitrogen, aromatic compounds and phosphorus metabolism in the BIOLAK sludge were 2.50%, 2.28% and 1.56%, respectively, which were higher than those in the sludge of United States and Australia. Among four processes of nitrogen metabolism, denitrification-related genes were most abundant (80.81%), followed by ammonification (12.78%), nitrification,(4.38%) and nitrogen fixation (2.04%). In conclusion, the BIOLAK activated sludge had amazing biodiversity, meanwhile

  1. Local analyses of Planck maps with Minkowski functionals

    Science.gov (United States)

    Novaes, C. P.; Bernui, A.; Marques, G. A.; Ferreira, I. S.

    2016-09-01

    Minkowski functionals (MF) are excellent tools to investigate the statistical properties of the cosmic background radiation (CMB) maps. Between their notorious advantages is the possibility to use them efficiently in patches of the CMB sphere, which allow studies in masked skies, inclusive analyses of small sky regions. Then, possible deviations from Gaussianity are investigated by comparison with MF obtained from a set of Gaussian isotropic simulated CMB maps to which are applied the same cut-sky masks. These analyses are sensitive enough to detect contaminations of small intensity like primary and secondary CMB anisotropies. Our methodology uses the MF, widely employed to study non-Gaussianities in CMB data, and asserts Gaussian deviations only when all of them points out an exceptional χ2 value, at more than 2.2σ confidence level, in a given sky patch. Following this rigorous procedure, we find 13 regions in the foreground-cleaned Planck maps that evince such high levels of non-Gaussian deviations. According to our results, these non-Gaussian contributions show signatures that can be associated to the presence of hot or cold spots in such regions. Moreover, some of these non-Gaussian deviations signals suggest the presence of foreground residuals in those regions located near the Galactic plane. Additionally, we confirm that most of the regions revealed in our analyses, but not all, have been recently reported in studies done by the Planck collaboration. Furthermore, we also investigate whether these non-Gaussian deviations can be possibly sourced by systematics, like inhomogeneous noise and beam effect in the released Planck data, or perhaps due to residual Galactic foregrounds.

  2. Local analyses of Planck maps with Minkowski Functionals

    CERN Document Server

    Novaes, C P; Marques, G A; Ferreira, I S

    2016-01-01

    Minkowski Functionals (MF) are excellent tools to investigate the statistical properties of the cosmic background radiation (CMB) maps. Between their notorious advantages is the possibility to use them efficiently in patches of the CMB sphere, which allow studies in masked skies, inclusive analyses of small sky regions. Then, possible deviations from Gaussianity are investigated by comparison with MF obtained from a set of Gaussian isotropic simulated CMB maps to which are applied the same cut-sky masks. These analyses are sensitive enough to detect contaminations of small intensity like primary and secondary CMB anisotropies. Our methodology uses the MF, widely employed to study non-Gaussianities in CMB data, and asserts Gaussian deviations only when all of them points out an exceptional $\\chi^2$ value, at more than $2.2 \\sigma$ confidence level, in a given sky patch. Following this rigorous procedure, we find 13 regions in the foreground-cleaned Planck maps that evince such high levels of non-Gaussian devia...

  3. Size and compositional analyses of biologically active aerosols from a CO2 and diode laser plume

    International Nuclear Information System (INIS)

    Modern medical procedures, including laser surgery, can generate fine aerosols that may carry biologically active agents. With such procedures becoming more commonplace, it is evident that we need to look at the health implications on hospital staff when dealing with highly contagious patients with bacterial and/or viral infections, such as AIDS. The focus of this study is not to determine what portion that population is actually harmful, only to deduce what segment is still biologically active after vaporization from tissues. We have developed procedures to collect and analyze aerosols by size (from >10 μm to less than 0.07 μm) and by time (from minutes to ∼4 hour increments). Health relevant size cuts for aerosols in a work environment have been adopted by the International Organization for Standardization and the Comite of European de Normalisation. We examined both the nature of the aerosols generated and the efficiency of hospital masks used by personnel in screening aerosols and simulated conditions under which aerosols might be inhaled. Four sets of data were recorded: Mask filtered physical, mask filtered biological, unfiltered physical and unfiltered biological. A combination of PIXE analyses on impactor and filter samples were matched with filters and strips plated on agarose plates and counted for colony forming units to determine the biologically active subset of the population. (author)

  4. Marine Carotenoids: Biological Functions and Commercial Applications

    NARCIS (Netherlands)

    Vilchez, C.; Forján, E.; Cuaresma, M.; Bédmar, F.; Garbayo, I.; Vega, J.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 functi

  5. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

    Science.gov (United States)

    Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian’an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O’Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tönu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

    2012-01-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have raised the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional follow-up of these newly discovered loci will further improve our understanding of glycemic control. PMID:22885924

  6. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways.

    Science.gov (United States)

    Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian'an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O'Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tõnu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

    2012-09-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control. PMID:22885924

  7. Theoretical study for a digital transfer function analyser

    International Nuclear Information System (INIS)

    This study deals with the harmonic analysis of the instantaneous counting rate of a pulse train. This arises from using a fission chamber for reactivity to power transfer function measurements by oscillation methods in reactors. The systematical errors due to the sampling process are computed. The integration carried out when sampling the signal modifies the formulae of the Nyquist theorem on spectrum folding. The statistical errors due to the noise are analysed: it is shown that the bandwidth of the spectral window applied to the noise frequency spectrum is equal to the inverse of the time duration of the experiment. A dead time of 25 per cent of the sampling time does not increase appreciably the bandwidth. A new method is proposed afterwards yielding very approximate results of the Fourier analysis during the experiment. The systematical errors arising from the measuring process are determined, and it is shown that the bandwidth of the corresponding spectral window is still given by the inverse of the time duration of the experiment. (author)

  8. Results from multi-trace-element neutron activation analyses of marine biological specimens

    International Nuclear Information System (INIS)

    In the course of this instrumental NAA study to date, a considerable body of data has been obtained on the Hg, Se and Zn levels in several different species of Pacific Ocean fish and mammals. Great biological variability has been noted. Three principal variables that effect the levels of these three trace elements in marine biological specimens include species, tissue and size or age of the specimen. There is also appreciable variation in these levels amongst different specimens of the same species and within a given tissue of even a given specimen. Because of these many variables, it is important that sample dissection be conducted carefully, that data such as specimen size be recorded, and large numbers of specimens are analyzed. The instrumental NAA procedure employed in this study has been checked by analyses of two recent NBS reference materials: orchard leaves and bovine liver. (T.G.)

  9. Tunable ultrasensitivity: functional decoupling and biological insights.

    Science.gov (United States)

    Wang, Guanyu; Zhang, Mengshi

    2016-01-01

    Sensitivity has become a basic concept in biology, but much less is known about its tuning, probably because allosteric cooperativity, the best known mechanism of sensitivity, is determined by rigid conformations of interacting molecules and is thus difficult to tune. Reversible covalent modification (RCM), owing to its systems-level ingenuity, can generate concentration based, tunable sensitivity. Using a mathematical model of regulated RCM, we find sensitivity tuning can be decomposed into two orthogonal modes, which provide great insights into vital biological processes such as tissue development and cell cycle progression. We find that decoupling of the two modes of sensitivity tuning is critical to fidelity of cell fate decision; the decoupling is thus important in development. The decomposition also allows us to solve the 'wasteful degradation conundrum' in budding yeast cell cycle checkpoint, which further leads to discovery of a subtle but essential difference between positive feedback and double negative feedback. The latter guarantees revocability of stress-induced cell cycle arrest; while the former does not. By studying concentration conditions in the system, we extend applicability of ultrasensitivity and explain the ubiquity of reversible covalent modification. PMID:26847155

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

    DEFF Research Database (Denmark)

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

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

  11. Printable Bioelectronics To Investigate Functional Biological Interfaces.

    Science.gov (United States)

    Manoli, Kyriaki; Magliulo, Maria; Mulla, Mohammad Yusuf; Singh, Mandeep; Sabbatini, Luigia; Palazzo, Gerardo; Torsi, Luisa

    2015-10-19

    Thin-film transistors can be used as high-performance bioelectronic devices to accomplish tasks such as sensing or controlling the release of biological species as well as transducing the electrical activity of cells or even organs, such as the brain. Organic, graphene, or zinc oxide are used as convenient printable semiconducting layers and can lead to high-performance low-cost bioelectronic sensing devices that are potentially very useful for point-of-care applications. Among others, electrolyte-gated transistors are of interest as they can be operated as capacitance-modulated devices, because of the high capacitance of their charge double layers. Specifically, it is the capacitance of the biolayer, being lowest in a series of capacitors, which controls the output current of the device. Such an occurrence allows for extremely high sensitivity towards very weak interactions. All the aspects governing these processes are reviewed here. PMID:26420480

  12. 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.

  13. Biological soil crust community types differ in key ecological functions

    OpenAIRE

    Pietrasiak, N; Regus, JU; Johansen, JR; LAM, D.; Sachs, JL; Santiago, LS

    2013-01-01

    Soil stability, nitrogen and carbon fixation were assessed for eight biological soil crust community types within a Mojave Desert wilderness site. Cyanolichen crust outperformed all other crusts in multi-functionality whereas incipient crust had the poorest performance. A finely divided classification of biological soil crust communities improves estimation of ecosystem function and strengthens the accuracy of landscape-scale assessments. © 2013 Elsevier Ltd.

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

    OpenAIRE

    Ye-Rang Yun; Jong Eun Won; Eunyi Jeon; Sujin Lee; Wonmo Kang; Hyejin Jo; Jun-Hyeog Jang; Ueon Sang Shin; Hae-Won Kim

    2010-01-01

    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 opt...

  15. Genomic Functionalization: The Next Revolution In Biology

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-01

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

  16. X-ray structure analyses of biological molecules and particles in Japan. A brief history and future prospect

    International Nuclear Information System (INIS)

    In Japan, X-ray structure analyses of molecules and particles from biology started in the 1970s. The structure analysis methods have been developed through the innovation of various techniques in advance, and have contributed for understanding the elementary and microscopic processes in life. Here we summarize briefly the history of X-ray structure analyses for structural biology in Japan and think about the prospect. (author)

  17. Labeling and functionalizing amphipols for biological applications.

    Science.gov (United States)

    Le Bon, Christel; Popot, Jean-Luc; Giusti, Fabrice

    2014-10-01

    Amphipols (APols) are short amphipathic polymers developed as an alternative to detergents for handling membrane proteins (MPs) in aqueous solution. MPs are, as a rule, much more stable following trapping with APols than they are in detergent solutions. The best-characterized APol to date, called A8-35, is a mixture of short-chain sodium polyacrylates randomly derivatized with octylamine and isopropylamine. Its solution properties have been studied in detail, and it has been used extensively for biochemical and biophysical studies of MPs. One of the attractive characteristics of APols is that it is relatively easy to label them, isotopically or otherwise, without affecting their physical-chemical properties. Furthermore, several variously modified APols can be mixed, achieving multiple functionalization of MP/APol complexes in the easiest possible manner. Labeled or tagged APols are being used to study the solution properties of APols, their miscibility, their biodistribution upon injection into living organisms, their association with MPs and the composition, structure and dynamics of MP/APol complexes, examining the exchange of surfactants at the surface of MPs, labeling MPs to follow their distribution in fractionation experiments or to immobilize them, increasing the contrast between APols and solvent or MPs in biophysical experiments, improving NMR spectra, etc. Labeling or functionalization of APols can take various courses, each of which has its specific constraints and advantages regarding both synthesis and purification. The present review offers an overview of the various derivatives of A8-35 and its congeners that have been developed in our laboratory and discusses the pros and cons of various synthetic routes. PMID:24696186

  18. Whole-Genome Analyses of LUNG FUNCTION, HEIGHT and SMOKING

    OpenAIRE

    Janss, Luc; Sigsgaard, Torben; Sorensen, Daniel

    2014-01-01

    A joint analysis of FEV1 (Forced Expiratory Volume after one second) and height is reported using novel methodology, as well as a single-trait analysis of smoking status. A first goal of the study was to incorporate dense genetic marker information in a random regression (Bayesian) model to quantify the relative contributions of genomic and environmental factors to the relationship between FEV1 and height. Smoking status was analysed using a probit random regression model and a second goal of...

  19. Functional analyses of NSF1 in wine yeast using interconnected correlation clustering and molecular analyses.

    Directory of Open Access Journals (Sweden)

    Kyrylo Bessonov

    Full Text Available Analyzing time-course expression data captured in microarray datasets is a complex undertaking as the vast and complex data space is represented by a relatively low number of samples as compared to thousands of available genes. Here, we developed the Interdependent Correlation Clustering (ICC method to analyze relationships that exist among genes conditioned on the expression of a specific target gene in microarray data. Based on Correlation Clustering, the ICC method analyzes a large set of correlation values related to gene expression profiles extracted from given microarray datasets. ICC can be applied to any microarray dataset and any target gene. We applied this method to microarray data generated from wine fermentations and selected NSF1, which encodes a C2H2 zinc finger-type transcription factor, as the target gene. The validity of the method was verified by accurate identifications of the previously known functional roles of NSF1. In addition, we identified and verified potential new functions for this gene; specifically, NSF1 is a negative regulator for the expression of sulfur metabolism genes, the nuclear localization of Nsf1 protein (Nsf1p is controlled in a sulfur-dependent manner, and the transcription of NSF1 is regulated by Met4p, an important transcriptional activator of sulfur metabolism genes. The inter-disciplinary approach adopted here highlighted the accuracy and relevancy of the ICC method in mining for novel gene functions using complex microarray datasets with a limited number of samples.

  20. [Biological experiments in microgravity: equilibrium function].

    Science.gov (United States)

    Gorgiladze, G I; Shipov, A A; Horn, E

    2012-01-01

    The review deals with the investigations of structural and functional modifications in the equilibrium organ (EO) in invertebrates (coelenterates, shells, crustaceans and insects) and vertebrates (fishes, amphibians, rats, primates) on different ontogenetic stages in the condition of microgravity and during readaptation to the Earth's gravity. Results of the investigations detail the adaptive strategy of terrestrial organism in the environment lacking the gravitational components that leads to the discrepancy of an inner model of the body-environment schema constructed by the central nervous system at 1 g and the novel reality. It is manifested by ataxic behavior and increased graviceptors' afferentation against efferent system inactivation. The new condition is defined as a sensibilization phase ensued by the eluding phase: behavior obeys the innate motion strategy, whereas graviceptors' afferentation decreases due to activation of the efferent system. Readaptation to 1 G takes several to 50 days and proceeds as a sequence of slow in motion behavior, ataxia and vestibular sensitization. Reactivity of the gravitosensory system to microgravity was found to be age-dependent. Gain in the EO inertial mass in microgravity and reduction with return to 1 g indicates gravity relevance to EO genesis. PMID:23402139

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

    Science.gov (United States)

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

    2014-01-01

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

  2. 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. PMID:26668171

  3. Assessing Ecological Impacts of Shrimp and Sewage Effluent: Biological Indicators with Standard Water Quality Analyses

    Science.gov (United States)

    Jones, A. B.; O'Donohue, M. J.; Udy, J.; Dennison, W. C.

    2001-01-01

    Despite evidence linking shrimp farming to several cases of environmental degradation, there remains a lack of ecologically meaningful information about the impacts of effluent on receiving waters. The aim of this study was to determine the biological impact of shrimp farm effluent, and to compare and distinguish its impacts from treated sewage effluent. Analyses included standard water quality/sediment parameters, as well as biological indicators including tissue nitrogen (N) content, stable isotope ratio of nitrogen (δ 15N), and amino acid composition of inhabitant seagrasses, mangroves and macroalgae. The study area consisted of two tidal creeks, one receiving effluent from a sewage treatment plant and the other from an intensive shrimp farm. The creeks discharged into the western side of Moreton Bay, a sub-tropical coastal embayment on the east coast of Australia. Characterization of water quality revealed significant differences between the creeks, and with unimpacted eastern Moreton Bay. The sewage creek had higher concentrations of dissolved nutrients (predominantly NO-3/NO-2 and PO3-4, compared to NH+4 in the shrimp creek). In contrast, the shrimp creek was more turbid and had higher phytoplankton productivity. Beyond 750 m from the creek mouths, water quality parameters were indistinguishable from eastern Moreton Bay values. Biological indicators detected significant impacts up to 4 km beyond the creek mouths (reference site). Elevated plant δ 15N values ranged from 10·4-19·6‰ at the site of sewage discharge to 2·9-4·5‰ at the reference site. The free amino acid concentration and composition of seagrass and macroalgae was used to distinguish between the uptake of sewage and shrimp derived N. Proline (seagrass) and serine (macroalgae) were high in sewage impacted plants and glutamine (seagrass) and alanine (macroalgae) were high in plants impacted by shrimp effluent. The δ 15N isotopic signatures and free amino acid composition of inhabitant

  4. Whole-Genome Analyses of lung function, height and smoking

    DEFF Research Database (Denmark)

    Janss, Luc; Sigsgaard, Torben; Sorensen, Daniel

    2014-01-01

    quantify the relative contributions of genomic and environmental factors to the relationship between FEV1 and height. Smoking status was analysed using a probit random regression model and a second goal of the study was to estimate the genomic heritability of smoking status. Estimates of genomic...... heritabilities for height and FEV1 are equal to 0.47 and to 0.30, respectively. The estimates of the genomic and environmental correlations between height and FEV1 are 0.78 and 0.34, respectively. The posterior mean of the genomic heritability of smoking status is equal to 0.14 and provides evidence for the...... presence of genetic factors associated with the trait. Under the data augmentation strategy introduced, the joint posterior distribution of FEV1 and height factorises into two independent posterior distributions. This simplifies programming and results in excellent numerical behaviour. The approach can be...

  5. Gene Discovery and Functional Analyses in the Model Plant Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Cai-Ping Feng; John Mundy

    2006-01-01

    The present mini-review describes newer methods and strategies, including transposon and T-DNA insertions,TILLING, Deleteagene, and RNA interference, to functionally analyze genes of interest in the model plant Arabidopsis. The relative advantages and disadvantages of the systems are also discussed.

  6. Gene Discovery and Functional Analyses in the Model Plant Arabidopsis

    DEFF Research Database (Denmark)

    Feng, Cai-ping; Mundy, J.

    2006-01-01

    The present mini-review describes newer methods and strategies, including transposon and T-DNA insertions, TILLING, Deleteagene, and RNA interference, to functionally analyze genes of interest in the model plant Arabidopsis. The relative advantages and disadvantages of the systems are also...

  7. Systematic Functional Annotation and Visualization of Biological Networks.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-06-22

    Large-scale biological networks represent relationships between genes, but our understanding of how networks are functionally organized is limited. Here, I describe spatial analysis of functional enrichment (SAFE), a systematic method for annotating biological networks and examining their functional organization. SAFE visualizes the network in 2D space and measures the continuous distribution of functional enrichment across local neighborhoods, producing a list of the associated functions and a map of their relative positioning. I applied SAFE to annotate the Saccharomyces cerevisiae genetic interaction similarity network and protein-protein interaction network with gene ontology terms. SAFE annotations of the genetic network matched manually derived annotations, while taking less than 1% of the time, and proved robust to noise and sensitive to biological signal. Integration of genetic interaction and chemical genomics data using SAFE revealed a link between vesicle-mediate transport and resistance to the anti-cancer drug bortezomib. These results demonstrate the utility of SAFE for examining biological networks and understanding their functional organization. PMID:27237738

  8. An abrupt stochastic damage function to analyse climate policy benefits

    OpenAIRE

    Ha-Duong, Minh; Dumas, Patrice

    2004-01-01

    Chapter in Alain Haurie and Laurent Viguier (eds.) 2005, The coupling of climate and economic dynamics, Essays on Integrated Assessment. Series: Advances in Global Change Research, Vol. 22 , Kluwerhttp://www.centre-cired.fr/perso/haduong/files/Dumas.ea-2004-AbruptStochasticDamage.pdf This paper studies uncertainty about the non-linearity of climate change impact. The DIAM 2.3 model is used to compute the sensitivity of optimal CO2 emissions paths with respect to damage function parameters....

  9. Lyapunov functions to analyse stability regions of aeroelastic equation

    Czech Academy of Sciences Publication Activity Database

    Pospíšil, Stanislav; Náprstek, Jiří

    Leuven : Katolieke Universiteit Leuven, 2011 - (Roeck, G.; Degrande, G.; Lombaert, G.; Műller, G.), s. 2035-2042 ISBN 9789076019314. [EURODYN2011 -International Conference on Structural Dynamics /8./. Leuven (BE), 04.06.2011-06.06.2011] R&D Projects: GA ČR(CZ) GA103/09/0094; GA AV ČR(CZ) IAA200710902 Institutional research plan: CEZ:AV0Z20710524 Keywords : nonlinear aeroelasticity * dynamic stability * Lyapunov function Subject RIV: JM - Building Engineering

  10. Screening and Functional Analyses of Nilaparvata lugens Salivary Proteome.

    Science.gov (United States)

    Huang, Hai-Jian; Liu, Cheng-Wen; Huang, Xiao-Hui; Zhou, Xiang; Zhuo, Ji-Chong; Zhang, Chuan-Xi; Bao, Yan-Yuan

    2016-06-01

    Most phloem-feeding insects secrete gelling and watery saliva during the feeding process. However, the functions of salivary proteins are poorly understood. In this study, our purpose was to reveal the components and functions of saliva in a rice sap-sucking insect pest, Nilaparvata lugens. The accomplishment of the whole genome and transcriptome sequencing in N. lugens would be helpful for elucidating the gene information and expression specificity of the salivary proteins. In this study, we have, for the first time, identified the abundant protein components from gelling and watery saliva in a monophagous sap-sucking insect species through shotgun proteomic detection combined with the genomic and transcriptomic analysis. Eight unknown secreted proteins were limited to N. lugens, indicating species-specific saliva components. A group of annexin-like proteins first identified in the secreted saliva displayed different domain structure and expression specificity with typical insect annexins. Nineteen genes encoding five annexin-like proteins, six salivaps (salivary glands-specific proteins with unknown function), seven putative enzymes, and a mucin-like protein showed salivary gland-specific expression pattern, suggesting their importance in the physiological mechanisms of salivary gland and saliva in this insect species. RNA interference revealed that salivap-3 is a key protein factor in forming the salivary sheath, while annexin-like5 and carbonic anhydrase are indispensable for N. lugens survival. These novel findings will greatly help to clarify the detailed functions of salivary proteins in the physiological process of N. lugens and elucidate the interaction mechanisms between N. lugens and the rice plant, which could provide important targets for the future management of rice pests. PMID:27142481

  11. Plant Ion Channels: Gene Families, Physiology, and Functional Genomics Analyses

    Science.gov (United States)

    Ward, John M.; Mäser, Pascal; Schroeder, Julian I.

    2016-01-01

    Distinct potassium, anion, and calcium channels in the plasma membrane and vacuolar membrane of plant cells have been identified and characterized by patch clamping. Primarily owing to advances in Arabidopsis genetics and genomics, and yeast functional complementation, many of the corresponding genes have been identified. Recent advances in our understanding of ion channel genes that mediate signal transduction and ion transport are discussed here. Some plant ion channels, for example, ALMT and SLAC anion channel subunits, are unique. The majority of plant ion channel families exhibit homology to animal genes; such families include both hyperpolarization-and depolarization-activated Shaker-type potassium channels, CLC chloride transporters/channels, cyclic nucleotide–gated channels, and ionotropic glutamate receptor homologs. These plant ion channels offer unique opportunities to analyze the structural mechanisms and functions of ion channels. Here we review gene families of selected plant ion channel classes and discuss unique structure-function aspects and their physiological roles in plant cell signaling and transport. PMID:18842100

  12. Analyses of functionally graded plates with a magnetoelectroelastic layer

    International Nuclear Information System (INIS)

    A meshless local Petrov–Galerkin (MLPG) method is presented for the analysis of functionally graded material (FGM) plates with a sensor/actuator magnetoelectroelastic layer localized on the top surface of the plate. The Reissner–Mindlin shear deformation theory is applied to describe the plate bending problem. The expressions for the bending moment, shear force and normal force are obtained by integration through the FGM plate and magnetoelectric layer for the corresponding constitutive equations. Then, the original three-dimensional (3D) thick-plate problem is reduced to a two-dimensional (2D) problem. Nodal points are randomly distributed over the mean surface of the considered plate. Each node is the center of a circle surrounding the node. The weak-form on small subdomains with a Heaviside step function as the test function is applied to derive local integral equations. After performing the spatial MLS approximation, a system of ordinary differential equations of the second order for certain nodal unknowns is obtained. The derived ordinary differential equations are solved by the Houbolt finite-difference scheme. Pure mechanical loads or electromagnetic potentials are prescribed on the top of the layered plate. Both stationary and transient dynamic loads are analyzed. (paper)

  13. Soil microbial community structure in diverse land use systems:A comparative study using Biolog,DGGE,and PLFA analyses

    Institute of Scientific and Technical Information of China (English)

    XUE Dong; YAO Huai-Ying; GE De-Yong; HUANG Chang-Yong

    2008-01-01

    Biolog,16S rRNA gene denaturing gradient gel electrophoresis (DGGE),and phospholipid fatty acid (PLFA) analyses were used to assess soil microbial community characteristics in a chronosequence of tea garden systems (8-,50-,and 90year-old tea gardens),an adjacent wasteland,and a 90-year-old forest.Biolog analysis showed that the average well color development (AWCD) of all carbon sources and the functional diversity based on the Shannon index decreased (P<0.05)in the following order:wasteland>forest>tea garden.For the DGGE analysis,the genetic diversity based on the Shannon index was significantly lower in the tea garden soils than in the wasteland.However,compared to the 90-year-old forest,the tea garden soils showed significantly higher genetic diversity.PLFA analysis showed that the ratio of Gram positive bacteria to Gram negative bacteria was significantly higher in the tea garden soils than in the wasteland,and the highest value was found in the 90-year-old forest.Both the fungal PLFA and the ratio of fungi to bacteria were significantly higher in the three tea garden soils than in the wasteland and forest,indicating that fungal PLFA was significantly affected by land-use change.Based on cluster analysis of the soil microbial community structure,all three analytical methods showed that land-use change had a greater effect on soil microbial community structure than tea garden age.

  14. Functional Analyses of Vertebrate TCF Proteins in C. elegans Embryos

    OpenAIRE

    Robertson, Scott M.; Lo, Miao-Chia; Odom, Ranaan; Yang, Xiao-Dong; Medina, Jessica; Huang, Shuyi; Lin, Rueyling

    2011-01-01

    In the canonical Wnt pathway, signaling results in the stabilization and increased levels of β-catenin in responding cells. β-catenin then enters the nucleus, functioning as a coactivator for the Wnt effector, TCF/LEF protein. In the absence of Wnt signaling, TCF is complexed with corepressors, together repressing Wnt target genes. In C. elegans, Wnt signaling specifies the E blastomere to become the endoderm precursor. Activation of endoderm genes in E requires not only an increase in β-cate...

  15. Development of Standards for NanoSIMS Analyses of Biological Materials

    Energy Technology Data Exchange (ETDEWEB)

    Davission, M L; Weber, P K; Pett-Ridge, J; Singer, S

    2008-07-31

    NanoSIMS is a powerful analytical technique for investigating element distributions at the nanometer scale, but quantifying elemental abundances requires appropriate standards, which are not readily available for biological materials. Standards for trace element analyses have been extensively developed for secondary ion mass spectrometry (SIMS) in the semiconductor industry and in the geological sciences. The three primary approaches for generating standards for SIMS are: (1) ion implantation (2) using previously characterized natural materials, and (3) preparing synthetic substances. Ion implantation is a reliable method for generating trace element standards, but it is expensive, which limits investigation of the analytical issues discussed above. It also requires low background levels of the elements of interest. Finding or making standard materials has the potential to provide more flexibility than ion implantation, but realizing homogeneity at the nano-scale is in itself a significant challenge. In this study, we experiment with all three approaches, but with an emphasis toward synthetic organic polymers in order to reduce costs, increase flexibility, and achieve a wide dynamic concentration range. This emphasis serves to meet the major challenge for biological samples of identifying matrix matched, homogeneous material. Biological samples themselves are typically heterogeneous at the scale of microns to 100s of microns, and therefore they are poor SIMS standards. Therefore, we focused on identifying 'biological-like' materials--either natural or synthetic--that can be used for standards. The primary criterion is that the material be as compositionally similar to biological samples as possible (primarily C, H, O, and N). For natural material we adsorbed organic colloids consisting of peptidoglycan (i.e., amino sugars), activated charcoal, and humic acids. Experiments conducted with Si on peptidoglycan showed low affinity as SiO{sub 2}, yet its

  16. Synthesis, spectroscopic characterization, biological screenings, DNA binding study and POM analyses of transition metal carboxylates

    Science.gov (United States)

    Uddin, Noor; Sirajuddin, Muhammad; Uddin, Nizam; Tariq, Muhammad; Ullah, Hameed; Ali, Saqib; Tirmizi, Syed Ahmed; Khan, Abdur Rehman

    2015-04-01

    This article contains the synthesis of a novel carboxylic acid derivative, its transition metal complexes and evaluation of biological applications. Six carboxylate complexes of transition metals, Zn(II) and Hg(II), have been successfully synthesized and characterized by FT-IR and NMR (1H, 13C). The ligand, HL, (4-[(2,6-Diethylphenyl)amino]-4-oxobutanoic acid) was also characterized by single crystal X-ray analysis. The complexation occurs via oxygen atoms of the carboxylate moiety. FT-IR date show the bidentate nature of the carboxylate moiety of the ligand as the Δν value in all complexes is less than that of the free ligand. The ligand and its complexes were screened for antifungal and antileishmanial activities. The results showed that the ligand and its complexes are active with few exceptions. UV-visible spectroscopy and viscometry results reveal that the ligand and its complexes interact with the DNA via intercalative mode of interaction. A new and efficient strategy to identify the pharmacophores and anti-pharmacophores sites in carboxylate derivatives for the antibacterial/antifungal activity using Petra, Osiris and Molinspiration (POM) analyses was also carried out.

  17. Micro-PIXE analyses of frozen-hydrated semi-thick biological sections

    International Nuclear Information System (INIS)

    Cryo-micro-PIXE system and methodology of microanalysis of frozen-hydrated semi-thick biological sections is described. A commercially available cryotransfer system used in electron microscopy has been adapted for this purpose. The analyzed material was frozen by metal–mirror method and sections of 20–50 micron thickness were prepared. Micro-PIXE and simultaneous proton backscattering was performed using 3 MeV proton beam. Monitoring of water vapour composition during the proton bombardment showed good stability of the analyzed material. The results of repetitive analyses of standards prepared from gelatin–glycerol solution with added known concentrations of K, Ni, Cu, Zn were in good agreement with expected, calculated values. Mass losses and changes of elemental composition were monitored. Elemental maps obtained for frozen-hydrated semi-thick section of Ni hyperaccumulator Senecio coronatus showed excellent preservation of leaf morphology and the distribution of elements. Quantitative elemental mapping of frozen-hydrated specimens compared with subsequent analysis of the same areas after freeze-drying revealed similar distribution pattern in both cases. It is clear, however, that freeze-drying induces some distortion of cell morphology and specimen shrinkage

  18. Micro-PIXE analyses of frozen-hydrated semi-thick biological sections

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.D., E-mail: yaodongw@tlabs.ac.za [Materials Research Department, iThemba LABS, National Research Foundation, P.O. Box 722, Somerset West 7129 (South Africa); Mesjasz-Przybylowicz, J., E-mail: mesjasz@tlabs.ac.za [Materials Research Department, iThemba LABS, National Research Foundation, P.O. Box 722, Somerset West 7129 (South Africa); Tylko, G., E-mail: grzegorz.tylko@uj.edu.pl [Department of Cell Biology and Imaging, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow (Poland); Barnabas, A.D., E-mail: alban@tlabs.ac.za [Materials Research Department, iThemba LABS, National Research Foundation, P.O. Box 722, Somerset West 7129 (South Africa); Przybylowicz, W.J., E-mail: Przybylowicz@tlabs.ac.za [Materials Research Department, iThemba LABS, National Research Foundation, P.O. Box 722, Somerset West 7129 (South Africa)

    2013-07-01

    Cryo-micro-PIXE system and methodology of microanalysis of frozen-hydrated semi-thick biological sections is described. A commercially available cryotransfer system used in electron microscopy has been adapted for this purpose. The analyzed material was frozen by metal–mirror method and sections of 20–50 micron thickness were prepared. Micro-PIXE and simultaneous proton backscattering was performed using 3 MeV proton beam. Monitoring of water vapour composition during the proton bombardment showed good stability of the analyzed material. The results of repetitive analyses of standards prepared from gelatin–glycerol solution with added known concentrations of K, Ni, Cu, Zn were in good agreement with expected, calculated values. Mass losses and changes of elemental composition were monitored. Elemental maps obtained for frozen-hydrated semi-thick section of Ni hyperaccumulator Senecio coronatus showed excellent preservation of leaf morphology and the distribution of elements. Quantitative elemental mapping of frozen-hydrated specimens compared with subsequent analysis of the same areas after freeze-drying revealed similar distribution pattern in both cases. It is clear, however, that freeze-drying induces some distortion of cell morphology and specimen shrinkage.

  19. Thermal post-bunkling analyses of functionally graded material rod

    Institute of Scientific and Technical Information of China (English)

    ZHAO Feng-qun; WANG Zhong-min; LIU Hong-zhao

    2007-01-01

    The non-linear governing differential equations of immovably simply supported functionally graded material (FGM) rod subjected to thermal loads were derived.The thermal post-buckling behaviors of FGM rod made of ZrO2 and Ti-6A1-4Vwere analyzed by shooting method. Firstly, the thermal post-buckling equilibrium paths of the FGM rod with different gradient index in the uniform temperature field were plotted,and compared with the behaviors of the homogeneous rods made of ZrO2 and Ti-6A1-4V materials, respectively. For given value of end rotation angles, the influence of gradient index on the thermal post-buckling behaviors of FGM rod was discussed. Secondly, the thermal post-buckling characteristics of the FGM rod were analyzed when the temperature difference parameter is changed while the bottom temperature parameter remains constant, and when the bottom temperature parameter is changed while the temperature difference parameter remains constant, and compared with the characteristics of the two homogeneous material rods.

  20. Biomarkers of Aging: From Function to Molecular Biology

    OpenAIRE

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

    2016-01-01

    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 sing...

  1. Diverse Biological Functions of Extracellular Collagen Processing Enzymes

    OpenAIRE

    Trackman, Philip C.

    2005-01-01

    Collagens are abundant proteins in higher organisms, and are formed by a complex biosynthetic pathway involving intracellular and extracellular post-translational modifications. Starting from simple soluble precursors, this interesting pathway produces insoluble functional fibrillar and non-fibrillar elements of the extracellular matrix. The present review highlights recent progress and new insights into biological regulation of extracellular procollagen processing, and some novel functions o...

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

    NARCIS (Netherlands)

    Enes Dapkevicius, M.L.N.

    2002-01-01

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

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

    Science.gov (United States)

    Cole, Daniel J; Hine, Nicholas D M

    2016-10-01

    Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality. PMID:27494095

  4. 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.

  5. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics

    Directory of Open Access Journals (Sweden)

    Yongqun eHe

    2012-02-01

    Full Text Available Brucella is a Gram-negative, facultative intracellular bacterium that causes zoonotic brucellosis in humans and various animals. Out of ten classified Brucella species, B. melitensis, B. abortus, B. suis, and B. canis are pathogenic to humans. In the past decade, the mechanisms of Brucella pathogenesis and host immunity have been extensively investigated using the cutting edge systems biology and bioinformatics approaches. This article provides a comprehensive review of the applications of Omics (including genomics, transcriptomics, and proteomics and bioinformatics technologies for the analysis of Brucella pathogenesis, host immune responses, and vaccine targets. Based on more than 30 sequenced Brucella genomes, comparative genomics is able to identify gene variations among Brucella strains that help to explain host specificity and virulence differences among Brucella species. Diverse transcriptomics and proteomics gene expression studies have been conducted to analyze gene expression profiles of wild type Brucella strains and mutants under different laboratory conditions. High throughput Omics analyses of host responses to infections with virulent or attenuated Brucella strains have been focused on responses by mouse and cattle macrophages, bovine trophoblastic cells, mouse and boar splenocytes, and ram buffy coat. Differential serum responses in humans and rams to Brucella infections have been analyzed using high throughput serum antibody screening technology. The Vaxign reverse vaccinology has been used to predict many Brucella vaccine targets. More than 180 Brucella virulence factors and their gene interaction networks have been identified using advanced literature mining methods. The recent development of community-based Vaccine Ontology and Brucellosis Ontology provides an efficient way for Brucella data integration, exchange, and computer-assisted automated reasoning.

  6. Loss-of-function analyses defines vital and redundant functions of the Plasmodium rhomboid protease family.

    Science.gov (United States)

    Lin, Jing-Wen; Meireles, Patrícia; Prudêncio, Miguel; Engelmann, Sabine; Annoura, Takeshi; Sajid, Mohammed; Chevalley-Maurel, Séverine; Ramesar, Jai; Nahar, Carolin; Avramut, Cristina M C; Koster, Abraham J; Matuschewski, Kai; Waters, Andrew P; Janse, Chris J; Mair, Gunnar R; Khan, Shahid M

    2013-04-01

    Rhomboid-like proteases cleave membrane-anchored proteins within their transmembrane domains. In apicomplexan parasites substrates include molecules that function in parasite motility and host cell invasion. While two Plasmodium rhomboids, ROM1 and ROM4, have been examined, the roles of the remaining six rhomboids during the malaria parasite's life cycle are unknown. We present systematic gene deletion analyses of all eight Plasmodium rhomboid-like proteins as a means to discover stage-specific phenotypes and potential functions in the rodent malaria model, P. berghei. Four rhomboids (ROM4, 6, 7 and 8) are refractory to gene deletion, suggesting an essential role during asexual blood stage development. In contrast ROM1, 3, 9 and 10 were dispensable for blood stage development and exhibited no, subtle or severe defects in mosquito or liver development. Parasites lacking ROM9 and ROM10 showed no major phenotypic defects. Parasites lacking ROM1 presented a delay in blood stage patency following liver infection, but in contrast to a previous study blood stage parasites had similar growth and virulence characteristics as wild type parasites. Parasites lacking ROM3 in mosquitoes readily established oocysts but failed to produce sporozoites. ROM3 is the first apicomplexan rhomboid identified to play a vital role in sporogony. PMID:23490234

  7. Morpho-chemistry and functionality of diseased biological tissues

    Science.gov (United States)

    Lange, Marta; Cicchi, Riccardo; Pavone, Francesco

    2014-09-01

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

  8. Functional Agents to Biologically Control Deoxynivalenol Contamination in Cereal Grains

    Science.gov (United States)

    Tian, Ye; Tan, Yanglan; Liu, Na; Liao, Yucai; Sun, Changpo; Wang, Shuangxia; Wu, Aibo

    2016-01-01

    Mycotoxins, as microbial secondary metabolites, frequently contaminate cereal grains and pose a serious threat to human and animal health around the globe. Deoxynivalenol (DON), a commonly detected Fusarium mycotoxin, has drawn utmost attention due to high exposure levels and contamination frequency in the food chain. Biological control is emerging as a promising technology for the management of DON contamination. Functional biological control agents (BCAs), which include antagonistic microbes, natural fungicides derived from plants and detoxification enzymes, can be used to control DON contamination at different stages of grain production. In this review, studies regarding different biological agents for DON control in recent years are summarized for the first time. Furthermore, this article highlights the significance of BCAs for controlling DON contamination, as well as the need for more practical and efficient BCAs concerning food safety. PMID:27064760

  9. Further Evaluation of Leisure Items in the Attention Condition of Functional Analyses

    OpenAIRE

    Roscoe, Eileen M; Carreau, Abbey; MacDonald, Jackie; Pence, Sacha T

    2008-01-01

    Research suggests that including leisure items in the attention condition of a functional analysis may produce engagement that masks sensitivity to attention. In this study, 4 individuals' initial functional analyses indicated that behavior was maintained by nonsocial variables (n  =  3) or by attention (n  =  1). A preference assessment was used to identify items for subsequent functional analyses. Four conditions were compared, attention with and without leisure items and control with and w...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-06-01

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

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

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

    Ghezzehei, Teamrat; Or, Dani

    2016-04-01

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

  13. Functionalized Conjugated Polyelectrolytes for Biological Sensing and Imaging.

    Science.gov (United States)

    Zhan, Ruoyu; Liu, Bin

    2016-06-01

    Conjugated polyelectrolytes (CPEs) are macromolecules with highly delocalized π-conjugated backbones and charged side chains, which are unique types of active materials, with wide applications in optoelectronics, sensing, imaging, and therapy. By attaching specific groups (e.g., recognition elements, magnetic resonance (MR) contrast agents, gene carriers, and drugs) to the side chain or backbone of CPEs, functionalized CPEs have been developed and used for specific biological applications. In this account, we summarize the recent progress of functionalized CPEs with respect to their synthesis and biomedical applications. Future perspectives are also discussed at the end. PMID:27230631

  14. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

    OpenAIRE

    Huang, Da Wei; Sherman, Brad T; Tan, Qina; Collins, Jack R; Alvord, W. Gregory; Roayaei, Jean; Stephens, Robert; Baseler, Michael W; Lane, H. Clifford; Lempicki, Richard A.

    2007-01-01

    The DAVID Gene Functional Classification Tool uses a novel agglomeration algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules. This organization is accomplished by mining the complex biological co-occurrences found in multiple sources of functional annotation. It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretat...

  15. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology

    OpenAIRE

    Campbell David; Moss Patrick; Deutsch Eric W; Marzolf Bruz; Johnson Michael H; Galitski Timothy

    2006-01-01

    Abstract Background The biological information in genomic expression data can be understood, and computationally extracted, in the context of systems of interacting molecules. The automation of this information extraction requires high throughput management and analysis of genomic expression data, and integration of these data with other data types. Results SBEAMS-Microarray, a module of the open-source Systems Biology Experiment Analysis Management System (SBEAMS), enables MIAME-compliant st...

  16. Mnk kinase pathway: Cellular functions and biological outcomes

    Institute of Scientific and Technical Information of China (English)

    Sonali; Joshi; Leonidas; C; Platanias

    2014-01-01

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

  17. 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; Cordeiro-da Silva, Anabela; 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; Nolte-'t Hoen, Esther N M; 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

  18. Systems analysis of biological networks in skeletal muscle function.

    Science.gov (United States)

    Smith, Lucas R; Meyer, Gretchen; Lieber, Richard L

    2013-01-01

    Skeletal muscle function depends on the efficient coordination among subcellular systems. These systems are composed of proteins encoded by a subset of genes, all of which are tightly regulated. In the cases where regulation is altered because of disease or injury, dysfunction occurs. To enable objective analysis of muscle gene expression profiles, we have defined nine biological networks whose coordination is critical to muscle function. We begin by describing the expression of proteins necessary for optimal neuromuscular junction function that results in the muscle cell action potential. That action potential is transmitted to proteins involved in excitation-contraction coupling enabling Ca(2+) release. Ca(2+) then activates contractile proteins supporting actin and myosin cross-bridge cycling. Force generated by cross-bridges is transmitted via cytoskeletal proteins through the sarcolemma and out to critical proteins that support the muscle extracellular matrix. Muscle contraction is fueled through many proteins that regulate energy metabolism. Inflammation is a common response to injury that can result in alteration of many pathways within muscle. Muscle also has multiple pathways that regulate size through atrophy or hypertrophy. Finally, the isoforms associated with fast muscle fibers and their corresponding isoforms in slow muscle fibers are delineated. These nine networks represent important biological systems that affect skeletal muscle function. Combining high-throughput systems analysis with advanced networking software will allow researchers to use these networks to objectively study skeletal muscle systems. PMID:23188744

  19. 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.

  20. Development of Analyses of Biological Steroids Using Chromatography--Special Reference to Vitamin D Compounds and Neurosteroids--

    Institute of Scientific and Technical Information of China (English)

    Kazutake Shimada; Tatsuya Higashi; Kuniko Mitamura

    2003-01-01

    Steroids comprise a large group of natural substances that must frequently be monitored in various biological materials. Due to the metabolic versatility of steroid molecules, extremely complex mixtures are often encountered, necessitating the use of a chromatographic procedure prior to measurement. In this article we present our work, that is, the development of analyses of biological steroids (especially vitamin D compounds and neurosteroids) using gas chromatography/mass spectrometry, high-performance liquid chromatography (including inclusion chromatography using cyclodextrin) and liquid chromatography/mass spectrometry.

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  2. Relative influences of establishing operations and reinforcement contingencies on self-injurious behavior during functional analyses.

    OpenAIRE

    Worsdell, A S; Iwata, B A; Conners, J; Kahng, S W; Thompson, R H

    2000-01-01

    In the typical functional analysis in which the antecedent and consequent events associated with problem behavior are manipulated, the control condition involves elimination of both the relevant establishing operation (EO) and its associated contingency through a schedule of noncontingent reinforcement (usually fixed-time [FT] 30 s). In some functional analyses, however, antecedent events are manipulated in the absence of differential consequences, and a common test condition in such analyses...

  3. Phenological response of a key ecosystem function to biological invasion.

    Science.gov (United States)

    Alp, Maria; Cucherousset, Julien; Buoro, Mathieu; Lecerf, Antoine

    2016-05-01

    Although climate warming has been widely demonstrated to induce shifts in the timing of many biological events, the phenological consequences of other prominent global change drivers remain largely unknown. Here, we investigated the effects of biological invasions on the seasonality of leaf litter decomposition, a crucial freshwater ecosystem function. Decomposition rates were quantified in 18 temperate shallow lakes distributed along a gradient of crayfish invasion and a temperature-based model was constructed to predict yearly patterns of decomposition. We found that, through direct detritus consumption, omnivorous invasive crayfish accelerated decomposition rates up to fivefold in spring, enhancing temperature dependence of the process and shortening the period of major detritus availability in the ecosystem by up to 39 days (95% CI: 15-61). The fact that our estimates are an order of magnitude higher than any previously reported climate-driven phenological shifts indicates that some powerful drivers of phenological change have been largely overlooked. PMID:26931804

  4. Lipids in the structure and functions of biological membranes

    Directory of Open Access Journals (Sweden)

    Kuznetsov V.I.

    2014-06-01

    Full Text Available Lipids are one of the main components of cellular membranes. Lipids make up 30-55% of the cell content depending on the types of cells. Phospholipids, sphingomyelins, cholesterol, etc. are characteristic to cellular membranes. The composition of lipids of the both sides of the membranes differs. This fact determines asymmetry of the structure of bili-pid layer. The reason for many pathologies is the changes in the properties of cellular membranes with the modification of their components. The study of structure and functioning of cellular biomembranes is essential for many researchers. The condition of membranes, their quality, their quantitative composition and modification under the influence of different factors as well as their interaction with carbohydrate and protein component are of great importance for the functioning of both membranes, cells and the body in general. Analysis and structuring of lipids and their functions in biological membranes are studied.

  5. The Impact of Collective Molecular Dynamics on Physiological and Biological Functionalities of Artificial and Biological Membranes

    Science.gov (United States)

    Rheinstadter, Maikel

    2008-03-01

    We use neutron, X-ray and light scattering techniques to determine dynamical and structural properties of artificial and biological membranes. The combination of various techniques enlarges the window to length scales from the nearest-neighbor distances of lipid molecules to more than 10-6m, covering time scales from about 0.1 ps to 1 s. The main research objective is to quantify collective molecular fluctuations in these systems and to establish relationships to physiological and biological functions of the bilayers, such as transmembrane transport. The motivation for this project is twofold: 1) By understanding fundamental properties of bilayers at the microscopic and mesoscopic level, we aim to tailor membranes with specific properties such as permeability and elasticity. 2) By relating dynamical fluctuations to physiological and biological functions, we can gain a deeper understanding of the bilayers on a molecular scale that may help optimizing the transmembrane transport of certain drugs. We show how bilayer permeability, elasticity and inter protein excitations can be determined from the experiments. M.C. Rheinstädter et al., Phys. Rev. Lett. 93, 108107 (2004); Phys. Rev. Lett. 97, 048103 (2006); Phys. Rev. E 75, 011907 (2007);J. Vac. Soc. Technol. A 24, 1191 (2006).

  6. Tubulin acetylation: responsible enzymes, biological functions and human diseases.

    Science.gov (United States)

    Li, Lin; Yang, Xiang-Jiao

    2015-11-01

    Microtubules have important functions ranging from maintenance of cell morphology to subcellular transport, cellular signaling, cell migration, and formation of cell polarity. At the organismal level, microtubules are crucial for various biological processes, such as viral entry, inflammation, immunity, learning and memory in mammals. Microtubules are subject to various covalent modifications. One such modification is tubulin acetylation, which is associated with stable microtubules and conserved from protists to humans. In the past three decades, this reversible modification has been studied extensively. In mammals, its level is mainly governed by opposing actions of α-tubulin acetyltransferase 1 (ATAT1) and histone deacetylase 6 (HDAC6). Knockout studies of the mouse enzymes have yielded new insights into biological functions of tubulin acetylation. Abnormal levels of this modification are linked to neurological disorders, cancer, heart diseases and other pathological conditions, thereby yielding important therapeutic implications. This review summarizes related studies and concludes that tubulin acetylation is important for regulating microtubule architecture and maintaining microtubule integrity. Together with detyrosination, glutamylation and other modifications, tubulin acetylation may form a unique 'language' to regulate microtubule structure and function. PMID:26227334

  7. Biological and physical oceanographic sensitivity analyses for subseabed disposal of high-level waste

    International Nuclear Information System (INIS)

    This report presents an investigation and sensitivity analysis of two segments of the MARINRAD system model - the physical oceanographic and biological transport of radionuclides. MARINRAD is a systems model developed by The Analytic Sciences Corporation to assess the consequences of releasing radioactive wastes into the ocean. The section on physical oceanography covers release rates, partition coefficients (sorption within the water column), and ocean transport parameters. The biological transport section investigates the relative importance of various pathways, concentration factors, and the contribution to the overall dose from the bioaccumulation of radionuclides in a deep-water aquatic food chain

  8. Functionalization of polydopamine coated magnetic nanoparticles with biological entities

    Science.gov (United States)

    Mǎgeruşan, Lidia; Mrówczyński, Radosław; Turcu, Rodica

    2015-12-01

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

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

    Indian Academy of Sciences (India)

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

    2009-10-01

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

  10. Suboptimal geometrical implantation of biological aortic valves provokes functional deficits.

    Science.gov (United States)

    Kuehnel, Ralf-Uwe; Wendt, Max O; Jainski, Ute; Hartrumpf, Martin; Pohl, Manfred; Albes, Johannes M

    2010-06-01

    Endovascular valves have become a valid option for patients not qualifying for conventional surgery. Biological valves mounted in a stent are currently used. After implantation, however, geometrical distortion of the valve can occur. We tested whether biological valves suitable for transcatheter implantation exhibit hemodynamic deficits after deployment in a distorted position. Two types of valves [bovine pericardium (BP) and porcine cusps], of 21 and 23 mm diameter, respectively were investigated. Mean transvalvular gradient (TVG), effective orifice area (EOA), and regurgitation fraction (REG) were measured prior to and after the 20% distortion of the original diameter. All valves exhibited an increase of TVG and reduction of EOA whereas REG increased only in BP valves after distortion. The 21 mm valves demonstrated a more pronounced alteration than the 23 mm valves. Even moderately distorted implantation of a biological valve results in a marked functional alteration. The susceptibility of pericardial valves is higher than that of porcine valves probably owing to better coaptation properties of native cusps even under deformed conditions when compared to valves constructed with pericardium. Care should therefore be taken during implantation of endovascular valves in order to avoid fixed hemodynamic deficits. Native valves may preferably be used as they demonstrate a more robust behavior regarding suboptimal implantation. PMID:20233809

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-10-24

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

  12. Functions of microRNAs in cardiovascular biology and disease.

    Science.gov (United States)

    Hata, Akiko

    2013-01-01

    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

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

    Science.gov (United States)

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

    2013-08-01

    Lactosucrose (O-β-D-galactopyranosyl-(1,4)-O-α-D-glucopyranosyl-(1,2)-β-D-fructofuranoside) is a trisaccharide formed from lactose and sucrose by enzymatic transglycosylation. This rare trisaccharide is a kind of indigestible carbohydrate, has good prebiotic effect, and promotes intestinal mineral absorption. It has been used as a functional ingredient in a range of food products which are approved as foods for specified health uses in Japan. Using lactose and sucrose as substrates, lactosucrose can be produced through transfructosylation by β-fructofuranosidase from Arthrobacter sp. K-1 or a range of levansucrases, or through transgalactosylation by β-galactosidase from Bacillus circulans. This article presented a review of recent studies on the physiological functions of lactosucrose and the biological production from lactose and sucrose by different enzymes. PMID:23828605

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

    International Nuclear Information System (INIS)

    To determine miRNAs and their predicted target proteins regulatory networks which are potentially involved in onset of pulmonary fibrosis in the bleomycin rat model, we conducted integrative miRNA microarray and iTRAQ-coupled LC-MS/MS proteomic analyses, and evaluated the significance of altered biological functions and pathways. We observed that alterations of miRNAs and proteins are associated with the early phase of bleomycin-induced pulmonary fibrosis, and identified potential target pairs by using ingenuity pathway analysis. Using the data set of these alterations, it was demonstrated that those miRNAs, in association with their predicted target proteins, are potentially involved in canonical pathways reflective of initial epithelial injury and fibrogenic processes, and biofunctions related to induction of cellular development, movement, growth, and proliferation. Prediction of activated functions suggested that lung cells acquire proliferative, migratory, and invasive capabilities, and resistance to cell death especially in the very early phase of bleomycin-induced pulmonary fibrosis. The present study will provide new insights for understanding the molecular pathogenesis of idiopathic pulmonary fibrosis. - Highlights: • We analyzed bleomycin-induced pulmonary fibrosis in the rat. • Integrative analyses of miRNA microarray and proteomics were conducted. • We determined the alterations of miRNAs and their potential target proteins. • The alterations may control biological functions and pathways in pulmonary fibrosis. • Our result may provide new insights of pulmonary fibrosis

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

    Energy Technology Data Exchange (ETDEWEB)

    Fukunaga, Satoki [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-Naka, Konohana-ku, Osaka 554-8558 (Japan); Kakehashi, Anna [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Sumida, Kayo; Kushida, Masahiko; Asano, Hiroyuki [Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-Naka, Konohana-ku, Osaka 554-8558 (Japan); Gi, Min [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Wanibuchi, Hideki, E-mail: wani@med.osaka-cu.ac.jp [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan)

    2015-08-01

    To determine miRNAs and their predicted target proteins regulatory networks which are potentially involved in onset of pulmonary fibrosis in the bleomycin rat model, we conducted integrative miRNA microarray and iTRAQ-coupled LC-MS/MS proteomic analyses, and evaluated the significance of altered biological functions and pathways. We observed that alterations of miRNAs and proteins are associated with the early phase of bleomycin-induced pulmonary fibrosis, and identified potential target pairs by using ingenuity pathway analysis. Using the data set of these alterations, it was demonstrated that those miRNAs, in association with their predicted target proteins, are potentially involved in canonical pathways reflective of initial epithelial injury and fibrogenic processes, and biofunctions related to induction of cellular development, movement, growth, and proliferation. Prediction of activated functions suggested that lung cells acquire proliferative, migratory, and invasive capabilities, and resistance to cell death especially in the very early phase of bleomycin-induced pulmonary fibrosis. The present study will provide new insights for understanding the molecular pathogenesis of idiopathic pulmonary fibrosis. - Highlights: • We analyzed bleomycin-induced pulmonary fibrosis in the rat. • Integrative analyses of miRNA microarray and proteomics were conducted. • We determined the alterations of miRNAs and their potential target proteins. • The alterations may control biological functions and pathways in pulmonary fibrosis. • Our result may provide new insights of pulmonary fibrosis.

  16. Ultra-Structure database design methodology for managing systems biology data and analyses

    Directory of Open Access Journals (Sweden)

    Hemminger Bradley M

    2009-08-01

    Full Text Available Abstract Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping. Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find

  17. PRODUCTION PROCESS DESIGN OF FUNCTIONAL FOOD PRODUCTS BASED ON FUNCTIONAL VALUE ANALYSES

    OpenAIRE

    Pershakova T. V.; Shubina L. N.; Derenkova I. A.; Naumov N. N.

    2015-01-01

    The article substantiates the feasibility of the method of functional value analysis application to ensure high efficiency for the production of functional food products. This article describes the design technique of food functionality based on the methodology of value analysis, allowing considering such factors as consumer preferences, nutritional, functional value, economic and technological indicators while developing product formulations and technologies. With the example of flour confec...

  18. Application of gold nanoparticles in electrokinetic analyses and separations of biologically active peptides

    Czech Academy of Sciences Publication Activity Database

    Sýkora, D.; Řezanka, P.; Zvatora, P.; Zimová, M.; Ehala, Sille; Čeřovský, Václav; Kašička, Václav

    2011-01-01

    Roč. 96, č. 4 (2011), s. 454-454. ISSN 1097-0282. [American Peptide Symposium /22./. 25.06.2011-30.06.2011, San Diego] R&D Projects: GA ČR(CZ) GA203/09/0675 Institutional research plan: CEZ:AV0Z40550506 Keywords : gold nanoparticles (GNPs) * opentubular capillary * electrochromatography (OT-CEC) * biologically active peptides Subject RIV: CC - Organic Chemistry

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

    Lifescience Database Archive (English)

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

  20. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

    Directory of Open Access Journals (Sweden)

    Wuyi Liu

    2013-01-01

    Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

  1. Ab initio computational study of vincristine as a biological active compound: NMR and NBO analyses

    Directory of Open Access Journals (Sweden)

    Shiva Joohari

    2015-06-01

    Full Text Available Vincristine is a biological active alkaloid that has been used clinically against a variety of neoplasms. In the current study we have theoretically investigated the magnetic properties of titled compound to predict physical and chemical properties of vincristine as a biological inhibitor. Ab initio computation using HF and B3LYP with 3-21G(d and 6-31G(d level of theory have been performed and then magnetic shielding tensor (, ppm, shielding asymmetry (, magnetic shielding anisotropy (aniso, ppm, the skew of a tensor (K, chemical shift anisotropy ( and chemical shift ( were calculated to indicate the details of the interaction mechanism between microtubules and vincristine. Moreover, EHOMO, ELUMO and Ebg were evaluated. The maximum and minimum values of Ebg were found in HF/3-21g and B3LYP/3-21g respectively. It was also uggested that O24, O37, O49 and O55 with minimum values of iso, are active sites of titled compound. Furthermore the calculated chemical shifts were compared with experimental data in DMSO and CDCl3 solvents.

  2. Use of FISH-translocations analyses for retrospective biological dosimetry: How stable are stable chromosome aberrations?

    International Nuclear Information System (INIS)

    Chromosome aberrations, in particular dicentrics, in peripheral blood lymphocytes are used to estimate the absorbed dose immediately following a radiation accident. However, difficulties for dose estimation arise with old exposures, due to a decline of cells containing unstable dicentric aberrations. The fluorescence in situ hybridisation (FISH) technique employing chromosome specific DNA libraries to 'paint' individual human chromosomes has opened new perspectives for rapid and reliable detection of stable chromosome aberrations such as translocations. The inherent stability of translocations over cell generations has enabled them to be used as a biodosemeter. However, due to the limited life of circulating T-lymphocytes, a level of uncertainty exists on the long-term persistence of stable translocations. The objectives of the present work are to present the current state of knowledge on the stability of translocations detected by FISH. The following aspects have been considered; (1) experience so far of retrospective biological dosimetry in humans following accidental and occupational over-exposure, (2) animal studies using mice and monkeys, (3) the influence of subsequent cell divisions on the yield and persistence of translocations following in vitro irradiation of human lymphocytes, and (4) the needs for further work to standardise and validate the use of FISH as a biological dosemeter, and to investigate the influence of various parameters such as radiation quality, dose rate and the discrimination of sub-types of translocations on persistence. (author)

  3. AFM imaging of functionalized carbon nanotubes on biological membranes

    Science.gov (United States)

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

    2009-10-01

    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.

  4. Biological activity of lactoferrin-functionalized biomimetic hydroxyapatite nanocrystals

    Directory of Open Access Journals (Sweden)

    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

  5. Genome-wide survey for biologically functional pseudogenes.

    Directory of Open Access Journals (Sweden)

    Orjan Svensson

    2006-05-01

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

  6. Genome-wide survey for biologically functional pseudogenes.

    Science.gov (United States)

    Svensson, Orjan; Arvestad, Lars; Lagergren, Jens

    2006-05-01

    According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological function. Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the human-mouse species split, and also a larger group of primate-specific ones found from human-chimpanzee searches. Two processed sequences are notable, their conservation since the human-mouse split being as high as most protein-coding genes; one is derived from the protein Ataxin 7-like 3 (ATX7NL3), and one from the Spinocerebellar ataxia type 1 protein (ATX1). Our approach is comparative and can be applied to any pair of species. It is implemented by a semi-automated pipeline based on cross-species BLAST comparisons and maximum-likelihood phylogeny estimations. To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios. PMID:16680195

  7. Biochemical Properties and Biological Functions of FET Proteins.

    Science.gov (United States)

    Schwartz, Jacob C; Cech, Thomas R; Parker, Roy R

    2015-01-01

    Members of the FET protein family, consisting of FUS, EWSR1, and TAF15, bind to RNA and contribute to the control of transcription, RNA processing, and the cytoplasmic fates of messenger RNAs in metazoa. FET proteins can also bind DNA, which may be important in transcription and DNA damage responses. FET proteins are of medical interest because chromosomal rearrangements of their genes promote various sarcomas and because point mutations in FUS or TAF15 can cause neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar dementia. Recent results suggest that both the normal and pathological effects of FET proteins are modulated by low-complexity or prion-like domains, which can form higher-order assemblies with novel interaction properties. Herein, we review FET proteins with an emphasis on how the biochemical properties of FET proteins may relate to their biological functions and to pathogenesis. PMID:25494299

  8. Comparative genomics of pectinacetylesterases: Insight on function and biology.

    Science.gov (United States)

    de Souza, Amancio José; Pauly, Markus

    2015-01-01

    Pectin acetylation influences the gelling ability of this important plant polysaccharide for the food industry. Plant apoplastic pectinacetylesterases (PAEs) play a key role in regulating the degree of pectin acetylation and modifying their expression thus represents one way to engineer plant polysaccharides for food applications. Identifying the major active enzymes within the PAE gene family will aid in our understanding of this biological phenomena as well as provide the tools for direct trait manipulation. Using comparative genomics we propose that there is a minimal set of 4 distinct PAEs in plants. Possible functional diversification of the PAE family in the grasses is also explored with the identification of 3 groups of PAE genes specific to grasses. PMID:26237162

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

    Directory of Open Access Journals (Sweden)

    Sara Franceschelli

    2013-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Daria Van Tyne

    2013-04-01

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

  11. Functionalized nanoparticles for biological imaging and detection applications

    Science.gov (United States)

    Mei, Bing C.

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

  12. Crucial role of detailed function, task, timeline, link and human vulnerability analyses in HRA

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, T.G.; Haney, L.N.; Ostrom, L.T.

    1992-10-01

    This paper addresses one major cause for large uncertainties in human reliability analysis (HRA) results, that is, an absence of detailed function, task, timeline, link and human vulnerability analyses. All too often this crucial step in the HRA process is done in a cursory fashion using word of mouth or written procedures which themselves may incompletely or inaccurately represent the human action sequences and human error vulnerabilities being analyzed. The paper examines the potential contributions these detailed analyses can make in achieving quantitative and qualitative HRA results which are: (1) creditable, that is, minimize uncertainty, (2) auditable, that is, systematically linking quantitative results and qualitative information from which the results are derived, (3) capable of supporting root cause analyses on human reliability factors determined to be major contributors to risk, and (4) capable of repeated measures and being combined with similar results from other analyses to examine HRA issues transcending individual systems and facilities. Based on experience analyzing test and commercial nuclear reactors, and medical applications of nuclear technology, an iterative process is suggested for doing detailed function, task, timeline, link and human vulnerability analyses using documentation reviews, open-ended and structured interviews, direct observations, and group techniques. Finally, the paper concludes that detailed analyses done in this manner by knowledgeable human factors practitioners, can contribute significantly to the credibility, auditability, causal factor analysis, and combining goals of the HRA.

  13. Lung function, biological monitoring, and biological effect monitoring of gemstone cutters exposed to beryls

    Science.gov (United States)

    Wegner, R.; Heinrich-Ramm, R.; Nowak, D.; Olma, K.; Poschadel, B.; Szadkowski, D.

    2000-01-01

    OBJECTIVES—Gemstone cutters are potentially exposed to various carcinogenic and fibrogenic metals such as chromium, nickel, aluminium, and beryllium, as well as to lead. Increased beryllium concentrations had been reported in the air of workplaces of beryl cutters in Idar-Oberstein, Germany. The aim of the survey was to study the excretion of beryllium in cutters and grinders with occupational exposure to beryls—for example, aquamarines and emeralds—to examine the prevalence of beryllium sensitisation with the beryllium lymphocyte transformation test (BeLT), to examine the prevalence of lung disease induced by beryllium, to describe the internal load of the respective metals relative to work process, and to screen for genotoxic effects in this particular profession.
METHODS—In a cross sectional investigation, 57 out of 100 gemstone cutters working in 12 factories in Idar-Oberstein with occupational exposure to beryls underwent medical examinations, a chest radiograph, lung function testing (spirometry, airway resistance with the interrupter technique), and biological monitoring, including measurements of aluminium, chromium, and nickel in urine as well as lead in blood. Beryllium in urine was measured with a newly developed direct electrothermal atomic absorption spectroscopy technique with a measurement limit of 0.06 µg/l. Also, cytogenetic tests (rates of micronuclei and sister chromatid exchange), and a BeLT were performed. Airborne concentrations of beryllium were measured in three factories. As no adequate local control group was available, the cutters were categorised into those with an exposure to beryls of >4 hours/week (group A) and ⩽4 hours/week (group B).
RESULTS—Clinical, radiological, or spirometric abnormalities indicating pneumoconiosis were detected in none of the gemstone cutters. Metal concentrations in biological material were far below the respective biological limit values, and beryllium in urine was only measurable in

  14. Functional analyses of the digestive ß-Glucosidase of Formosan Subterranean Termites (Coptotermes formosanus)

    Science.gov (United States)

    The research was to elucidate the function of the ß-glucosidase of Formosan subterranean termites in vitro and in vivo. Quantitative RT-PCR analyses indicated that the gene transcript was relatively more abundant in the foraging worker caste than in other castes and salivary glands were the major ex...

  15. Chemical and Biological Analyses of the Essential Oils and Main Constituents of Piper Species

    Directory of Open Access Journals (Sweden)

    Leonor Laura Leon

    2012-02-01

    Full Text Available The essential oils obtained from leaves of Piper duckei and Piper demeraranum by hydrodistillation were analyzed by gas chromatography-mass spectrometry. The main constituents found in P. demeraranum oil were limonene (19.3% and β-elemene (33.1% and in P. duckei oil the major components found were germacrene D (14.7% and trans-caryophyllene (27.1%. P. demeraranum and P. duckei oils exhibited biological activity, with IC50 values between 15 to 76 μg mL−1 against two Leishmania species, P. duckei oil being the most active. The cytotoxicity of the essential oils on mice peritoneal macrophage cells was insignificant, compared with the toxicity of pentamidine. The main mono- and sesquiterpene, limonene (IC50 = 278 μM and caryophyllene (IC50 = 96 μM, were tested against the strains of Leishmania amazonensis, and the IC50 values of these compounds were lower than those found for the essential oils of the Piper species. The HET-CAM test was used to evaluate the irritation potential of these oils as topical products, showing that these oils can be used as auxiliary medication in cases of cutaneous leishmaniasis, with less side effects and lower costs.

  16. Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution.

    Directory of Open Access Journals (Sweden)

    Sabrina Renaud

    Full Text Available Geometric morphometrics aims to characterize of the geometry of complex traits. It is therefore by essence multivariate. The most popular methods to investigate patterns of differentiation in this context are (1 the Principal Component Analysis (PCA, which is an eigenvalue decomposition of the total variance-covariance matrix among all specimens; (2 the Canonical Variate Analysis (CVA, a.k.a. linear discriminant analysis (LDA for more than two groups, which aims at separating the groups by maximizing the between-group to within-group variance ratio; (3 the between-group PCA (bgPCA which investigates patterns of between-group variation, without standardizing by the within-group variance. Standardizing within-group variance, as performed in the CVA, distorts the relationships among groups, an effect that is particularly strong if the variance is similarly oriented in a comparable way in all groups. Such shared direction of main morphological variance may occur and have a biological meaning, for instance corresponding to the most frequent standing genetic variation in a population. Here we undertake a case study of the evolution of house mouse molar shape across various islands, based on the real dataset and simulations. We investigated how patterns of main variance influence the depiction of among-group differentiation according to the interpretation of the PCA, bgPCA and CVA. Without arguing about a method performing 'better' than another, it rather emerges that working on the total or between-group variance (PCA and bgPCA will tend to put the focus on the role of direction of main variance as line of least resistance to evolution. Standardizing by the within-group variance (CVA, by dampening the expression of this line of least resistance, has the potential to reveal other relevant patterns of differentiation that may otherwise be blurred.

  17. Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution.

    Science.gov (United States)

    Renaud, Sabrina; Dufour, Anne-Béatrice; Hardouin, Emilie A; Ledevin, Ronan; Auffray, Jean-Christophe

    2015-01-01

    Geometric morphometrics aims to characterize of the geometry of complex traits. It is therefore by essence multivariate. The most popular methods to investigate patterns of differentiation in this context are (1) the Principal Component Analysis (PCA), which is an eigenvalue decomposition of the total variance-covariance matrix among all specimens; (2) the Canonical Variate Analysis (CVA, a.k.a. linear discriminant analysis (LDA) for more than two groups), which aims at separating the groups by maximizing the between-group to within-group variance ratio; (3) the between-group PCA (bgPCA) which investigates patterns of between-group variation, without standardizing by the within-group variance. Standardizing within-group variance, as performed in the CVA, distorts the relationships among groups, an effect that is particularly strong if the variance is similarly oriented in a comparable way in all groups. Such shared direction of main morphological variance may occur and have a biological meaning, for instance corresponding to the most frequent standing genetic variation in a population. Here we undertake a case study of the evolution of house mouse molar shape across various islands, based on the real dataset and simulations. We investigated how patterns of main variance influence the depiction of among-group differentiation according to the interpretation of the PCA, bgPCA and CVA. Without arguing about a method performing 'better' than another, it rather emerges that working on the total or between-group variance (PCA and bgPCA) will tend to put the focus on the role of direction of main variance as line of least resistance to evolution. Standardizing by the within-group variance (CVA), by dampening the expression of this line of least resistance, has the potential to reveal other relevant patterns of differentiation that may otherwise be blurred. PMID:26192946

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

    Science.gov (United States)

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

    2016-03-01

    The study examined how the interplay between children's cortisol response and family income is related to executive function (EF) skills. The sample included one hundred and two 5- to 6-year-olds (64% minority). EF skills were measured using laboratory tasks and observer ratings. Physiological reactivity was assessed via cortisol response during a laboratory visit. A consistent, positive association between family income and EF skills emerged only for children who showed high cortisol response, a marker of biological sensitivity to context. In contrast, family income was not related to EF skills in children who displayed low cortisol response. Follow-up analyses revealed a disordinal interaction, suggesting that differential susceptibility can be detected at the level of basic cognitive and self-regulatory skills that support adaptive functioning. PMID:26709089

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

    Science.gov (United States)

    Meng, Linghui

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

  20. Resilin-Like Polypeptide Hydrogels Engineered for Versatile Biological Functions.

    Science.gov (United States)

    Li, Linqing; Tong, Zhixiang; Jia, Xinqiao; Kiick, Kristi L

    2013-01-01

    Natural resilin, the rubber-like protein that exists in specialized compartments of most arthropods, possesses excellent mechanical properties such as low stiffness, high resilience and effective energy storage. Recombinantly-engineered resilin-like polypeptides (RLPs) that possess the favorable attributes of native resilin would be attractive candidates for the modular design of biomaterials for engineering mechanically active tissues. Based on our previous success in creating a novel RLP-based hydrogel and demonstrating useful mechanical and cell-adhesive properties, we have produced a suite of new RLP-based constructs, each equipped with 12 repeats of the putative resilin consensus sequence and a single, distinct biologically active domain. This approach allows independent control over the concentrations of cell-binding, MMP-sensitive, and polysaccharide-sequestration domains in hydrogels comprising mixtures of the various RLPs. The high purity, molecular weight and correct compositions of each new polypeptide have been confirmed via high performance liquid chromatography (HPLC), sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), and amino acid analysis. These RLP-based polypeptides exhibit largely random-coil conformation, both in solution and in the cross-linked hydrogels, as indicated by circular dichroic and infrared spectroscopic analyses. Hydrogels of various compositions, with a range of elastic moduli (1kPa to 25kPa) can be produced from these polypeptides, and the activity of the cell-binding and matrix metalloproteinase (MMP) sensitive domains was confirmed. Tris(hydroxymethyl phosphine) cross-linked RLP hydrogels were able to maintain their mechanical integrity as well as the viability of encapsulated primary human mesenchymal stem cells (MSCs). These results validate the promising properties of these RLP-based elastomeric biomaterials. PMID:23505396

  1. Heme-nitrosyls: electronic structure implications for function in biology.

    Science.gov (United States)

    Hunt, Andrew P; Lehnert, Nicolai

    2015-07-21

    The question of why mammalian systems use nitric oxide (NO), a potentially hazardous and toxic diatomic, as a signaling molecule to mediate important functions such as vasodilation (blood pressure control) and nerve signal transduction initially perplexed researchers when this discovery was made in the 1980s. Through extensive research over the past two decades, it is now well rationalized why NO is used in vivo for these signaling functions, and that heme proteins play a dominant role in NO signaling in mammals. Key insight into the properties of heme-nitrosyl complexes that make heme proteins so well poised to take full advantage of the unique properties of NO has come from in-depth structural, spectroscopic, and theoretical studies on ferrous and ferric heme-nitrosyls. This Account highlights recent findings that have led to greater understanding of the electronic structures of heme-nitrosyls, and the contributions that model complex studies have made to elucidate Fe-NO bonding are highlighted. These results are then discussed in the context of the biological functions of heme-nitrosyls, in particular in soluble guanylate cyclase (sGC; NO signaling), nitrophorins (NO transport), and NO-producing enzymes. Central to this Account is the thermodynamic σ-trans effect of NO, and how this relates to the activation of the universal mammalian NO sensor sGC, which uses a ferrous heme as the high affinity "NO detection unit". It is shown via detailed spectroscopic and computational studies that the strong and very covalent Fe(II)-NO σ-bond is at the heart of the strong thermodynamic σ-trans effect of NO, which greatly weakens the proximal Fe-NHis (or Fe-SCys) bond in six-coordinate ferrous heme-nitrosyls. In sGC, this causes the dissociation of the proximally bound histidine ligand upon NO binding to the ferrous heme, inducing a significant conformational change that activates the sGC catalytic domain for the production of cGMP. This, in turn, leads to vasodilation and

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

    Directory of Open Access Journals (Sweden)

    Vojvodić Svetlana

    2010-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Nicole Shangming Hou

    2012-05-01

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

  4. Phytochrome from Green Plants: Properties and biological Function

    Energy Technology Data Exchange (ETDEWEB)

    Quail, Peter H.

    2014-07-25

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

  5. radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar

    Directory of Open Access Journals (Sweden)

    Matkovich Carolyn

    2010-10-01

    Full Text Available Abstract Background Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Results Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card and extracts and retains information of biological relevance (i.e. moving targets. Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Conclusions Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets.

  6. Comparative transcriptome analyses of seven anurans reveal functions and adaptations of amphibian skin

    Science.gov (United States)

    Huang, Li; Li, Jun; Anboukaria, Housseni; Luo, Zhenhua; Zhao, Mian; Wu, Hua

    2016-01-01

    Animal skin, which is the tissue that directly contacts the external surroundings, has evolved diverse functions to adapt to various environments. Amphibians represent the transitional taxon from aquatic to terrestrial life. Exploring the molecular basis of their skin function and adaptation is important to understand the survival and evolutionary mechanisms of vertebrates. However, comprehensive studies on the molecular mechanisms of skin functions in amphibians are scarce. In this study, we sequenced the skin transcriptomes of seven anurans belonging to three families and compared the similarities and differences in expressed genes and proteins. Unigenes and pathways related to basic biological processes and special functions, such as defense, immunity, and respiration, were enriched in functional annotations. A total of 108 antimicrobial peptides were identified. The highly expressed genes were similar in species of the same family but were different among families. Additionally, the positively selected orthologous groups were involved in biosynthesis, metabolism, immunity, and defense processes. This study is the first to generate extensive transcriptome data for the skin of seven anurans and provides unigenes and pathway candidates for further studies on amphibian skin function and adaptation. PMID:27040083

  7. Comparative analyses of quaternary arrangements in homo-oligomeric proteins in superfamilies: Functional implications.

    Science.gov (United States)

    Sudha, Govindarajan; Srinivasan, Narayanaswamy

    2016-09-01

    A comprehensive analysis of the quaternary features of distantly related homo-oligomeric proteins is the focus of the current study. This study has been performed at the levels of quaternary state, symmetry, and quaternary structure. Quaternary state and quaternary structure refers to the number of subunits and spatial arrangements of subunits, respectively. Using a large dataset of available 3D structures of biologically relevant assemblies, we show that only 53% of the distantly related homo-oligomeric proteins have the same quaternary state. Considering these homologous homo-oligomers with the same quaternary state, conservation of quaternary structures is observed only in 38% of the pairs. In 36% of the pairs of distantly related homo-oligomers with different quaternary states the larger assembly in a pair shows high structural similarity with the entire quaternary structure of the related protein with lower quaternary state and it is referred as "Russian doll effect." The differences in quaternary state and structure have been suggested to contribute to the functional diversity. Detailed investigations show that even though the gross functions of many distantly related homo-oligomers are the same, finer level differences in molecular functions are manifested by differences in quaternary states and structures. Comparison of structures of biological assemblies in distantly and closely related homo-oligomeric proteins throughout the study differentiates the effects of sequence divergence on the quaternary structures and function. Knowledge inferred from this study can provide insights for improved protein structure classification and function prediction of homo-oligomers. Proteins 2016; 84:1190-1202. © 2016 Wiley Periodicals, Inc. PMID:27177429

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

    OpenAIRE

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

    2013-01-01

    Background 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 natu...

  9. Enzyme analyses of the acute damage of liver function by LP-TAE treatment

    International Nuclear Information System (INIS)

    Objective: To evaluate the changes of enzyme for acute damage to liver function during the treatment of big hepatic carcinoma by Lipiodol-Transcatheter Arterial Embolization (LP-TAE) and analyze the influence to acute liver function change concerned with different doses of Lipiodol (LP). Methods: 30 patients of big hepatic carcinoma diagnosed by CT, MRI, DSA etc. were collected with the venous blood samples before and the third day after by Lp-TAE treatment together with analyses of the relation between the changes of enzyme and the doses of Lipiodol (LP). Results: All cases suffered from acute liver dysfunction to a greater or less extent correlative with different doses of lipiodol. Conclusions: The proper proportion of doses between lipiodol and anti-cancerous drugs should be emphasized during treatment of LP-TAE in big hepatic cancers for prevention of liver dis-function, furthermore with hope to have a rule for lipiodol dosage

  10. Molecular eco-systems biology: towards an understanding of community function

    OpenAIRE

    Raes, J.; Bork, P.

    2008-01-01

    Systems-biology approaches, which are driven by genome sequencing and high-throughput functional genomics data, are revolutionizing single-cell-organism biology. With the advent of various high-throughput techniques that aim to characterize complete microbial ecosystems (metagenomics, meta-transcriptomics and meta-metabolomics), we propose that the time is ripe to consider molecular systems biology at the ecosystem level (eco-systems biology). Here, we discuss the necessary data types that ar...

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

    OpenAIRE

    Knüpfer, Christian; Beckstein, Clemens

    2013-01-01

    Background 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. Results In this paper we describe different functional aspects of dynamic models. This descriptio...

  12. The IWOP Technique and Wigner-Function Approach to Quantum Effect of Mesoscopic Biological Cell

    Science.gov (United States)

    Wang, Xiu-Xia

    2014-09-01

    Using the IWOP technique, Wigner function theory and TFD theory, the quantization of a mesoscopic biological cell equivalent circuit is proposed, The quantum fluctuations of the mesoscopic biological cell are researched in thermal vacuum state and vacuum state. It is shown that the IWOP technique, Wigner function theory and Umezawa-Takahashi's TFD theory play the key role in quantizing a mesoscopic biological cell at finite temperature and the fluctuations and uncertainty increase with increasing temperature and decrease with prolonged time.

  13. Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function.

    Directory of Open Access Journals (Sweden)

    Wenbo Tang

    Full Text Available Genome-wide association studies (GWAS have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function.We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1 in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis.The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P  =  5.71 × 10(-7. In addition, meta-analysis using the five cohorts with ≥3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P  =  2.18 × 10(-8 at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively.In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function.

  14. Large-Scale Genome-Wide Association Studies and Meta-Analyses of Longitudinal Change in Adult Lung Function

    Science.gov (United States)

    Tang, Wenbo; Kowgier, Matthew; Loth, Daan W.; Soler Artigas, María; Joubert, Bonnie R.; Hodge, Emily; Gharib, Sina A.; Smith, Albert V.; Ruczinski, Ingo; Gudnason, Vilmundur; Mathias, Rasika A.; Harris, Tamara B.; Hansel, Nadia N.; Launer, Lenore J.; Barnes, Kathleen C.; Hansen, Joyanna G.; Albrecht, Eva; Aldrich, Melinda C.; Allerhand, Michael; Barr, R. Graham; Brusselle, Guy G.; Couper, David J.; Curjuric, Ivan; Davies, Gail; Deary, Ian J.; Dupuis, Josée; Fall, Tove; Foy, Millennia; Franceschini, Nora; Gao, Wei; Gläser, Sven; Gu, Xiangjun; Hancock, Dana B.; Heinrich, Joachim; Hofman, Albert; Imboden, Medea; Ingelsson, Erik; James, Alan; Karrasch, Stefan; Koch, Beate; Kritchevsky, Stephen B.; Kumar, Ashish; Lahousse, Lies; Li, Guo; Lind, Lars; Lindgren, Cecilia; Liu, Yongmei; Lohman, Kurt; Lumley, Thomas; McArdle, Wendy L.; Meibohm, Bernd; Morris, Andrew P.; Morrison, Alanna C.; Musk, Bill; North, Kari E.; Palmer, Lyle J.; Probst-Hensch, Nicole M.; Psaty, Bruce M.; Rivadeneira, Fernando; Rotter, Jerome I.; Schulz, Holger; Smith, Lewis J.; Sood, Akshay; Starr, John M.; Strachan, David P.; Teumer, Alexander; Uitterlinden, André G.; Völzke, Henry; Voorman, Arend; Wain, Louise V.; Wells, Martin T.; Wilk, Jemma B.; Williams, O. Dale; Heckbert, Susan R.; Stricker, Bruno H.; London, Stephanie J.; Fornage, Myriam; Tobin, Martin D.; O′Connor, George T.; Hall, Ian P.; Cassano, Patricia A.

    2014-01-01

    Background Genome-wide association studies (GWAS) have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function. Methods We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1) in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis. Results The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P  =  5.71 × 10-7). In addition, meta-analysis using the five cohorts with ≥3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P  =  2.18 × 10-8) at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively. Conclusions In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function. PMID:24983941

  15. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S

    2014-06-12

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  16. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    Directory of Open Access Journals (Sweden)

    Ari J S Ferreira

    Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...

  18. The effects of ropivacaine hydrochloride on platelet function: an assessment using the platelet function analyser (PFA-100).

    LENUS (Irish Health Repository)

    Porter, J

    2012-02-03

    Amide local anaesthetics impair blood clotting in a concentration-dependent manner by inhibition of platelet function and enhanced fibrinolysis. We hypothesised that the presence of ropivacaine in the epidural space could decrease the efficacy of an epidural blood patch, as this technique requires that the injected blood can clot in order to be effective. Ropivacaine is an aminoamide local anaesthetic used increasingly for epidural analgesia during labour. The concentration of local anaesthetic in blood achieved in the epidural space during the performance of an epidural blood patch is likely to be the greatest which occurs (intentionally) in any clinical setting. This study was undertaken to investigate whether concentrations of ropivacaine in blood, which could occur: (i) clinically in the epidural space and (ii) in plasma during an epidural infusion of ropivacaine, alter platelet function. A platelet function analyser (Dade PFA-100, Miami) was employed to assess the effects of ropivacaine-treated blood on platelet function. The greater concentrations of ropivacaine studied (3.75 and 1.88 mg x ml(-1)), which correspond to those which could occur in the epidural space, produced significant inhibition of platelet aggregation. We conclude that the presence of ropivacaine in the epidural space may decrease the efficacy of an early or prophylactic epidural blood patch.

  19. Structural and functional analyses of the putrescine binding protein PotF from Xanthomonas citri

    International Nuclear Information System (INIS)

    Full text: The focus of our group is to determinate the role of ABC transporters in the physiology and growth of Xanthomonas citri, a phytopathogenic bacteria that infects citrus plants causing significant losses for the economy. One of the ABC transporters identified in the X. citri genome and that was showed to be active during the infection in Citrus sinensis plants was the putrescine transporter. This transporter consists of two internal membrane proteins PotG and PotH that form a pore, a cytoplasmic protein that gives energy for the transport and the periplasmic-binding protein PotF, which is responsible for the affinity and specificity of the system. Its function is associated to the microbial carcinogenesis, biofilm formation, escape from phagolysosomes, bacteriocin production, toxin activity and protection from oxidative and acid stress. In this work, we show for the first time, the expression, purification, functional and structural analyses of the X. citri PotF protein. The PotF was expressed from Escherichia coli cells strain Arctic, as a 40 kDa soluble protein, after induction of IPTG for twenty four hours at thirteen deg C. Using immobilized metal affinity chromatography for purification, the protein was eluted in the fractions with 10-500 mM of imidazole. To test the folding and cability to bind putrescine, spectroscopic analyses were performed using circular dichroism and intrinsic fluorescence. The data showed that PotF suffers conformational changes in presence of ligands and in different pH, suggesting a possible interaction with the tested ligand. Moreover, based on bioinformatics studies and molecular modeling analyses, we showed that X. citri PotF is highly conserved when compared to orthologs present in other bacteria, including the residues that form the ligand-binding site. The production of PotF in a soluble and stable form will allow us to start the crystallization trials in attempt to solve its structure. (author)

  20. Structural and functional analyses of the putrescine binding protein PotF from Xanthomonas citri

    Energy Technology Data Exchange (ETDEWEB)

    Santana, L.D.F.; Balan, A. [Laboratorio Nacional de Biociencias - LNBIO, Campinas, SP (Brazil)

    2012-07-01

    Full text: The focus of our group is to determinate the role of ABC transporters in the physiology and growth of Xanthomonas citri, a phytopathogenic bacteria that infects citrus plants causing significant losses for the economy. One of the ABC transporters identified in the X. citri genome and that was showed to be active during the infection in Citrus sinensis plants was the putrescine transporter. This transporter consists of two internal membrane proteins PotG and PotH that form a pore, a cytoplasmic protein that gives energy for the transport and the periplasmic-binding protein PotF, which is responsible for the affinity and specificity of the system. Its function is associated to the microbial carcinogenesis, biofilm formation, escape from phagolysosomes, bacteriocin production, toxin activity and protection from oxidative and acid stress. In this work, we show for the first time, the expression, purification, functional and structural analyses of the X. citri PotF protein. The PotF was expressed from Escherichia coli cells strain Arctic, as a 40 kDa soluble protein, after induction of IPTG for twenty four hours at thirteen deg C. Using immobilized metal affinity chromatography for purification, the protein was eluted in the fractions with 10-500 mM of imidazole. To test the folding and cability to bind putrescine, spectroscopic analyses were performed using circular dichroism and intrinsic fluorescence. The data showed that PotF suffers conformational changes in presence of ligands and in different pH, suggesting a possible interaction with the tested ligand. Moreover, based on bioinformatics studies and molecular modeling analyses, we showed that X. citri PotF is highly conserved when compared to orthologs present in other bacteria, including the residues that form the ligand-binding site. The production of PotF in a soluble and stable form will allow us to start the crystallization trials in attempt to solve its structure. (author)

  1. Functional analyses of cellulose synthase genes in flax (Linum usitatissimum) by virus-induced gene silencing.

    Science.gov (United States)

    Chantreau, Maxime; Chabbert, Brigitte; Billiard, Sylvain; Hawkins, Simon; Neutelings, Godfrey

    2015-12-01

    Flax (Linum usitatissimum) bast fibres are located in the stem cortex where they play an important role in mechanical support. They contain high amounts of cellulose and so are used for linen textiles and in the composite industry. In this study, we screened the annotated flax genome and identified 14 distinct cellulose synthase (CESA) genes using orthologous sequences previously identified. Transcriptomics of 'primary cell wall' and 'secondary cell wall' flax CESA genes showed that some were preferentially expressed in different organs and stem tissues providing clues as to their biological role(s) in planta. The development for the first time in flax of a virus-induced gene silencing (VIGS) approach was used to functionally evaluate the biological role of different CESA genes in stem tissues. Quantification of transcript accumulation showed that in many cases, silencing not only affected targeted CESA clades, but also had an impact on other CESA genes. Whatever the targeted clade, inactivation by VIGS affected plant growth. In contrast, only clade 1- and clade 6-targeted plants showed modifications in outer-stem tissue organization and secondary cell wall formation. In these plants, bast fibre number and structure were severely impacted, suggesting that the targeted genes may play an important role in the establishment of the fibre cell wall. Our results provide new fundamental information about cellulose biosynthesis in flax that should facilitate future plant improvement/engineering. PMID:25688574

  2. To What Extent do Biology Textbooks Contribute to Scientific Literacy? Criteria for Analysing Science-Technology-Society-Environment Issues

    Directory of Open Access Journals (Sweden)

    Florbela M. Calado

    2015-10-01

    Full Text Available Our article proposes a set of six criteria for analysing science-technology-society-environment (STSE issues in regular textbooks as to how they are expected to contribute to students’ scientific literacy. We chose genetics and gene technology as fields prolific in STSE issues. We derived our criteria (including 26 sub-criteria from a literature review of the debate in science education on how to increase scientific literacy. We inspected the textbooks regarding the relationships between science, technology, society, and environment, and considered the presence of the decontextualized and socially neutral view of science as distorted view. We, qualitatively and quantitatively, applied our set of criteria to two German Biology textbooks and identified, in total, 718 STSE statements. Based on the frequencies of different criteria and sub-criteria in the textbooks, we drew conclusions concerning STSE issues and the underlying conceptions of science and technology, which might hinder the furtherance of scientific literacy. The applicability of our approach in other science education contexts is discussed.

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

    Directory of Open Access Journals (Sweden)

    Xiaowei eMa

    2014-02-01

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

  4. Normal form from biological motion despite impaired ventral stream function

    OpenAIRE

    Gilaie-Dotan, S.; Bentin, S.; Harel, M; Rees, G.; Saygin, A.P.

    2011-01-01

    We explored the extent to which biological motion perception depends on ventral stream integration by studying LG, an unusual case of developmental visual agnosia. LG has significant ventral stream processing deficits but no discernable structural cortical abnormality. LG's intermediate visual areas and object-sensitive regions exhibit abnormal activation during visual object perception, in contrast to area V5/MT+ which responds normally to visual motion (Gilaie-Dotan, Perry, Bonneh, Malach, ...

  5. Computational Exploration of the Biological Basis of Black-Scholes Expected Utility Function

    OpenAIRE

    Sukanto Bhattacharya; Kuldeep Kumar

    2007-01-01

    It has often been argued that there exists an underlying biological basis of utility functions. Taking this line of argument a step further in this paper, we have aimed to computationally demonstrate the biological basis of the Black-Scholes functional form as applied to classical option pricing and hedging theory. The evolutionary optimality of the classical Black-Scholes function has been computationally established by means of a haploid genetic algorithm model. The objective was to minimiz...

  6. Computational Exploration of the Biological Basis of Black-Scholes Expected Utility Function

    OpenAIRE

    Kuldeep Kumar; Sukanto Bhattacharya

    2007-01-01

    It has often been argued that there exists an underlying biological basis of utility functions. Taking this line of argument a step further in this paper, we have aimed to computationally demonstrate the biological basis of the Black-Scholes functional form as applied to classical option pricing and hedging theory. The evolutionary optimality of the classical Black-Scholes function has been computationally established by means of a haploid genetic algorithm model. The objective was to mi...

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

    International Nuclear Information System (INIS)

    The H2O substitution for D2O 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)

  8. 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/. PMID:27446133

  9. Phenetic and functional analyses of the distal ulna of Australopithecus afarensis and Australopithecus africanus.

    Science.gov (United States)

    Tallman, Melissa

    2015-01-01

    The morphology of the distal portion of the hominoid ulna is poorly studied despite its important functional role at the wrist joint. There are five qualitatively well-described fossil hominin distal ulnae belonging to Australopithecus afarensis and Australopithecus africanus, but there have been few efforts to quantify their morphology or relate it to their functional abilities. This article presents an effort to do so, using three-dimensional geometric morphometrics to analyze the shape of the distal ulna of the Plio-Pleistocene hominins and an extant comparative sample of great apes and humans. For the extant taxa, results show that the morphology of Pan and Pongo is distinct from that of Homo, and that these differences are likely related to climbing, clambering and below-branch suspension in the former, and the release of the limbs from locomotion and (potentially) tool manufacture in the latter. For the australopiths, results indicate that the A. afarensis sample is relatively heterogeneous. These results are driven by the morphology of A.L. 333-12, which is the largest ulna in the sample and has a unique combination of traits when compared with the other two A. afarensis specimens. Overall, the morphology of all the hominins was most consistent with the pattern displayed by extant great apes, and specifically Pan and Pongo; however, large overlap in shape in the distal ulna in the extant sample indicates that other areas of the skeleton may be more informative for functional analyses. PMID:25529241

  10. Inferring biological functions of guanylyl cyclases with computational methods

    KAUST Repository

    Alquraishi, May Majed

    2013-09-03

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

  11. Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury.

    Science.gov (United States)

    Duan, Hongmei; Ge, Weihong; Zhang, Aifeng; Xi, Yue; Chen, Zhihua; Luo, Dandan; Cheng, Yin; Fan, Kevin S; Horvath, Steve; Sofroniew, Michael V; Cheng, Liming; Yang, Zhaoyang; Sun, Yi E; Li, Xiaoguang

    2015-10-27

    Spinal cord injury (SCI) is considered incurable because axonal regeneration in the central nervous system (CNS) is extremely challenging, due to harsh CNS injury environment and weak intrinsic regeneration capability of CNS neurons. We discovered that neurotrophin-3 (NT3)-loaded chitosan provided an excellent microenvironment to facilitate nerve growth, new neurogenesis, and functional recovery of completely transected spinal cord in rats. To acquire mechanistic insight, we conducted a series of comprehensive transcriptome analyses of spinal cord segments at the lesion site, as well as regions immediately rostral and caudal to the lesion, over a period of 90 days after SCI. Using weighted gene coexpression network analysis (WGCNA), we established gene modules/programs corresponding to various pathological events at different times after SCI. These objective measures of gene module expression also revealed that enhanced new neurogenesis and angiogenesis, and reduced inflammatory responses were keys to conferring the effect of NT3-chitosan on regeneration. PMID:26460053

  12. Non-coding RNAs: Classification, Biology and Functioning.

    Science.gov (United States)

    Hombach, Sonja; Kretz, Markus

    2016-01-01

    One of the long-standing principles of molecular biology is that DNA acts as a template for transcription of messenger RNAs, which serve as blueprints for protein translation. A rapidly growing number of exceptions to this rule have been reported over the past decades: they include long known classes of RNAs involved in translation such as transfer RNAs and ribosomal RNAs, small nuclear RNAs involved in splicing events, and small nucleolar RNAs mainly involved in the modification of other small RNAs, such as ribosomal RNAs and transfer RNAs. More recently, several classes of short regulatory non-coding RNAs, including piwi-associated RNAs, endogenous short-interfering RNAs and microRNAs have been discovered in mammals, which act as key regulators of gene expression in many different cellular pathways and systems. Additionally, the human genome encodes several thousand long non-protein coding RNAs >200 nucleotides in length, some of which play crucial roles in a variety of biological processes such as epigenetic control of chromatin, promoter-specific gene regulation, mRNA stability, X-chromosome inactivation and imprinting. In this chapter, we will introduce several classes of short and long non-coding RNAs, describe their diverse roles in mammalian gene regulation and give examples for known modes of action. PMID:27573892

  13. Evaluation of an extraction method for a mixture of endocrine disrupters in sediment using chemical and in vitro biological analyses.

    Science.gov (United States)

    Creusot, Nicolas; Dévier, Marie-Hélène; Budzinski, Hélène; Aït-Aïssa, Selim

    2016-06-01

    Aquatic sediments are contaminated by a wide diversity of organic pollutants such as endocrine-disrupting chemicals (EDCs) which encompass a broad range of chemical classes having natural and anthropogenic origins. The use of in vitro bioassays is now widely accepted as an alternative method for their detection in complex samples. However, based on the diversity of EDC chemical properties, their common extraction is difficult and comprehensive validation of extraction methods for a bioanalysis purpose is still weakly documented. In this study, we compared the performance of several organic solvents, i.e., acetone, methanol, dichloromethane, heptane, dichloromethane/acetone (50:50, v/v), dichloromethane/methanol (50:50, v/v), heptane/acetone (50:50, v/v), and heptane/methanol (50:50, v/v), to extract a diversity of active chemicals from a spiked sediment matrix using pressurized liquid extraction. For this purpose, we defined a mixture of 12 EDCs with a wide range of polarity (2 PCB-126, 2,3,7,8 TCDD, benzo[k]fluoranthene, and dibenzo[a,h]anthracene). Working concentrations of each individual compound in the mixture were determined as equipotent concentrations on the basis of the concentration-addition (CA) model applied to in vitro estrogenic, dioxin-like, and pregnane X receptor (PXR)-like activities. Extraction efficiencies based on both chemical and biological analyses were assessed in triplicate in artificial blank sediment spiked with this mixture and in natural sediment contaminated by native EDCs. In both spiked and natural sediment, MeOH/DCM yields the best recovery while heptane was the least efficient solvent. Our study provided the validation of a sediment extraction methodology for EDC bioanalysis purposes, which can be used for comprehensive environmental contamination characterization. PMID:26832862

  14. Simplivariate Models: Uncovering the Underlying Biology in Functional Genomics Data

    OpenAIRE

    Edoardo Saccenti; Westerhuis, Johan A.; Smilde, Age K.; van der Werf, Mariët J; Jos A Hageman; Hendriks, Margriet M. W. B.

    2011-01-01

    One of the first steps in analyzing high-dimensional functional genomics data is an exploratory analysis of such data. Cluster Analysis and Principal Component Analysis are then usually the method of choice. Despite their versatility they also have a severe drawback: they do not always generate simple and interpretable solutions. On the basis of the observation that functional genomics data often contain both informative and non-informative variation, we propose a method that finds sets of va...

  15. Comparison of functional proteomic analyses of human breast cancer cell lines T47D and MCF7.

    Directory of Open Access Journals (Sweden)

    Juliette Adjo Aka

    Full Text Available T47D and MCF7 are two human hormone-dependent breast cancer cell lines which are widely used as experimental models for in vitro and in vivo (tumor xenografts breast cancer studies. Several proteins involved in cancer development were identified in these cell lines by proteomic analyses. Although these studies reported the proteomic profiles of each cell line, until now, their differential protein expression profiles have not been established. Here, we used two-dimensional gel and mass spectrometry analyses to compare the proteomic profiles of the two cell lines, T47D and MCF7. Our data revealed that more than 164 proteins are differentially expressed between them. According to their biological functions, the results showed that proteins involved in cell growth stimulation, anti-apoptosis mechanisms and cancerogenesis are more strongly expressed in T47D than in MCF7. These proteins include G1/S-specific cyclin-D3 and prohibitin. Proteins implicated in transcription repression and apoptosis regulation, including transcriptional repressor NF-X1, nitrilase homolog 2 and interleukin-10, are, on the contrary, more strongly expressed in MCF7 as compared to T47D. Five proteins that were previously described as breast cancer biomarkers, namely cathepsin D, cathepsin B, protein S100-A14, heat shock protein beta-1 (HSP27 and proliferating cell nuclear antigen (PCNA, are found to be differentially expressed in the two cell lines. A list of differentially expressed proteins between T47D and MCF7 was generated, providing useful information for further studies of breast cancer mechanisms with these cell lines as models.

  16. 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.

  17. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals.

    Science.gov (United States)

    Daugherty, Matthew D; Schaller, Aaron M; Geballe, Adam P; Malik, Harmit S

    2016-01-01

    IFIT (interferon-induced with tetratricopeptide repeats) proteins are critical mediators of mammalian innate antiviral immunity. Mouse IFIT1 selectively inhibits viruses that lack 2'O-methylation of their mRNA 5' caps. Surprisingly, human IFIT1 does not share this antiviral specificity. Here, we resolve this discrepancy by demonstrating that human and mouse IFIT1 have evolved distinct functions using a combination of evolutionary, genetic and virological analyses. First, we show that human IFIT1 and mouse IFIT1 (renamed IFIT1B) are not orthologs, but are paralogs that diverged >100 mya. Second, using a yeast genetic assay, we show that IFIT1 and IFIT1B proteins differ in their ability to be suppressed by a cap 2'O-methyltransferase. Finally, we demonstrate that IFIT1 and IFIT1B have divergent antiviral specificities, including the discovery that only IFIT1 proteins inhibit a virus encoding a cap 2'O-methyltransferase. These functional data, combined with widespread turnover of mammalian IFIT genes, reveal dramatic species-specific differences in IFIT-mediated antiviral repertoires. PMID:27240734

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

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  19. VISUALIZATION APPROACH TO STRUCTURE-FUNCTION RELATIONSHIP IN BIOLOGICAL MACROMOLECULES

    Directory of Open Access Journals (Sweden)

    M. Luetić

    2015-08-01

    Full Text Available Introduction: Most of recent research in the field of education strongly recommends the use of visualization in the daily teacher’s practice, especially when it comes to teaching science. Objectives: We investigated the impact of different kinds of visualization on student’s accomplishments, and the relationship between 2D and 3D visualization on the learning outcomes in biochemistry teaching, as well as gender-related differences in 2D vs 3D perception abilities. Materials and Methods: The research study was conducted on a sample of 149 senior secondary school students, devided into three groups: control group (usual teaching approach, and two experimental groups taught using different kinds of visualization: E1 (2D and 3D static visualization tools, and E2 (3D dynamic visualization tools, in addition. Discussion and results: We measured the students’ learning outcomes in biochemistry, as well as the level of satisfaction with different teaching methods. The data were interpreted by performing statistical measures and analyses. In order to validate our hypothesis, we used one-tail and two-tail ANOVA analyses (along with the t-test.Conclusions: There was no statistical significance regarding 2D vs 3D visualization tools in biochemistry teaching. Although there existed some gender-related differences in students’ achievements (in favor of females, it was not established that they were related to the type of visualization (2D or 3D tools applied. However students from the E2 group (additional computer animations were more interested and involved in this kind of teaching. Although the results do not show a statistical significance in favor of 3D visualization, we must conclude that in teaching biochemistry it is certainly a more efficient approach than traditional teacher-oriented lessons. By using this kind of visualization tools in everyday teaching practice, chemistry teachers are given the opportunity to enlighten students with somewhat

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

    OpenAIRE

    Mazereeuw, M.

    2013-01-01

    This thesis reports on a design research project about a learning, supervising and teaching strategy to enable students in agricultural preparatory vocational secondary education (VMBO) to recognize the functionality of biological knowledge of reproduction in work placement sites. Although biological knowledge can be functionally used in many work placement sites it is not evident that students recognize that this is the case. Workplace characteristics, participation in work actions and workp...

  1. Analysis of Boolean Functions based on Interaction Graphs and their influence in System Biology

    OpenAIRE

    Das, Jayanta Kumar; Rout, Ranjeet Kumar; Choudhury, Pabitra Pal

    2014-01-01

    Interaction graphs provide an important qualitative modeling approach for System Biology. This paper presents a novel approach for construction of interaction graph with the help of Boolean function decomposition. Each decomposition part (Consisting of 2-bits) of the Boolean functions has some important significance. In the dynamics of a biological system, each variable or node is nothing but gene or protein. Their regulation has been explored in terms of interaction graphs which are generate...

  2. Mapping The Variations Of Moho Depth And Poisson's Ratio In China With Receiver Function Analyses

    Science.gov (United States)

    Chen, Y.; Niu, F.; Liu, R.; Huang, Z.; Chan, W.; Sun, L.

    2007-12-01

    We collected and processed a large amount of high-quality broadband teleseismic waveforms recorded at all 48 stations in the Chinese National Digital Seismic Network (CNDSN) to estimate the lateral variations of Moho depth and crustal Vp/Vs ratio (hence Poisson's ratio) in China by receiver function analyses. A cross-correlation based method was used to select mutually coherent receiver functions, which yielded over 200 traces for most of the stations. Because multiple maxima often present within a thin band in the H-k domain due to the depth- velocity trade-off, we stabilized this method by weighing each H-k grid using the cross-correlation between Ps converted phase and other Moho multiples. An nth-root stacking method was also applied to reduce uncorrelated noise relative to the linear stack. These modifications successfully ruled out any unrealistic results from H-k search. Relatively reliable crustal thickness and Poisson's ratio were consistently obtained from both the RZ (radial and vertical components) and SP (components concentrate SV- and P- wave energy in a skew coordinate system) based receiver function data. Although we utilized average crustal P- wave velocities obtained from Pn/Sn tomographic studies in projecting time to depth, the crustal thickness and Poisson's ratio obtained from receiver functions still show significant discrepancies with those inferred from Pn and Sn waves. For the stations along the east coast of China, the crustal thickness varies from 29km to 37km and the Vp/Vs ratio is about 1.70 on average. While for the stations at the middle section of China across the Sino-Korean platform and the Yangtze platform, the crust turns to be 39km on average, and the Vp/Vs ratios are higher than those to the east coast. The results presented beneath the stations in the west of China well illustrated the complicated and active tectonic complexion in this region. Along the Tianshan fold system, the Moho is at about 53 km on average, whereas in

  3. The practical impact of differential item functioning analyses in a health-related quality of life instrument

    DEFF Research Database (Denmark)

    Scott, Neil W; Fayers, Peter M; Aaronson, Neil K;

    2009-01-01

    Differential item functioning (DIF) analyses are commonly used to evaluate health-related quality of life (HRQoL) instruments. There is, however, a lack of consensus as to how to assess the practical impact of statistically significant DIF results.......Differential item functioning (DIF) analyses are commonly used to evaluate health-related quality of life (HRQoL) instruments. There is, however, a lack of consensus as to how to assess the practical impact of statistically significant DIF results....

  4. Part task trainer applications: The KWU nuclear plant analyser and the KWU functional trainer

    International Nuclear Information System (INIS)

    The paper covers two themes. (1) The need for supplementing full scope simulator training by other more cost effective devices led KWU to the development of two part task trainer applications. The KWU 'nuclear plant analyser' (NPA) is a real time engineering simulator. It is based on the KWU computer programs for transient analysis and licensing and is used for analysis, operational support and training purposes for managerial personnel. The transient code NLOOP runs on the mainframe computer in the KWU computing centre which feeds via telephone line four colour graphic displays controlled by a dedicated graphic computer. (2) An evaluation over two years of full scope simulator training led KWU to the conclusion that up to 80% of the total training can be provided by representing only 30% of the full scope control room. The design of the 'functional trainer' (FT) calls for the simulation of the primary system, the auxiliary systems directly connected, the secondary system being simulated as a closed cycle and the detailed simulation and representation of the reactor control system, limitation system, protection system and the turbine control system. Other systems are represented by replacement simulation. The KWU FT is mainly used for practical exercises and familiarization with the reactor control system, limitation system, turbine controls and reactor protection system. It can also be used for design-objective-oriented strategy and behaviour training. In the version 'OPAL' (on-line predictive analysing and learning system) the KWU FT can be linked in parallel to the real plant via the data acquisition computers. (author). 5 refs, 7 figs

  5. Functionalization of carbon nanotube and nanofiber electrodes with biological macromolecules: Progress toward a nanoscale biosensor

    Science.gov (United States)

    Baker, Sarah E.

    The integration of nanoscale carbon-based electrodes with biological recognition and electrical detection promises unparalleled biological detection systems. First, biologically modified carbon-based materials have been shown to have superior long-term chemical stability when compared to other commonly used materials for biological detection such as silicon, gold, and glass surfaces. Functionalizing carbon electrodes for biological recognition and using electrochemical methods to transduce biological binding information will enable real-time, hand-held, lower cost and stable biosensing devices. Nanoscale carbon-based electrodes allow the additional capability of fabricating devices with high densities of sensing elements, enabling multi-analyte detection on a single chip. We have worked toward the integration of these sensor components by first focusing on developing and characterizing the chemistry required to functionalize single-walled carbon nanotubes and vertically aligned carbon nanofibers with oligonucleotides and proteins for specific biological recognition. Chemical, photochemical and electrochemical methods for functionalizing these materials with biological molecules were developed. We determined, using fluorescence and colorimetric techniques, that these biologically modified nanoscale carbon electrodes are biologically active, selective, and stable. A photochemical functionalization method enabled facile functionalization of dense arrays vertically aligned carbon nanofiber forests. We found that much of the vertically aligned carbon nanofiber sidewalls were functionalized and biologically accessible by this method---the absolute number of DNA molecules hybridized to DNA-functionalized nanofiber electrodes was ˜8 times higher than the number of DNA molecules hybridized to flat glassy carbon electrodes and implies that nanofiber forest sensors may facilitate higher sensitivity to target DNA sequences per unit area. We also used the photochemical method

  6. Functional Nanostructured Platforms for Chemical and Biological Sensing

    Energy Technology Data Exchange (ETDEWEB)

    Letant, S E

    2006-03-20

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

  7. MicroRNA function in NK cell biology

    OpenAIRE

    Beaulieu, AM; Bezman, NA; Lee, JE; Matloubian, M; Sun, JC; Lanier, LL

    2013-01-01

    The important role of microRNAs in directing immune responses has become increasingly clear. Here, we highlight discoveries uncovering the role of specific microRNAs in regulating the development and function of natural killer (NK) cells. Furthermore, we discuss the impact of NK cells on the entire immune system during global and specific microRNA ablation in the settings of inflammation, infection, and immune dysregulation. © 2013 John Wiley & Sons A/S.

  8. Towards Functional Zoning: Importance, Vulnerability and Sectoral Conflict Analyses via GIS

    Science.gov (United States)

    Tanik, A.; Seker, D. Z.; Ozturk, I.

    2011-12-01

    Functional zoning of the Akcakoca District located along the Western Black Sea Coast of Turkey is achieved by implementing the 'Methodology for Spatial Planning for the Coastal Zone' that has been developed specifically for coastal areas by the European Union within the framework of EuropeAid-TACIS project. According to this methodology, the database comprises of three main groups of GIS layers; natural components, social and demographic components, and geographical components. Prior to importance and vulnerability analyses, authors worked on data collection, generation of GIS based digital maps, processing of environmental, socio-economic and land-use information, determination of sectoral conflicts and on displaying the current land-use distribution in the form of maps. For each of the GIS layers under the main group's, importance and vulnerability scores are determined and by the help of these grades, necessary information and maps are produced for spatial planning. Identical grading system has been developed and applied to each GIS layer formed in order to achieve the overall importance and vulnerability maps of the district. Functional zoning map was then produced via these maps together with the information gained through stakeholders meetings and site visits. The findings and the maps produced are targeted to be utilized by the decision-makers to further build up spatial planning of the district. The lack of a national coastal management strategy attracted the interest of all stakeholders participated in the mutual discussions held during the field trips realized during the implementation of the methodology. Public awareness on land-use policy seems to be an essential step towards effective planning and establishment of human-induced activities together with the necessity of setting a national strategy for integrated coastal zone management. All these efforts aimed to put forth the priority uses of both land and water resources of the district.

  9. [Dialectic of the interrelationship between structure and function in biology and medicine].

    Science.gov (United States)

    Strukov, A I; Kakturskiĭ, L V

    1977-01-01

    The paper deals with some aspects of the dialectics of structure and function relationships in biological objects normally and pathologically. Idealistic and metaphysical concepts of the structure-function relationships (morphological idealism, holism, physiological idealism, functionalism) are critisized, and historical premises of these concepts are characterized. The principle of indissoluble unity and interconnection of changes in structure and function is emphasized, while the thesis of the primacy of function in the shaping of the form and the concept of functional diseases are rejected. Much attention is paid to the methodological principles of the study of structure and function based on the systemic approach to the investigation of biological objects from the point of view of structural levels and integratism. The groundlessness of the principles of reductionism and organicism in the solution of this problem is indicated. The connection of the concepts of structure and function with categories and laws of materialistic dialectics is dwelt on. PMID:880057

  10. Spruce Budworm (Lepidoptera: Tortricidae) Oral Secretions I: Biology and Function.

    Science.gov (United States)

    Eveleigh, Eldon; Silk, Peter; Leclair, Gaëtan; Mayo, Peter; Francis, Brittany; Williams, Martin

    2015-12-01

    The potential roles of the oral secretions (OS) of spruce budworm (SBW; Choristoneura fumiferana Clemens) larvae and factors that may affect the volume of OS disgorged were investigated in the laboratory. Experiments revealed that diet-fed SBW larvae readily disgorge OS when induced ("milked"), with minimal overall cost to their development and eventual pupal weight. Exposure of conspecific larvae to OS throughout larval development negatively affected survival and male pupal weight; however, male development time was faster when exposed to OS. Female pupal weight and development time were not affected. Preliminary experiments suggested that OS had a repellent effect on a co-occurring herbivore, the false hemlock looper, Nepytia canosaria (Walker). OS produced by larvae that fed on three host tree species and on artificial diet significantly increased the grooming time of ants (Camponotus sp.), indicating that SBW OS have an anti-predator function. The volume of OS is significantly greater in L6 than in L4 or L5, with the volume produced by L6 depending on weight and age as well as feeding history at time of milking. These findings indicate that SBW OS function as both an intra- and interspecific epideictic pheromone and as an anti-predator defensive mechanism, while incurring minimal metabolic costs. PMID:26454475

  11. Is kinase activity essential for biological functions of BRI1?

    Institute of Scientific and Technical Information of China (English)

    Weihui Xu; Juan Huang; Baohua Li; Jiayang Li; Yonghong Wang

    2008-01-01

    Brassinosteroids (BRs) are a major group of plant hormones that regulate plant growth and development. BRI1, a protein localized to the plasma membrane, functions as a BR receptor and it has been proposed that its kinase activity has an essential role in BR-regulated plant growth and development. Here we report the isolation and molecular characterization of a new allele of bril, bril-301, which shows moderate morphological phenotypes and a reduced response to BRs under normal growth conditions. Sequence analysis identified a two-base alteration from GG to AT, resulting in a conversion of 989G to 9891 in the BRI1 kinase domain. An in vitro assay of kinase activity showed that bril-301 has no detectable autophosphorylation activity or phosphorylation activity towards the BRI1 substrates TTL and BAK1. Furthermore, our results suggest that bril-301, even with extremely impaired kinase activity, still retains partial function in regulating plant growth and development, which raises the question of whether BRI1 kinase activity is essential for BR-mediated growth and development in higher plants.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-15

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

  14. The biology and function of exosomes in cancer.

    Science.gov (United States)

    Kalluri, Raghu

    2016-04-01

    Humans circulate quadrillions of exosomes at all times. Exosomes are a class of extracellular vesicles released by all cells, with a size range of 40-150 nm and a lipid bilayer membrane. Exosomes contain DNA, RNA, and proteins. Exosomes likely remove excess and/or unnecessary constituents from the cells, functioning like garbage bags, although their precise physiological role remains unknown. Additionally, exosomes may mediate specific cell-to-cell communication and activate signaling pathways in cells they fuse or interact with. Exosomes are detected in the tumor microenvironment, and emerging evidence suggests that they play a role in facilitating tumorigenesis by regulating angiogenesis, immunity, and metastasis. Circulating exosomes can be used as liquid biopsies and noninvasive biomarkers for early detection, diagnosis, and treatment of cancer patients. PMID:27035812

  15. The functions of biological diversity in an age of extinction.

    Science.gov (United States)

    Naeem, Shahid; Duffy, J Emmett; Zavaleta, Erika

    2012-06-15

    Ecosystems worldwide are rapidly losing taxonomic, phylogenetic, genetic, and functional diversity as a result of human appropriation of natural resources, modification of habitats and climate, and the spread of pathogenic, exotic, and domestic plants and animals. Twenty years of intense theoretical and empirical research have shown that such biotic impoverishment can markedly alter the biogeochemical and dynamic properties of ecosystems, but frontiers remain in linking this research to the complexity of wild nature, and in applying it to pressing environmental issues such as food, water, energy, and biosecurity. The question before us is whether these advances can take us beyond merely invoking the precautionary principle of conserving biodiversity to a predictive science that informs practical and specific solutions to mitigate and adapt to its loss. PMID:22700920

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

    Directory of Open Access Journals (Sweden)

    Oksana eKaidanovich-Beilin

    2011-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Ritu Kumar

    2014-10-01

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

  18. Non-random distribution of homo-repeats: links with biological functions and human diseases.

    Science.gov (United States)

    Lobanov, Michail Yu; Klus, Petr; Sokolovsky, Igor V; Tartaglia, Gian Gaetano; Galzitskaya, Oxana V

    2016-01-01

    The biological function of multiple repetitions of single amino acids, or homo-repeats, is largely unknown, but their occurrence in proteins has been associated with more than 20 hereditary diseases. Analysing 122 bacterial and eukaryotic genomes, we observed that the number of proteins containing homo-repeats is significantly larger than expected from theoretical estimates. Analysis of statistical significance indicates that the minimal size of homo-repeats varies with amino acid type and proteome. In an attempt to characterize proteins harbouring long homo-repeats, we found that those containing polar or small amino acids S, P, H, E, D, K, Q and N are enriched in structural disorder as well as protein- and RNA-interactions. We observed that E, S, Q, G, L, P, D, A and H homo-repeats are strongly linked with occurrence in human diseases. Moreover, S, E, P, A, Q, D and T homo-repeats are significantly enriched in neuronal proteins associated with autism and other disorders. We release a webserver for further exploration of homo-repeats occurrence in human pathology at http://bioinfo.protres.ru/hradis/. PMID:27256590

  19. 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...

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

    Science.gov (United States)

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

    2010-12-01

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

  1. Matrix metalloproteinases: their biological functions and clinical implications.

    Science.gov (United States)

    Hijova, E

    2005-01-01

    Matrix metalloproteinases (MMPs), which are also known as matrixins, are proteinases that participate in extracellular matrix remodelling and degradation. Under normal physiological conditions, the activities of MMPs are precisely regulated at the level of transcription, at that of activation of the pro-MMP precursor zymogenes as well as at that of inhibition by endogenous inhibitors (tissue inhibitors of metalloproteinases, TIMPs). Alterations in the regulation of MMP activity are implicated in diseases such as cancer, fibrosis, arthritis and atherosclerosis. The pathological effects of MMPs and TIMPs in cardiovascular diseases involve vascular remodelling, atherosclerotic plaque instability and cardiac remodelling in congestive heart failure or after myocardial infarction. Since excessive tissue remodelling and increased matrix metalloproteinases activity have been demonstrated during atherosclerotic lesion progression (including plaque disruption), MMPs represent a potential target for therapeutic intervention aimed at the modification of vascular pathology by restoring the physiological balance between MMPs and TIMPs. Recent findings suggest that MMPs are also involved in cancer initiation, invasion and metastasis; MMP inhibitors could be considered for evaluation as cancer chemopreventive molecules. This review describes the members of MMP and TIMP families and discusses the structure, function and regulation of MMP activity. (Tab. 1, Ref: 45.) PMID:16026148

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

    International Nuclear Information System (INIS)

    Graphical abstract: -- Highlights: •Derivatization of diamond nanopowder as IMAC and RP. •Characterization with SEM, EDX and FT-IR. •Phosphopeptide enrichment from standard as well as real samples. •Desalting and human serum profiling with reproducible results. •MALDI-MS analysis with database identification. -- Abstract: Diamond is known for its high affinity and biocompatibility towards biomolecules and is used exclusively in separation sciences and life science research. In present study, diamond nanopowder is derivatized as Immobilized Metal Ion Affinity Chromatographic (IMAC) material for the phosphopeptides enrichment and as Reversed Phase (C-18) media for the desalting of complex mixtures and human serum profiling through MALDI-TOF-MS. Functionalized diamond nanopowder is characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Diamond-IMAC is applied to the standard protein (β-casein), spiked human serum, egg yolk and non-fat milk for the phosphopeptides enrichment. Results show the selectivity of synthesized IMAC-diamond immobilized with Fe3+ and La3+ ions. To comprehend the elaborated use, diamond-IMAC is also applied to the serum samples from gall bladder carcinoma for the potential biomarkers. Database search is carried out by the Mascot program ( (www.matrixscience.com)) for the assignment of phosphorylation sites. Diamond nanopowder is thus a separation media with multifunctional use and can be applied to cancer protein profiling for the diagnosis and biomarker identification

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

    Directory of Open Access Journals (Sweden)

    K. Michaelian

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-05-02

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

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

    Science.gov (United States)

    Michaelian, K.

    2011-01-01

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

  6. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

    Directory of Open Access Journals (Sweden)

    Stéphane Uroz

    Full Text Available In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France. The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource

  7. Function and significance of bell beaker pottery according to data from residue analyses

    Directory of Open Access Journals (Sweden)

    Guerra Doce, Elisa

    2006-06-01

    Full Text Available Traditionally, Bell Beakers have been thought to contain alcoholic beverages which were consumed in the course of male feasting ceremonies. Recent residue analyses have shed some light on the question of their function. However, whilst beer and mead have been identified from certain examples, not all Beakers were drinking cups. Some were used as reduction pots to smelt copper ores, others have some organic residues associated with food, and still others were employed as funerary urns. Yet, while the evidence points to a diversity of uses, it is argued that an ideological connection can be observed. Beakers were probably a special form of pottery with a ritual character, related to activities that imply some kind of transformation.

    Los vasos campaniformes suelen relacionarse con el consumo de bebidas alcohólicas durante la celebración de banquetes ceremoniales de exaltación masculina. Si bien las analíticas de residuos han identificado cerveza e hidromiel en unos cuantos ejemplares, no todos los campaniformes desempeñaron esta misma función. Algunos hicieron las veces de vasijas-horno para reducir el mineral de cobre, en otros se han detectado restos de alimentos y también se emplearon como urnas funerarias. A pesar de esta diversidad de usos, creemos que existe una conexión ideológica entre ellos, de tal manera que habría que considerar a los campaniformes como una cerámica singular con un carácter ritual, destinada a actividades que conllevan algún tipo de transformación.

  8. Comparing Surface-Based and Volume-Based Analyses of Functional Neuroimaging Data in Patients with Schizophrenia

    OpenAIRE

    Anticevic, Alan; Dierker, Donna L.; Gillespie, Sarah K.; Repovs, Grega; Csernansky, John G.; Van Essen, David C.; Deanna M Barch

    2008-01-01

    A major challenge in functional neuroimaging is to cope with individual variability in cortical structure and function. Most analyses of cortical function compensate for variability using affine or low-dimensional nonlinear volume-based registration (VBR) of individual subjects to an atlas, which does not explicitly take into account the geometry of cortical convolutions. A promising alternative is to use surface-based registration (SBR), which capitalizes on explicit surface representations ...

  9. 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. PMID:27111421

  10. Social inclusion enhances biological motion processing: A functional near-infrared spectroscopy study

    OpenAIRE

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

    2012-01-01

    Humans are especially tuned to the movements of other people. Neural correlates of this social attunement have been proposed to lie in and around the right posterior superior temporal sulcus (STS) region, which robustly responds to biological motion in contrast to a variety of non-biological motions. This response persists even when no form information is provided, as in point-light displays (PLDs). The aim of the current study was to assess the ability of functional near-infrared spectroscop...

  11. The Acute Effects of Grape Polyphenols Supplementation on Endothelial Function in Adults: Meta-Analyses of Controlled Trials

    OpenAIRE

    Shao-Hua Li; Hong-Bo Tian; Hong-Jin Zhao; Liang-Hua Chen; Lian-Qun Cui

    2013-01-01

    BACKGROUND: The acute effects of grape polyphenols on endothelial function in adults are inconsistent. Here, we performed meta-analyses to determine these acute effects as measured by flow-mediated dilation (FMD). METHODS: Trials were searched in PubMed, Embase and the Cochrane Library database. Summary estimates of weighted mean differences (WMDs) and 95% CIs were obtained by using random-effects models. Meta-regression and subgroup analyses were performed to identify the source of heterogen...

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

    OpenAIRE

    Schultz, M.J.; Spronk, P.E.; 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 receive CVVH? A second aim was to answer a relevant question in ICUs in resource-poor settings, i.e., can novel biological markers predict development of AKI and need for RRT in patients with sever...

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

    OpenAIRE

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

    2013-01-01

    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 a...

  14. Exergames: neuroplastic hypothesis about cognitive improvement and biological effects on physical function of institutionalized older persons

    OpenAIRE

    Renato Sobral Monteiro; César Augusto Otero Vaghetti; Osvaldo José M. Nascimento; Jerson Laks; Andrea Camaz Deslandes

    2016-01-01

    Exergames can be considered a dual task because the games are performed by a man-videogame interface, requiring cognitive and motor functions simultaneously. Although the literature has shown improvements of cognitive and physical functions due to exergames, the intrinsic mechanisms involved in these functional changes have still not been elucidated. The aims of the present study were (1) to demonstrate the known biological mechanisms of physical exercise regarding muscle adaptation and estab...

  15. Application of femtosecond-pulsed lasers for direct optical manipulation of biological functions

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jonghee; Park, Junseong; Jong Choi, Won [Department of Bio and Brain Engineering, KAIST, Daejeon (Korea, Republic of); Choi, Myunghwan [Graduate School of Nanoscience and Technology, KAIST, Daejeon (Korea, Republic of); Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA (United States); Choi, Chulhee [Department of Bio and Brain Engineering, KAIST, Daejeon (Korea, Republic of); KAIST Institute for the BioCentury, KAIST, Daejeon (Korea, Republic of)

    2013-03-15

    Absorption of photon energy by cells or tissue can evoke photothermal, photomechanical, and photochemical effects, depending on the density of the deposited energy. Photochemical effects require a low energy density and can be used for reversible modulation of biological functions. Ultrashort-pulsed lasers have a high intensity due to the short pulse duration, despite its low average energy. Through nonlinear absorption, these lasers can deliver very high peak energy into the submicrometer focus area without causing collateral damage. Absorbed energy delivered by ultrashort-pulsed laser irradiation induces free electrons, which can be readily converted to reactive oxygen species (ROS) and related free radicals in the localized region. Free radicals are best known to induce irreversible biological effects via oxidative modification; however, they have also been proposed to modulate biological functions by releasing calcium ions from intracellular organelles. Calcium can evoke variable biological effects in both excitable and nonexcitable cell types. Controlled stimulation by ultrashort laser pulses generate intracellular calcium waves that can modulate many biological functions, such as cardiomyocyte beat rate, muscle contractility, and blood-brain barrier (BBB) permeability. This article presents optical methods that are useful therapeutic and research tools in the biomedical field and discuss the possible mechanisms responsible for biological modulation by ultrashort-pulsed lasers, especially femtosecond-pulsed lasers. (copyright 2012 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

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

  17. Two-stage coal liquefaction process materials from the Wilsonville Facility operated in the nonintegrated and integrated modes: chemical analyses and biological testing

    Energy Technology Data Exchange (ETDEWEB)

    Later, D.W.

    1985-01-01

    This document reports the results from chemical analyses and biological testing of process materials sampled during operation of the Wilsonville Advanced Coal Liquefaction Research and Development Facility (Wilsonville, Alabama) in both the noncoupled or nonintegrated (NTSL Run 241) and coupled or integrated (ITSL Run 242) two-stage liquefaction operating modes. Mutagenicity and carcinogenicity assays were conducted in conjunction with chromatographic and mass spectrometric analyses to provide detailed, comparative chemical and biological assessments of several NTSL and ITSL process materials. In general, the NTSL process materials were biologically more active and chemically more refractory than analogous ITSL process materials. To provide perspective, the NTSL and ITSL results are compared with those from similar testing and analyses of other direct coal liquefaction materials from the solvent refined coal (SRC) I, SRC II and EDS processes. Comparisons are also made between two-stage coal liquefaction materials from the Wilsonville pilot plant and the C.E. Lummus PDU-ITSL Facility in an effort to assess scale-up effects in these two similar processes. 36 references, 26 figures, 37 tables.

  18. Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?

    CERN Document Server

    Kolb, Brian; 10.1142/S1793984412300063

    2012-01-01

    Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory---a framework that can treat thousands of atoms on firm theoretical ground---can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent ...

  19. A systematic literature review on reviews and meta-analyses of biologically based CAM-practices for cancer patients

    DEFF Research Database (Denmark)

    Paludan-Müller, Christine; Lunde, Anita; Johannessen, Helle

    2010-01-01

    for the improvement of quality of life. Breast cancer was the most common single type of cancer reviewed (8 reviews), all focused on the relief of side effects, primarily by supplements containing soy/plant hormones. The use of these supplements should be discouraged due to a risk for progression of breast cancer...... patients. There is a need for future studies on specific type of practices in relation to side effects and quality of life parameters. Research Methods: -Systematic reviews, meta analysis Funding: The research was funded by The Danish Cancer Society and the University of Southern Denmark.......Purpose To provide an overview and evaluate the evidence of biologically based CAM-practices for cancer patients. Methods Pubmed, Social Science Citation Index, AMED and the Cochrane library were systematically searched for reviews on effects of biologically based CAM-practices, including herbal...

  20. An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB

    OpenAIRE

    Bell, Michael J; Colin S Gillespie; Swan, Daniel; Lord, Phillip

    2012-01-01

    Motivation: Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases ...

  1. Crucial role of detailed function, task, timeline, link and human vulnerability analyses in HRA. [Human Reliability Analysis (HRA)

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, T.G.; Haney, L.N.; Ostrom, L.T.

    1992-01-01

    This paper addresses one major cause for large uncertainties in human reliability analysis (HRA) results, that is, an absence of detailed function, task, timeline, link and human vulnerability analyses. All too often this crucial step in the HRA process is done in a cursory fashion using word of mouth or written procedures which themselves may incompletely or inaccurately represent the human action sequences and human error vulnerabilities being analyzed. The paper examines the potential contributions these detailed analyses can make in achieving quantitative and qualitative HRA results which are: (1) creditable, that is, minimize uncertainty, (2) auditable, that is, systematically linking quantitative results and qualitative information from which the results are derived, (3) capable of supporting root cause analyses on human reliability factors determined to be major contributors to risk, and (4) capable of repeated measures and being combined with similar results from other analyses to examine HRA issues transcending individual systems and facilities. Based on experience analyzing test and commercial nuclear reactors, and medical applications of nuclear technology, an iterative process is suggested for doing detailed function, task, timeline, link and human vulnerability analyses using documentation reviews, open-ended and structured interviews, direct observations, and group techniques. Finally, the paper concludes that detailed analyses done in this manner by knowledgeable human factors practitioners, can contribute significantly to the credibility, auditability, causal factor analysis, and combining goals of the HRA.

  2. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

    NARCIS (Netherlands)

    Scott, Robert A.; Lagou, Vasiliki; Welch, Ryan P.; Wheeler, Eleanor; Montasser, May E.; Luan, Jian'an; Maegi, Reedik; Strawbridge, Rona J.; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J.; Yengo, Loic; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C. D.; Jukema, J. Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V.; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J.; Evans, David M.; St Pourcain, Beate; Wu, Ying; Andrews, Jeanette S.; Hui, Jennie; Bielak, Lawrence F.; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O'Connell, Jeffrey R.; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tonu; Mihailov, Evelin; Fraser, Ross M.; Fall, Tove; Voight, Benjamin F.; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M.; Morris, Andrew P.; Rayner, Nigel W.; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S.; Willems, Sara M.; Chines, Peter S.; Jackson, Anne U.; Kang, Hyun Min; Stringham, Heather M.; Song, Kijoung; Tanaka, Toshiko; Peden, John F.; Goel, Anuj; Hicks, Andrew A.; An, Ping; Mueller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J.; Bruinenberg, Marcel; Pankow, James S.; North, Kari E.; Forouhi, Nita G.; Loos, Ruth J. F.; Edkins, Sarah; Varga, Tibor V.; Hallmans, Goeran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J. L.; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B.; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L.; Rivadeneira, Fernando; Uitterlinden, Andre G.; Palmer, Colin N. A.; Doney, Alex S. F.; Willemsen, Gonneke; Smit, Johannes H.; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L.; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L.; Fowkes, Gerard R.; Kovacs, Peter; Lindstrom, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H.; Basart, Hanneke V.; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E.; Boehm, Bernhard O.; Peters, Annette; Pramstaller, Peter P.; Province, Michael A.; Borecki, Ingrid B.; Hastie, Nicholas D.; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M.; Bergman, Richard N.; Collins, Francis S.; Tuomilehto, Jaakko; Watanabe, Richard M.; de Geus, Eco J. C.; Penninx, Brenda W.; Hofman, Albert; Oostra, Ben A.; Psaty, Bruce M.; Vollenweider, Peter; Wilson, James F.; Wright, Alan F.; Hovingh, G. Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K. E.; Kyvik, Kirsten O.; Kaprio, Jaakko; Price, Jackie F.; Dedoussis, George V.; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R.; van Duijn, Cornelia M.; Morris, Andrew D.; Toenjes, Anke; Peyser, Patricia A.; Beilby, John P.; Koerner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R.; Schwarz, Peter E. H.; Lakka, Timo A.; Rauramaa, Rainer; Adair, Linda S.; Smith, George Davey; Spector, Tim D.; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Boomsma, Dorret I.; Stefansson, Kari; van der Harst, Pim; Dupuis, Josee; Pedersen, Nancy L.; Sattar, Naveed; Harris, Tamara B.; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L.; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J.; Bouatia-Naji, Nabila; McCarthy, Mark I.; Franks, Paul W.; Meigs, James B.; Teslovich, Tanya M.; Florez, Jose C.; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Ines

    2012-01-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes ri

  3. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

    DEFF Research Database (Denmark)

    Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P;

    2012-01-01

    Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes...

  4. Metagenomics and in situ analyses reveal Propionivibrio spp. to be abundant GAO in biological wastewater treatment systems

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Albertsen, Mads; Stokholm-Bjerregaard, Mikkel;

    to be present at equal levels. Metagenomics was employed to elucidate the identity and recover genomes from the abundant community members. Phylogenetic analyses revealed closely related “Ca. Accumulibacter” and Propionivibrio genera were co-dominant and were both targeted by the PAOmix probes. In situ staining...

  5. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation

    OpenAIRE

    Stéphane Uroz; Panos Ioannidis; Juliette Lengelle; Aurélie Cébron; Emmanuelle Morin; Marc Buée; Francis Martin

    2013-01-01

    In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation...

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

    Science.gov (United States)

    Price, S A; Schmitz, L

    2016-04-01

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

  7. Exergames: neuroplastic hypothesis about cognitive improvement and biological effects on physical function of institutionalized older persons

    Science.gov (United States)

    Monteiro-Junior, Renato Sobral; Vaghetti, César Augusto Otero; Nascimento, Osvaldo José M.; Laks, Jerson; Deslandes, Andrea Camaz

    2016-01-01

    Exergames can be considered a dual task because the games are performed by a man-videogame interface, requiring cognitive and motor functions simultaneously. Although the literature has shown improvements of cognitive and physical functions due to exergames, the intrinsic mechanisms involved in these functional changes have still not been elucidated. The aims of the present study were (1) to demonstrate the known biological mechanisms of physical exercise regarding muscle adaptation and establish a relationship with exergames; and (2) to present a neurobiological hypothesis about the neuroplastic effects of exergames on the cognitive function of institutionalized older persons. These hypotheses are discussed. PMID:27073355

  8. Exergames: neuroplastic hypothesis about cognitive improvement and biological effects on physical function of institutionalized older persons.

    Science.gov (United States)

    Monteiro-Junior, Renato Sobral; Vaghetti, César Augusto Otero; Nascimento, Osvaldo José M; Laks, Jerson; Deslandes, Andrea Camaz

    2016-02-01

    Exergames can be considered a dual task because the games are performed by a man-videogame interface, requiring cognitive and motor functions simultaneously. Although the literature has shown improvements of cognitive and physical functions due to exergames, the intrinsic mechanisms involved in these functional changes have still not been elucidated. The aims of the present study were (1) to demonstrate the known biological mechanisms of physical exercise regarding muscle adaptation and establish a relationship with exergames; and (2) to present a neurobiological hypothesis about the neuroplastic effects of exergames on the cognitive function of institutionalized older persons. These hypotheses are discussed. PMID:27073355

  9. To What Extent do Biology Textbooks Contribute to Scientific Literacy? Criteria for Analysing Science-Technology-Society-Environment Issues

    OpenAIRE

    Florbela M. Calado; Franz-Josef Scharfenberg; Bogner, Franz X.

    2015-01-01

    Our article proposes a set of six criteria for analysing science-technology-society-environment (STSE) issues in regular textbooks as to how they are expected to contribute to students’ scientific literacy. We chose genetics and gene technology as fields prolific in STSE issues. We derived our criteria (including 26 sub-criteria) from a literature review of the debate in science education on how to increase scientific literacy. We inspected the textbooks regarding the relationships between sc...

  10. Gene-based GWAS and -biological pathway analysis of the resilience of executive functioning

    OpenAIRE

    Mukherjee, Shubhabrata; Kim, Sungeun; Ramanan, Vijay K.; Gibbons, Laura E.; Nho, Kwangsik; Glymour, M. Maria; Ertekin-Taner, Nilüfer; Thomas J Montine; Saykin, Andrew J; Crane, Paul K.

    2014-01-01

    Resilience in executive functioning (EF) is characterized by high EF measured by neuropsychological test performance despite structural brain damage from neurodegenerative conditions. We previously reported single nucleotide polymorphism (SNP) genome-wide association study (GWAS) results for EF resilience. Here, we report gene- and pathway-based analyses of the same resilience phenotype, using an optimal SNP-set (Sequence) Kernel Association Test (SKAT) for gene-based analyses (conservative t...

  11. Systems analysis of mechanical biological waste treatment plants in Germany; Systemtechnische Analyse der mechanisch-biologischen Abfallbehandlungsanlagen in Deutschland

    Energy Technology Data Exchange (ETDEWEB)

    Thiel, S. [Thome-Kozmiensky Ingenieure, Nietwerder (Germany)

    2006-07-01

    The present article starts with a presentation of the state of the art of mechanical biological waste treatment in Germany. This is followed by a description of the various process concepts, the technical configurations they use and the output fractions they produce and where they end up. The final part is dedicated to a comparison, based on selected example plants, of the mass balances and secondary fuel yields of the individual process concepts in cases where high-grade secondary fuels are produced, e.g. for use in power plants and cement works.

  12. Role of Biological Sex in Normal Cardiac Function and in its Disease Outcome – A Review

    OpenAIRE

    Prabhavathi, K.; Selvi, K.Tamarai; Poornima, K.N.; Sarvanan, A.

    2014-01-01

    Biological sex plays an important role in normal cardiac physiology as well as in the heart‘s response to cardiac disease. Women generally have better cardiac function and survival than do men in the face of cardiac disease; however, this is progressively lost when comparing postmenopausal women with age matched men. Animal model of cardiac disease mirror what is seen in humans. Sex hormones contribute significantly to sex based difference in cardiac functioning and in its disease outcome. Es...

  13. Exploratory Analysis of Biological Networks through Visualization, Clustering, and Functional Annotation in Cytoscape.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-01-01

    Biological networks define how genes, proteins, and other cellular components interact with one another to carry out specific functions, providing a scaffold for understanding cellular organization. Although in-depth network analysis requires advanced mathematical and computational knowledge, a preliminary visual exploration of biological networks is accessible to anyone with basic computer skills. Visualization of biological networks is used primarily to examine network topology, identify functional modules, and predict gene functions based on gene connectivity within the network. Networks are excellent at providing a bird's-eye view of data sets and have the power of illustrating complex ideas in simple and intuitive terms. In addition, they enable exploratory analysis and generation of new hypotheses, which can then be tested using rigorous statistical and experimental tools. This protocol describes a simple procedure for visualizing a biological network using the genetic interaction similarity network for Saccharomyces cerevisiae as an example. The visualization procedure described here relies on the open-source network visualization software Cytoscape and includes detailed instructions on formatting and loading the data, clustering networks, and overlaying functional annotations. PMID:26988373

  14. Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function

    NARCIS (Netherlands)

    D.B. Hancock (Dana); M. Eijgelsheim (Mark); J.B. Wilk (Jemma); S.A. Gharib (Sina); L.R. Loehr (Laura); K. Marciante (Kristin); N. Franceschini (Nora); Y.M.T.A. van Durme; T.H. Chen; R.G. Barr (Graham); M.B. Schabath (Matthew); D.J. Couper (David); G.G. Brusselle (Guy); B.M. Psaty (Bruce); P. Tikka-Kleemola (Päivi); J.I. Rotter (Jerome); A.G. Uitterlinden (André); A. Hofman (Albert); N.M. Punjabi (Naresh); F. Rivadeneira Ramirez (Fernando); A.C. Morrison (Alanna); P.L. Enright (Paul); K.E. North (Kari); S.R. Heckbert (Susan); T. Lumley (Thomas); B.H.Ch. Stricker (Bruno); G.T. O'Connor (George); S.J. London (Stephanie)

    2010-01-01

    textabstractSpirometric measures of lung function are heritable traits that reflect respiratory health and predict morbidity and mortality. We meta-analyzed genome-wide association studies for two clinically important lung-function measures: forced expiratory volume in the first second (FEV1) and it

  15. Short term recovery of soil biological functions in a new vineyard cultivated in organic farming

    Science.gov (United States)

    Costantini, Edoardo; Agnelli, Alessandro; Fabiani, Arturo; Gagnarli, Elena; Mocali, Stefano; Priori, Simone; Simoni, Sauro; Valboa, Giuseppe

    2014-05-01

    Deep earthwork activities carried out before vineyard plantation completely upset soil profile and characteristics. The resulting soil features are often much more similar to the underlying substratum than original soil profile. The time needed to recover soil functions is ecologically relevant and affects vine phenology and grape yield, particularly in organic viticulture. The general aim of this research work was to investigate the time needed to recover soil functions after the earthworks made before vine plantation. This study compared for a four years period physical and chemical properties, microbial and mesofauna communities, in new and old vineyards, cultivated on the same soil type. The experiment was conducted in a farm of the Chianti Classico district (Central Italy), on hills of high altitude (400-500 m a.s.l.) on clayey-calcareous flysches, with stony and calcareous soils (Haplic Cambisol (Calcaric, Skeletic)). The reference vine cultivar was Sangiovese. The older vineyard was planted in 2000, after slope reshaping by bulldozing and back hoe ploughing down to about 0.8-1.0 m. The new vineyard was planted in 2011 after an equivalent earthwork carried out in the summer of 2009. Both vineyards were organically managed and only compost at the rate of 1,000 kg ha-1 -a was added every year. The new vineyard was periodically cultivated by mechanical tillage, while the older only at alternate rows. Soil samples from the first 15 cm depth were collected in 4 replicates in the younger as well as in the older vineyard during the springtime of 2010-2013; in the older vineyard, two samples were from the periodically cultivated swaths and two under permanent grass cover. Samples were analysed for physical (particle size, field capacity, wilting point), chemical (pH, electrical conductivity, lime, active lime, organic carbon, total nitrogen), microbiological (soil respiration, microbial biomass, DGGE), and mesofauna features (abundance, taxa richness, BSQ index and

  16. Overview of a surface-ripened cheese community functioning by meta-omics analyses

    OpenAIRE

    Dugat-Bony, Eric; Straub, Cecile; Teissandier, Aurélie; Onesime, Djamila; Loux, Valentin; Monnet, Christophe; Irlinger, Francoise; LANDAUD-LIAUTAUD, Sophie; Leclercq-Perlat, Marie Noelle; Bento, Pascal; Fraud, Sébastien; Gibrat, Jean-Francois; Aubert, Julie; Fer, Frédéric; Guedon, Eric

    2015-01-01

    Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an exp...

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

    DEFF Research Database (Denmark)

    Rosenkilde, Per

    1995-01-01

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

  18. Evaluating the Accuracy of Results for Teacher Implemented Trial-Based Functional Analyses.

    Science.gov (United States)

    Rispoli, Mandy; Ninci, Jennifer; Burke, Mack D; Zaini, Samar; Hatton, Heather; Sanchez, Lisa

    2015-09-01

    Trial-based functional analysis (TBFA) allows for the systematic and experimental assessment of challenging behavior in applied settings. The purposes of this study were to evaluate a professional development package focused on training three Head Start teachers to conduct TBFAs with fidelity during ongoing classroom routines. To assess the accuracy of the TBFA results, the effects of a function-based intervention derived from the TBFA were compared with the effects of a non-function-based intervention. Data were collected on child challenging behavior and appropriate communication. An A-B-A-C-D design was utilized in which A represented baseline, and B and C consisted of either function-based or non-function-based interventions counterbalanced across participants, and D represented teacher implementation of the most effective intervention. Results showed that the function-based intervention produced greater decreases in challenging behavior and greater increases in appropriate communication than the non-function-based intervention for all three children. PMID:26069219

  19. 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...... 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...

  20. 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....... This paper 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....

  1. Functional and phylogenetic analyses of chromosome 21 promoters and hominid-specific transcription factor binding sites

    OpenAIRE

    Querfurth, Robert

    2011-01-01

    The focus of this work addresses functional studies of human and primate promoters, and the genome-wide localization and validation of human-specific transcription factor binding sites of the essential transcription factor GABPa. In this context, the development of an improved PCR protocol, including the careful adjustment of PCR additives to compose an efficient enhancer mix, was central to the amplification of large GC-rich promoter fragments used as source for the functional studies. Based...

  2. Functional Analyses of Bitter Taste Receptors in Domestic Cats (Felis catus).

    Science.gov (United States)

    Lei, Weiwei; Ravoninjohary, Aurore; Li, Xia; Margolskee, Robert F; Reed, Danielle R; Beauchamp, Gary K; Jiang, Peihua

    2015-01-01

    Cats are obligate carnivores and under most circumstances eat only animal products. Owing to the pseudogenization of one of two subunits of the sweet receptor gene, they are indifferent to sweeteners, presumably having no need to detect plant-based sugars in their diet. Following this reasoning and a recent report of a positive correlation between the proportion of dietary plants and the number of Tas2r (bitter receptor) genes in vertebrate species, we tested the hypothesis that if bitter perception exists primarily to protect animals from poisonous plant compounds, the genome of the domestic cat (Felis catus) should have lost functional bitter receptors and they should also have reduced bitter receptor function. To test functionality of cat bitter receptors, we expressed cat Tas2R receptors in cell-based assays. We found that they have at least 7 functional receptors with distinct receptive ranges, showing many similarities, along with some differences, with human bitter receptors. To provide a comparative perspective, we compared the cat repertoire of intact receptors with those of a restricted number of members of the order Carnivora, with a range of dietary habits as reported in the literature. The numbers of functional bitter receptors in the terrestrial Carnivora we examined, including omnivorous and herbivorous species, were roughly comparable to that of cats thereby providing no strong support for the hypothesis that a strict meat diet influences bitter receptor number or function. Maintenance of bitter receptor function in terrestrial obligate carnivores may be due to the presence of bitter compounds in vertebrate and invertebrate prey, to the necessary role these receptors play in non-oral perception, or to other unknown factors. We also found that the two aquatic Carnivora species examined had fewer intact bitter receptors. Further comparative studies of factors driving numbers and functions of bitter taste receptors will aid in understanding the forces

  3. Functional Analyses of Bitter Taste Receptors in Domestic Cats (Felis catus.

    Directory of Open Access Journals (Sweden)

    Weiwei Lei

    Full Text Available Cats are obligate carnivores and under most circumstances eat only animal products. Owing to the pseudogenization of one of two subunits of the sweet receptor gene, they are indifferent to sweeteners, presumably having no need to detect plant-based sugars in their diet. Following this reasoning and a recent report of a positive correlation between the proportion of dietary plants and the number of Tas2r (bitter receptor genes in vertebrate species, we tested the hypothesis that if bitter perception exists primarily to protect animals from poisonous plant compounds, the genome of the domestic cat (Felis catus should have lost functional bitter receptors and they should also have reduced bitter receptor function. To test functionality of cat bitter receptors, we expressed cat Tas2R receptors in cell-based assays. We found that they have at least 7 functional receptors with distinct receptive ranges, showing many similarities, along with some differences, with human bitter receptors. To provide a comparative perspective, we compared the cat repertoire of intact receptors with those of a restricted number of members of the order Carnivora, with a range of dietary habits as reported in the literature. The numbers of functional bitter receptors in the terrestrial Carnivora we examined, including omnivorous and herbivorous species, were roughly comparable to that of cats thereby providing no strong support for the hypothesis that a strict meat diet influences bitter receptor number or function. Maintenance of bitter receptor function in terrestrial obligate carnivores may be due to the presence of bitter compounds in vertebrate and invertebrate prey, to the necessary role these receptors play in non-oral perception, or to other unknown factors. We also found that the two aquatic Carnivora species examined had fewer intact bitter receptors. Further comparative studies of factors driving numbers and functions of bitter taste receptors will aid in

  4. Functional performance of a total ankle replacement: thorough assessment by combining gait and fluoroscopic analyses

    OpenAIRE

    Cenni, Francesco; Leardini, Alberto; Pieri, Maddalena; Berti, Lisa; Belvedere, Claudio; Romagnoli, Matteo; Giannini, Sandro

    2013-01-01

    BACKGROUND: A thorough assessment of patients after total ankle replacement during activity of daily living can provide complete evidence of restored function in the overall lower limbs and replaced ankle. This study analyzes how far a possible restoration of physiological mobility in the replaced ankle can also improve the function of the whole locomotor apparatus. METHODS: Twenty patients implanted with an original three-part ankle prosthesis were analyzed 12 months after surgery d...

  5. Consequences of species loss for ecosystem functioning: meta-analyses of data from biodiversity experiments

    OpenAIRE

    Schmid, B; Balvanera, P; Cardinale, B J; Godbold, J; Pfisterer, A B; Raffaelli, D; Solan, M.; Srivastava, D S

    2009-01-01

    A large number of studies have now explicitly examined the relationship between species loss and ecosystem functions. The results from such “biodiversity experiments” have previously been collated and analyzed by two independent groups of authors. Both data sets show that reductions in species diversity generally result in reduced ecosystem functioning, even though the studies cover a wide range of ecosystems, diversity manipulations, and response variables. In this chapter, we analyze the tw...

  6. Radiotoxicological analyses of 239+240Pu and 241Am in biological samples by anion-exchange and extraction chromatography: a preliminary study for internal contamination evaluations

    International Nuclear Information System (INIS)

    Many biological samples (urines and faeces) have been analysed by means of chromatographic extraction columns, utilising two different resins (AG 1-X2 resin chloride and T.R.U.), in order to detect the possible internal contamination of 239+240Pu and 241Am, for some workers of a reprocessing nuclear plant in the decommissioning phase. The results obtained show on one hand the great suitability of the first resin for the determination of plutonium, and on the other the great selectivity of the second one for the determination of americium

  7. In actio optophysiological analyses reveal functional diversification of dopaminergic neurons in the nematode C. elegans

    Science.gov (United States)

    Tanimoto, Yuki; Zheng, Ying Grace; Fei, Xianfeng; Fujie, Yukako; Hashimoto, Koichi; Kimura, Koutarou D.

    2016-05-01

    Many neuronal groups such as dopamine-releasing (dopaminergic) neurons are functionally divergent, although the details of such divergence are not well understood. Dopamine in the nematode Caenorhabditis elegans modulates various neural functions and is released from four left-right pairs of neurons. The terminal identities of these dopaminergic neurons are regulated by the same genetic program, and previous studies have suggested that they are functionally redundant. In this study, however, we show functional divergence within the dopaminergic neurons of C. elegans. Because dopaminergic neurons of the animals were supposedly activated by mechanical stimulus upon entry into a lawn of their food bacteria, we developed a novel integrated microscope system that can auto-track a freely-moving (in actio) C. elegans to individually monitor and stimulate the neuronal activities of multiple neurons. We found that only head-dorsal pair of dopaminergic neurons (CEPD), but not head-ventral or posterior pairs, were preferentially activated upon food entry. In addition, the optogenetic activation of CEPD neurons alone exhibited effects similar to those observed upon food entry. Thus, our results demonstrated functional divergence in the genetically similar dopaminergic neurons, which may provide a new entry point toward understanding functional diversity of neurons beyond genetic terminal identification.

  8. Multi-functionalized single-walled carbon nanotubes as tumor cell targeting biological transporters

    International Nuclear Information System (INIS)

    Multi-functionalized single walled carbon nanotubes (SWNTs) were prepared and applied as tumor cell targeting biological transporters. A positive charge was introduced on SWNTs to get high loading efficiency of fluorescein (FAM) labeled short double strands DNA (20 base pairs). The SWNTs were encapsulated with the folic acid modified phospholipids for active targeting into tumor cell. The tumor cell-targeting properties of these multi-functionalized SWNTs were investigated by active targeting into mouse ovarian surface epithelial cells. The experimental results show that these multi-functionalized SWNTs have good tumor cell targeting property

  9. The Structure of a Gene Co-Expression Network Reveals Biological Functions Underlying eQTLs

    Science.gov (United States)

    Villa-Vialaneix, Nathalie; Liaubet, Laurence; Laurent, Thibault; Cherel, Pierre; Gamot, Adrien; SanCristobal, Magali

    2013-01-01

    What are the commonalities between genes, whose expression level is partially controlled by eQTL, especially with regard to biological functions? Moreover, how are these genes related to a phenotype of interest? These issues are particularly difficult to address when the genome annotation is incomplete, as is the case for mammalian species. Moreover, the direct link between gene expression and a phenotype of interest may be weak, and thus difficult to handle. In this framework, the use of a co-expression network has proven useful: it is a robust approach for modeling a complex system of genetic regulations, and to infer knowledge for yet unknown genes. In this article, a case study was conducted with a mammalian species. It showed that the use of a co-expression network based on partial correlation, combined with a relevant clustering of nodes, leads to an enrichment of biological functions of around 83%. Moreover, the use of a spatial statistics approach allowed us to superimpose additional information related to a phenotype; this lead to highlighting specific genes or gene clusters that are related to the network structure and the phenotype. Three main results are worth noting: first, key genes were highlighted as a potential focus for forthcoming biological experiments; second, a set of biological functions, which support a list of genes under partial eQTL control, was set up by an overview of the global structure of the gene expression network; third, pH was found correlated with gene clusters, and then with related biological functions, as a result of a spatial analysis of the network topology. PMID:23577081

  10. Quantitative and qualitative validations of a sonication-based DNA extraction approach for PCR-based molecular biological analyses.

    Science.gov (United States)

    Dai, Xiaohu; Chen, Sisi; Li, Ning; Yan, Han

    2016-05-15

    The aim of this study was to comprehensively validate the sonication-based DNA extraction method, in hope of the replacement of the so-called 'standard DNA extraction method' - the commercial kit method. Microbial cells in the digested sludge sample, containing relatively high amount of PCR-inhibitory substances, such as humic acid and protein, were applied as the experimental alternatives. The procedure involving solid/liquid separation of sludge sample and dilution of both DNA templates and inhibitors, the minimum templates for PCR-based analyses, and the in-depth understanding from the bias analysis by pyrosequencing technology were obtained and confirmed the availability of the sonication-based DNA extraction method. PMID:26774955

  11. Cotyledonary somatic embryos of Pinus pinaster Ait. most closely resemble fresh, maturing cotyledonary zygotic embryos: biological, carbohydrate and proteomic analyses.

    Science.gov (United States)

    Morel, Alexandre; Trontin, Jean-François; Corbineau, Françoise; Lomenech, Anne-Marie; Beaufour, Martine; Reymond, Isabelle; Le Metté, Claire; Ader, Kevin; Harvengt, Luc; Cadene, Martine; Label, Philippe; Teyssier, Caroline; Lelu-Walter, Marie-Anne

    2014-11-01

    Cotyledonary somatic embryos (SEs) of maritime pine are routinely matured for 12 weeks before being germinated and converted to plantlets. Although regeneration success is highly dependent on SEs quality, the date of harvesting is currently determined mainly on the basis of morphological features. This empirical method does not provide any accurate information about embryo quality with respect to storage compounds (proteins, carbohydrates). We first analyzed SEs matured for 10, 12 and 14 weeks by carrying out biological (dry weight, water content) and biochemical measurements (total protein and carbohydrate contents). No difference could be found between collection dates, suggesting that harvesting SEs after 12 weeks is appropriate. Cotyledonary SEs were then compared to various stages, from fresh to fully desiccated, in the development of cotyledonary zygotic embryos (ZEs). We identified profiles that were similar using hierarchical ascendant cluster analysis (HCA). Fresh and dehydrated ZEs could be distinguished, and SEs clustered with fresh ZEs. Both types of embryo exhibited similar carbohydrate and protein contents and signatures. This high level of similarity (94.5 %) was further supported by proteome profiling. Highly expressed proteins included storage, stress-related, late embryogenesis abundant and energy metabolism proteins. By comparing overexpressed proteins in developing and cotyledonary SEs or ZEs, some (23 proteins) could be identified as candidate biomarkers for the late, cotyledonary stage. This is the first report of useful generic protein markers for monitoring embryo development in maritime pine. Our results also suggest that improvements of SEs quality may be achieved if the current maturation conditions are refined. PMID:25115559

  12. Functional Connectivity Analyses in Imaging Genetics: Considerations on Methods and Data Interpretation

    OpenAIRE

    Bedenbender, Johannes; Paulus, Frieder M.; Krach, Sören; Pyka, Martin; Sommer, Jens; Krug, Axel; Witt, Stephanie H; Rietschel, Marcella; Laneri, Davide; Kircher, Tilo; Jansen, Andreas

    2011-01-01

    Functional magnetic resonance imaging (fMRI) can be combined with genotype assessment to identify brain systems that mediate genetic vulnerability to mental disorders (“imaging genetics”). A data analysis approach that is widely applied is “functional connectivity”. In this approach, the temporal correlation between the fMRI signal from a pre-defined brain region (the so-called “seed point”) and other brain voxels is determined. In this technical note, we show how the choice of freely selecta...

  13. PLANT LIPIDOMICS: DISCERNING BIOLOGICAL FUNCTION BY PROFILING PLANT COMPLEX LIPIDS USING MASS SPECTROMETRY

    Science.gov (United States)

    Since 2002, plant biologists have begun to apply mass spectrometry to the comprehensive analysis of complex lipids. Such lipidomic analyses have been used to uncover roles for lipids in plant response to stresses and to identify in vivo functions of genes involved in lipid metabolism....

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

    Directory of Open Access Journals (Sweden)

    Carmel McDougall

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

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

    Science.gov (United States)

    McDougall, Carmel; Woodcroft, Ben J.

    2016-01-01

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

  16. Scaling and Spectral Analyses Based on Spatial Correlation Functions of Urban Form

    CERN Document Server

    Chen, Yanguang

    2012-01-01

    Urban form has been empirically demonstrated to be of scaling invariance and can be described with fractal geometry. However, the valid range of fractal dimension and the relationships between various fractal indicators of cities are not yet revealed in theory. Especially, systematic methods of spatial analysis have not yet been developed for fractal cities. By mathematical deduction and transformation (e.g. Fourier transform), I find that scaling analysis, spectral analysis, and spatial correlation analysis are all associated with fractal concepts and can be integrated into a new approach to fractal analysis of cities. This method can be termed '3S analyses' of urban form. Using the 3S analysis, I derived a set of fractal parameter equations, by which different fractal parameters of cities can be linked up with one another. Each fractal parameter has its own reasonable range of values. According to the fractal parameter equations, the intersection of the rational ranges of different fractal parameters sugges...

  17. Classifying social anxiety disorder using multivoxel pattern analyses of brain function and structure

    NARCIS (Netherlands)

    Frick, A.; Gingnell, M.; Marquand, A.F.; Howner, K.; Fischer, H.; Kristiansson, M.; Williams, S.C.; Fredrikson, M.; Furmark, T.

    2014-01-01

    Functional neuroimaging of social anxiety disorder (SAD) support altered neural activation to threat-provoking stimuli focally in the fear network, while structural differences are distributed over the temporal and frontal cortices as well as limbic structures. Previous neuroimaging studies have inv

  18. Differential item functioning (DIF) analyses of health-related quality of life instruments using logistic regression

    DEFF Research Database (Denmark)

    Scott, Neil W.; Fayers, Peter M.; Aaronson, Neil K.;

    2010-01-01

    Differential item functioning (DIF) methods can be used to determine whether different subgroups respond differently to particular items within a health-related quality of life (HRQoL) subscale, after allowing for overall subgroup differences in that scale. This article reviews issues that arise...

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

    DEFF Research Database (Denmark)

    Petersen, Anders; Andersen, Tobias

    modelling human performance in whole and partial report tasks in which multiple simultaneously presented letters are to be reported (Shibuya & Bundesen, 1988). Therefore, we investigated visual letter identification as a function of exposure duration. On each trial, a single randomly chosen letter (A-Z) was...

  20. Analyses of multiplicity distributions by means of the Modified Negative Binomial Distribution and its KNO scaling function

    OpenAIRE

    OSADA, T; Nakajima, N; Biyajima, M.; Suzuki, N.

    1998-01-01

    We analyze various data of multiplicity distributions by means of the Modified Negative Binomial Distribution (MNBD) and its KNO scaling function, since this MNBD explains the oscillating behavior of the cumulant moment observed in e^+e^- annihilations, h-h collisions and e-p collisions. In the present analyses, we find that the MNBD(discrete distributions) describes the data of charged particles in e^+e^- annihilations much better than the Negative Binomial Distribution (NBD). To investigate...

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

    Science.gov (United States)

    Zammito, John

    2006-12-01

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

  2. Biological Sampling and Analysis in Sinclair and Dyes Inlets, Washington: Chemical Analyses for 2007 Puget Sound Biota Study

    Energy Technology Data Exchange (ETDEWEB)

    Brandenberger, Jill M.; Suslick, Carolynn R.; Johnston, Robert K.

    2008-10-09

    Evaluating spatial and temporal trends in contaminant residues in Puget Sound fish and macroinvertebrates are the objectives of the Puget Sound Ambient Monitoring Program (PSAMP). In a cooperative effort between the ENVironmental inVESTment group (ENVVEST) and Washington State Department of Fish and Wildlife, additional biota samples were collected during the 2007 PSAMP biota survey and analyzed for chemical residues and stable isotopes of carbon (δ13C) and nitrogen (δ15N). Approximately three specimens of each species collected from Sinclair Inlet, Georgia Basin, and reference locations in Puget Sound were selected for whole body chemical analysis. The muscle tissue of specimens selected for chemical analyses were also analyzed for δ13C and δ15N to provide information on relative trophic level and food sources. This data report summarizes the chemical residues for the 2007 PSAMP fish and macro-invertebrate samples. In addition, six Spiny Dogfish (Squalus acanthias) samples were necropsied to evaluate chemical residue of various parts of the fish (digestive tract, liver, embryo, muscle tissue), as well as, a weight proportional whole body composite (WBWC). Whole organisms were homogenized and analyzed for silver, arsenic, cadmium, chromium, copper, nickel, lead, zinc, mercury, 19 polychlorinated biphenyl (PCB) congeners, PCB homologues, percent moisture, percent lipids, δ13C, and δ15N.

  3. Phylogenetic analyses and characterization of RNase X25 from Drosophila melanogaster suggest a conserved housekeeping role and additional functions for RNase T2 enzymes in protostomes.

    Directory of Open Access Journals (Sweden)

    Linda Ambrosio

    Full Text Available Ribonucleases belonging to the RNase T2 family are enzymes associated with the secretory pathway that are almost absolutely conserved in all eukaryotes. Studies in plants and vertebrates suggest they have an important housekeeping function in rRNA recycling. However, little is known about this family of enzymes in protostomes. We characterized RNase X25, the only RNase T2 enzyme in Drosophila melanogaster. We found that RNase X25 is the major contributor of ribonuclease activity in flies as detected by in gel assays, and has an acidic pH preference. Gene expression analyses showed that the RNase X25 transcript is present in all adult tissues and developmental stages. RNase X25 expression is elevated in response to nutritional stresses; consistent with the hypothesis that this enzyme has a housekeeping role in recycling RNA. A correlation between induction of RNase X25 expression and autophagy was observed. Moreover, induction of gene expression was triggered by oxidative stress suggesting that RNase X25 may have additional roles in stress responses. Phylogenetic analyses of this family in protostomes showed that RNase T2 genes have undergone duplication events followed by divergence in several phyla, including the loss of catalytic residues, and suggest that RNase T2 proteins have acquired novel functions. Among those, it is likely that a role in host immunosuppression evolved independently in several groups, including parasitic Platyhelminthes and parasitoid wasps. The presence of only one RNase T2 gene in the D. melanogaster genome, without any other evident secretory RNase activity detected, makes this organism an ideal system to study the cellular functions of RNase T2 proteins associated with RNA recycling and maintenance of cellular homeostasis. On the other hand, the discovery of gene duplications in several protostome genomes also presents interesting new avenues to study additional biological functions of this ancient family of proteins.

  4. Aminopyrine breath test for evaluation of liver function. How to analyse the 14CO2 data

    International Nuclear Information System (INIS)

    Previous studies in our laboratory have shown that breath analysis of 14CO2, following administration of specifically labelled 14C-dimethylaminoantipyrine, allows assessment of Vsub(max) and Ksub(m) of in vivo demethylation in the rat. Consequently, this procedure was modified for application in man. Whereas in 23 liver normals the disappearance constant ksub(B) of 14CO2 from breath was 21+-SD4%/h, ksub(B) was significantly reduced in 14 patients with alcoholic cirrhosis (8+-4%/h). Breath analysis is suggested as a non-invasive, convenient and valid method for measuring hepatic microsomal demethylation. Breath analysis discriminates between liver normals and patients with impaired liver function as well as established quantitative liver function tests (disappearance rate of BSP, galactose elimination capacity)

  5. Proteomic and functional analyses reveal a mitochondrial dysfunction in P301L tau transgenic mice

    OpenAIRE

    David, D C; Hauptmann, S.; Scherping, I; Schuessel, K; U. Keil; Rizzu, P.; Ravid, R; Dröse, S; Brandt, U.; Müller, W E; Eckert, A; Götz, J.

    2005-01-01

    Transgenic mice overexpressing the P301L mutant human tau protein exhibit an accumulation of hyperphosphorylated tau and develop neurofibrillary tangles. The consequences of tau pathology were investigated here by proteomics followed by functional analysis. Mainly metabolism-related proteins including mitochondrial respiratory chain complex components, antioxidant enzymes, and synaptic proteins were identified as modified in the proteome pattern of P301L tau mice. Significantly, the reduction...

  6. Chemical and functional analyses of the plant cuticle as leaf transpiration barrier

    OpenAIRE

    Schuster, Ann-Christin

    2016-01-01

    Cuticles cover all above-ground primary plant organs and are lipoid in nature consisting of a cutin matrix with cuticular waxes embedded within or deposited on its surface. The foremost function of the plant cuticle is the limitation of transpirational water loss into the surrounding atmosphere. Transpiration of water vapour from plants differs between stomatal and cuticular transpiration. Stomatal closure minimises the stomatal water loss and the remaining, much lower water transpiration occ...

  7. Differential item functioning (DIF) analyses of health-related quality of life instruments using logistic regression

    DEFF Research Database (Denmark)

    Scott, Neil W; Fayers, Peter M; Aaronson, Neil K;

    2010-01-01

    Differential item functioning (DIF) methods can be used to determine whether different subgroups respond differently to particular items within a health-related quality of life (HRQoL) subscale, after allowing for overall subgroup differences in that scale. This article reviews issues that arise...... when testing for DIF in HRQoL instruments. We focus on logistic regression methods, which are often used because of their efficiency, simplicity and ease of application....

  8. Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

    OpenAIRE

    Mochida, Keiichi; Shinozaki, Kazuo

    2011-01-01

    Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progre...

  9. Functional Genomic Analyses Identify Pathways Dysregulated by Progranulin Deficiency Implicating Wnt Signaling

    OpenAIRE

    Rosen, Ezra Y.; Wexler, Eric M; Versano, Revital; Coppola, Giovanni; Gao, Fuying; Winden, Kellen D.; Oldham, Michael C.; Martens, Lauren Herl; Zhou, Ping; Farese, Robert V; Geschwind, Daniel H.

    2011-01-01

    Progranulin (GRN) mutations cause frontotemporal dementia (FTD), but GRN’s function in the CNS remains largely unknown. To identify the pathways downstream of GRN, we used weighted gene co-expression network analysis (WGCNA) to develop a systems-level view of transcriptional alterations in a human neural progenitor model of GRN-deficiency. This highlighted key pathways such as apoptosis and ubiquitination in GRN deficient human neurons, while revealing an unexpected major role for the Wnt sig...

  10. Functional analyses of carnivorous plant-specific amino acid residues in S-like ribonucleases.

    Science.gov (United States)

    Arai, Naoki; Nishimura, Emi; Kikuchi, Yo; Ohyama, Takashi

    2015-09-11

    Unlike plants with no carnivory, carnivorous plants seem to use S-like ribonucleases (RNases) as an enzyme for carnivory. Carnivorous plant-specific conserved amino acid residues are present at four positions around the conserved active site (CAS). The roles of these conserved amino acid residues in the enzymatic function were explored in the current study by preparing five recombinant variants of DA-I, the S-like RNase of Drosera adelae. The kcat and kcat/Km values of the enzymes revealed that among the four variants with a single mutation, the serine to glycine mutation at position 111 most negatively influenced the enzymatic activity. The change in the bulkiness of the amino acid residue side-chain seemed to be the major cause of the above effect. Modeling of the three dimensional (3D) structures strongly suggested that the S to G mutation at 111 greatly altered the overall enzyme conformation. The conserved four amino acid residues are likely to function in keeping the two histidine residues, which are essential for the cleavage of RNA strands, and the CAS in the most functional enzymatic conformation. PMID:26235877

  11. 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.

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

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function....... system (the cell), also at the quantitative level, and this is the goal of systems biology. Clearly this will have a significant impact on microbial physiology as well as on metabolic engineering.......Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function....... With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has...

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

    International Nuclear Information System (INIS)

    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

  14. Phlebotomus orientalis sand flies from two geographically distant Ethiopian localities: biology, genetic analyses and susceptibility to Leishmania donovani.

    Directory of Open Access Journals (Sweden)

    Veronika Seblova

    Full Text Available BACKGROUND: Phlebotomus orientalis Parrot (Diptera: Psychodidae is the main vector of visceral leishmaniasis (VL caused by Leishmania donovani in East Africa. Here we report on life cycle parameters and susceptibility to L. donovani of two P. orientalis colonies originating from different sites in Ethiopia: a non-endemic site in the lowlands - Melka Werer (MW, and an endemic focus of human VL in the highlands - Addis Zemen (AZ. METHODOLOGY/PRINCIPAL FINDINGS: Marked differences in life-cycle parameters between the two colonies included distinct requirements for larval food and humidity during pupation. However, analyses using Random Amplified Polymorphic DNA (RAPD PCR and DNA sequencing of cytB and COI mitochondrial genes did not reveal any genetic differences. F1 hybrids developed successfully with higher fecundity than the parental colonies. Susceptibility of P. orientalis to L. donovani was studied by experimental infections. Even the lowest infective dose tested (2×10(3 per ml was sufficient for successful establishment of L. donovani infections in about 50% of the P. orientalis females. Using higher infective doses, the infection rates were around 90% for both colonies. Leishmania development in P. orientalis was fast, the presence of metacyclic promastigotes in the thoracic midgut and the colonization of the stomodeal valve by haptomonads were recorded in most P. orientalis females by day five post-blood feeding. CONCLUSIONS: Both MW and AZ colonies of P. orientalis were highly susceptible to Ethiopian L. donovani strains. As the average volume of blood-meals taken by P. orientalis females are about 0.7 µl, the infective dose at the lowest concentration was one or two L. donovani promastigotes per sand fly blood-meal. The development of L. donovani was similar in both P. orientalis colonies; hence, the absence of visceral leishmaniasis in non-endemic area Melka Werer cannot be attributed to different susceptibility of local P. orientalis

  15. Influence of Lipid Oxidization on Structures and Functions of Biological Membranes

    OpenAIRE

    Korytowski, Agatha Anna

    2016-01-01

    The primary aim of this thesis is to clarify how the structures and functions of biological membranes are influenced by the oxidative damage mediated by free radicals. As a precisely defined model systems, artificially reconstituted lipid membranes (Langmuir monolayers, vesicles, supported membranes, multilamellar membranes) incorporating two oxidized phospholipids bearing aldehyde or carboxyl groups at the end of truncated sn-2 acyl chains were fabricated. By the combination of various exper...

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

    OpenAIRE

    Mancuso, James J.; Jie Cheng

    2014-01-01

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

  17. The SYK tyrosine kinase: a crucial player in diverse biological functions

    OpenAIRE

    Mócsai, Attila; Ruland, Jürgen; Tybulewicz, Victor L.J.

    2010-01-01

    Spleen tyrosine kinase (SYK) has been known to relay adaptive immune receptor signalling. However, recent reports indicate that SYK also mediates other, unexpectedly diverse biological functions including cellular adhesion, innate immune recognition, osteoclast maturation, platelet activation and vascular development. SYK is activated by C-type lectins and integrins, and activates novel targets including the CARD9/CARMA1–BCL10–MALT1 pathway and the NLRP3 inflammasome. Drosophila studies indic...

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

    Science.gov (United States)

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

    2015-05-01

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

  19. Functional and fluorescence analyses of tryptophan residues in H+-pyrophosphatase of Clostridium tetani.

    Science.gov (United States)

    Chen, Yen-Wei; Lee, Ching-Hung; Huang, Yun-Tzu; Pan, Yih-Jiuan; Lin, Shih-Ming; Lo, Yueh-Yu; Lee, Chien-Hsien; Huang, Lin-Kun; Huang, Yu-Fen; Hsu, Yu-Di; Pan, Rong-Long

    2014-04-01

    Homodimeric proton-translocating pyrophosphatase (H+-PPase; EC 3.6.1.1) maintains the cytoplasmic pH homeostasis of many bacteria and higher plants by coupling pyrophosphate (PPi) hydrolysis and proton translocation. H+-PPase accommodates several essential motifs involved in the catalytic mechanism, including the PPi binding motif and Acidic I and II motifs. In this study, 3 intrinsic tryptophan residues, Trp-75, Trp-365, and Trp-602, in H+-PPase from Clostridium tetani were used as internal probes to monitor the local conformational state of the periplasm domain, transmembrane region, and cytoplasmic domain, respectively. Upon binding of the substrate analog Mg-imidodiphosphate (Mg-IDP), local structural changes prevented the modification of tryptophan residues by N-bromosuccinimide (NBS), especially at Trp-602. Following Mg-Pi binding, Trp-75 and Trp-365, but not Trp-602, were slightly protected from structural modifications by NBS. These results reveal the conformation of H+-PPase is distinct in the presence of different ligands. Moreover, analyses of the Stern-Volmer relationship and steady-state fluorescence anisotropy also indicate that the local structure around Trp-602 is more exposed to solvent and varied under different environments. In addition, Trp-602 was identified to be a crucial residue in the H+-PPase that may potentially be involved in stabilizing the structure of the catalytic region by site-directed mutagenesis analysis. PMID:24121937

  20. System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach.

    Science.gov (United States)

    Ran, Jihua; Li, Hui; Li, Huiwu

    2016-01-01

    Background. KDM6A (Lysine (K)-Specific Demethylase 6A) is the driver gene related to esophageal squamous cell carcinoma (ESCC). In order to provide more biological insights into KDM6A, in this paper, we treat PPI (protein-protein interaction) network derived from KDM6A as a conceptual framework and follow it to review its biological function. Method. We constructed a PPI network with Cytoscape software and performed clustering of network with Clust&See. Then, we evaluate the pathways, which are statistically involved in the network derived from KDM6A. Lastly, gene ontology analysis of clusters of genes in the network was conducted. Result. The network includes three clusters that consist of 74 nodes connected via 453 edges. Fifty-five pathways are statistically involved in the network and most of them are functionally related to the processes of cell cycle, gene expression, and carcinogenesis. The biology themes of clusters 1, 2, and 3 are chromatin modification, regulation of gene expression by transcription factor complex, and control of cell cycle, respectively. Conclusion. The PPI network presents a panoramic view which can facilitate for us to understand the function role of KDM6A. It is a helpful way by network approach to perform system review on a certain gene. PMID:27294188

  1. Hydrologic and biogeochemical functioning of intensively managed catchments: A synthesis of top-down analyses

    Science.gov (United States)

    Basu, Nandita B.; Thompson, Sally E.; Rao, P. Suresh C.

    2011-10-01

    This paper synthesizes a 3-year collaborative effort to characterize the biogeochemical and hydrological features of intensively managed agricultural catchments by combining data analysis, modeling, and preliminary hypothesis testing. The specific focus was on the Midwestern region of the United States. The results suggest that: (1) water management, specifically the homogenization of evapotranspiration losses driven by mono-cultural vegetation cover, and the homogenization of runoff generation driven by artificial drainage, has created engineered, predictable hydrologic systems; (2) nutrient and pesticide management, specifically their regular applications have created two kinds of biogeochemical export regimes: chemostatic (low variability in concentration as exhibited by nitrate) and episodic (high variability in concentration as exhibited by pesticides); (3) coupled mass-balance models for water and solutes reproduce these two regimes as a function of chemical rate constants. Phosphorus transport regimes were found to be episodic at smaller spatial scales, but chemostatic at larger scales. Chemostatic response dominates in transport-limited catchments that have internal sources of the solute to buffer the periodicity in episodic inputs, while episodic response dominates in source-limited catchments. The shift from episodic nitrate export in pristine catchments to chemostatic regimes in managed watersheds was attributed to legacy stores of nitrogen (built from continued fertilizer applications) that buffer interannual variations in biogeochemical processing. Fast degradation kinetics of pesticides prevents the build-up of legacy sources, and leads to episodic export. Analytical expressions were derived for the probability density functions of solute delivery ratio as a function of the stochastics of rainfall-runoff events and biogeochemical controls.

  2. Domain III function of Mu transposase analysed by directed placement of subunits within the transpososome

    Indian Academy of Sciences (India)

    Susana Mariconda; Soon-Young Namgoong; Ki-Hoon Yoon; Hong Jiang; Rasika M Harshey

    2000-12-01

    Assembly of the functional tetrameric form of Mu transposase (MuA protein) at the two att ends of Mu depends on interaction of MuA with multiple att and enhancer sites on supercoiled DNA, and is stimulated by MuB protein. The N-terminal domain I of MuA harbours distinct regions for interaction with the att ends and enhancer; the C-terminal domain III contains separate regions essential for tetramer assembly and interaction with MuB protein (III and III, respectively). Although the central domain II (the ‘DDE’ domain) of MuA harbours the known catalytic DDE residues, a 26 amino acid peptide within III also has a non-specific DNA binding and nuclease activity which has been implicated in catalysis. One model proposes that active sites for Mu transposition are assembled by sharing structural/catalytic residues between domains II and III present on separate MuA monomers within the MuA tetramer. We have used substrates with altered att sites and mixtures of MuA proteins with either wild-type or altered att DNA binding specificities, to create tetrameric arrangements wherein specific MuA subunits are nonfunctional in II, III or III domains. From the ability of these oriented tetramers to carry out DNA cleavage and strand transfer we conclude that domain III or III function is not unique to a specific subunit within the tetramer, indicative of a structural rather than a catalytic function for domain III in Mu transposition.

  3. Functional connectivity analyses in imaging genetics: considerations on methods and data interpretation.

    Directory of Open Access Journals (Sweden)

    Johannes Bedenbender

    Full Text Available Functional magnetic resonance imaging (fMRI can be combined with genotype assessment to identify brain systems that mediate genetic vulnerability to mental disorders ("imaging genetics". A data analysis approach that is widely applied is "functional connectivity". In this approach, the temporal correlation between the fMRI signal from a pre-defined brain region (the so-called "seed point" and other brain voxels is determined. In this technical note, we show how the choice of freely selectable data analysis parameters strongly influences the assessment of the genetic modulation of connectivity features. In our data analysis we exemplarily focus on three methodological parameters: (i seed voxel selection, (ii noise reduction algorithms, and (iii use of additional second level covariates. Our results show that even small variations in the implementation of a functional connectivity analysis can have an impact on the connectivity pattern that is as strong as the potential modulation by genetic allele variants. Some effects of genetic variation can only be found for one specific implementation of the connectivity analysis. A reoccurring difficulty in the field of psychiatric genetics is the non-replication of initially promising findings, partly caused by the small effects of single genes. The replication of imaging genetic results is therefore crucial for the long-term assessment of genetic effects on neural connectivity parameters. For a meaningful comparison of imaging genetics studies however, it is therefore necessary to provide more details on specific methodological parameters (e.g., seed voxel distribution and to give information how robust effects are across the choice of methodological parameters.

  4. Functional connectivity analyses in imaging genetics: considerations on methods and data interpretation.

    Science.gov (United States)

    Bedenbender, Johannes; Paulus, Frieder M; Krach, Sören; Pyka, Martin; Sommer, Jens; Krug, Axel; Witt, Stephanie H; Rietschel, Marcella; Laneri, Davide; Kircher, Tilo; Jansen, Andreas

    2011-01-01

    Functional magnetic resonance imaging (fMRI) can be combined with genotype assessment to identify brain systems that mediate genetic vulnerability to mental disorders ("imaging genetics"). A data analysis approach that is widely applied is "functional connectivity". In this approach, the temporal correlation between the fMRI signal from a pre-defined brain region (the so-called "seed point") and other brain voxels is determined. In this technical note, we show how the choice of freely selectable data analysis parameters strongly influences the assessment of the genetic modulation of connectivity features. In our data analysis we exemplarily focus on three methodological parameters: (i) seed voxel selection, (ii) noise reduction algorithms, and (iii) use of additional second level covariates. Our results show that even small variations in the implementation of a functional connectivity analysis can have an impact on the connectivity pattern that is as strong as the potential modulation by genetic allele variants. Some effects of genetic variation can only be found for one specific implementation of the connectivity analysis. A reoccurring difficulty in the field of psychiatric genetics is the non-replication of initially promising findings, partly caused by the small effects of single genes. The replication of imaging genetic results is therefore crucial for the long-term assessment of genetic effects on neural connectivity parameters. For a meaningful comparison of imaging genetics studies however, it is therefore necessary to provide more details on specific methodological parameters (e.g., seed voxel distribution) and to give information how robust effects are across the choice of methodological parameters. PMID:22220190

  5. Expression and functional analyses of the Arabidopsis QUA1 gene in light signal transduction.

    Science.gov (United States)

    Zhaojin, Chen; Chuanyu, Ding; Yuan, Zheng

    2016-05-01

    Plants not only use light as an energy source for photosynthesis, but also have to monitor the light quality and quantity input to execute appropriate physiological and developmental responses, such as cell differentiation, structural and functional changes, as well as the formation of tissues and organs. The process is referred to as photomorphogenesis. Arabidopsis QUA1 (QUASIMODO1), which functions in pectin synthesis, is identified as a member of glycosyltransferases. Previously, the hypocotyl elongation of the qua1-1 mutant was shown to be inhibited under dark conditions. In this study, we used the qua1-1/cry1 and qua1-1/phyB double mutants as the materials to study the function of the QUA1 gene in light signal transduction. The results showed that QUA1 not only participated in hypocotyl elongation under dark conditions, but also in blue light, red light and far red light conditions. In qua1-1 mutant seedlings, both the cell length of hypocotyl and the light-regulated gene expression were affected. Compared with cry1 and phyB mutants, qua1-1/cry1 and qua1-1/phyB double mutants had the shorter hypocotyl. Light-regulated gene expression was also affected in the double mutants. These data indicated that QUA1 might participate in the light signal transduction regulated by CRY1 and PHYB. Hence, the QUA1 gene may play multiple roles in light signal transduction by regulating the cell elongation and light-regulated gene expression. PMID:27232492

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

    Directory of Open Access Journals (Sweden)

    Kathleen H Wood

    2016-05-01

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

  7. Tuning of nanoparticle biological functionality through controlled surface chemistry and characterisation at the bioconjugated nanoparticle surface

    Science.gov (United States)

    Hristov, Delyan R.; Rocks, Louise; Kelly, Philip M.; Thomas, Steffi S.; Pitek, Andrzej S.; Verderio, Paolo; Mahon, Eugene; Dawson, Kenneth A.

    2015-12-01

    We have used a silica - PEG based bionanoconjugate synthetic scheme to study the subtle connection between cell receptor specific recognition and architecture of surface functionalization chemistry. Extensive physicochemical characterization of the grafted architecture is capable of capturing significant levels of detail of both the linker and grafted organization, allowing for improved reproducibility and ultimately insight into biological functionality. Our data suggest that scaffold details, propagating PEG layer architecture effects, determine not only the rate of uptake of conjugated nanoparticles into cells but also, more significantly, the specificity of pathways via which uptake occurs.

  8. RESPONDING AND ANALYSING: STAGES OF TEACHING FUNCTIONAL GRAMMAR IN INDONESIAN CONTEXT

    Directory of Open Access Journals (Sweden)

    Lala Bumela

    2014-07-01

    Full Text Available Abstract: This paper offers an alternative to the teaching of a functional grammar course in Indonesian TEFL tertiary level context. An issue raised here is whether the course should directly require students to undertake textual analysis or provide them first with subjective reading experiences.  This issue is inspired by Jones and Lock¹s approach to teaching grammar in context (2011. This paper reports on a study that focused on two related phases of dealing with texts: responding and analyzing.  In the first phase, students were encouraged to take a personalised approach in responding to written English texts.  They had the freedom to decide whether the texts were meaningful for them in certain ways. Mckee (2003 and Lehtonen (2000 posit that as the sole decision maker in meaning negotiation, readers perceive the meaningfulness of texts in very diverse ways. In the second phase of the study, the students undertook an individual analysis of different text types.  This study reveals that a successful textual analysis is determined by how students make sense of the texts. The analysis of context of situation, for example, becomes meaningful to students after they demonstrate a proper position as a reader.  This, in turn, helps them in gaining insights into the structure and grammar of those texts.   Keywords: systemic functional linguistics, genre-based approach, textual analysis

  9. Morphological and functional analyses of two infants with obstructive renal dysplasia.

    Science.gov (United States)

    Miura, Kenichiro; Sekine, Takashi; Nishimura, Riki; Kanamori, Yutaka; Yanagisawa, Atsuhiro; Sakai, Kiyohide; Nagata, Michio; Igarashi, Takashi

    2011-08-01

    Renal dysplasia associated with urinary tract obstruction comprises two distinct phenotypes, i.e., multicystic dysplastic kidney (MCDK) and obstructive renal dysplasia (ORD). MCDK is a common manifestation in infants with renal dysplasia, which is characterized by multiloculated thin-walled cysts with no functional parenchyma and an atretic ureter owing to pyelocalyceal occlusion early in fetal life. In contrast, ORD is an extremely rare condition which is caused by severe obstruction of the distal ureter or urethra. Here, we report two infants with ORD. Both patients manifested unilateral kidney enlargement with multiple cortical cysts, mild hydronephrosis, and marked dilatation of the ipsilateral ureter. Contralateral kidneys and urinary tracts revealed no apparent radiological abnormalities. Serial ultrasonographic studies of fetal and neonatal kidneys in both cases revealed that ureteral dilatation was evident at gestational week 16 and 27, respectively, and most of the cortical cysts disappeared within 1-3 months after birth. The functions of the affected kidneys were severely impaired but evident at the time of birth. These manifestations were consistent with a diagnosis of ORD, and were distinct from the features of MCDK. Our observation of fetal and infantile kidneys in these two cases provides us with a better understanding of the pathogenesis of ORD. PMID:21455661

  10. Tetrahydrolipstatin Inhibition, Functional Analyses, and Three-dimensional Structure of a Lipase Essential for Mycobacterial Viability

    Energy Technology Data Exchange (ETDEWEB)

    Crellin, Paul K.; Vivian, Julian P.; Scoble, Judith; Chow, Frances M.; West, Nicholas P.; Brammananth, Rajini; Proellocks, Nicholas I.; Shahine, Adam; Le Nours, Jerome; Wilce, Matthew C.J.; Britton, Warwick J.; Coppel, Ross L.; Rossjohn, Jamie; Beddoe, Travis (Monash); (Centenary)

    2010-09-17

    The highly complex and unique mycobacterial cell wall is critical to the survival of Mycobacteria in host cells. However, the biosynthetic pathways responsible for its synthesis are, in general, incompletely characterized. Rv3802c from Mycobacterium tuberculosis is a partially characterized phospholipase/thioesterase encoded within a genetic cluster dedicated to the synthesis of core structures of the mycobacterial cell wall, including mycolic acids and arabinogalactan. Enzymatic assays performed with purified recombinant proteins Rv3802c and its close homologs from Mycobacterium smegmatis (MSMEG{_}6394) and Corynebacterium glutamicum (NCgl2775) show that they all have significant lipase activities that are inhibited by tetrahydrolipstatin, an anti-obesity drug that coincidently inhibits mycobacterial cell wall biosynthesis. The crystal structure of MSMEG{_}6394, solved to 2.9 {angstrom} resolution, revealed an {alpha}/{beta} hydrolase fold and a catalytic triad typically present in esterases and lipases. Furthermore, we demonstrate direct evidence of gene essentiality in M. smegmatis and show the structural consequences of loss of MSMEG{_}6394 function on the cellular integrity of the organism. These findings, combined with the predicted essentiality of Rv3802c in M. tuberculosis, indicate that the Rv3802c family performs a fundamental and indispensable lipase-associated function in mycobacteria.

  11. Functional and comparative genomics analyses of pmp22 in medaka fish

    Directory of Open Access Journals (Sweden)

    Kawarabayasi Yutaka

    2009-06-01

    Full Text Available Abstract Background Pmp22, a member of the junction protein family Claudin/EMP/PMP22, plays an important role in myelin formation. Increase of pmp22 transcription causes peripheral neuropathy, Charcot-Marie-Tooth disease type1A (CMT1A. The pathophysiological phenotype of CMT1A is aberrant axonal myelination which induces a reduction in nerve conduction velocity (NCV. Several CMT1A model rodents have been established by overexpressing pmp22. Thus, it is thought that pmp22 expression must be tightly regulated for correct myelin formation in mammals. Interestingly, the myelin sheath is also present in other jawed vertebrates. The purpose of this study is to analyze the evolutionary conservation of the association between pmp22 transcription level and vertebrate myelin formation, and to find the conserved non-coding sequences for pmp22 regulation by comparative genomics analyses between jawed fishes and mammals. Results A transgenic pmp22 over-expression medaka fish line was established. The transgenic fish had approximately one fifth the peripheral NCV values of controls, and aberrant myelination of transgenic fish in the peripheral nerve system (PNS was observed. We successfully confirmed that medaka fish pmp22 has the same exon-intron structure as mammals, and identified some known conserved regulatory motifs. Furthermore, we found novel conserved sequences in the first intron and 3'UTR. Conclusion Medaka fish undergo abnormalities in the PNS when pmp22 transcription increases. This result indicates that an adequate pmp22 transcription level is necessary for correct myelination of jawed vertebrates. Comparison of pmp22 orthologs between distantly related species identifies evolutionary conserved sequences that contribute to precise regulation of pmp22 expression.

  12. Liver function in Huntington's disease assessed by blood biochemical analyses in a clinical setting

    DEFF Research Database (Denmark)

    Nielsen, Signe Marie Borch; Vinther-Jensen, Tua; Nielsen, Jørgen E.;

    2016-01-01

    Huntington's disease (HD) is a dominantly inherited, progressive neurological disorder caused by a CAG repeat elongation in the huntingtin gene. In addition to motor-, psychiatric- A nd cognitive dysfunction, peripheral disease manifestations in the form of metabolic changes and cellular...... indicated by the Unified Huntington's disease rating scale-Total Functional Capacity Score (UHDRS-TFC). For gamma-glutamyl transferase, elevated levels were more frequent in the manifest groups than in both the HD gene-expansion negative controls and premanifest HD gene-expansion carriers. Finally, the...... premanifest HD gene-expansion carriers and controls, using a clinically applied panel of LFTs. Here, we demonstrate that the level of alkaline phosphatase is increased in manifest HD gene-expansion carriers compared to premanifest HD gene-expansion carriers and correlate with increased disease severity...

  13. Functional genomic analyses identify pathways dysregulated by progranulin deficiency, implicating Wnt signaling.

    Science.gov (United States)

    Rosen, Ezra Y; Wexler, Eric M; Versano, Revital; Coppola, Giovanni; Gao, Fuying; Winden, Kellen D; Oldham, Michael C; Martens, Lauren Herl; Zhou, Ping; Farese, Robert V; Geschwind, Daniel H

    2011-09-22

    Progranulin (GRN) mutations cause frontotemporal dementia (FTD), but GRN's function in the CNS remains largely unknown. To identify the pathways downstream of GRN, we used weighted gene coexpression network analysis (WGCNA) to develop a systems-level view of transcriptional alterations in a human neural progenitor model of GRN-deficiency. This highlighted key pathways such as apoptosis and ubiquitination in GRN deficient human neurons, while revealing an unexpected major role for the Wnt signaling pathway, which was confirmed by analysis of gene expression data from postmortem FTD brain. Furthermore, we observed that the Wnt receptor Fzd2 was one of only a few genes upregulated at 6 weeks in a GRN knockout mouse, and that FZD2 reduction caused increased apoptosis, while its upregulation promoted neuronal survival in vitro. Together, these in vitro and in vivo data point to an adaptive role for altered Wnt signaling in GRN deficiency-mediated FTD, representing a potential therapeutic target. PMID:21943601

  14. Testing of global pressure/temperature (GPT) model and global mapping function (GMF) in GPS analyses

    Science.gov (United States)

    Kouba, J.

    2009-03-01

    Several sources of a priori meteorological data have been compared for their effects on geodetic results from GPS precise point positioning (PPP). The new global pressure and temperature model (GPT), available at the IERS Conventions web site, provides pressure values that have been used to compute a priori hydrostatic (dry) zenith path delay z h estimates. Both the GPT-derived and a simple height-dependent a priori constant z h performed well for low- and mid-latitude stations. However, due to the actual variations not accounted for by the seasonal GPT model pressure values or the a priori constant z h, GPS height solution errors can sometimes exceed 10 mm, particularly in Polar Regions or with elevation cutoff angles less than 10 degrees. Such height errors are nearly perfectly correlated with local pressure variations so that for most stations they partly (and for solutions with 5-degree elevation angle cutoff almost fully) compensate for the atmospheric loading displacements. Consequently, unlike PPP solutions utilizing a numerical weather model (NWM) or locally measured pressure data for a priori z h, the GPT-based PPP height repeatabilities are better for most stations before rather than after correcting for atmospheric loading. At 5 of the 11 studied stations, for which measured local meteorological data were available, the PPP height errors caused by a priori z h interpolated from gridded Vienna Mapping Function-1 (VMF1) data (from a NWM) were less than 0.5 mm. Height errors due to the global mapping function (GMF) are even larger than those caused by the GPT a priori pressure errors. The GMF height errors are mainly due to the hydrostatic mapping and for the solutions with 10-degree elevation cutoff they are about 50% larger than the GPT a priori errors.

  15. System biology approach to detect and assign biological functions and regulator genes to feed efficiency traits in Nellore cattle

    DEFF Research Database (Denmark)

    Alexandre, Pâmela; Kogelman, Lisette; Santana, Miguel; Eler, Joanir; Kadarmideen, Haja; Fukumasu, Heidge

    The objective of this study was to use a system biology approach to identify biological mechanisms involved on feed efficiency in Nellore cattle and its possible regulator genes. Two modules of co-expressed and highly inter-connected genes correlated to feed efficiency were identified as well as ...

  16. Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Christer; Sun, Chuanxin; Ghebramedhin, Haile; Hoglund, Anna-Stina; Jansson, Christer

    2008-01-15

    Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN technology in studies on starch branching enzyme activities in barley leaves. We also comment on the mechanism for ODN uptake in plant cells. Antisense ODNs are short (12-25 nt-long) stretches of single-stranded ODNs that hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. They are naturally occurring in both prokaryotes and eukaryotes where they partake in gene regulation and defense against viral infection. The mechanisms for antisense ODN inhibition are not fully understood but it is generally considered that the ODN either sterically interferes with translation or promotes transcript degradation by RNase H activation. The earliest indication of the usefulness of antisense ODN technology for the purposes of molecular biology and medical therapy was the demonstration in 1978 that synthetic ODNs complementary to Raos sarcoma virus could inhibit virus replication in tissue cultures of chick embryo fibroblasts. Since then the antisense ODN technology has been widely used in animal sciences and as an important emerging therapeutic approach in clinical medicine. However, antisense ODN inhibition has been an under-exploited strategy for plant tissues, although the prospects for plant cells in suspension cultures to take up single-stranded ODNs was reported over a decade ago. In 2001, two reports from Malho and coworker demonstrated the use of cationic-complexed antisense ODNs to suppress expression of genes encoding pollen

  17. Genetic and functional analyses demonstrate a role for abnormal glycinergic signaling in autism.

    Science.gov (United States)

    Pilorge, M; Fassier, C; Le Corronc, H; Potey, A; Bai, J; De Gois, S; Delaby, E; Assouline, B; Guinchat, V; Devillard, F; Delorme, R; Nygren, G; Råstam, M; Meier, J C; Otani, S; Cheval, H; James, V M; Topf, M; Dear, T N; Gillberg, C; Leboyer, M; Giros, B; Gautron, S; Hazan, J; Harvey, R J; Legendre, P; Betancur, C

    2016-07-01

    Autism spectrum disorder (ASD) is a common neurodevelopmental condition characterized by marked genetic heterogeneity. Recent studies of rare structural and sequence variants have identified hundreds of loci involved in ASD, but our knowledge of the overall genetic architecture and the underlying pathophysiological mechanisms remains incomplete. Glycine receptors (GlyRs) are ligand-gated chloride channels that mediate inhibitory neurotransmission in the adult nervous system but exert an excitatory action in immature neurons. GlyRs containing the α2 subunit are highly expressed in the embryonic brain, where they promote cortical interneuron migration and the generation of excitatory projection neurons. We previously identified a rare microdeletion of the X-linked gene GLRA2, encoding the GlyR α2 subunit, in a boy with autism. The microdeletion removes the terminal exons of the gene (GLRA2(Δex8-9)). Here, we sequenced 400 males with ASD and identified one de novo missense mutation, p.R153Q, absent from controls. In vitro functional analysis demonstrated that the GLRA2(Δex8)(-)(9) protein failed to localize to the cell membrane, while the R153Q mutation impaired surface expression and markedly reduced sensitivity to glycine. Very recently, an additional de novo missense mutation (p.N136S) was reported in a boy with ASD, and we show that this mutation also reduced cell-surface expression and glycine sensitivity. Targeted glra2 knockdown in zebrafish induced severe axon-branching defects, rescued by injection of wild type but not GLRA2(Δex8-9) or R153Q transcripts, providing further evidence for their loss-of-function effect. Glra2 knockout mice exhibited deficits in object recognition memory and impaired long-term potentiation in the prefrontal cortex. Taken together, these results implicate GLRA2 in non-syndromic ASD, unveil a novel role for GLRA2 in synaptic plasticity and learning and memory, and link altered glycinergic signaling to social and cognitive

  18. Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

    Directory of Open Access Journals (Sweden)

    Isganitis Timothy

    2006-02-01

    Full Text Available Abstract Background Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. Results We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. Conclusion Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at http://biozon.org.

  19. Statistical improvements in functional magnetic resonance imaging analyses produced by censoring high-motion data points.

    Science.gov (United States)

    Siegel, Joshua S; Power, Jonathan D; Dubis, Joseph W; Vogel, Alecia C; Church, Jessica A; Schlaggar, Bradley L; Petersen, Steven E

    2014-05-01

    Subject motion degrades the quality of task functional magnetic resonance imaging (fMRI) data. Here, we test two classes of methods to counteract the effects of motion in task fMRI data: (1) a variety of motion regressions and (2) motion censoring ("motion scrubbing"). In motion regression, various regressors based on realignment estimates were included as nuisance regressors in general linear model (GLM) estimation. In motion censoring, volumes in which head motion exceeded a threshold were withheld from GLM estimation. The effects of each method were explored in several task fMRI data sets and compared using indicators of data quality and signal-to-noise ratio. Motion censoring decreased variance in parameter estimates within- and across-subjects, reduced residual error in GLM estimation, and increased the magnitude of statistical effects. Motion censoring performed better than all forms of motion regression and also performed well across a variety of parameter spaces, in GLMs with assumed or unassumed response shapes. We conclude that motion censoring improves the quality of task fMRI data and can be a valuable processing step in studies involving populations with even mild amounts of head movement. PMID:23861343

  20. Functional evolution of ADAMTS genes: Evidence from analyses of phylogeny and gene organization

    Directory of Open Access Journals (Sweden)

    Van Meir Erwin G

    2005-02-01

    Full Text Available Abstract Background The ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs proteins are a family of metalloproteases with sequence similarity to the ADAM proteases, that contain the thrombospondin type 1 sequence repeat motifs (TSRs common to extracellular matrix proteins. ADAMTS proteins have recently gained attention with the discovery of their role in a variety of diseases, including tissue and blood disorders, cancer, osteoarthritis, Alzheimer's and the genetic syndromes Weill-Marchesani syndrome (ADAMTS10, thrombotic thrombocytopenic purpura (ADAMTS13, and Ehlers-Danlos syndrome type VIIC (ADAMTS2 in humans and belted white-spotting mutation in mice (ADAMTS20. Results Phylogenetic analysis and comparison of the exon/intron organization of vertebrate (Homo, Mus, Fugu, chordate (Ciona and invertebrate (Drosophila and Caenorhabditis ADAMTS homologs has elucidated the evolutionary relationships of this important gene family, which comprises 19 members in humans. Conclusions The evolutionary history of ADAMTS genes in vertebrate genomes has been marked by rampant gene duplication, including a retrotransposition that gave rise to a distinct ADAMTS subfamily (ADAMTS1, -4, -5, -8, -15 that may have distinct aggrecanase and angiogenesis functions.

  1. Structural and functional analyses of DM43, a snake venom metalloproteinase inhibitor from Didelphis marsupialis serum.

    Science.gov (United States)

    Neves-Ferreira, Ana G C; Perales, Jonas; Fox, Jay W; Shannon, John D; Makino, Débora L; Garratt, Richard C; Domont, Gilberto B

    2002-04-12

    DM43, an opossum serum protein inhibitor of snake venom metalloproteinases, has been completely sequenced, and its disulfide bond pattern has been experimentally determined. It shows homology to human alpha(1)B-glycoprotein, a plasma protein of unknown function and a member of the immunoglobulin supergene family. Size exclusion and dynamic laser light scattering data indicated that two monomers of DM43, each composed of three immunoglobulin-like domains, associated to form a homodimer in solution. Analysis of its glycan moiety showed the presence of N-acetylglucosamine, mannose, galactose, and sialic acid, most probably forming four biantennary N-linked chains. DM43 inhibited the fibrinogenolytic activities of bothrolysin and jararhagin and formed 1:1 stoichiometric stable complexes with both metalloproteinases. DM43 was ineffective against atrolysin C or A. No complex formation was detected between DM43 and jararhagin C, indicating the essential role of the metalloproteinase domain for interaction. Homology modeling based on the crystal structure of a killer cell inhibitory receptor suggested the existence of an I-type Ig fold, a hydrophobic dimerization surface and six surface loops potentially forming the metalloproteinase-binding surface on DM43. PMID:11815628

  2. Molecular biological approaches to study myosin functions in cytokinesis of Dictyostelium.

    Science.gov (United States)

    Uyeda, T Q; Yumura, S

    2000-04-15

    The cellular slime mold Dictyostelium discoideum is amenable to biochemical, cell biological, and molecular genetic analyses, and offers a unique opportunity for multifaceted approaches to dissect the mechanism of cytokinesis. One of the important questions that are currently under investigation using Dictyostelium is to understand how cleavage furrows or contractile rings are assembled in the equatorial region. Contractile rings consist of a number of components including parallel filaments of actin and myosin II. Phenotypic analyses and in vivo localization studies of cells expressing mutant myosin IIs have demonstrated that myosin II's transport to and localization at the equatorial region does not require regulation by phosphorylation of myosin II, specific amino acid sequences of myosin II, or the motor activity of myosin II. Rather, the transport appears to depend on a myosin II-independent flow of cortical cytoskeleton. What drives the flow of cortical cytoskeleton is still elusive. However, a growing number of mutants that affect assembly of contractile rings have been accumulated. Analyses of these mutations, identification of more cytokinesis-specific genes, and information deriving from other experimental systems, should allow us to understand the mechanism of contractile ring formation and other aspects of cytokinesis. PMID:10816252

  3. Shaping Small Bioactive Molecules to Untangle Their Biological Function: A Focus on Fluorescent Plant Hormones.

    Science.gov (United States)

    Lace, Beatrice; Prandi, Cristina

    2016-08-01

    Modern biology overlaps with chemistry in explaining the structure and function of all cellular processes at the molecular level. Plant hormone research is perfectly located at the interface between these two disciplines, taking advantage of synthetic and computational chemistry as a tool to decipher the complex biological mechanisms regulating the action of plant hormones. These small signaling molecules regulate a wide range of developmental processes, adapting plant growth to ever changing environmental conditions. The synthesis of small bioactive molecules mimicking the activity of endogenous hormones allows us to unveil many molecular features of their functioning, giving rise to a new field, plant chemical biology. In this framework, fluorescence labeling of plant hormones is emerging as a successful strategy to track the fate of these challenging molecules inside living organisms. Thanks to the increasing availability of new fluorescent probes as well as advanced and innovative imaging technologies, we are now in a position to investigate many of the dynamic mechanisms through which plant hormones exert their action. Such a deep and detailed comprehension is mandatory for the development of new green technologies for practical applications. In this review, we summarize the results obtained so far concerning the fluorescent labeling of plant hormones, highlighting the basic steps leading to the design and synthesis of these compelling molecular tools and their applications. PMID:27378726

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

    Institute of Scientific and Technical Information of China (English)

    Ying Zhao; Yachen Wang; Wei-Guo Zhu

    2011-01-01

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

  5. Integrated 'Omics', Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability.

    Science.gov (United States)

    Lutz, Stefanie; Anesio, Alexandre M; Field, Katie; Benning, Liane G

    2015-01-01

    Snow algae are poly-extremophilic microalgae and important primary colonizers and producers on glaciers and snow fields. Depending on their pigmentation they cause green or red mass blooms during the melt season. This decreases surface albedo and thus further enhances snow and ice melting. Although the phenomenon of snow algal blooms has been known for a long time, large aspects of their physiology and ecology sill remain cryptic. This study provides the first in-depth and multi-omics investigation of two very striking adjacent green and red snow fields on a glacier in Svalbard. We have assessed the algal community composition of green and red snow including their associated microbiota, i.e., bacteria and archaea, their metabolic profiles (targeted and non-targeted metabolites) on the bulk and single-cell level, and assessed the feedbacks between the algae and their physico-chemical environment including liquid water content, pH, albedo, and nutrient availability. We demonstrate that green and red snow clearly vary in their physico-chemical environment, their microbial community composition and their metabolic profiles. For the algae this likely reflects both different stages of their life cycles and their adaptation strategies. Green snow represents a wet, carbon and nutrient rich environment and is dominated by the algae Microglena sp. with a metabolic profile that is characterized by key metabolites involved in growth and proliferation. In contrast, the dry and nutrient poor red snow habitat is colonized by various Chloromonas species with a high abundance of storage and reserve metabolites likely to face upcoming severe conditions. Combining a multitude of techniques we demonstrate the power of such complementary approaches in elucidating the function and ecology of extremophiles such as green and red snow algal blooms, which play crucial roles in glacial ecosystems. PMID:26635781

  6. Functional groups and elemental analyses of cuticular morphotypes of Cordaites principalis (Germar) Geinitz, Carboniferous Maritimes Basin, Canada

    Science.gov (United States)

    Zodrow, E.L.; Mastalerz, Maria; Orem, W.H.; Simunek, Z.; Bashforth, A.R.

    2000-01-01

    Well-preserved cuticles were isolated from Cordaites principalis (Germar) Geinitz leaf compressions, i.e., foliage from extinct gymnosperm trees Coniferophyta: Order Cordaitales. The specimens were collected from the Sydney. Stellarton and Bay St. George subbasins of the once extensive Carboniferous Maritimes Basin of Atlantic Canada. Fourier transformation of infrared spectra (FTIR) and elemental analyses indicate that the ca. 300-306-million-year-old fossil cuticles share many of the functional groups observed in modern cuticles. The similarities of the functional groups in each of the three cuticular morphotypes studied support the inclusion into a single cordaite-leaf taxon, i.e., C. principalis (Germar), confirming previous morphological investigations. Vitrinite reflectance measurements on coal seams in close proximity to the fossil-bearing sediments reveal that the Bay St. George sample site has the lowest thermal maturity, whereas the sites in Sydney and Stellarton are more mature. IR absorption and elemental analyses of the cordaite compressions corroborate this trend, which suggests that the coalified mesophyll in the leaves follows a maturation path similar to that of vitrinite. Comparison of functional groups of the cordaite cuticles with those from certain pteridosperms previously studied from the Sydney Subbasin shows that in the cordaite cuticles highly conjugated C-O (1632 cm-1) bands dominate over carbonyl stretch that characterizes the pteridosperm cuticles. The differences demonstrate the potential of chemotaxonomy as a valuable tool to assist distinguishing between Carboniferous plant-fossil groups. Published by Elsevier Science B.V.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-15

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

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

    International Nuclear Information System (INIS)

    In this article, we report the design and synthesis of a series of well-dispersed superparamagnetic iron oxide nanoparticles (SPIONs) using chitosan as a surface modifying agent to develop a potential T2 contrast probe for magnetic resonance imaging (MRI). The amine, carboxyl, hydroxyl, and thiol functionalities were introduced on chitosan-coated magnetic probe via simple reactions with small reactive organic molecules to afford a series of biofunctionalized nanoparticles. Physico-chemical characterizations of these functionalized nanoparticles were performed by TEM, XRD, DLS, FTIR, and VSM. The colloidal stability of these functionalized iron oxide nanoparticles was investigated in presence of phosphate buffer saline, high salt concentrations and different cell media for 1 week. MRI analysis of human cervical carcinoma (HeLa) cell lines treated with nanoparticles elucidated that the amine-functionalized nanoparticles exhibited higher amount of signal darkening and lower T2 relaxation in comparison to the others. The cellular internalization efficacy of these functionalized SPIONs was also investigated with HeLa cancer cell line by magnetically activated cell sorting (MACS) and fluorescence microscopy and results established selectively higher internalization efficacy of amine-functionalized nanoparticles to cancer cells. These positive attributes demonstrated that these nanoconjugates can be used as a promising platform for further in vitro and in vivo biological evaluations.

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

    Directory of Open Access Journals (Sweden)

    James J Mancuso

    2014-11-01

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

  10. SCALE: a modular code system for performing standardized computer analyses for licensing evaluation. Volume 2. Functional modules

    International Nuclear Information System (INIS)

    This manual provides documentation for a new multi-faceted computational system called SCALE (Standardized Computer Analyses for Licensing Evaluation) that has been developed to provide a standard analysis tool for use by the NRC staff and licensees in evaluating nuclear facilities and package designs. Volume 2 describes the computer codes (functional modules) used within the criticality, shielding, and heat transfer calculation control modules. Separate abstracts are provided for the functional modules available: resonance self-shielding by the Bondarenko method; resonance self-shielding by the Nordheim method; a one-dimensional discrete-ordinates program for transport analysis; calculation of fluxes and dose rates outside a shield; improved Monte Carlo criticality program; processing of problem-dependent cross sections and neutron spectral data; calculation of fuel depletion, transmutation, fission product buildup and decay; mixing of multigroup cross sections; neutron and photon Monte Carlo transport analyses (advanced geometry); heat conduction (finite difference formulation); 3-D geometry plotting program; temperature distribution plotting programs; and plotting program to verify heat transfer input data

  11. [The influences of anterior disc displacement on oral mandibular function and morphology and their biological mechanisms].

    Science.gov (United States)

    Xia, W D; Fu, K Y

    2016-03-01

    Anterior disc displacement is a common subtype seen in temporomandibular disorders (TMD) patients. It may cause mandibular movement disorders, such as clicking of joint, intermittent closed lock, limitation of mouth opening, etc. These disorders may affect the life qualities of patients. Anterior disc displacement may also cause mandibular malformations, especially among adolescents, which may affect the growth of condyle, therefore may have a correlation with mandibular retrusion or mandibular deviation when grown up. This paper going to review the influences of anterior disc displacement on oral mandibular function and morphology and their biological mechanisms. PMID:26980658

  12. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

    Science.gov (United States)

    Ruder, Warren C.; Hsu, Chia-Pei D.; Edelman, Brent D.; Schwartz, Russell; LeDuc, Philip R.

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe3O4) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures.

  13. Role of PET/CT functional imaging on constructing a tumor radiotherapeutic biological target volume

    International Nuclear Information System (INIS)

    In studies on intensity modulated radiotherapy with conventional fractionation, different radiosensitivity areas require different irradiation doses. In tumor radiotherapy areas CR, boosts in radiotherapy doses should be determined according to whether there are survived tumor cells or not. To those survived cells, CT imaging has become the key tool to delineate the radiotherapy target. Thus, the study on the construction of biological target volume with PET/CT functional imaging, which could reflect either radiosensitivity or cell proliferation-related cell metabolism, anoxia and DNA number of various cell cycle phases, is an important research area. (authors)

  14. [Plasma antioxidant activity--a test for impaired biological functions of endoecology, exotrophy, and inflammation reactions].

    Science.gov (United States)

    Titov, V N; Krylin, V V; Dmitriev, V A; Iashin, Ia I

    2010-07-01

    The authors discuss the diagnostic value of a test for total serum antioxidant activity determined by an electrochemistry method on a liquid chromatograph (without a column), by using an amperometric detector, as well as the composition of the endogenously synthesized hydrophilic and hydrophobic acceptors of reactive oxygen species (ROS). Uric acid is a major hydrophilic acceptor of ROS; monoenic oleic fatty acid acts as its major lipophilic acceptor. The constant determined by the authors for of 03 oleic acid oxidation during automatic titration in the organic medium is an order of magnitude higher than that for alpha-tocopherol, beta-carotene and linoleic fatty acid; its concentration is also an order of magnitude higher. In oxidative stress, the adrenal steroid hormone dehydroepiandrosterone initiates oleic acid synthesis via expression of palmitoyl elongase and steatoryl desaturase. In early steps of phylogenesis in primates, spontaneous mutation resulted in ascorbic acid synthesis gene knockout; phylogenetically, further other mutation knocked out the gene encoding the synthesis of uricase and the conversion of uric acid to alantoin. In primates, uric acid became not only a catabolite of purine bases in vivo, but also the major endogenous hydrophilic acceptor of ROS. This philogenetic order makes it clear why the epithelium in the proximal nephron tubule entirely reabsorbs uric acid (a catabolite?) from primary urine and then secretes it again to urine depending on the impairment of biological functions of endoecology (the intercellular medium being contaminated with biological rubbish), the activation of a biological inflammatory reaction, the cellular production of ROS, and the reduction in serum total antioxidant activity. With each biological reaction, there was an increase in the blood content of uric acid as a hydrophilic acceptor of ROS, by actively lowering its secretion into urine. Uric acid is a diagnostic test of inflammation, or rather compensatory

  15. Virus-induced gene silencing as a tool for functional analyses in the emerging model plant Aquilegia (columbine, Ranunculaceae

    Directory of Open Access Journals (Sweden)

    Kramer Elena M

    2007-04-01

    Full Text Available Abstract Background The lower eudicot genus Aquilegia, commonly known as columbine, is currently the subject of extensive genetic and genomic research aimed at developing this taxon as a new model for the study of ecology and evolution. The ability to perform functional genetic analyses is a critical component of this development process and ultimately has the potential to provide insight into the genetic basis for the evolution of a wide array of traits that differentiate flowering plants. Aquilegia is of particular interest due to both its recent evolutionary history, which involves a rapid adaptive radiation, and its intermediate phylogenetic position between core eudicot (e.g., Arabidopsis and grass (e.g., Oryza model species. Results Here we demonstrate the effective use of a reverse genetic technique, virus-induced gene silencing (VIGS, to study gene function in this emerging model plant. Using Agrobacterium mediated transfer of tobacco rattle virus (TRV based vectors, we induce silencing of PHYTOENE DESATURASE (AqPDS in Aquilegia vulgaris seedlings, and ANTHOCYANIDIN SYNTHASE (AqANS and the B-class floral organ identity gene PISTILLATA in A. vulgaris flowers. For all of these genes, silencing phenotypes are associated with consistent reduction in endogenous transcript levels. In addition, we show that silencing of AqANS has no effect on overall floral morphology and is therefore a suitable marker for the identification of silenced flowers in dual-locus silencing experiments. Conclusion Our results show that TRV-VIGS in Aquilegia vulgaris allows data to be rapidly obtained and can be reproduced with effective survival and silencing rates. Furthermore, this method can successfully be used to evaluate the function of early-acting developmental genes. In the future, data derived from VIGS analyses will be combined with large-scale sequencing and microarray experiments already underway in order to address both recent and ancient evolutionary

  16. Clustering of DNA words and biological function: a proof of principle.

    Science.gov (United States)

    Hackenberg, Michael; Rueda, Antonio; Carpena, Pedro; Bernaola-Galván, Pedro; Barturen, Guillermo; Oliver, José L

    2012-03-21

    Relevant words in literary texts (key words) are known to be clustered, while common words are randomly distributed. Given the clustered distribution of many functional genome elements, we hypothesize that the biological text per excellence, the DNA sequence, might behave in the same way: k-length words (k-mers) with a clear function may be spatially clustered along the one-dimensional chromosome sequence, while less-important, non-functional words may be randomly distributed. To explore this linguistic analogy, we calculate a clustering coefficient for each k-mer (k=2-9bp) in human and mouse chromosome sequences, then checking if clustered words are enriched in the functional part of the genome. First, we found a positive general trend relating clustering level and word enrichment within exons and Transcription Factor Binding Sites (TFBSs), while a much weaker relation exists for repeats, and no relation at all exists for introns. Second, we found that 38.45% of the 200 top-clustered 8-mers, but only 7.70% of the non-clustered words, are represented in known motif databases. Third, enrichment/depletion experiments show that highly clustered words are significantly enriched in exons and TFBSs, while they are depleted in introns and repetitive DNA. Considering exons and TFBSs together, 1417 (or 72.26%) in human and 1385 (or 72.97%) in mouse of the top-clustered 8-mers showed a statistically significant association to either exons or TFBSs, thus strongly supporting the link between word clustering and biological function. Lastly, we identified a subset of clustered, diagnostic words that are enriched in exons but depleted in introns, and therefore might help to discriminate between these two gene regions. The clustering of DNA words thus appears as a novel principle to detect functionality in genome sequences. As evolutionary conservation is not a prerequisite, the proof of principle described here may open new ways to detect species-specific functional DNA sequences

  17. Evaluation of jaw and neck muscle activities while chewing using EMG-EMG transfer function and EMG-EMG coherence function analyses in healthy subjects.

    Science.gov (United States)

    Ishii, Tomohiro; Narita, Noriyuki; Endo, Hiroshi

    2016-06-01

    This study aims to quantitatively clarify the physiological features in rhythmically coordinated jaw and neck muscle EMG activities while chewing gum using EMG-EMG transfer function and EMG-EMG coherence function analyses in 20 healthy subjects. The chewing side masseter muscle EMG signal was used as the reference signal, while the other jaw (non-chewing side masseter muscle, bilateral anterior temporal muscles, and bilateral anterior digastric muscles) and neck muscle (bilateral sternocleidomastoid muscles) EMG signals were used as the examined signals in EMG-EMG transfer function and EMG-EMG coherence function analyses. Chewing-related jaw and neck muscle activities were aggregated in the first peak of the power spectrum in rhythmic chewing. The gain in the peak frequency represented the power relationships between jaw and neck muscle activities during rhythmic chewing. The phase in the peak frequency represented the temporal relationships between the jaw and neck muscle activities, while the non-chewing side neck muscle presented a broad range of distributions across jaw closing and opening phases. Coherence in the peak frequency represented the synergistic features in bilateral jaw closing muscles and chewing side neck muscle activities. The coherence and phase in non-chewing side neck muscle activities exhibited a significant negative correlation. From above, the bilateral coordination between the jaw and neck muscle activities is estimated while chewing when the non-chewing side neck muscle is synchronously activated with the jaw closing muscles, while the unilateral coordination is estimated when the non-chewing side neck muscle is irregularly activated in the jaw opening phase. Thus, the occurrence of bilateral or unilateral coordinated features in the jaw and neck muscle activities may correspond to the phase characteristics in the non-chewing side neck muscle activities during rhythmical chewing. Considering these novel findings in healthy subjects, EMG

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

    International Nuclear Information System (INIS)

    Hydroxyapatite (HA) [Ca10(PO4)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

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

    Energy Technology Data Exchange (ETDEWEB)

    Rabiei, Afsaneh [Department of Mechanical and Aerospace Engineering, North Carolina State University, 3211 Broughton Hall, 2601 Stinson Dr., Campus Box 7910, Raleigh, NC 27695-7910 (United States)]. E-mail: arabiei@eos.ncsu.edu; Blalock, Travis [Department of Mechanical and Aerospace Engineering, North Carolina State University, 3211 Broughton Hall, 2601 Stinson Dr., Campus Box 7910, Raleigh, NC 27695-7910 (United States); Thomas, Brent [Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695 (United States); Cuomo, Jerry [Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695 (United States); Yang, Y. [Biomedical Engineering and Orthopedic Surgery, University of Tennessee Health Science Center, 920 Madison Ave., Suite 1005, Memphis, TN 38163 (United States); Ong, Joo [Biomedical Engineering and Orthopedic Surgery, University of Tennessee Health Science Center, 920 Madison Ave., Suite 1005, Memphis, TN 38163 (United States)

    2007-04-15

    Hydroxyapatite (HA) [Ca{sub 10}(PO{sub 4}){sub 6}(OH){sub 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.

  20. Biological functionality of extracellular matrix-ornamented three-dimensional printed hydroxyapatite scaffolds.

    Science.gov (United States)

    Kumar, A; Nune, K C; Misra, R D K

    2016-06-01

    Three-dimensional (3D) printing is considered an ideally suitable method to fabricate patient specific implantable devices. The approach enabled to produce a porous scaffold with tailored physical, mechanical, and biological properties because of the flexibility to tune the scaffold architecture. The objective of the study described was to elucidate the determining role of cell-laid extracellular matrix (ECM) in impacting biological response. In this regard, to mimic the natural ECM environment or the attributes of the native tissue, a natural ECM analogue surface was produced on the 3D printed and sintered hydroxyapatite (HA) scaffold surface by the mineralized ECM of the osteoblast. This involved the growth of osteoblast on 3D printed scaffolds, followed by differentiation to deposit the mineralized ECM on the biomaterial surface. The cells were removed from the mineralized matrix using freeze-thaw cycles to obtain a decellularized extracellular matrix (dECM) on the biomaterial surface. Subsequently, seeding of osteoblast on dECM-ornamented HA scaffolds led to 3D growth with enhanced expression of prominent proteins, actin and vinculin. Based on preliminary observations of present study, it was underscored that HA scaffolds-ornamented with dECM provided an optimized microenvironment conducive to the growth of 3D structural tissue and favorably promoted biological functionality because of the availability of an environment that promoted cell-cell and cell-scaffold interaction. The primary advantage of dECM is that it enabled constructive remodeling and promoted the formation of tissue in lieu of less functional tissue. The study opens-up a new path for printing of 3D structures suitable to treat segmental bone defects. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1343-1351, 2016. PMID:26799466

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-02

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

  2. 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.

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

    Science.gov (United States)

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

    2016-08-01

    To study the biological performance of surface-modified biomedical polymer materials, a model of the functional mechanism of nonspecific adsorption resistance was constructed. Cell behavior on the surface and in vivo transplantation features of intraocular lens (IOL) materials, such as hydrophobic acrylic ester and polymethyl methacrylate (PMMA), were investigated. The results of cell adhesion and proliferation studies showed that the addition of hirudin can significantly resist epithelial cell adhesion, better than the pure amination process, and thereby inhibit excessive proliferation on the surface. Experiments on the eyes of rabbits indicated that the IOL surfaces with hirudin modification reduced the incidence of cell aggregation and inflammation. Combined with a study of protein-resistant layer construction with recombinant hirudin on the material surface, the mechanism of surface functionalization was determined. The biological performance indicated that nonspecific adsorption is greatly decreased due to the existence of amphiphilic ions or hydration layers, which lead to stability and long-term resistance to nonspecific adsorption. These results offer a theoretical basis for the use of traditional biomedical polymer materials in long-term clinical applications. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1961-1967, 2016. PMID:27027387

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

    Science.gov (United States)

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

    2014-12-16

    Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses-the so-called transfer function-and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined. PMID:25404136

  5. Translating Lung Function Genome-Wide Association Study (GWAS) Findings: New Insights for Lung Biology.

    Science.gov (United States)

    Kheirallah, A K; Miller, S; Hall, I P; Sayers, I

    2016-01-01

    Chronic respiratory diseases are a major cause of worldwide mortality and morbidity. Although hereditary severe deficiency of α1 antitrypsin (A1AD) has been established to cause emphysema, A1AD accounts for only ∼1% of Chronic Obstructive Pulmonary Disease (COPD) cases. Genome-wide association studies (GWAS) have been successful at detecting multiple loci harboring variants predicting the variation in lung function measures and risk of COPD. However, GWAS are incapable of distinguishing causal from noncausal variants. Several approaches can be used for functional translation of genetic findings. These approaches have the scope to identify underlying alleles and pathways that are important in lung function and COPD. Computational methods aim at effective functional variant prediction by combining experimentally generated regulatory information with associated region of the human genome. Classically, GWAS association follow-up concentrated on manipulation of a single gene. However association data has identified genetic variants in >50 loci predicting disease risk or lung function. Therefore there is a clear precedent for experiments that interrogate multiple candidate genes in parallel, which is now possible with genome editing technology. Gene expression profiling can be used for effective discovery of biological pathways underpinning gene function. This information may be used for informed decisions about cellular assays post genetic manipulation. Investigating respiratory phenotypes in human lung tissue and specific gene knockout mice is a valuable in vivo approach that can complement in vitro work. Herein, we review state-of-the-art in silico, in vivo, and in vitro approaches that may be used to accelerate functional translation of genetic findings. PMID:26915270

  6. SCALE: A modular code system for performing standardized computer analyses for licensing evaluation: Functional modules, F9-F11

    International Nuclear Information System (INIS)

    This Manual represents Revision 5 of the user documentation for the modular code system referred to as SCALE. The history of the SCALE code system dates back to 1969 when the current Computational Physics and Engineering Division at Oak Ridge National Laboratory (ORNL) began providing the transportation package certification staff at the U.S. Atomic Energy Commission with computational support in the use of the new KENO code for performing criticality safety assessments with the statistical Monte Carlo method. From 1969 to 1976 the certification staff relied on the ORNL staff to assist them in the correct use of codes and data for criticality, shielding, and heat transfer analyses of transportation packages. However, the certification staff learned that, with only occasional use of the codes, it was difficult to become proficient in performing the calculations often needed for an independent safety review. Thus, shortly after the move of the certification staff to the U.S. Nuclear Regulatory Commission (NRC), the NRC staff proposed the development of an easy-to-use analysis system that provided the technical capabilities of the individual modules with which they were familiar. With this proposal, the concept of the Standardized Computer Analyses for Licensing Evaluation (SCALE) code system was born. This volume consists of the section of the manual dealing with three of the functional modules in the code. Those are the Morse-SGC for the SCALE system, Heating 7.2, and KENO V.a. The manual describes the latest released versions of the codes

  7. SCALE: A modular code system for performing standardized computer analyses for licensing evaluation: Functional modules, F9-F11

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    This Manual represents Revision 5 of the user documentation for the modular code system referred to as SCALE. The history of the SCALE code system dates back to 1969 when the current Computational Physics and Engineering Division at Oak Ridge National Laboratory (ORNL) began providing the transportation package certification staff at the U.S. Atomic Energy Commission with computational support in the use of the new KENO code for performing criticality safety assessments with the statistical Monte Carlo method. From 1969 to 1976 the certification staff relied on the ORNL staff to assist them in the correct use of codes and data for criticality, shielding, and heat transfer analyses of transportation packages. However, the certification staff learned that, with only occasional use of the codes, it was difficult to become proficient in performing the calculations often needed for an independent safety review. Thus, shortly after the move of the certification staff to the U.S. Nuclear Regulatory Commission (NRC), the NRC staff proposed the development of an easy-to-use analysis system that provided the technical capabilities of the individual modules with which they were familiar. With this proposal, the concept of the Standardized Computer Analyses for Licensing Evaluation (SCALE) code system was born. This volume consists of the section of the manual dealing with three of the functional modules in the code. Those are the Morse-SGC for the SCALE system, Heating 7.2, and KENO V.a. The manual describes the latest released versions of the codes.

  8. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.

    Science.gov (United States)

    Warde-Farley, David; Donaldson, Sylva L; Comes, Ovi; Zuberi, Khalid; Badrawi, Rashad; Chao, Pauline; Franz, Max; Grouios, Chris; Kazi, Farzana; Lopes, Christian Tannus; Maitland, Anson; Mostafavi, Sara; Montojo, Jason; Shao, Quentin; Wright, George; Bader, Gary D; Morris, Quaid

    2010-07-01

    GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist. PMID:20576703

  9. Genome-wide linkage, exome sequencing and functional analyses identify ABCB6 as the pathogenic gene of dyschromatosis universalis hereditaria.

    Directory of Open Access Journals (Sweden)

    Hong Liu

    Full Text Available BACKGROUND: As a genetic disorder of abnormal pigmentation, the molecular basis of dyschromatosis universalis hereditaria (DUH had remained unclear until recently when ABCB6 was reported as a causative gene of DUH. METHODOLOGY: We performed genome-wide linkage scan using Illumina Human 660W-Quad BeadChip and exome sequencing analyses using Agilent SureSelect Human All Exon Kits in a multiplex Chinese DUH family to identify the pathogenic mutations and verified the candidate mutations using Sanger sequencing. Quantitative RT-PCR and Immunohistochemistry was performed to verify the expression of the pathogenic gene, Zebrafish was also used to confirm the functional role of ABCB6 in melanocytes and pigmentation. RESULTS: Genome-wide linkage (assuming autosomal dominant inheritance mode and exome sequencing analyses identified ABCB6 as the disease candidate gene by discovering a coding mutation (c.1358C>T; p.Ala453Val that co-segregates with the disease phenotype. Further mutation analysis of ABCB6 in four other DUH families and two sporadic cases by Sanger sequencing confirmed the mutation (c.1358C>T; p.Ala453Val and discovered a second, co-segregating coding mutation (c.964A>C; p.Ser322Lys in one of the four families. Both mutations were heterozygous in DUH patients and not present in the 1000 Genome Project and dbSNP database as well as 1,516 unrelated Chinese healthy controls. Expression analysis in human skin and mutagenesis interrogation in zebrafish confirmed the functional role of ABCB6 in melanocytes and pigmentation. Given the involvement of ABCB6 mutations in coloboma, we performed ophthalmological examination of the DUH carriers of ABCB6 mutations and found ocular abnormalities in them. CONCLUSION: Our study has advanced our understanding of DUH pathogenesis and revealed the shared pathological mechanism between pigmentary DUH and ocular coloboma.

  10. Comparing Surface-Based and Volume-Based Analyses of Functional Neuroimaging Data in Patients with Schizophrenia

    Science.gov (United States)

    Anticevic, Alan; Dierker, Donna L.; Gillespie, Sarah K.; Repovs, Grega; Csernansky, John G.; Van Essen, David C.; Barch, Deanna M.

    2008-01-01

    A major challenge in functional neuroimaging is to cope with individual variability in cortical structure and function. Most analyses of cortical function compensate for variability using affine or low-dimensional nonlinear volume-based registration (VBR) of individual subjects to an atlas, which does not explicitly take into account the geometry of cortical convolutions. A promising alternative is to use surface-based registration (SBR), which capitalizes on explicit surface representations of cortical folding patterns in individual subjects. In this study, we directly compare results from SBR and affine VBR in a study of working memory in healthy controls and patients with schizophrenia (SCZ). Each subject's structural scan was used for cortical surface reconstruction using the SureFit method. fMRI data were mapped directly onto individual cortical surface models, and each hemisphere was registered to the population-average PALS-B12 atlas using landmark-constrained SBR. The precision with which cortical sulci were aligned was much greater for SBR than VBR. SBR produced superior alignment precision across the entire cortex, and this benefit was greater in patients with schizophrenia. We demonstrate that spatial smoothing on the surface provides better resolution and signal preservation than a comparable degree of smoothing in the volume domain. Lastly, the statistical power of functional activation in the working memory task was greater for SBR than for VBR. These results indicate that SBR provides significant advantages over affine VBR when analyzing cortical fMRI activations. Furthermore, these improvements can be even greater in disorders that have associated structural abnormalities. PMID:18434199

  11. New approaches to recognizing functional domains in biological sequences. Final report, April 1, 1993--March 31, 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-01

    The purpose of this project is to develop new approaches and programs for determining the function of DNA domains. This will aid in the understanding of the sequence data obtained through the Human Genome Project. One of the great challenges of that project is to abstract important biological information from the raw sequences that emerge. The efforts have focused on several areas determining the protein coding regions in genomic DNA; recognizing patterns of DNA binding proteins, including nucleosomes, from the sequence using multi-alphabet analyses; better recognition methods for RNA genes and other patterns where structural considerations are important along with sequence; enhancing the ``Sequence Landscape`` approach to pattern recognition and applying it to various problems in domain classification. GeneParser is the program the authors developed to identify optimal classification boundaries in genomic DNA. This was the first approach to combine several types of evidence into the classification and obtain optimal and suboptimal predictions by a Dynamic Programming algorithm. The authors also explored the use of neural networks to obtain the optimal weighting of the different types of evidence.

  12. The neuronal correlates of digits backward are revealed by voxel-based morphometry and resting-state functional connectivity analyses.

    Directory of Open Access Journals (Sweden)

    Rui Li

    Full Text Available Digits backward (DB is a widely used neuropsychological measure that is believed to be a simple and effective index of the capacity of the verbal working memory. However, its neural correlates remain elusive. The aim of this study is to investigate the neural correlates of DB in 299 healthy young adults by combining voxel-based morphometry (VBM and resting-state functional connectivity (rsFC analyses. The VBM analysis showed positive correlations between the DB scores and the gray matter volumes in the right anterior superior temporal gyrus (STG, the right posterior STG, the left inferior frontal gyrus and the left Rolandic operculum, which are four critical areas in the auditory phonological loop of the verbal working memory. Voxel-based correlation analysis was then performed between the positive rsFCs of these four clusters and the DB scores. We found that the DB scores were positively correlated with the rsFCs within the salience network (SN, that is, between the right anterior STG, the dorsal anterior cingulate cortex and the right fronto-insular cortex. We also found that the DB scores were negatively correlated with the rsFC within an anti-correlation network of the SN, between the right posterior STG and the left posterior insula. Our findings suggest that DB performance is related to the structural and functional organizations of the brain areas that are involved in the auditory phonological loop and the SN.

  13. Exploring new biological functions of amyloids: bacteria cell agglutination mediated by host protein aggregation.

    Directory of Open Access Journals (Sweden)

    Marc Torrent

    Full Text Available Antimicrobial proteins and peptides (AMPs are important effectors of the innate immune system that play a vital role in the prevention of infections. Recent advances have highlighted the similarity between AMPs and amyloid proteins. Using the Eosinophil Cationic Protein as a model, we have rationalized the structure-activity relationships between amyloid aggregation and antimicrobial activity. Our results show how protein aggregation can induce bacteria agglutination and cell death. Using confocal and total internal reflection fluorescence microscopy we have tracked the formation in situ of protein amyloid-like aggregates at the bacteria surface and on membrane models. In both cases, fibrillar aggregates able to bind to amyloid diagnostic dyes were detected. Additionally, a single point mutation (Ile13 to Ala can suppress the protein amyloid behavior, abolishing the agglutinating activity and impairing the antimicrobial action. The mutant is also defective in triggering both leakage and lipid vesicle aggregation. We conclude that ECP aggregation at the bacterial surface is essential for its cytotoxicity. Hence, we propose here a new prospective biological function for amyloid-like aggregates with potential biological relevance.

  14. The relationship between the connecting peptide of recombined single chain insulin and its biological function

    Institute of Scientific and Technical Information of China (English)

    黄一丁; 梁镇和; 冯佑民

    2001-01-01

    To investigate the relationship between the biological activity of recombined single chain insulin and the length of the connecting peptide, we designed and prepared three single chain insulin molecules, namely, PIP, [A]5PIP and [A]10PIP, by site-directed mutagenesis, in which B30 and A1 were linked through dipeptide A-K, heptapeptide A-A-A-A-A-A-K, and dodecapeptide A-A-A-A-A-A-A-A-A-A-A-K, respectively. Their receptor binding capacities were 0.14%, 14.3% and 11.1% of that of insulin respectively and their in vivo biological activities were in consistence with their receptor binding capacity; whereas their growth promoting activities were 17%, 116.3% and 38% of that of insulin. These results suggested the following conclusions. (i) The recombined single chain insulin could also possess the same metabolic and mitogenic function as insulin. (ii) The receptor binding capacity of recombined single chain insulin to insulin receptor was closely related to the length and amino acid composition of the connecting peptide and could change from 0 to 100% of insulin depending on the different connecting peptides. This result further illustrated the necessity of B chain C-terminus swaying away from A chain N-terminus when insulin binds to its receptor. (iii) The mitogenic activity of recombined single chain insulin also depended on the length and the amino acid composition of the connecting peptide and was higher than its metabolic activity.

  15. Species composition,distribution patterns and ecological functions of biological soil crusts in the Gurbantunggut Desert

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    As one of the most important biological factors that maintain the stability of the largest fixed and semi-fixed desert in China,the Gurbantunggut Desert,the biological soil crusts (BSCs) develop well and play critical ecological roles in the desert ecosystem. In this paper,we briefly summarize our research findings since 2002 including species composition,distribution pattern and ecological functions of BSCs in the desert. Our results indicate abundant species diversity of BSCs in the Gurbantunggut Desert in comparison to other deserts in China. At the scales of sand dune or whole desert,the distribution patterns of BSCs are location-specific. The existence of BSCs in this desert could:(1) accelerate the formation of desert soil and the weathering of minerals; (2) accumulate organic matter in surface soil through related species in soil crusts; (3) enhance the abilities of sand surface to resist wind erosion; (4) influence seed germination of vascular plants; and (5) enhance the production of dew deposition on sandy soil surface.

  16. 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.

  17. Friendly Fire: Biological Functions and Consequences of Chromosomal Targeting by CRISPR-Cas Systems.

    Science.gov (United States)

    Heussler, Gary E; O'Toole, George A

    2016-05-15

    Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) systems in bacteria and archaea target foreign elements, such as bacteriophages and conjugative plasmids, through the incorporation of short sequences (termed spacers) from the foreign element into the CRISPR array, thereby allowing sequence-specific targeting of the invader. Thus, CRISPR-Cas systems are typically considered a microbial adaptive immune system. While many of these incorporated spacers match targets on bacteriophages and plasmids, a noticeable number are derived from chromosomal DNA. While usually lethal to the self-targeting bacteria, in certain circumstances, these self-targeting spacers can have profound effects in regard to microbial biology, including functions beyond adaptive immunity. In this minireview, we discuss recent studies that focus on the functions and consequences of CRISPR-Cas self-targeting, including reshaping of the host population, group behavior modification, and the potential applications of CRISPR-Cas self-targeting as a tool in microbial biotechnology. Understanding the effects of CRISPR-Cas self-targeting is vital to fully understanding the spectrum of function of these systems. PMID:26929301

  18. Structural and biological function of NYD-SP15 as a new member of cytidine deaminases.

    Science.gov (United States)

    Xu, Yidan; Li, Lei; Li, Jianmin; Liu, Qinghuai

    2016-05-25

    Recent studies were mainly focus on the cytidine deaminase family genes, which contained a lot of members that varied on the function of catalytic deamination in RNA or DNA and were involved in the process of growth maintenance, host immunity, retroviral infection, tumorigenesis, and drug resistance with a feature of C-U deamination. In this study, we identified a new member of cytidine deaminase family, NYD-SP15. Previous work showed that the deduced structure of the protein contained two dCMP_cyt_deam domains, which were involved in zinc ion binding. NYD-SP15 was expressed variably in a wide range of tissues, indicating its worthy biological function and creative significances. Sequence analysis, RT-PCR, western blot, flow cytometry, direct-site mutation and GST pull-down assay were performed to analyze the construction and function of NYD-SP15. The results in our studies showed that NYD-SP15 was closely related to deoxycytidylate deaminase and cytidine deaminase, with authentic cytidine deaminase activity in vivo and vitro as well as homo dimerization effects. NYD-SP15 contained nuclear localization sequence (NLS) and nuclear export-signal (NES) and could dynamically shuttle between the nucleus and cytoplasm. Furthermore, NYD-SP15 gene over-expression reduced the cells growth and blocked G1 to S phase, which implied a potential inhibition effect on cell growth. PMID:26945630

  19. 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.

  20. The universality and biological significance of signal molecules with intracellular-extracellular compatible functions

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Generally,cell signal molecules are classified into the extracellular signal molecules (the first messengers) and the intracellular signal ones (the second messengers).Cyclic adenosine monophosphate (cAMP),calcium ions and calmodulin (CaM) are the traditional intracellular messengers,but they are also present in extracellular matrix (ECM).Some of them have been discovered to act as the first messengers through cell surface receptors.Other second messengers,such as cyclic guanosine monophosphate (cGMP),cyclic adenosine diphosphate ribose (cADPR) and annexin,are also found existing outside animal and plant cells.The existence of these messengers with intracellular-extracellular compatible functions in cells may be a regular biological phenomenon.These compatible messengers might be the communication factors between intracellular and extracellular regions or among the cell populations,and are also important in regulating cell development procedure.

  1. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid.

    Science.gov (United States)

    Ruder, Warren C; Hsu, Chia-Pei D; Edelman, Brent D; Schwartz, Russell; Leduc, Philip R

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe(3)O(4)) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures. PMID:22952408

  2. [Historic and functional biology: the inadequacy of a system theory of evolution].

    Science.gov (United States)

    Regelmann, J P

    1982-01-01

    In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and

  3. Mapping the functional properties of soft biological tissues under shear loading

    Science.gov (United States)

    Buckley, Mark Raymond

    The structure and composition of articular cartilage and other load-bearing biological tissues are highly complex and heterogeneous. As a result, their functional mechanical properties exhibit clear spatial variations. Unlocking the structure-function relationship in these materials is critical for devising strategies to restore tissue impaired by injury or disease and can provide a template for successful implant design. Here, we describe a tissue deformation imaging stage (TDIS) allowing for simultaneous force measurement and visualization of microscale deformation in soft biological tissues under controlled shear strain. In combination with a fast confocal microscope, the TDIS is used to test the microscale response of articular cartilage to shear loading. To obtain the location-specific shear modulus of this tissue, we employ a high-resolution technique that involves tracking the deformation of a line photobleached into a fluorescently stained sample loaded in the TDIS. We find that the quasi-static and dynamic shear moduli are lowest roughly 100 mum below the articular surface. Here, articular cartilage is highly nonlinear, stiffening under increased shear strain and becoming more compliant under increased compressive strain. Using a simple thought model, we relate these results to structural features of the collagen network in articular cartilage. Furthermore, we demonstrate that the region of maximum compliance is also the primary site of shear energy dissipation in articular cartilage. Our findings suggest that damage to or surgical removal of the surface of this tissue will increase the joint's susceptibility to shear-induced damage. Finally, similar experiments are performed on intervertebral disc and growth plate, demonstrating the versatility of our in-situ strain mapping techniques.

  4. Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity.

    Directory of Open Access Journals (Sweden)

    Guan-Feng Wang

    2015-02-01

    Full Text Available Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR. Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC, a nucleotide binding (NB-ARC and a leucine rich repeat (LRR domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance.

  5. Genetic Analyses Reveal Functions for MAP2K3 and MAP2K6 in Mouse Testis Determination.

    Science.gov (United States)

    Warr, Nick; Siggers, Pam; Carré, Gwenn-Aël; Wells, Sara; Greenfield, Andy

    2016-05-01

    Testis determination in mammals is initiated by expression of SRY in somatic cells of the embryonic gonad. Genetic analyses in the mouse have revealed a requirement for mitogen-activated protein kinase (MAPK) signaling in testis determination: targeted loss of the kinases MAP3K4 and p38 MAPK causes complete XY embryonic gonadal sex reversal. These kinases occupy positions at the top and bottom level, respectively, in the canonical three-tier MAPK-signaling cascade: MAP3K, MAP2K, MAPK. To date, no role in sex determination has been attributed to a MAP2K, although such a function is predicted to exist. Here, we report roles for the kinases MAP2K3 and MAP2K6 in testis determination. C57BL/6J (B6) embryos lacking MAP2K3 exhibited no significant abnormalities of testis development, whilst those lacking MAP2K6 exhibited a minor delay in testis determination. Compound mutants lacking three out of four functional alleles at the two loci also exhibited delayed testis determination and transient ovotestis formation as a consequence, suggestive of partially redundant roles for these kinases in testis determination. Early lethality of double-knockout embryos precludes analysis of sexual development. To reveal their roles in testis determination more clearly, we generated Map2k mutant B6 embryos using a weaker Sry allele (Sry(AKR)). Loss of Map2k3 on this highly sensitized background exacerbates ovotestis development, whilst loss of Map2k6 results in complete XY gonadal sex reversal associated with reduction of Sry expression at 11.25 days postcoitum. Our data suggest that MAP2K6 functions in mouse testis determination, via positive effects on Sry, and also indicate a minor role for MAP2K3. PMID:27009039

  6. SCALE: A modular code system for performing standardized computer analyses for licensing evaluation: Functional modules F1-F8

    International Nuclear Information System (INIS)

    This Manual represents Revision 5 of the user documentation for the modular code system referred to as SCALE. The history of the SCALE code system dates back to 1969 when the current Computational Physics and Engineering Division at Oak Ridge National Laboratory (ORNL) began providing the transportation package certification staff at the U.S. Atomic Energy Commission with computational support in the use of the new KENO code for performing criticality safety assessments with the statistical Monte Carlo method. From 1969 to 1976 the certification staff relied on the ORNL staff to assist them in the correct use of codes and data for criticality, shielding, and heat transfer analyses of transportation packages. However, the certification staff learned that, with only occasional use of the codes, it was difficult to become proficient in performing the calculations often needed for an independent safety review. Thus, shortly after the move of the certification staff to the U.S. Nuclear Regulatory Commission (NRC), the NRC staff proposed the development of an easy-to-use analysis system that provided the technical capabilities of the individual modules with which they were familiar. With this proposal, the concept of the Standardized Computer Analyses for Licensing Evaluation (SCALE) code system was born. This volume consists of the section of the manual dealing with eight of the functional modules in the code. Those are: BONAMI - resonance self-shielding by the Bondarenko method; NITAWL-II - SCALE system module for performing resonance shielding and working library production; XSDRNPM - a one-dimensional discrete-ordinates code for transport analysis; XSDOSE - a module for calculating fluxes and dose rates at points outside a shield; KENO IV/S - an improved monte carlo criticality program; COUPLE; ORIGEN-S - SCALE system module to calculate fuel depletion, actinide transmutation, fission product buildup and decay, and associated radiation source terms; ICE

  7. SCALE: A modular code system for performing standardized computer analyses for licensing evaluation: Functional modules F1-F8

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    This Manual represents Revision 5 of the user documentation for the modular code system referred to as SCALE. The history of the SCALE code system dates back to 1969 when the current Computational Physics and Engineering Division at Oak Ridge National Laboratory (ORNL) began providing the transportation package certification staff at the U.S. Atomic Energy Commission with computational support in the use of the new KENO code for performing criticality safety assessments with the statistical Monte Carlo method. From 1969 to 1976 the certification staff relied on the ORNL staff to assist them in the correct use of codes and data for criticality, shielding, and heat transfer analyses of transportation packages. However, the certification staff learned that, with only occasional use of the codes, it was difficult to become proficient in performing the calculations often needed for an independent safety review. Thus, shortly after the move of the certification staff to the U.S. Nuclear Regulatory Commission (NRC), the NRC staff proposed the development of an easy-to-use analysis system that provided the technical capabilities of the individual modules with which they were familiar. With this proposal, the concept of the Standardized Computer Analyses for Licensing Evaluation (SCALE) code system was born. This volume consists of the section of the manual dealing with eight of the functional modules in the code. Those are: BONAMI - resonance self-shielding by the Bondarenko method; NITAWL-II - SCALE system module for performing resonance shielding and working library production; XSDRNPM - a one-dimensional discrete-ordinates code for transport analysis; XSDOSE - a module for calculating fluxes and dose rates at points outside a shield; KENO IV/S - an improved monte carlo criticality program; COUPLE; ORIGEN-S - SCALE system module to calculate fuel depletion, actinide transmutation, fission product buildup and decay, and associated radiation source terms; ICE.

  8. Differential function of lip residues in the mechanism and biology of an anthrax hemophore.

    Directory of Open Access Journals (Sweden)

    MarCia T Ekworomadu

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  11. Functional connectivity of coral reef fishes in a tropical seascape assessed by compound-specific stable isotope analyses

    KAUST Repository

    McMahon, Kelton W.

    2011-01-01

    The ecological integrity of tropical habitats, including mangroves, seagrass beds and coral reefs, is coming under increasing pressure from human activities. Many coral reef fish species are thought to use mangroves and seagrass beds as juvenile nurseries before migrating to coral reefs as adults. Identifying essential habitats and preserving functional linkages among these habitats is likely necessary to promote ecosystem health and sustainable fisheries on coral reefs. This necessitates quantitative assessment of functional connectivity among essential habitats at the seascape level. This thesis presents the development and first application of a method for tracking fish migration using amino acid (AA) δ13C analysis in otoliths. In a controlled feeding experiment with fish reared on isotopically distinct diets, we showed that essential AAs exhibited minimal trophic fractionation between consumer and diet, providing a δ13C record of the baseline isoscape. We explored the potential for geochemical signatures in otoliths of snapper to act as natural tags of residency in seagrass beds, mangroves and coral reefs in the Red Sea, Caribbean Sea and Eastern Pacific Ocean. The δ13C values of otolith essential AAs varied as a function of habitat type and provided a better tracer of residence in juvenile nursery habitats than conventional bulk stable isotope analyses (SIA). Using our otolith AA SIA approach, we quantified the relative contribution of coastal wetlands and reef habitats to Lutjanus ehrenbergii populations on coastal, shelf and oceanic coral reefs in the Red Sea. L. ehrenbergii made significant ontogenetic migrations, traveling more than 30 km from juvenile nurseries to coral reefs and across deep open water. Coastal wetlands were important nurseries for L. ehrenbergii; however, there was significant plasticity in L. ehrenbergii juvenile habitat requirements. Seascape configuration played an important role in determining the functional connectivity of L

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

    Science.gov (United States)

    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. PMID:27596431

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

    Directory of Open Access Journals (Sweden)

    Zahra YADEGARI

    2015-10-01

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

  14. Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control.

    Science.gov (United States)

    Medeiros, David B; Daloso, Danilo M; Fernie, Alisdair R; Nikoloski, Zoran; Araújo, Wagner L

    2015-08-01

    Stomata control the concomitant exchange of CO2 and transpiration in land plants. While a constant supply of CO2 is need to maintain the rate of photosynthesis, the accompanying water losses must be tightly regulated to prevent dehydration and undesired metabolic changes. The factors affecting stomatal movement are directly coupled with the cellular networks of guard cells. Although the guard cell has been used as a model for characterization of signaling pathways, several important questions about its functioning remain elusive. Current modeling approaches describe the stomatal conductance in terms of relatively few easy-to-measure variables being unsuitable for in silico design of genetic manipulation strategies. Here, we argue that a system biology approach, combining modeling and high-throughput experiments, may be used to elucidate the mechanisms underlying stomata control and to determine targets for modulation of stomatal responses to environment. In support of our opinion, we review studies demonstrating how high-throughput approaches have provided a systems-view of guard cells. Finally, we emphasize the opportunities and challenges of genome-scale modeling and large-scale data integration for in silico manipulation of guard cell functions to improve crop yields, particularly under stress conditions which are of pertinence both to climate change and water use efficiency. PMID:25689387

  15. Development of Spectral Domain Optical Coherence Tomography for in vivo Functional Imaging of Biological Tissues

    Science.gov (United States)

    An, Lin

    Optical coherence tomography is a rapidly developing optical imaging modality capable of noninvasively providing depth resolved information of biological tissue at micrometer scale. In this thesis, we described several OCT technologies that can be used to double the imaging depth, realize functional vasculature imaging of biological tissue and increase the imaging speed of OCT system. Aim 1: Use of a scanner to introduce spatial frequency modulation to OCT spectral interferograms for in vivo full-range Fourier-domain optical coherence tomography. A novel method was developed that could easily introduce a modulation frequency onto the X-direction (i.e., B-scan) of the FDOCT scanning system, enabling full-range Fourier-domain Optical Coherence Tomography (frFDOCT). Compared to the conventional FDOCT system, the newly developed frFDOCT system can provide increased system sensitivity and deeper imaging depth. The previous technology that can achieve frFDOCT either needed multiple steps for data capturing, which is time consuming, or required additional components which increased the system's complexity. The newly developed method generates a modulation spatial frequency in the spectral interferogram by simply offsetting the probe beam at the X-scanner. Aim 2: Using optical micro-angiography to achieve in vivo volumetric imaging of vascular perfusion within human retina and choroids. Optical Micro-Angiography (OMAG) is a functional extension of FDOCT technology. It can achieve visualization of vasculature network of biological tissue. In order to apply the OMAG method to image vasculature map of human retina and choroid, a phase compensation algorithm was developed, which could minimize the motion artifacts generated by the movements of human eye and head. Aim 3: Developing ultrahigh sensitive optical micro-angiography to achieve micro vasculature imaging of biological tissue. To improve the vasculature image quality, we developed ultrahigh sensitive OMAG (UHS

  16. Structure and functions of water-membrane interfaces and their role in proto-biological evolution

    Science.gov (United States)

    Pohorille, A.; Wilson, M.; Macelroy, R. D.

    1991-01-01

    Among the most important developments in proto-biological evolution was the emergence of membrane-like structures. These are formed by spontaneous association of relatively simple amphiphilic molecules that would have been readily available in the primordial environment. The resulting interfacial regions between water and nonpolar interior of the membrane have several properties which made them uniquely suitable for promoting subsequent evolution. They can (1) selectively attract organic material and mediate its transport, (2) serve as simple catalysts for chemical reactions, and (3) promote the formation of trans-membrane electrical and chemical gradients which could provide energy sources for proto-cells. Understanding the structure of interfaces, their interactions with organic molecules and molecular mechanisms of their functions is an essential step to understanding proto-biological evolution. In our computer simulation studies, we showed that the structure of water at interfaces with nonpolar media is significantly different from that in the bulk. In particular, the average surface dipole density points from the vapor to the liquid. As a result, negative ions can approach the interface more easily than positive ions. Amphiphilic molecules composed of hydrocarbon conjugated rings and polar substituents (e.g., phenol) assume at the interface rigid orientations in which polar groups are buried in water while hydrocarbon parts are located in the nonpolar environment. These orientational differences are of special interest in connection with the ability of some of these molecules to efficiently absorb photons. Flexible molecules with polar substituents often adopt at interfaces conformations different from those in the bulk aquaeous solution and in the gas phase. As a result, in many instances both specificity and kinetics of chemical reactions in which these molecules can participate is modified by the presence of surfaces. Of special interest is the mechanism by

  17. Physical Activity, Exercise, and Mammalian Testis Function: Emerging Preclinical Protein Biomarker and Integrative Biology Insights.

    Science.gov (United States)

    Gomes, Mariana; Freitas, Maria João; Fardilha, Margarida

    2015-09-01

    Exercise and physical activity have long been recognized for health promotion and to delay the onset of many pathological situations such as diabetes and cancers. Still, there appears to be an upper limit on the beneficial health effects regarding intensity and frequency of exercise training. In humans, the effect of exercise training in the male reproductive system has been studied mainly through the analysis of semen quality parameters, with inconsistent results. Less is known on molecular biomarkers of exercise-related changes in testis at the protein/proteome level. This review offers an in-depth analysis on the small scale protein studies available primarily from the preclinical studies and interprets their functional impact on the reproductive health with a view to humans. In all, exercise training in preclinical models seems to negatively modulate, in the course of health, critical functions that directly affect spermatogenesis, such as testosterone biosynthesis, energy supply, and antioxidant system components. Exercise training induces apoptosis, leading to the impairment of spermatogenesis and, consequently, to male infertility. In pathological conditions, an improvement in the testicular functions is observed by increases in steroidogenic enzymes and antioxidant defenses, and reductions in activity of inflammatory pathways. Importantly, the mechanisms by which exercise training modulates the reproductive function are far from being fully understood. The analyses of the testis proteome in varying exercise conditions would inform the molecular mechanisms involved and identify putative theranostics opportunities. Such future research is a cornerstone for health promotion in the pursuit of reproductive health informed by omics systems sciences. PMID:26284990

  18. Recent advances in alveolar biology: evolution and function of alveolar proteins.

    Science.gov (United States)

    Orgeig, Sandra; Hiemstra, Pieter S; Veldhuizen, Edwin J A; Casals, Cristina; Clark, Howard W; Haczku, Angela; Knudsen, Lars; Possmayer, Fred

    2010-08-31

    This review is focused on the evolution and function of alveolar proteins. The lung faces physical and environmental challenges, due to changing pressures/volumes and foreign pathogens, respectively. The pulmonary surfactant system is integral in protecting the lung from these challenges via two groups of surfactant proteins - the small molecular weight hydrophobic SPs, SP-B and -C, that regulate interfacial adsorption of the lipids, and the large hydrophilic SPs, SP-A and -D, which are surfactant collectins capable of inhibiting foreign pathogens. Further aiding pulmonary host defence are non-surfactant collectins and antimicrobial peptides that are expressed across the biological kingdoms. Linking to the first symposium session, which emphasised molecular structure and biophysical function of surfactant lipids and proteins, this review begins with a discussion of the role of temperature and hydrostatic pressure in shaping the evolution of SP-C in mammals. Transitioning to the role of the alveolus in innate host defence we discuss the structure, function and regulation of antimicrobial peptides, the defensins and cathelicidins. We describe the recent discovery of novel avian collectins and provide evidence for their role in preventing influenza infection. This is followed by discussions of the roles of SP-A and SP-D in mediating host defence at the alveolar surface and in mediating inflammation and the allergic response of the airways. Finally we discuss the use of animal models of lung disease including knockouts to develop an understanding of the role of these proteins in initiating and/or perpetuating disease with the aim of developing new therapeutic strategies. PMID:20433956

  19. High-throughput generation of an activation-tagged mutant library for functional genomic analyses in tobacco.

    Science.gov (United States)

    Liu, Feng; Gong, Daping; Zhang, Qian; Wang, Dawei; Cui, Mengmeng; Zhang, Zhiguo; Liu, Guanshan; Wu, Jinxia; Wang, Yuanying

    2015-03-01

    Tobacco (Nicotiana tabacum L.) is an ideal model system for molecular biological and genetic studies. In this study, activation tagging was used to generate approximately 100,000 transgenic tobacco plants. Southern blot analysis indicated that there were 1.6 T-DNA inserts per line on average in our transformed population. The phenotypes observed include abnormalities in leaf and flower morphology, plant height, flowering time, branching, and fertility. Among 6,000 plants in the T0 generation, 57 displayed obvious phenotypes. Among 4,105 lines in the T1 generation, 311 displayed abnormal phenotypes. Fusion primer and nested integrated PCR was used to identify 963 independent genomic loci of T-DNA insertion sites in 1,257 T1 lines. The distribution of T-DNA insertions was non-uniform and correlated well with the predicted gene density along each chromosome. The insertions were biased toward genic regions and noncoding regions within 5 kb of a gene. Fifteen plants that showed the same phenotype as their parent with a dominant pattern in the T2 generation were chosen randomly to detect the expression levels of genes adjacent to the T-DNA integration sites by semi-quantitative RT-PCR. Fifteen candidate genes were identified. Activation was observed in 7 out of the 15 adjacent genes, including one that was located 13.1 kb away from the enhancer sequence. The activation-tagged population described in this paper will be a highly valuable resource for tobacco functional genomics research using both forward and reverse genetic approaches. PMID:25408504

  20. Analysing the Effect of Mutation on Protein Function and Discovering Potential Inhibitors of CDK4: Molecular Modelling and Dynamics Studies.

    Directory of Open Access Journals (Sweden)

    Nagasundaram N

    Full Text Available The cyclin-dependent kinase 4 (CDK4-cyclin D1 complex plays a crucial role in the transition from the G1 phase to S phase of the cell cycle. Among the CDKs, CDK4 is one of the genes most frequently affected by somatic genetic variations that are associated with various forms of cancer. Thus, because the abnormal function of the CDK4-cyclin D1 protein complex might play a vital role in causing cancer, CDK4 can be considered a genetically validated therapeutic target. In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4-cyclin D1 and protein-ligand (CDK4-flavopiridol interactions. This analysis resulted in the identification of possible inhibitors of mutant CDK4 proteins that bind the conformations induced by deleterious nsSNPs. Using computational prediction methods, we identified five nsSNPs as highly deleterious: R24C, Y180H, A205T, R210P, and R246C. From molecular docking and molecular dynamic studies, we observed that these deleterious nsSNPs affected CDK4-cyclin D1 and CDK4-flavopiridol interactions. Furthermore, in a virtual screening approach, the drug 5_7_DIHYDROXY_ 2_ (3_4_5_TRI HYDROXYPHENYL _4H_CHROMEN_ 4_ONE displayed good binding affinity for proteins with the mutations R24C or R246C, the drug diosmin displayed good binding affinity for the protein with the mutation Y180H, and the drug rutin displayed good binding affinity for proteins with the mutations A205T and R210P. Overall, this computational investigation of the CDK4 gene highlights the link between genetic variation and biological phenomena in human cancer and aids in the discovery of molecularly targeted therapies for personalized treatment.

  1. Exploring biological and pathological functions of TGFβ family member activin C

    International Nuclear Information System (INIS)

    Activins and their antagonists inhibins are cytokines of the transforming growth factor β family (TGFβ), with important regulatory functions in a wide array of physiological processes. Activins are homo- or heterodimers consisting of two disulfide-linked β subunits, four mammalian activin β subunits - βA, βB, βC, βE - have been identified in mammalian cells. Inhibins in contrast are heterodimers composed of an β subunit and a β subunit. Whereas the expression of βA and βB subunits is high and widely distributed in many organs, the βC and βE subunits are predominantly expressed in the liver. Activin A is by far the best investigated activin. It has been implicated for instance in reproductive biology, embryonic development, homeostasis, inflammation and tissue repair. In the liver it contributes to regulation of cell growth, apoptosis and tissue architecture. Additionally, deregulation of activin A signaling accounts for pathologic conditions such as hepatic inflammation, fibrosis and carcinogenesis. The biological functions of the other family members and their involvement in liver biology and diseases are still poorly understood. The first part of this work deals with the mRNA expression pattern of the complete inhibin gene family to obtain novel insights into possible functions of activins and inhibins in human hepatocellular carcinogenesis. Using quantitative real-time PCR analysis we found strongly increased inhibin β subunit expression comparing samples of hepatocellular carcinoma and tumor surrounding tissue to samples from healthy donors. All four β subunits were expressed in normal and patient samples, whereas expression of βB subunit increased from normal to malignant samples. This study is the first to report a significant relation of the inhibin β and inhibin βB mRNA levels to human hepatocellular carcinoma. Furthermore, these data, different from those in rodent model systems, suggest a tumor promoting role of inhibin and activin

  2. Nitrification inhibition as measured by RNA- and DNA-based function-specific assays and microbial community structure analyses

    Science.gov (United States)

    Abstract: The biological removal of ammonia in conventional wastewater treatment plants (WWTPs) is performed by promoting nitrification, which transforms ammonia into nitrate, which in turn is converted into nitrogen gas by denitrifying bacteria. The first step in nitrification, ...

  3. Functional assessment of intestinal motility and gut wall inflammation in rodents: analyses in a standardized model of intestinal manipulation.

    Science.gov (United States)

    Vilz, Tim O; Overhaus, Marcus; Stoffels, Burkhard; Websky, Martin von; Kalff, Joerg C; Wehner, Sven

    2012-01-01

    Inflammation of the gastrointestinal tract is a common reason for a variety of human diseases. Animal research models are critical in investigating the complex cellular and molecular of intestinal pathology. Although the tunica mucosa is often the organ of interest in many inflammatory diseases, recent works demonstrated that the muscularis externa (ME) is also a highly immunocompetent organ that harbours a dense network of resident immunocytes.(1,2) These works were performed within the standardized model of intestinal manipulation (IM) that leads to inflammation of the bowel wall, mainly limited to the ME. Clinically this inflammation leads to prolonged intestinal dysmotility, known as postoperative ileus (POI) which is a frequent and unavoidable complication after abdominal surgery.(3) The inflammation is characterized by liberation of proinflammatory mediators such as IL-6(4) or IL-1β or inhibitory neurotransmitters like nitric oxide (NO).(5) Subsequently, tremendous numbers of immunocytes extravasate into the ME, dominated by polymorphonuclear neutrophils (PMN) and monocytes and finally maintain POI.(2) Lasting for days, this intestinal paralysis leads to an increased risk of aspiration, bacterial translocation and infectious complications up to sepsis and multi organ failure and causes a high economic burden.(6) In this manuscript we demonstrate the standardized model of IM and in vivo assessment of gastrointestinal transit (GIT) and colonic transit. Furthermore we demonstrate a method for separation of the ME from the tunica mucosa followed by immunological analysis, which is crucial to distinguish between the inflammatory responses in these both highly immunoactive bowel wall compartments. All analyses are easily transferable to any other research models, affecting gastrointestinal function. PMID:22990580

  4. Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach

    OpenAIRE

    Luan Yihui; Nunez-Iglesias Juan; Wang Wenhui; Sun Fengzhu

    2009-01-01

    Abstract Background Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks. Results ...

  5. Somatostatin receptor expression and biological functions in endocrine pancreatic cells: review based on a doctoral thesis.

    Science.gov (United States)

    Ludvigsen, Eva

    2007-01-01

    Type 1 diabetes is resulting from the selective destruction of insulin-producing betacells within the pancreatic islets. Somatostatin acts as an inhibitor of hormone secretion through specific receptors (sst1-5). All ssts were expressed in normal rat and mouse pancreatic islets, although the expression intensity and the co-expression pattern varied between ssts as well as between species. This may reflect a difference in response to somatostatin in islet cells of the two species. The Non-Obese Diabetic (NOD) mouse model is an experimental model of type 1 diabetes, with insulitis accompanied by spontaneous hyperglycaemia. Pancreatic specimens from NOD mice at different age and stage of disease were stained for ssts. The islet cells of diabetic NOD mice showed increased islet expression of sst2-5 compared to normoglycemic NOD mice. The increase in sst2-5 expression in the islets cells may suggest either a contributing factor in the process leading to diabetes, or a defense response against ongoing beta-cell destruction. Somatostatin analogues were tested on a human endocrine pancreatic tumour cell line and cultured pancreatic islets. Somatostatin analogues had an effect on cAMP accumulation, chromogranin A secretion and MAP kinase activity in the cell line. Treatment of rat pancreatic islets with somatostatin analogues with selective receptor affinity was not sufficient to induce an inhibition of insulin and glucagon secretion. However, a combination of selective analogues or non-selective analogues via costimulation of receptors can cause inhibition of hormone production. For insulin and glucagon, combinations of sst2 + sst5 and sst1 + sst2, respectively, showed a biological effect. In summary, knowledge of islet cell ssts expression and the effect of somatostatin analogues with high affinity to ssts may be valuable in the future attempts to influence beta-cell function in type 1 diabetes mellitus, since down-regulation of beta-cell function may promote survival of

  6. Multiple functional UV devices based on III-Nitride quantum wells for biological warfare agent detection

    Science.gov (United States)

    Wang, Qin; Savage, Susan; Persson, Sirpa; Noharet, Bertrand; Junique, Stéphane; Andersson, Jan Y.; Liuolia, Vytautas; Marcinkevicius, Saulius

    2009-02-01

    We have demonstrated surface normal detecting/filtering/emitting multiple functional ultraviolet (UV) optoelectronic devices based on InGaN/GaN, InGaN/AlGaN and AlxGa1-xN/AlyGa1-yN multiple quantum well (MQW) structures with operation wavelengths ranging from 270 nm to 450 nm. Utilizing MQW structure as device active layer offers a flexibility to tune its long cut-off wavelength in a wide UV range from solar-blind to visible by adjusting the well width, well composition and barrier height. Similarly, its short cut-off wavelength can be adjusted by using a GaN or AlGaN block layer on a sapphire substrate when the device is illuminated from its backside, which further provides an optical filtering effect. When a current injects into the device under forward bias the device acts as an UV light emitter, whereas the device performs as a typical photodetector under reverse biases. With applying an alternating external bias the device might be used as electroabsorption modulator due to quantum confined Stark effect. In present work fabricated devices have been characterized by transmission/absorption spectra, photoresponsivity, electroluminescence, and photoluminescence measurements under various forward and reverse biases. The piezoelectric effect, alloy broadening and Stokes shift between the emission and absorption spectra in different InGaN- and AlGaN-based QW structures have been investigated and compared. Possibilities of monolithic or hybrid integration using such multiple functional devices for biological warfare agents sensing application have also be discussed.

  7. Carbohydrate/glycan-binding specificity of legume lectins in respect to their proposed biological functions

    Directory of Open Access Journals (Sweden)

    Márcio Viana Ramos

    2000-01-01

    Full Text Available The lectins, proteins which specifically recognize carbohydrate moieties, have been extensively studied in many biochemical and structural aspects in order to establish the molecular basis of this non-catalytic event. On the other hand, their clinical and agricultural potentials have been growing fast. Although lectins, mainly those from legume plants, had been investigated for biological properties, studies about the physiological functions of lectins are scarce in literature. Therefore, despite the accumulated data on lectins (as proteins, the role played by these signalizing molecules is poorly discussed. In the light of our accumulated results on legume lectins, specially those obtained from plants belonging to the Diocleinae sub-tribe and available data in literature, we discuss here the main hypothesis of their functions according to their carbohydrate/glycan-binding specificity.As lectinas, proteinas que especificamente reconhecem estruturas que contém carboidratos, têm sido extensivamente estudadas em muitos aspectos bioquímicos e estruturais, objetivando estabelecer as bases moleculares deste evento não-catalítico. Por outro lado, os potenciais clínicos e agriculturais destas proteínas têm crescido rapidamente. Embora as lectinas, principalmente aquelas de legumes tenham sido bastante investigadas em suas propriedades biológicas, estudos sobre as funcões fisiológicas de lectinas são escassos na literatura. Além disto, a despeito da quantidade de dados acumulados sobre lectinas (como proteínas, o papel desempenhado por estas moléculas de sinalização é pobremente discutido. Valendo-se de nossos estudos sobre lectinas de leguminosas, principalmente da sub-tribo Diocleinae, e outros dados presentes na literatura, discutimos aqui, as principais hipóteses de suas funções com base na especificidade por carboidratos e glicanos complexos.

  8. The biology and functional morphology of Macoma biota (Bivalvia: Tellinidae: Macominae

    Directory of Open Access Journals (Sweden)

    Pedro Ribeiro Piffer

    2011-06-01

    Full Text Available Macoma biota Arruda & Domaneschi, 2005, is a recently described species known only from the intertidal zone of Praia da Cidade, Caraguatatuba Bay, in the state of São Paulo, southeastern Brazil. The main purpose of the present paper is to describe the biology of M. biota, beginning with a detailed analysis of its anatomy and functional morphology and how these attributes are correlated with its habitat and life history. The morphology of the organs in the pallial cavity and their sorting devices indicate that this species has efficient mechanisms to process large amounts of particles that enter this cavity via the inhalant current. M. biota can rapidly select the material suitable for ingestion and direct the undesired excess to the rejection mantle tracts. These characteristics along with the siphon's behavior and the digestive tract configuration reveal that this species can be classified primarily as a deposit feeder, like other species of the genus; however, it can also behave as a suspension feeder, depending on the environmental conditions.

  9. Melatonin and its potential biological functions in the fruits of sweet cherry.

    Science.gov (United States)

    Zhao, Yu; Tan, Dun-Xian; Lei, Qiong; Chen, Hao; Wang, Lin; Li, Qing-tian; Gao, Yinan; Kong, Jin

    2013-08-01

    Melatonin is a well-known molecule which possesses many beneficial effects on human health. Many agriculture products provide natural melatonin in the diet. Cherry is one such fruit as they are rich in melatonin. In order to understand the biological roles of melatonin in cherry fruit, melatonin synthesis and its changes over 24 hr period were systematically monitored both during their development and in the ripe cherries in two cultivars, 'Hongdeng' (Prunus avium L. cv. Hongdeng) and 'Rainier' (Prunus avium L. cv. Rainier). It was found that both darkness and oxidative stress induced melatonin synthesis, which led to dual melatonin synthetic peaks during a 24 hr period. The high levels of malondialdehyde induced by high temperature and high intensity light exposure were directly related to up-regulated melatonin production. A primary function of melatonin in cherry fruits is speculated to be as an antioxidant to protect the cherry from the oxidative stress. Importantly, plant tryptophan decaboxylase gene (PaTDC) was identified in cherry fruits. Our data shows that PaTDC expression is positively related to the melatonin production in the cherry. This provides additional information to suggest that tryptophan decaboxylase is a rate-limiting enzyme of melatonin synthesis in plants. PMID:23480341

  10. The formation, function and regulation of amyloids: insights from structural biology.

    Science.gov (United States)

    Landreh, M; Sawaya, M R; Hipp, M S; Eisenberg, D S; Wüthrich, K; Hartl, F U

    2016-08-01

    Amyloid diseases are characterized by the accumulation of insoluble, β-strand-rich aggregates. The underlying structural conversions are closely associated with cellular toxicity, but can also drive the formation of functional protein assemblies. In recent years, studies in the field of structural studies have revealed astonishing insights into the origins, mechanisms and implications of amyloid formation. Notably, high-resolution crystal structures of peptides in amyloid-like fibrils and prefibrillar oligomers have become available despite their challenging chemical nature. Nuclear magnetic resonance spectroscopy has revealed that dynamic local polymorphisms in the benign form of the prion protein affect the transformation into amyloid fibrils and the transmissibility of prion diseases. Studies of the structures and interactions of chaperone proteins help us to understand how the cellular proteostasis network is able to recognize different stages of aberrant protein folding and prevent aggregation. In this review, we will focus on recent developments that connect the different aspects of amyloid biology and discuss how understanding the process of amyloid formation and the associated defence mechanisms can reveal targets for pharmacological intervention that may become the first steps towards clinically viable treatment strategies. PMID:27237473

  11. Expression of a Magnaporthe grisea Elicitor and Its Biological Function in Activating Resistance in Rice

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The expression of a protein elicitor from Magnaporthe griesea and its biological function in activating resistance in rice (Oryza sativa L) were reported. The gene of elicitor was expressed in Escherichia coli cells and produced a His6-fusion protein with 42 kD apparent molecular weight on SDS-PAGE. The purified protein could induce the resistance to blast disease, with the control efficiency of 46.47% and 36.41% at the 14th day and the 21st day after blast inoculation, respectively.After treatment with the expressed protein, the phenylalanine ammonia-lyase (PAL) and peroxidase (POD) activities were promoted in rice plants, meanwhile, the transcription levels of STKM, FAD, PBZ1 and PR1 genes were increased in rice plants. Moreover, after comparing the profile of total rice leaf proteins on two-dimensional eiectrophoresis gel, about 14proteins were found to be increased in expression level after the expressed protein treatment. All the results indicated that the expressed protein could act as an elicitor to trigger the resistance in rice.

  12. Analyses of WOX4 transgenics provide further evidence for the evolution of the WOX gene family during the regulation of diverse stem cell functions

    OpenAIRE

    Ji, Jiabing; Shimizu, Rena; Sinha, Neelima; Scanlon, Michael J.

    2010-01-01

    The WOX (WUSCHEL-RELATED HOMEOBOX) gene family of Arabidopsis comprises fifteen plant-specific transcriptional factors that play important development roles. Genetic, phylogenetic and genomic analyses suggest that WOX genes generally act non-autonomously to organize stem-cell and initial-cell populations within plant meristems and organ anlagen. Previous cross-complementation analyses indicate that the functional diversification of distinct WOX paralogs may be explained largely by promoter ev...

  13. 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...... motions. Design/methodology/approach – Each joint is driven by a pair of virtual agonist-antagonist mechanism (VAAM, i.e., passive components). The muscle-like functions as well as the variable joint compliance are simply achieved by tuning the damping coefficient of the VAAM. Findings – With the VAAM......, 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...

  14. Quantitative assessments of morphological and functional properties of biological trees based on their fractal nature.

    Science.gov (United States)

    Kamiya, Akira; Takahashi, Tatsuhisa

    2007-06-01

    The branching systems in our body (vascular and bronchial trees) and those in the environment (plant trees and river systems) are characterized by a fractal nature: the self-similarity in the bifurcation pattern. They increase their branch density toward terminals according to a power function with the exponent called fractal dimension (D). From a stochastic model based-on this feature, we formulated the fractal-based integrals to calculate such morphological parameters as aggregated branch length, surface area, and content volume for any given range of radius (r). It was followed by the derivation of branch number and cross-sectional area, by virtue of the logarithmic sectioning of the r axis and of the branch radius-length relation also given by a power function of r with an exponent (alpha). These derivatives allowed us to quantify various hydrodynamic parameters of vascular and bronchial trees as fluid conduit systems, including the individual branch flow rate, mean flow velocity, wall shear rate and stress, internal pressure, and circumferential tension. The validity of these expressions was verified by comparing the outcomes with actual data measured in vivo in the vascular beds. From additional analyses of the terminal branch number, we found a simple equation relating the exponent (m) of the empirical power law (Murray's so-called cube law) to the other exponents as (m=D+alpha). Finally, allometric studies of mammalian vascular trees revealed uniform and scale-independent distributions of terminal arterioles in organs, which afforded an infarct index, reflecting the severity of tissue damage following arterial infarction. PMID:17347385

  15. Biological dosimetry: benefit of a serial biological profile in major radiation accidents; Dosimetrie biologique: interet de l`analyse d`un bilan biologique multiparametrique lors d`une surexposition accidentelle

    Energy Technology Data Exchange (ETDEWEB)

    Martin, S.; Denis, J.; Agay, D.; Abadie, B.; Serbat, A.; Fatome, M.

    1995-12-31

    Supposing there is, for each irradiated individual, a specific biological profile, the kinetics and multi-parametric statistical analysis of which allows to sort irradiated. The parameters of this serial biological profile were researched using a primate experimental model. A biological profile bas been defined which allows as soon as the 6. hour and during 72 hours, to point out doses > 4 Gy and/or prognosis. (author). 2 refs.

  16. Functionalization of titanium with chitosan via silanation: evaluation of biological and mechanical performances.

    Directory of Open Access Journals (Sweden)

    Pauline Renoud

    Full Text Available Complications in dentistry and orthopaedic surgery are mainly induced by peri-implant bacterial infections and current implant devices do not prevent such infections. The coating of antibacterial molecules such as chitosan on its surface would give the implant bioactive properties. The major challenge of this type of coating is the attachment of chitosan to a metal substrate. In this study, we propose to investigate the functionalization of titanium with chitosan via a silanation. Firstly, the surface chemistry and mechanical properties of such coating were evaluated. We also verified if the coated chitosan retained its biocompatibility with the peri-implant cells, as well as its antibacterial properties. FTIR and Tof-SIMS analyses confirmed the presence of chitosan on the titanium surface. This coating showed great scratch resistance and was strongly adhesive to the substrate. These mechanical properties were consistent with an implantology application. The Chitosan-coated surfaces showed strong inhibition of Actinomyces naeslundii growth; they nonetheless showed a non significant inhibition against Porphyromonas gingivalis after 32 hours in liquid media. The chitosan-coating also demonstrated good biocompatibility to NIH3T3 fibroblasts. Thus this method of covalent coating provides a biocompatible material with improved bioactive properties. These results proved that covalent coating of chitosan has significant potential in biomedical device implantation.

  17. Functionalization of titanium with chitosan via silanation: evaluation of biological and mechanical performances.

    Science.gov (United States)

    Renoud, Pauline; Toury, Bérangère; Benayoun, Stéphane; Attik, Ghania; Grosgogeat, Brigitte

    2012-01-01

    Complications in dentistry and orthopaedic surgery are mainly induced by peri-implant bacterial infections and current implant devices do not prevent such infections. The coating of antibacterial molecules such as chitosan on its surface would give the implant bioactive properties. The major challenge of this type of coating is the attachment of chitosan to a metal substrate. In this study, we propose to investigate the functionalization of titanium with chitosan via a silanation. Firstly, the surface chemistry and mechanical properties of such coating were evaluated. We also verified if the coated chitosan retained its biocompatibility with the peri-implant cells, as well as its antibacterial properties. FTIR and Tof-SIMS analyses confirmed the presence of chitosan on the titanium surface. This coating showed great scratch resistance and was strongly adhesive to the substrate. These mechanical properties were consistent with an implantology application. The Chitosan-coated surfaces showed strong inhibition of Actinomyces naeslundii growth; they nonetheless showed a non significant inhibition against Porphyromonas gingivalis after 32 hours in liquid media. The chitosan-coating also demonstrated good biocompatibility to NIH3T3 fibroblasts. Thus this method of covalent coating provides a biocompatible material with improved bioactive properties. These results proved that covalent coating of chitosan has significant potential in biomedical device implantation. PMID:22859940

  18. Along-arc variation in water distribution in the upper mantle beneath Kyushu, Japan, as derived from receiver function analyses

    Science.gov (United States)

    Abe, Y.; Ohkura, T.; Hirahara, K.; Shibutani, T.

    2013-12-01

    The Kyushu district, Japan, under which the Philippine Sea (PHS) plate is subducting in a WNW direction, has several active volcanoes. On the volcanic front in Kyushu, a 110 km long gap in volcanism exists in the central part of Kyushu and volcanic rocks with various degrees of contamination by slab-derived fluid are distributed. To reveal the causes of the gap in volcanism and the chemical properties of volcanic rocks and to understand the process of magma genesis and water transportation, we should reveal along-arc variation in water distribution beneath Kyushu. We investigated the seismic velocity discontinuities in the upper mantle beneath Kyushu, with seismic waveform data from 65 stations of Hi-net, which are established by National Research Institute for Earth Science and Disaster Prevention, and 55 stations of the J-array, which are established by Japan Meteorological Agency, Kyushu University, Kagoshima University and Kyoto University. We used receiver function analyses developed especially for discontinuities with high dipping angles (Abe et al., 2011, GJI). We obtained the geometry and velocity contrasts of the continental Moho, the oceanic Moho, and the upper boundary of the PHS slab. From the geometry of these discontinuities and contrast in S wave velocities, we interpreted that the oceanic crust of the PHS slab has a low S wave velocity and is hydrated to a depth of 70 km beneath south Kyushu, to a depth of 80-90 km beneath central Kyushu, and to a depth of no more than 50 km beneath north Kyushu. We also interpreted that the fore-arc mantle beneath central Kyushu has a low velocity region (Vs < 3.2 km/s) that can contain hydrated materials and free aqueous fluid. Such a low velocity fore-arc mantle does not exist beneath north and south Kyushu. Beneath north Kyushu, the oceanic crust does not appear to convey much water in the mantle wedge. Beneath south Kyushu, water dehydrated from the slab could move to the back-arc side and cause arc volcanism

  19. Stability of heroin, 6-monoacetylmorphine, and morphine in biological samples and validation of an LC–MS assay for delayed analyses of pharmacokinetic samples in rats

    OpenAIRE

    Jones, Jessica M.; Raleigh, Michael D.; Pentel, Paul R.; Harmon, Theresa M.; Keyler, Daniel E.; Remmel, Rory P.; Birnbaum, Angela K

    2012-01-01

    Degradation of heroin to 6-monoacetylmorphine (6-MAM) and then morphine happens rapidly in vivo and in vitro. The rates of heroin and 6-MAM degradation depend on the type of biological samples, and the duration and conditions of storage. In order to optimize conditions for measuring heroin and its metabolites in samples collected for pharmacokinetic studies in rats, we investigated the time course of degradation of heroin, 6-MAM, and morphine in four biological matrices: rat blood, rat brain ...

  20. Interaction of hepatitis B virus with tumor suppressor gene p53: its significance and biological function

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The mechanism of the interaction of hepatitis B virus (HBV) with tumor suppressor p53 and its role in the hepatocarcinogenesis have been studied by PCR-directed sequencing, gel shift assays and in situ ultraviolet cross-linking assay. The biological function of the interaction of HBV with p53 gene was investigated by co-transfection of chloramphenicol acetyltransferase (CAT) reporter gene, p53 and HBV DNA, and quantitative PCR. Among the 16 primary hepatocellular carcinoma (PHC) samples, 13 were HBV-DNA positive,10 HBxAg positive and 9 p53 protein positive. The p53 gene point mutation was found in 5 samples, one of which had a G to T substitution located at codon 249. After analyzing the HBV genome by a computer program, a p53 response element binding sequence was found in HBV genome at upstream of enhancer I, from 1047 to 1059 nucleotides. This sequence could specifically bind to p53 protein, increase p53 protein accumulation in the PHC cells and stimulate the transactivating activity of p53 and HBV replication .The results also revealed that HBxAg could combine with p53 protein to form a complex in the cells and enhance CAT expression. Immunocytochemical staining showed that p53 protein complex was located in the cytoplasm and the process of p53 entry to nuclei was, in part, blocked. From our results, we conclude that the mutation of p53 gene at codon 249 is infrequent in HBV-associated PHC, the DNA-protein binding between HBV and p53, and the protein-protein binding between HBxAg and p53 might lead to the reduction or inactivation of p53 protein, which in turn resulting in HBV-associated hepatocarcinogenesis.

  1. Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach.

    Directory of Open Access Journals (Sweden)

    Chia-Wei Hu

    Full Text Available BACKGROUND: Rhodopseudomonas palustris (R. palustris is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin-Benson-Bassham (CBB cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach. METHODOLOGY/PRINCIPAL FINDINGS: By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth

  2. Rapidly restoring biological soil crusts and ecosystem functions in a severely disturbed desert ecosystem.

    Science.gov (United States)

    Chiquoine, Lindsay P; Abella, Scott R; Bowker, Matthew A

    2016-06-01

    Restoring biological soil crusts (biocrusts) in degraded drylands can contribute to recovery of ecosystem functions that have global implications, including erosion resistance and nutrient cycling. To examine techniques for restoring biocrusts, we conducted a replicated, factorial experiment on recently abandoned road surfaces by applying biocrust inoculation (salvaged and stored dry for two years), salvaged topsoil, an abiotic soil amendment (wood shavings), and planting of a dominant perennial shrub (Ambrosia dumosa). Eighteen months after treatments, we measured biocrust abundance and species composition, soil chlorophyll a content and fertility, and soil resistance to erosion. Biocrust addition significantly accelerated biocrust recovery on disturbed soils, including increasing lichen and moss cover and cyanobacteria colonization. Compared to undisturbed controls, inoculated plots had similar lichen and moss composition, recovered 43% of total cyanobacteria density, had similar soil chlorophyll content, and exhibited recovery of soil fertility and soil stability. Inoculation was the only treatment that generated lichen and moss cover. Topsoil application resulted in partial recovery of the cyanobacteria community and soil properties. Compared to untreated disturbed plots, topsoil application without inoculum increased cyanobacteria density by 186% and moderately improved soil chlorophyll and ammonium content and soil stability. Topsoil application produced 22% and 51% of the cyanobacteria density g⁻¹ soil compared to undisturbed and inoculated plots, respectively. Plots not treated with either topsoil or inoculum had significantly lower cyanobacteria density, soil chlorophyll and ammonium concentrations, and significantly higher soil nitrate concentration. Wood shavings and Ambrosia had no influence on biocrust lichen and moss species recovery but did affect cyanobacteria composition and soil fertility. Inoculation of severely disturbed soil with native

  3. The first characterization of gene structure and biological function for echinoderm translationally controlled tumor protein (TCTP).

    Science.gov (United States)

    Ren, Chunhua; Chen, Ting; Jiang, Xiao; Wang, Yanhong; Hu, Chaoqun

    2014-12-01

    Translationally controlled tumor protein (TCTP) is a multifunctional protein that existed ubiquitously in different eukaryote species and distributed widely in various tissues and cell types. In this study, the gene structure and biological function of TCTP were first characterized in echinoderm. An echinoderm TCTP named StmTCTP was identified from sea cucumber (Stichopus monotuberculatus) by expression sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The StmTCTP cDNA is 1219 bp in length, containing a 5'-untranslated region (UTR) of 77 bp, a 3'-UTR of 623 bp and an open reading frame (ORF) of 519 bp that encoding a protein of 172 amino acids with a deduced molecular weight of 19.80 kDa and a predicted isolectric point of 4.66. Two deduced signal signatures termed TCTP1 and TCTP2, a microtubule binding domain, a Ca(2+) binding domain and the conserved residues forming Rab GTPase binding surface were found in the StmTCTP amino acid sequence. For the gene structure, StmTCTP contains four exons separated by three introns. The anti-oxidation and heat shock protein activities of recombinant TCTP protein were also demonstrated in this study. In addition, the expression of StmTCTP was found to be significantly upregulated by polyriboinosinic polyribocytidylic acid [poly (I:C)], lipopolysaccharides (LPS) or inactivated bacteria challenge in in vitro primary culture experiments of coelomocytes, suggested that the sea cucumber TCTP might play critical roles not only in the defense against oxidative and thermal stresses, but also in the innate immune defense against bacterial and viral infections. PMID:25193395

  4. What should be computed to understand and model brain function? from robotics, soft computing, biology and neuroscience to cognitive philosophy

    CERN Document Server

    Kitamura, Tadashi

    2001-01-01

    This volume is a guide to two types of transcendence of academic borders which seem necessary for understanding and modelling brain function. The first type is technical transcendence needed to make intelligent machines such as a humanoid robot, an animal-like behavior architecture, an interpreter of fiction, and an evolving learning machine. This technical erosion is conducted into areas such as biology, ethology, neuroscience and psychology, as well as robotics and soft computing. The second type of transcendence of cross-disciplinary boundaries cuts across scientific areas such as biology a

  5. 2K09 and Thereafter : The Coming Era of Integrative Bioinformatics, Systems Biology and Intelligent Computing for Functional Genomics and Personalized Medicine Research

    OpenAIRE

    2010-01-01

    Abstract Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Co...

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

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    . With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has...... system (the cell), also at the quantitative level, and this is the goal of systems biology. Clearly this will have a significant impact on microbial physiology as well as on metabolic engineering....

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

    International Nuclear Information System (INIS)

    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

  8. 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

  9. New method for the determination of the correction function of a hemisperical electron analyser based on elastic electron images

    International Nuclear Information System (INIS)

    Highlights: • Determination of correction function of a hemispherical analyzer (HSA). • Visualization of analysis area using elastic backscattered electron images. • Dependence of analysis area and transmission function with the kinetic energy. • Efficiency of these functions for quantitative interpretations of XPS. • Description of the general methodology to use these functions. - Abstract: The correction function of a hemispherical analyzer (HSA) is determined for quantitative interpretations of electron spectroscopy. In this way, electron elastic images are performed using a scanning electron gun. This new method allowed the determination of the analysis area A(EK) of a HSA for the first time. An important result is the dependence of this analysis area on the electron kinetic energy EK. Indeed, results show that A(EK) varies as EK−1.2 regardless of the spectrometer configuration. This parameter is different from the so-called transmission function and must be taken into account for quantitative interpretation. Moreover, the transmission function T(EK) is also determined in this work and varies as a power function EKx where x is a fitting parameter which depends only on the width in the energy dispersive direction of the hemisphere entrance slit. These two apparatus functions are then validated thanks to XPS measurements by comparing results obtained on two different Ag surfaces. Then a general methodology to use these functions is given

  10. New method for the determination of the correction function of a hemisperical electron analyser based on elastic electron images

    Energy Technology Data Exchange (ETDEWEB)

    Mahjoub, Mohamed Aymen [Clermont Université, Université Blaise Pascal, Institut Pascal, BP 10448, F-63000 Clermont-Ferrand (France); CNRS, UMR 6602, IP, F-63171 Aubière (France); Monier, Guillaume, E-mail: guillaume.monier@univ-bpclermont.fr [Clermont Université, Université Blaise Pascal, Institut Pascal, BP 10448, F-63000 Clermont-Ferrand (France); CNRS, UMR 6602, IP, F-63171 Aubière (France); Robert-Goumet, Christine; Bideux, Luc; Gruzza, Bernard [Clermont Université, Université Blaise Pascal, Institut Pascal, BP 10448, F-63000 Clermont-Ferrand (France); CNRS, UMR 6602, IP, F-63171 Aubière (France)

    2014-12-15

    Highlights: • Determination of correction function of a hemispherical analyzer (HSA). • Visualization of analysis area using elastic backscattered electron images. • Dependence of analysis area and transmission function with the kinetic energy. • Efficiency of these functions for quantitative interpretations of XPS. • Description of the general methodology to use these functions. - Abstract: The correction function of a hemispherical analyzer (HSA) is determined for quantitative interpretations of electron spectroscopy. In this way, electron elastic images are performed using a scanning electron gun. This new method allowed the determination of the analysis area A(E{sub K}) of a HSA for the first time. An important result is the dependence of this analysis area on the electron kinetic energy E{sub K}. Indeed, results show that A(E{sub K}) varies as E{sub K}{sup −1.2} regardless of the spectrometer configuration. This parameter is different from the so-called transmission function and must be taken into account for quantitative interpretation. Moreover, the transmission function T(E{sub K}) is also determined in this work and varies as a power function E{sub K}{sup x} where x is a fitting parameter which depends only on the width in the energy dispersive direction of the hemisphere entrance slit. These two apparatus functions are then validated thanks to XPS measurements by comparing results obtained on two different Ag surfaces. Then a general methodology to use these functions is given.

  11. Spectroscopic studies, thermal analyses and biological evaluation of new V(IV), Zr(IV) and U(VI) moxifloxacin complexes

    Science.gov (United States)

    Sadeek, Sadeek A.; El-Shwiniy, Walaa H.; Zordok, Wael A.; Kotb, Essam

    2011-12-01

    The synthesis and characterization of the new solid complexes [VO(MOX) 2H 2O]SO 4·11H 2O, [ZrO(MOX) 2Cl]Cl·15H 2O and [UO 2(MOX) 3](NO 3) 2·3H 2O formed in the interaction of moxifloxacin (MOX) with VOSO 4·H 2O, ZrOCl 2·8H 2O and UO 2(NO 3) 2·6H 2O in methanol and acetone as a solvents at room temperature were reported. The isolated solid complexes have been characterized with melting points, elemental analysis, molar conductance, magnetic moments studies, spectral (UV-Visible, IR and 1HNMR) as well as thermal analyses (TGA and DTG). The results support the formation of the complexes and indicate that moxifloxacin reacts as a bidentate ligand chelate to the metal ion through the pyridone oxygen and one carboxylato oxygen. The kinetic parameters of thermogravimetric (TGA) and its differential (DTG), such as activation energies, E*, enthalpies, Δ H*, entropies, Δ S* and Gibbs free energies, Δ G*, have been evaluated by using Coats-Redfern (CR) and Horowitz-Metzeger (HM) methods. The proposed structure of the ligand and their complexes were detected by using the density functional theory (DFT) at the B3LYP/CEP-31G level of theory. The bond stretching force constant and length of the U dbnd O for the [UO 2(MOX) 3](NO 3) 2·3H 2O complex were calculated. The antibacterial activity of the free moxifloxacin ligand and their metal complexes have been tested against some selected bacterial strains such as: Streptococcus aureus K1, Bacillus subtilis K22, Brevibacterium otitidis K76, Escherichia coli K32, Pseudomonas aeruginosa SW1 and Klebsiella oxytoca K42. The complexes showed good antibacterial effect to the selected bacterial strains as compared to the free ligand and Zr(IV) complex is very highly significant compared with the other two complexes.

  12. Best Practices for Promoting Functional Biology Education: Activity-Based, Laboratory-Oriented Instruction

    Directory of Open Access Journals (Sweden)

    Abigail Mgboyibo Osuafor

    2016-08-01

    Full Text Available A major goal of science education is fostering students’ intellectual competencies. This goal can only be achieved when students are actively involved in the teaching-learning process. This study therefore, investigated the extent to which the biology teachers employ pupil-centered activities such as laboratory/practical instructional methods in order to improve the learning outcome of their students. The descriptive survey involved 73 Biology teachers randomly selected from all the six education zones of Anambra state, Nigeria. Four research questions and two hypotheses guided the conduct of the study. A 32-item structured questionnaire which has reliability co-efficient of 0.82 was used to collect data. Data were analyzed using mean, standard deviation and t-test. Results show that Biology teachers adopt practical-oriented strategies in teaching biology, conduct practical activities to a high extent, and perceive practical exercises as essential to effective teaching and learning of the subject. Provision of adequate number of laboratory materials, employment of adequate number of biology teachers, making provision for well designed laboratory activities in the curriculum and training of teachers on how to effectively combine theory with practical are some of the strategies that will encourage biology teachers to conduct practical lessons. There was no significant difference between male and female biology teachers in their responses to the different aspects investigated. Based on these findings, some recommendations were made which include that curriculum designers should incorporate guides for practical activities that go with each topic in the curriculum so as to encourage the teachers to teach theory with practical.

  13. The Implemetation of Interventions for Problem Behavior Based on the Results of Precursor Functional Analyses in the Early Childhood Setting

    OpenAIRE

    Halversen, Hayley

    2016-01-01

    This study consisted of three parts. We first used a video observation method and statistical analysis to identify benign behaviors that occurred before the problem behavior. These benign behaviors are known as precursor behaviors. We then used a precursor functional analysis to identify the function of the precursor behaviors. Lastly, we developed and implemented an intervention based on the results of the precursor functional analysis. The interventions effectively reduced problem behavior ...

  14. Life sciences payloads analyses and technical program planning studies. [project planning of space missions of space shuttles in aerospace medicine and space biology

    Science.gov (United States)

    1976-01-01

    Contractural requirements, project planning, equipment specifications, and technical data for space shuttle biological experiment payloads are presented. Topics discussed are: (1) urine collection and processing on the space shuttle, (2) space processing of biochemical and biomedical materials, (3) mission simulations, and (4) biomedical equipment.

  15. Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea.

    Science.gov (United States)

    Díaz-Pérez, Leopoldo; Rodríguez-Zaragoza, Fabián Alejandro; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María Del Carmen

    2016-01-01

    This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea. PMID:27579575

  16. Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region

    Science.gov (United States)

    Bowker, M.A.; Miller, M.E.; Belnap, J.; Sisk, T.D.; Johnson, N.C.

    2008-01-01

    Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r = 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands. ?? 2008 Society for Conservation Biology.

  17. 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...... 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...... 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...

  18. UV effects on the primary productivity of picophytoplankton: biological weighting functions and exposure response curves of Synechococcus

    OpenAIRE

    Neale, P.J.; A. L. Pritchard; R. Ihnacik

    2014-01-01

    A model that predicts UV effects on marine primary productivity using a biological weighting function (BWF) coupled to the photosynthesis–irradiance response (BWF/P-E model) has been implemented for two strains of the picoplanktonic cyanobacteria Synechococcus, WH7803 and WH8102, which were grown at two irradiances (77 and 174 μmol m−2 s−1 photosynthetically available radiation (PAR)) and two temperatures (20 and 26 °C). The model was fit using photosynthesis measured in a ...

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

    OpenAIRE

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

    2011-01-01

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

  20. The biology of myeloid-derived suppressor cells: The blessing and the curse of morphological and functional heterogeneity

    OpenAIRE

    Youn, Je-in; Gabrilovich, Dmitry I.

    2010-01-01

    Myeloid-derived suppressor cells (MDSC) play an important role in the cellular network regulating immune responses in cancer, chronic infectious diseases, autoimmunity, and in other pathologic conditions. Morphological, phenotypic and functional heterogeneity is a hallmark of MDSC. This heterogeneity demonstrates the plasticity of this immune suppressive myeloid compartment, and shows how various tumors and infectious agents can have similar biological effects on myeloid cells despite the dif...

  1. A Decade of Systems Biology

    OpenAIRE

    Chuang, Han-Yu; Hofree, Matan; Ideker, Trey

    2010-01-01

    Systems biology provides a framework for assembling models of biological systems from systematic measurements. Since the field was first introduced a decade ago, considerable progress has been made in technologies for global cell measurement and in computational analyses of these data to map and model cell function. It has also greatly expanded into the translational sciences, with approaches pioneered in yeast now being applied to elucidate human development and disease. Here, we review the ...

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

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

    This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project...

  3. Discovering and validating biological hypotheses from coherent patterns in functional genomics data

    Energy Technology Data Exchange (ETDEWEB)

    Joachimiak, Marcin Pawel

    2008-08-12

    The area of transcriptomics analysis is among the more established in computational biology, having evolved in both technology and experimental design. Transcriptomics has a strong impetus to develop sophisticated computational methods due to the large amounts of available whole-genome datasets for many species and because of powerful applications in regulatory network reconstruction as well as elucidation and modeling of cellular transcriptional responses. While gene expression microarray data can be noisy and comparisons across experiments challenging, there are a number of sophisticated methods that aid in arriving at statistically and biologically significant conclusions. As such, computational transcriptomics analysis can provide guidance for analysis of results from newer experimental technologies. More recently, search methods have been developed to identify modules of genes, which exhibit coherent expression patterns in only a subset of experimental conditions. The latest advances in these methods allow to integrate multiple data types anddatasets, both experimental and computational, within a single statistical framework accounting for data confidence and relevance to specific biological questions. Such frameworks provide a unified environment for the exploration of specific biological hypothesis and for the discovery of coherent data patterns along with the evidence supporting them.

  4. FUNCTION IN BIOLOGY: ETIOLOGICAL AND ORGANIZATIONAL PERSPECTIVES Función en Biología: perspectivas etiológicas y organizacionales

    Directory of Open Access Journals (Sweden)

    CHARBEL NIÑO EL-HANI

    Full Text Available In this paper, we argue for a taxonomy of approaches to function based on different epistemological perspectives assumed with regard to the treatment of this central concept in the life sciences. We distinguish between etiological and organizational perspectives on function, analyzing distinct theories: Wright's selectionist etiological approach and Godfrey-Smith's modern history theory of functions, in the case of the etiological perspective; and Cummins' functional analysis and Collier's interactivist approach to function, among organizational accounts. We explain differences and similarities between these theories and the broader perspectives on function, arguing for a particular way of understanding the consensus without unity in debates about function. While explaining the accounts of function, we also deal with the relationship between this concept and other important biological concepts, such as adaptation, selection, complexity, and autonomy. We also advance an argument for the limits and prospects of the explanatory role of function in evolution. By arguing that changes in functionality are always grounded on changes in systems' organization, we show that function can never explain the origins of traits. Nevertheless, it can explain the spread of traits in populations, but only when we are dealing with functionally novel traits. Finally, we stress that organizational accounts of function are needed to understand how new functions appear by means of changes in systems' organization.En este artículo, argumentamos a favor de una taxonomía de abordajes del concepto función basada en diferentes perspectivas epistemológicas de acuerdo al tratamiento de este concepto central en las ciencias de la vida. Distinguimos entre perspectivas etiológicas y organizacionales sobre la noción de función, analizando teorías distintas: la teoría etiológica seleccionista de Wright y la teoría de la historia moderna de Godfrey-Smith, en el caso de

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

    Science.gov (United States)

    Upadhyayula, Venkata K K

    2012-02-17

    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 biothreat pathogens through any of the four sensory means mentioned previously. PMID:22244163

  6. Mechanical and biological properties of the micro-/nano-grain functionally graded hydroxyapatite bioceramics for bone tissue engineering.

    Science.gov (United States)

    Zhou, Changchun; Deng, Congying; Chen, Xuening; Zhao, Xiufen; Chen, Ying; Fan, Yujiang; Zhang, Xingdong

    2015-08-01

    Functionally graded materials (FGM) open the promising approach for bone tissue repair. In this study, a novel functionally graded hydroxyapatite (HA) bioceramic with micrograin and nanograin structure was fabricated. Its mechanical properties were tailored by composition of micrograin and nanograin. The dynamic mechanical analysis (DMA) indicated that the graded HA ceramics had similar mechanical property compared to natural bones. Their cytocompatibility was evaluated via fluorescent microscopy and MTT colorimetric assay. The viability and proliferation of rabbit bone marrow mesenchymal stem cells (BMSCs) on ceramics indicated that this functionally graded HA ceramic had better cytocompatibility than conventional HA ceramic. This study demonstrated that functionally graded HA ceramics create suitable structures to satisfy both the mechanical and biological requirements of bone tissues. PMID:25910818

  7. Application of time-series analyses to the hydrological functioning of an Alpine karstic system: the case of Bange-L’Eau-Morte

    Directory of Open Access Journals (Sweden)

    T. Mathevet

    2004-01-01

    Full Text Available This paper analyses the hydrological functioning of the Bange-L’Eau-Morte karstic system using classical and original techniques, recession curves, correlation and spectral analyses, noise analysis and wavelet analyses. The main characteristics that can be deduced are the recession coefficients, the dynamic volume of storage, the response time of the system, the quickflow and baseflow components and the snowmelt characteristics. The non-stationary and timescale-dependent behaviour of the system is studied and particular features of the runoff are shown. The step-by-step use of these different techniques provides a general methodology applicable to different karstic systems to provide quantifiable and objective criteria for differentiation and comparison of karstic systems. Keywords: karstic hydrology, Bauges mountains, recession curves, correlation and spectral analysis, wavelet analysis, snowmelt

  8. Functional analyses of two tomato APETALA3 genes demonstrate diversification in their roles in regulating floral development.

    Science.gov (United States)

    de Martino, Gemma; Pan, Irvin; Emmanuel, Eyal; Levy, Avraham; Irish, Vivian F

    2006-08-01

    The floral homeotic APETALA3 (AP3) gene in Arabidopsis thaliana encodes a MADS box transcription factor required for specifying petal and stamen identities. AP3 is a member of the euAP3 lineage, which arose by gene duplication coincident with radiation of the core eudicots. Although Arabidopsis lacks genes in the paralogous Tomato MADS box gene 6 (TM6) lineage, tomato (Solanum lycopersicum) possesses both euAP3 and TM6 genes, which have functionally diversified. A loss-of-function mutation in Tomato AP3 (TAP3) resulted in homeotic transformations of both petals and stamens, whereas RNA interference-induced reduction in TM6 function resulted in flowers with homeotic defects primarily in stamens. The functional differences between these genes can be ascribed partly to different expression domains. When overexpressed in an equivalent domain, both genes can partially rescue the tap3 mutant, indicating that relative levels as well as spatial patterns of expression contribute to functional differences. Our results also indicate that the two proteins have differing biochemical capabilities. Together, these results suggest that TM6 and TAP3 play qualitatively different roles in floral development; they also support the ideas that the ancestral role of AP3 lineage genes was in specifying stamen development and that duplication and divergence in the AP3 lineage allowed for the acquisition of a role in petal specification in the core eudicots. PMID:16844904

  9. Biological Soil Crusts Influence Hydrologic Function Differently in Various Deserts And Future Climate and Land Use will Affect These Relationships

    Science.gov (United States)

    Belnap, J.; Wilcox, B.; Barger, N.; Herrick, J.; van Soyoc, M.

    2012-04-01

    Biological soil crusts (biocrusts) can completely cover plant interspaces in dryland regions, and can constitute 70% or more of the living ground cover. In these areas, where precipitation is low and soils have low fertility, native plants often rely on intact biological soil crusts to provide water and nutrient flow to the broadly scattered vegetation. In cool desert systems, well-developed biocrusts (dominated by lichens and mosses) roughen the soil surface, increasing residence time of surface water flow. This results in increased and relatively homogenous infiltration of water into the soils. Filaments associated with cyanobacteria, fungi, mosses and lichens increase aggregate formation and stabilize soils, thus reducing sediment production, with well-developed biocrusts conferring much more stability on soils than less developed cyanobacterial dominated biocrusts. In hot and hyper-arid desert systems, biocrusts are generally less developed and dominated by cyanobacteria. These biocrusts generally increase runoff from plant interspaces to downslope vegetation. While reduced infiltration may seem to be negative, it can actually be advantageous to the downslope plants, as they may require small watersheds above them to provide the needed amount of water and nutrients required for their growth. Thus, infiltration and nutrient additions are more heterogenous than in cool desert systems. Soil surface disturbance and climate change have the potential to dramatically alter the species composition and thereby function of biological soil crusts in different deserts. Compressional disturbances results in reduced cover and a loss of lichen and moss species. Changes in climate regimes, such as an increase in temperature or a shift in the amount, timing, or intensity of rainfall, will influence the composition and physiological functioning of biological soil crusts, as various crust components have different photosynthetic and respiration responses to temperature and

  10. An experimental study of the anisotropy of the electron distribution function in an ECR plasma by means of a double retarding field analyser

    International Nuclear Information System (INIS)

    A double retarding field analyser for use in axially inhomogeneous axisymmetric magnetic field configurations is described and applied for measuring anisotropic electron distribution functions in an ECR discharge. The analyser uses the velocity transformation due to the constancy of the magnetic moment at adiabatic motion in an axially varying magnetic field. Its principles of operation and construction are described and discussed. An application to measuring the distribution function of electrons escaping through the mirror throat from an ECR discharge confined by a magnetic mirror trap clearly indicates an anisotropy in the energy distribution. The kinetic temperature of the gyrational motion of the electrons exceeds that of the motion parallel to the field lines. (author)

  11. A Structure of Biological System and Functionality using Artificial Neural Networks

    Directory of Open Access Journals (Sweden)

    Khaled Mohammed Beer Gamal

    2014-07-01

    Full Text Available Artificial neural networks have, as initial motivation, the structure of biological systems, and constitute an alternative computability paradigm. For that reason we will review some aspects of the way in which biological systems perform information processing. The fascination which still pervades this research field has much to do with the points of contact with the surprisingly elegant methods used by neurons in order to process information at the cellular level. Several million years of evolution have led to very sophisticated solutions to the problem of dealing with an uncertain environment. In this chapter we will discuss some elements of these strategies in order to determine what features we want to adopt in our abstract models of neural networks.

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

    OpenAIRE

    Kurita, Kenji Long

    2015-01-01

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

  13. Biological rhythms, higher brain function, and behavior: gaps, opportunities and challenges”

    OpenAIRE

    Benca, Ruth; Duncan, Marilyn J.; Frank, Ellen; McClung, Colleen; Nelson, Randy J.; Vicentic, Aleksandra

    2009-01-01

    Increasing evidence suggests that disrupted temporal organization impairs behavior, cognition, and affect; further, disruption of circadian clock genes impairs sleep/wake cycle and social rhythms which may be implicated in mental disorders. Despite this strong evidence, a gap in understanding the neural mechanisms of this interaction obscures whether biological rhythms disturbances are the underlying causes or merely symptoms of these diseases. Here, we review current understanding, emerging ...

  14. Beyond the hydrophobic effect: Critical function of water at biological phase boundaries--A hypothesis.

    Science.gov (United States)

    Damodaran, Srinivasan

    2015-07-01

    Many life-sustaining processes in living cells occur at the membrane-water interface. The pertinent questions that need to be asked are what is the evolutionary reason for biology to choose the membrane-water interface as the site for performing and/or controlling crucial biological reactions and what is the key physical principle that is singular to the membrane-water interface that biology exploits for regulating metabolic processes in cells? In this review, a hypothesis is developed, which espouses that cells control activities of membrane-bound enzymes and receptor activated processes via manipulating the thermodynamic activity of water at the membrane-water interfacial region. In support of this hypothesis, first we establish that the surface pressure of a lipid monolayer is a direct measure of a reduction in the thermodynamic activity of interfacial water. Second, we show that the surface pressure-dependent activation/inactivation of interfacial enzymes is fundamentally related to their dependence on interfacial water activity. We extend this argument to infer that cells might manipulate activities of membrane-associated biological processes via manipulating the activity of interfacial water via localized compression or expansion of the interface. In this paper, we critically analyze literature data on mechano-activation of large pore ion channels in Escherichia coli spheroplasts and G-proteins in reconstituted lipid vesicles, and show that these pressure-induced activation processes are fundamentally and quantitatively related to changes in the thermodynamic state of interfacial water, caused by mechanical stretching of the bilayer. PMID:25888225

  15. Adipocyte-derived basement membrane extract with biological activity: applications in hepatocyte functional augmentation in vitro

    OpenAIRE

    Sharma, Nripen S.; Nagrath, Deepak; Martin L Yarmush

    2010-01-01

    Natural and synthetic biomaterials utilized in tissue engineering applications require a dynamic interplay of complex macromolecular compositions of hydrated extracellular matrices (ECMs) and soluble growth factors. The challenges in utilizing synthetic ECMs is the effective control of temporal and spatial complexity of multiple signal presentation, as compared to natural ECMs that possess the inherent properties of biological recognition, including presentation of receptor-binding ligands, s...

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

    OpenAIRE

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

    2014-01-01

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

  17. Identification of Distinct Breast Cancer Stem Cell Populations Based on Single-Cell Analyses of Functionally Enriched Stem and Progenitor Pools

    OpenAIRE

    Nina Akrap; Daniel Andersson; Eva Bom; Pernilla Gregersson; Anders Ståhlberg; Göran Landberg

    2016-01-01

    Summary The identification of breast cancer cell subpopulations featuring truly malignant stem cell qualities is a challenge due to the complexity of the disease and lack of general markers. By combining extensive single-cell gene expression profiling with three functional strategies for cancer stem cell enrichment including anchorage-independent culture, hypoxia, and analyses of low-proliferative, label-retaining cells derived from mammospheres, we identified distinct stem cell clusters in b...

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

    International Nuclear Information System (INIS)

    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.

  19. Interrogating the Role of Receptor-Mediated Mechanisms: Biological Fate of Peptide-Functionalized Radiolabeled Gold Nanoparticles in Tumor Mice.

    Science.gov (United States)

    Silva, Francisco; Zambre, Ajit; Campello, Maria Paula Cabral; Gano, Lurdes; Santos, Isabel; Ferraria, Ana Maria; Ferreira, Maria João; Singh, Amolak; Upendran, Anandhi; Paulo, António; Kannan, Raghuraman

    2016-04-20

    To get a better insight on the transport mechanism of peptide-conjugated nanoparticles to tumors, we performed in vivo biological studies of bombesin (BBN) peptide functionalized gold nanoparticles (AuNPs) in human prostate tumor bearing mice. Initially, we sought to compare AuNPs with thiol derivatives of acyclic and macrocyclic chelators of DTPA and DOTA types. The DTPA derivatives were unable to provide a stable coordination of (67)Ga, and therefore, the functionalization with the BBN analogues was pursued for the DOTA-containing AuNPs. The DOTA-coated AuNPs were functionalized with BBN[7-14] using a unidentate cysteine group or a bidentate thioctic group to attach the peptide. AuNPs functionalized with thioctic-BBN displayed the highest in vitro cellular internalization (≈ 25%, 15 min) in gastrin releasing peptide (GRP) receptor expressing cancer cells. However, these results fail to translate to in vivo tumor uptake. Biodistribution studies following intravenous (IV) and intraperitoneal (IP) administration of nanoconjugates in tumor bearing mice indicated that the presence of BBN influences to some degree the biological profile of the nanoconstructs. For IV administration, the receptor-mediated pathway appears to be outweighed by the EPR effect. By contrast, in IP administration, it is reasoned that the GRPr-mediated mechanism plays a role in pancreas uptake. PMID:27003101

  20. Effect of side-stream phosphorus recovery on biological phosphorus removal performance investigated by chemical and microbial analyses in a novel BNR-IC process.

    Science.gov (United States)

    Zou, H M; Lu, X W; Li, T

    2014-01-01

    The aim of this study was to assess the effect of side-stream ratio (SSR) on performance of phosphorus (P) removal and recovery in a novel process linking biological nutrients removal (BNR) and induced crystallization (IC). Results showed that P removal efficiency was significantly enhanced when given an appropriate SSR, resulting in effluent P concentrations decreasing from 0.75 to 0.39 mg/L with an increase of SSR from 0 to 35%, where a maximum of 7.19 mg/L P recovery amount was obtained at 35% of SSR. Increasing the SSR can favor the P recovery, while an excessively high SSR (more than 35%) would have a negative effect on the subsequent biological P removal in the BNR-IC system. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis showed that in total, 11 DGGE bands of highest species richness were visually detected and significant changes in microbial community structure were found, with SSR variations ranging from 0 to 55%. Moreover, an increase in SSR can cause an increase in microbial community biodiversity; where microbial populations correspond to the 11 bands, they were generally classified into five different phyla or classes (Beta-, Gamma-, and Deltaproteobacteria, as well as Clostridia and Flavobacteria) based on the evolutionary tree analysis. PMID:25401306

  1. Integrative functional transcriptomic analyses implicate specific molecular pathways in pulmonary toxicity from exposure to aluminum oxide nanoparticles.

    Science.gov (United States)

    Li, Xiaobo; Zhang, Chengcheng; Bian, Qian; Gao, Na; Zhang, Xin; Meng, Qingtao; Wu, Shenshen; Wang, Shizhi; Xia, Yankai; Chen, Rui

    2016-09-01

    Gene expression profiling has developed rapidly in recent years and it can predict and define mechanisms underlying chemical toxicity. Here, RNA microarray and computational technology were used to show that aluminum oxide nanoparticles (Al2O3 NPs) were capable of triggering up-regulation of genes related to the cell cycle and cell death in a human A549 lung adenocarcinoma cell line. Gene expression levels were validated in Al2O3 NPs exposed A549 cells and mice lung tissues, most of which showed consistent trends in regulation. Gene-transcription factor network analysis coupled with cell- and animal-based assays demonstrated that the genes encoding PTPN6, RTN4, BAX and IER play a role in the biological responses induced by the nanoparticle exposure, which caused cell death and cell cycle arrest in the G2/S phase. Further, down-regulated PTPN6 expression demonstrated a core role in the network, thus expression level of PTPN6 was rescued by plasmid transfection, which showed ameliorative effects of A549 cells against cell death and cell cycle arrest. These results demonstrate the feasibility of using gene expression profiling to predict cellular responses induced by nanomaterials, which could be used to develop a comprehensive knowledge of nanotoxicity. PMID:26830206

  2. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

    OpenAIRE

    Warde-Farley, David; Sylva L. Donaldson; Comes, Ovi; Zuberi, Khalid; Badrawi, Rashad; Chao, Pauline; Franz, Max; Grouios, Chris; Kazi, Farzana; Lopes, Christian Tannus; Maitland, Anson; Mostafavi, Sara; Montojo, Jason; Shao, Quentin; Wright, George

    2010-01-01

    GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis t...

  3. Urban gravity model based on cross-correlation function and Fourier analyses of spatio-temporal process

    International Nuclear Information System (INIS)

    This paper is devoted to gaining a new insight into urban physics in the right perspective. The conventional urban gravity model based on Newton's Law of Universal Gravitation is made into a new expression based on a cross-correlation function. Endowed with a time-lag parameter and time functions, the developed model can integrate temporal dimension into spatial process of cities. A pair of gravity spectra can be given for spatial interaction of any two cities with Fourier transform, and the series of attraction quantity are proved to be the average values of interaction volumes from the traditional model. The method is applied to four cities in China, illustrating how to employ the improved model to characterize the spatio-temporal process of urban interaction. The new gravity model reveals the relationship between the concept of energy and the notion of interaction, and suggests asymmetric interaction between cities, commonly observed in the real world.

  4. Functional outcomes following ankle arthrodesis in males with haemophilia: analyses using the CDC’s Universal Data Collection surveillance project

    OpenAIRE

    LANE, H.; SIDDIQI, A.-E.-A.; INGRAM-RICH, R.; TOBASE, P.; WARD, R. SCOTT

    2014-01-01

    In persons with haemophilia (PWH), repeated ankle haemarthroses lead to pain, loss of joint range of motion (ROM), and limitations in activity and participation in society. PWH are offered ankle arthrodesis (AA) to eliminate pain. In our experience, PWH are hesitant to proceed to AA due to concerns regarding gait anomalies, functional decline and complete loss of ROM. The aim of this study was to report outcomes in ROM, assistive device (AD)/wheelchair use, activity scale and work/school abse...

  5. 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

  6. Functional degradation of the water-sediment regulation scheme in the lower Yellow River: Spatial and temporal analyses.

    Science.gov (United States)

    Miao, Chiyuan; Kong, Dongxian; Wu, Jingwen; Duan, Qingyun

    2016-05-01

    Heavy sedimentation has led to the phenomenon of a secondary perched river in the lower reaches of the Yellow River. The water-sediment regulation scheme (WSRS) using the Xiaolangdi Reservoir was first implemented in 2002 to try to solve this problem. In this study, we analyzed the spatial and temporal effects of the current WSRS (2005-2013) on the lower Yellow River. Our results suggest that the current WSRS is exhibiting a tendency towards functional degradation, meaning that the scheme is no longer as effective as it was initially for the lower Yellow River. Although the main river channel has been fully scoured in the lower reaches since the implementation of the WSRS, we found that the degree of erosion declined gradually in a top-down fashion from the braided reach, through the transitional reach, to the meandering reach. Of the total eroded sediment, 69.64% came from the braided reach and only 6.61% came from the meandering reach. In addition, the reduction in riverbed elevation-a key function of the WSRS-has clearly slowed since 2005. We discuss the mechanisms underlying this functional degradation of the current WSRS and future challenges for the management of the lower Yellow River. Insights gained from this study will likely be of use to those weighing up options for future implementations of the WSRS. PMID:26874756

  7. The dynamics of the biological membrane surrounding the buffalo milk fat globule investigated as a function of temperature.

    Science.gov (United States)

    Nguyen, Hanh T H; Madec, Marie-Noëlle; Ong, Lydia; Kentish, Sandra E; Gras, Sally L; Lopez, Christelle

    2016-08-01

    The biological membrane surrounding fat globules in milk (the MFGM) is poorly understood, despite its importance in digestion and in determining the properties of fat globules. In this study, in situ structural investigations of buffalo MFGM were performed as a function of temperature (4-60°C), using confocal microscopy. We demonstrate that temperature and rate of temperature change affected the lipid domains formed in the MFGM with the lateral segregation (i) of high Tm lipids and cholesterol in a Lo phase for both TTm and (ii) of high Tm lipids in a gel phase for Tfunction of temperature, could modulate the functions of fat globules during processing and digestion. PMID:26988511

  8. The relationship between the connecting peptide of recombined single chain insulin and its biological function

    Institute of Scientific and Technical Information of China (English)

    HUANG; Yiding; (

    2001-01-01

    [1]Straus, D. S., Growth-stimulatory of insulin in vitro and in vivo, Endocr. Rev., 1984, 5(2): 356-369.[2]Svenningsen, A. F., Kanje, M., Insulin and the insulin-like growth factors I and II are mitogenic to cultured rat sciatic nerve segments and stimulate [3H] thuymidine incorporation through their respective receptors, Glia, 1996, 18(1): 68-72.[3]Ogihara, S., Yamada, M., Saito, T. et al., Insulin potentiates mitogenic effect of epidermal growth factor on cultured guinea pig gastric mucous cells, Am. J. Physiol., 1996, 271(1 Pt 1): G104-121.[4]Steiner, D. F., Oyer, P. E., The biosynthesis of insulin and a probable precursor of insulin by a human islet cell adenoma, Proc. Nalt. Acad. Sci. USA, 1967, 57(2): 473-480.[5]King, G. L., Kahn, C. R., The growth-promoting effects of insulin, in Growth and Maturation Factors(ed. Guroff, G.), New York: John Wiley & Sons, 1984, 223-265.[6]Peavy, D. E., Brunner, M. R., Duckworth, W. C. et al., Receptor binding and biological potency of several split forms (conversion intermediates) of human proinsulin, Studies in cultured IM-9 lymphocytes and in vivo and in vitro in rats, J. Biol. Chem., 1985, 260: 13989-13994.[7]Derewenda, U., Derewenda, Z., Dodson, E. J. et al., X-ray analysis of the single chain B29-A1 peptide-linked insulin molecule. A completely inactive analogue, J. Mol. Biol., 1991, 220: 425-433.[8]Hua, Q. X., Shoelson, S. E., Kochoyan, M. et al., Receptor binding redefined by a structural switch in a mutant human insulin, Nature, 1991, 354: 238-241.[9]Hua, Q. X., Gozani, S. N., Chance, R. E. et al., Structure of a protein in a kinetic trap, Nat. Struc. Boil, 1995, 2: 129-138.[10]Kristensen, C., Andersen, A. S., Hach, M., A single-chain insulin-like growth factor I/insulin hybrid binds with high affinity to the insulin receptor, Biochem. J., 1995, 305: 981-986.[11]Humbel, R. E., Insulin-like growth factors I and II, Euro. J. Biochem., 1990, 190: 445-462.[12]Cooke, R. M

  9. The relationship between the connecting peptide of recombined single chain insulin and its biological function

    Institute of Scientific and Technical Information of China (English)

    HUANG; Yiding; (

    2001-01-01

    [1]Straus, D. S., Growth-stimulatory of insulin in vitro and in vivo, Endocr. Rev., 1984, 5(2): 356-369.[2]Svenningsen, A. F., Kanje, M., Insulin and the insulin-like growth factors I and II are mitogenic to cultured rat sciatic nerve segments and stimulate [3H] thuymidine incorporation through their respective receptors, Glia, 1996, 18(1): 68-72.[3]Ogihara, S., Yamada, M., Saito, T. et al., Insulin potentiates mitogenic effect of epidermal growth factor on cultured guinea pig gastric mucous cells, Am. J. Physiol., 1996, 271(1 Pt 1): G104-121.[4]Steiner, D. F., Oyer, P. E., The biosynthesis of insulin and a probable precursor of insulin by a human islet cell adenoma, Proc. Nalt. Acad. Sci. USA, 1967, 57(2): 473-480.[5]King, G. L., Kahn, C. R., The growth-promoting effects of insulin, in Growth and Maturation Factors(ed. Guroff, G.), New York: John Wiley & Sons, 1984, 223-265.[6]Peavy, D. E., Brunner, M. R., Duckworth, W. C. et al., Receptor binding and biological potency of several split forms (conversion intermediates) of human proinsulin, Studies in cultured IM-9 lymphocytes and in vivo and in vitro in rats, J. Biol. Chem., 1985, 260: 13989-13994.[7]Derewenda, U., Derewenda, Z., Dodson, E. J. et al., X-ray analysis of the single chain B29-A1 peptide-linked insulin molecule. A completely inactive analogue, J. Mol. Biol., 1991, 220: 425-433.[8]Hua, Q. X., Shoelson, S. E., Kochoyan, M. et al., Receptor binding redefined by a structural switch in a mutant human insulin, Nature, 1991, 354: 238-241.[9]Hua, Q. X., Gozani, S. N., Chance, R. E. et al., Structure of a protein in a kinetic trap, Nat. Struc. Boil, 1995, 2: 129-138.[10]Kristensen, C., Andersen, A. S., Hach, M., A single-chain insulin-like growth factor I/insulin hybrid binds with high affinity to the insulin receptor, Biochem. J., 1995, 305: 981-986.[11]Humbel, R. E., Insulin-like growth factors I and II, Euro. J. Biochem., 1990, 190: 445-462.[12]Cooke, R. M

  10. Novel function of polyaniline for biological environments: Cultivation of paramecium in the presence of polyaniline

    International Nuclear Information System (INIS)

    The reduced form of polyaniline (PANI, emeraldine base) functions as water purification to extend the lives of paramecia. The emeraldine base can absorb discharged waste from the planktons such as nitrogenous compounds and salts. This is a new function of π-conjugated polymers for micro-organisms

  11. Novel function of polyaniline for biological environments: Cultivation of paramecium in the presence of polyaniline

    Science.gov (United States)

    Goto, Hiromasa

    2014-03-01

    The reduced form of polyaniline (PANI, emeraldine base) functions as water purification to extend the lives of paramecia. The emeraldine base can absorb discharged waste from the planktons such as nitrogenous compounds and salts. This is a new function of π-conjugated polymers for micro-organisms.

  12. Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES.

    Science.gov (United States)

    Kado, Yuji; Mizohata, Eiichi; Nagatoishi, Satoru; Iijima, Mariko; Shinoda, Keiko; Miyafusa, Takamitsu; Nakayama, Taisuke; Yoshizumi, Takuma; Sugiyama, Akira; Kawamura, Takeshi; Lee, Young-Hun; Matsumura, Hiroyoshi; Doi, Hirofumi; Fujitani, Hideaki; Kodama, Tatsuhiko; Shibasaki, Yoshikazu; Tsumoto, Kouhei; Inoue, Tsuyoshi

    2016-01-29

    Epiregulin (EPR) is a ligand of the epidermal growth factor (EGF) family that upon binding to its epidermal growth factor receptor (EGFR) stimulates proliferative signaling, especially in colon cancer cells. Here, we describe the three-dimensional structure of the EPR antibody (the 9E5(Fab) fragment) in the presence and absence of EPR. Among the six complementarity-determining regions (CDRs), CDR1-3 in the light chain and CDR2 in the heavy chain predominantly recognize EPR. In particular, CDR3 in the heavy chain dramatically moves with cis-trans isomerization of Pro(103). A molecular dynamics simulation and mutational analyses revealed that Arg(40) in EPR is a key residue for the specific binding of 9E5 IgG. From isothermal titration calorimetry analysis, the dissociation constant was determined to be 6.5 nm. Surface plasmon resonance analysis revealed that the dissociation rate of 9E5 IgG is extremely slow. The superimposed structure of 9E5(Fab)·EPR on the known complex structure of EGF·EGFR showed that the 9E5(Fab) paratope overlaps with Domains I and III on the EGFR, which reveals that the 9E5(Fab)·EPR complex could not bind to the EGFR. The 9E5 antibody will also be useful in medicine as a neutralizing antibody specific for colon cancer. PMID:26627827

  13. Biological half-life of iodine in adults with intact thyroid function and in athyreotic persons

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, G.H.; Hauck, B.M.; Chamberlain, M.J

    2002-07-01

    A joint project between the Human Monitoring Laboratory (HML) and the Ottawa Hospital has measured the retention of {sup 131}I in patients who have received the radioiodine diagnostically. Thirty-nine subjects with intact thyroid glands and nine athyreotic subjects were measured in the HML's whole-body/thyroid counter to determine the retention of {sup 131}I following its medical administration. The average biological half-life of {sup 131}I in 26 euthyroid subjects was found to be 66.1{+-}6.3 days which may be statistically significantly lower than the ICRP recommended value of 80 days. Nine hyperthyroid patients had a mean biological half-life of 38.2{+-}8.6 days and in three hypothyroid patients the corresponding value was 29.3{+-}8.8 days. Thyroid {sup 131}I uptake was measured in a conventional clinical fashion at the Ottawa Hospital Civic campus 24 h after oral administration of the radioiodine using a collimated thick sodium iodide detector placed over the neck arteriorly. Measured values were 0.144{+-}0.009, 0.314{+-}0.035 and 0.045{+-}0.010 of the administered dose in euthyroid, hyperthyroid and hypothyroid patients respectively. The euthyroid range at the hospital is 0.06-0.22. Uptake was significantly lower for the euthyroid group than the ICRP value of 0.3. The radioiodine retention in athyreotic subjects followed a two compartment model with biological half-lives of 1.0{+-}0.2 days and 18.4{+-}1.1. days. (author)

  14. Isolation and Functional Analyses of a Putative Floral Homeotic C-Function Gene in a Basal Eudicot London Plane Tree (Platanus acerifolia)

    OpenAIRE

    Zhang, Jiaqi; Li, Zhineng; Guo, Cong; Liu, Guofeng; Bao, Manzhu

    2013-01-01

    The identification of mutants in model plant species has led to the isolation of the floral homeotic function genes that play crucial roles in flower organ specification. However, floral homeotic C-function genes are rarely studied in basal eudicots. Here, we report the isolation and characterization of the AGAMOUS (AG) orthologous gene (PaAG) from a basal eudicot London plane tree (Platanus acerifolia Willd). Phylogenetic analysis showed that PaAG belongs to the C- clade AG group of genes. P...

  15. Differential item functioning in Patient Reported Outcomes Measurement Information System® (PROMIS®) Physical Functioning short forms: Analyses across ethnically diverse groups

    OpenAIRE

    Jones, Richard N.; Doug Tommet; Mildred Ramirez; Roxanne Jensen; Teresi, Jeanne A.

    2016-01-01

    We analyzed physical functioning short form items derived from the PROMIS® item bank (PF16) using data from more than 5,000 recently diagnosed, ethnically diverse cancer patients. Our goal was to determine if the short form items demonstrated evidence of differential item functioning (DIF) according to sociodemographic characteristics in this clinical sample. We evaluated respons-es for evidence of unidimensionality, local independence (given a single common factor), differen-tial item functi...

  16. Interferon-γ: biological function and application for study of cellular immune response

    Directory of Open Access Journals (Sweden)

    A. A. Lutckii

    2015-01-01

    Full Text Available Cellular immune response plays a central role in control of intracellular pathogens like viruses, some bacteria and parasites. Evaluation of presence, specificity and strength of cellular immune response can be done by investigation of reaction of immune cells to specific stimulus, like antigen. The major cellular reactions to antigen stimulation are production of cytokines, proliferation and cytotoxicity. This review is focused on interferon-gamma as one of the central Th1 cytokines: its biology, immunological role and application as marker of cellular immune response.

  17. Iduronic Acid in Chondroitin/Dermatan Sulfate: Biosynthesis and Biological Function

    OpenAIRE

    Malmström, Anders; Bartolini, Barbara; Thelin, Martin A.; Pacheco, Benny; Maccarana, Marco

    2012-01-01

    The ability of chondroitin/dermatan sulfate (CS/DS) to convey biological information is enriched by the presence of iduronic acid. DS-epimerases 1 and 2 (DS-epi1 and 2), in conjunction with DS-4-O-sulfotransferase 1, are the enzymes responsible for iduronic acid biosynthesis and will be the major focus of this review. CS/DS proteoglycans (CS/DS-PGs) are ubiquitously found in connective tissues, basement membranes, and cell surfaces or are stored intracellularly. Such wide distr...

  18. Data on polyphenols and biological activity analyses of an Andean tomato collection and their relationships with tomato traits and geographical origin.

    Science.gov (United States)

    Di Paola Naranjo, Romina D; Otaiza, Santiago; Saragusti, Alejandra C; Baroni, Veronica; Carranza, A V; Peralta, Iris E; Valle, Estela M; Carrari, Fernando; Asis, Ramón

    2016-06-01

    Data provide information about a tomato collection composed of accessions from the Andean Valley, commercial accessions and wild species. Antioxidant metabolites were measured in mature fruits of this collection, and their biological activities were assessed by both in vitro and in vivo methods. In this work, the parameters used to identify and quantify polyphenols compounds in tomato fruit by liquid chromatography coupled to diode array detector and quadrupole time of flight mass spectrometer are described. Moreover, data supporting a procedure to characterize the properties of tomato fruits to revert death by thermal stress in Caenorhabditis elegans are explained in detail. Lastly, principal component analysis and hierarchical cluster analysis of metabolites composition, antioxidant activities (in vivo and in vitro), tomato traits and geographical origin of the tomatoes collection are shown. The data presented here are related to the research article entitled "Hydrophilic antioxidants from Andean Tomato Landraces assessed by their bioactivities in vitro and in vivo" [1]. PMID:27222844

  19. Swedish State Power Board activities related to man-machine analyses and optimization of the control room function

    International Nuclear Information System (INIS)

    As a result of new government requirements, the accident management of the Swedish State Power Board (SSPB) nuclear power plants is being strengthened as regards safety. This will influence control room environment, emergency operation procedure, training and organization. The paper mainly deals with current activities related to the control room environment. To meet the new requirements SSPB has (1) introduced a new general function/state oriented emergency operating procedure (EOP) for the shift engineer; (2) introduced an advanced safety parameter display system (SPDS); (3) enhanced simulator training of shift management; (4) reinforced the process image for the critical safety functions in the conventional control panels by grouping primary instrumentation. Some examples of retrofitting under way in the conventional control panels are: (a) the new BWRs are being retrofitted with process overview panels to assist operator actions during early stages of a transient; (b) the control panel for reactor vessel instrumentation (critical safety function: core cooling) has been changed in the old BWR to optimize actions when core cooling is jeopardized; (c) development of core cooling instrumentation for PWRs has been studied in simulators and retrofitting and modification are planned. The new EOP, SPDS, control room retrofits have been validated in simulators (and in the real world). Experience from simulator validation has shown that: (1) It is important for the reactor/turbine operator to follow the process response during an accident. It is therefore important that the EOP be simple to follow and the process system image be easy to understand. (2) The advanced SPDS has been valuable in giving the shift supervisor an overview and an independent verification of EOP actions. (3) Reactor pressure vessel instrumentation in PWRs has a positive impact on operator actions (especially those of the shift supervisor) during severe transients if it always reflects the actual

  20. A novel method of analysing the damping function of VSC based facts control : multi-machine power systems

    Energy Technology Data Exchange (ETDEWEB)

    Du, W. [Southeast Univ., Nanjing (China)]|[Bath Univ., Bath (United Kingdom); Wang, H.F. [Queen' s Univ. of Belfast, Belfast (United Kingdom); Dunn, R. [Bath Univ., Bath (United Kingdom)

    2008-07-01

    Oscillations in power transmission can be mitigated by adding a supplementary damping function to the normal control task of a flexible AC transmission systems (FACTS). When properly designed, FACTS stabilizers can contribute positive damping to power system oscillations. This paper proposed and presented a general analytical approach to study the effectiveness of damping control. The approach was used to describe the damping function of voltage source converter (VSC) based FACTS stabilizers. The proposed method was derived based on the equal-area criterion and small-signal stability analysis. The paper discussed a single-machine infinite-bus power system installed with a VSC based FACTS device; the damping effect of VSC based FACTS damping control; and demonstrations of example power systems. These examples included a shunt VSC based FACTS with damping control; interaction of FACTS voltage and damping control; feedback signal of FACTS damping control; and extension to the case of a multi-machine power system. The effectiveness of VSC based FACTS stabilizers in damping power system oscillations was clearly explained with the proposed method. The proposed method could also be readily extended to multi-machine power systems. 6 refs., 7 figs.

  1. Molecular and Functional Analyses of the Fast Skeletal Myosin Light Chain2 Gene of the Korean Oily Bitterling, Acheilognathus koreensis

    Directory of Open Access Journals (Sweden)

    Hyun Kook Cho

    2013-08-01

    Full Text Available We identified and characterized the primary structure of the Korean oily bitterling Acheilognathus koreensis fast skeletal myosin light chain 2 (Akmlc2f, gene. Encoded by seven exons spanning 3955 bp, the deduced 168-amino acid AkMLC2f polypeptide contained an EF-hand calcium-binding motif and showed strong homology (80%–98% with the MLC2 proteins of Ictalurus punctatus and other species, including mammals. Akmlc2f mRNA was highly enriched in skeletal muscles, and was detectable in other tissues. The upstream regions of Akmlc2f included a TATA box, one copy of a putative MEF-2 binding site and several putative C/EBPβ binding sites. The functional activity of the promoter region of Akmlc2f was examined using luciferase and red fluorescent protein reporters. The Akmlc2f promoter-driven reporter expressions were detected and increased by the C/EBPβ transcription factor in HEK293T cells. The activity of the promoter of Akmlc2f was also confirmed in the developing zebrafish embryo. Although the detailed mechanism underlying the expression of Akmlc2f remains unknown, these results suggest the muscle-specific expression of Akmlc2f transcript and the functional activation of Akmlc2f promoter by C/EBPβ.

  2. Functional assessment of glioma pathogenesis by in vivo multi-parametric magnetic resonance imaging and in vitro analyses

    Science.gov (United States)

    Yao, Nai-Wei; Chang, Chen; Lin, Hsiu-Ting; Yen, Chen-Tung; Chen, Jeou-Yuan

    2016-01-01

    Gliomas are aggressive brain tumors with poor prognosis. In this study, we report a novel approach combining both in vivo multi-parametric MRI and in vitro cell culture assessments to evaluate the pathogenic development of gliomas. Osteopontin (OPN), a pleiotropic factor, has been implicated in the formation and progression of various human cancers, including gliomas, through its functions in regulating cell proliferation, survival, angiogenesis, and migration. Using rat C6 glioma model, the combined approach successfully monitors the acquisition and decrease of cancer hallmarks. We show that knockdown of the expression of OPN reduces C6 cell proliferation, survival, viability and clonogenicity in vitro, and reduces tumor burden and prolongs animal survival in syngeneic rats. OPN depletion is associated with reduced tumor growth, decreased angiogenesis, and an increase of tumor-associated metabolites, as revealed by T2-weighted images, diffusion-weighted images, Ktrans maps, and 1H-MRS, respectively. These strategies allow us to define an important role of OPN in conferring cancer hallmarks, which can be further applied to assess the functional roles of other candidate genes in glioma. In particular, the non-invasive multi-parametric MRI measurement of cancer hallmarks related to proliferation, angiogenesis and altered metabolism may serve as a useful tool for diagnosis and for patient management. PMID:27198662

  3. Structural and functional analyses of Barth syndrome-causing mutations and alternative splicing in the tafazzin acyltransferase domain

    Directory of Open Access Journals (Sweden)

    Atsushi Hijikata

    2015-06-01

    Full Text Available Tafazzin is a mitochondrial phospholipid transacylase, and its mutations cause Barth syndrome (BTHS. Human tafazzin gene produces four distinct alternatively spliced transcripts. To understand the molecular mechanisms of tafazzin deficiency, we performed an atomic resolution analysis of the influence of the BTHS mutations and of alternative splicing on the structure and function of tafazzin. From the three-dimensional (3D homology modeling of tafazzin, we identified candidate amino acid residues that contribute to cardiolipin binding and to mitochondrial membrane associations that facilitate acyl-transfer reactions. Primate specific exon 5, which is alternatively spliced, is predicted to correspond to an intrinsically unstructured region in the protein. We proposed that this region should change the substrate-binding affinity and/or contribute to primate-specific molecular interactions. Exon 7, another alternatively spliced exon, encodes a region forming a part of the putative substrate-binding cleft, suggesting that the gene products lacking exon 7 will lose their substrate-binding ability. We demonstrate a clear localization of the BTHS mutations at residues responsible for membrane association, substrate binding, and the conformational stability of tafazzin. These findings provide new insights into the function of defective tafazzin and the pathogenesis of BTHS at the level of protein 3D structure and the evolution of alternatively spliced exons in primates.

  4. Structural and functional analyses of Barth syndrome-causing mutations and alternative splicing in the tafazzin acyltransferase domain.

    Science.gov (United States)

    Hijikata, Atsushi; Yura, Kei; Ohara, Osamu; Go, Mitiko

    2015-06-01

    Tafazzin is a mitochondrial phospholipid transacylase, and its mutations cause Barth syndrome (BTHS). Human tafazzin gene produces four distinct alternatively spliced transcripts. To understand the molecular mechanisms of tafazzin deficiency, we performed an atomic resolution analysis of the influence of the BTHS mutations and of alternative splicing on the structure and function of tafazzin. From the three-dimensional (3D) homology modeling of tafazzin, we identified candidate amino acid residues that contribute to cardiolipin binding and to mitochondrial membrane associations that facilitate acyl-transfer reactions. Primate specific exon 5, which is alternatively spliced, is predicted to correspond to an intrinsically unstructured region in the protein. We proposed that this region should change the substrate-binding affinity and/or contribute to primate-specific molecular interactions. Exon 7, another alternatively spliced exon, encodes a region forming a part of the putative substrate-binding cleft, suggesting that the gene products lacking exon 7 will lose their substrate-binding ability. We demonstrate a clear localization of the BTHS mutations at residues responsible for membrane association, substrate binding, and the conformational stability of tafazzin. These findings provide new insights into the function of defective tafazzin and the pathogenesis of BTHS at the level of protein 3D structure and the evolution of alternatively spliced exons in primates. PMID:25941633

  5. Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses.

    Science.gov (United States)

    Costa, Rodrigo; Gomes, Newton C M; Krögerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia

    2007-09-01

    The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene-based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured Pseudomonas in bulk and rhizosphere soils. Pseudomonas-specific gacA fingerprints of total-community (TC) rhizosphere DNA were surprisingly diverse, plant-specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture-dependent and independent surveys, a group of Pseudomonas isolates antagonistic towards V. dahliae was shown to be genotypically conserved, to carry the phlD biosynthetic locus (involved in the biosynthesis of 2,4-diacetylphloroglucinol - 2,4-DAPG), and to correspond to a dominant and highly frequent Pseudomonas population in the rhizosphere of field-grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the Pseudomonas fluorescens phylogenetic lineage and showed closest relatedness to P. fluorescens strain F113 (97% gacA gene sequence identity in 492-bp sequences), a biocontrol agent and 2,4-DAPG producer. Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis. PMID:17686023

  6. Analyses of WOX4 transgenics provide further evidence for the evolution of the WOX gene family during the regulation of diverse stem cell functions.

    Science.gov (United States)

    Ji, Jiabing; Shimizu, Rena; Sinha, Neelima; Scanlon, Michael J

    2010-07-01

    The WOX (WUSCHEL-related homeobox) gene family of Arabidopsis comprises fifteen plant-specific transcriptional factors that play important development roles. Genetic, phylogenetic, and genomic analyses suggest that WOX genes generally act non-autonomously to organize stem-cell and initial-cell populations within plant meristems and organ anlagen. Previous cross-complementation analyses indicate that the functional diversification of distinct WOX paralogs may be explained largely by promoter evolution, although paralog-specific protein::protein interactions are also implicated. A recent report described WOX4 function during development of the procambium, which comprises the meristematic tissues of the plant vasculature. Here we show that WOX4 fails to complement PRS1/WOX3 function, when driven from the PRS1/WOX3 native promoter. These data suggest that WOX4 identifies different DNA targets and/or interacting proteins during development of the vasculature procambium than does PRS1/WOX3 during the specification of lateral organ initial cells. The identification of super-compound leaf phenotypes induced by overexpression of the SlWOX4 ortholog in tomato suggests a functional link between vascular patterning and leaf complexity. PMID:20495368

  7. Surface functionalization of bioactive glasses with natural molecules of biological significance, part II: Grafting of polyphenols extracted from grape skin

    Science.gov (United States)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Polyphenols, as one of the most important family of phytochemicals protective substances from grape fruit, possess various biological activities and health-promoting benefits, for example: inhibition of some degenerative diseases, cardiovascular diseases and certain types of cancers, reduction of plasma oxidative stress and slowing aging. The combination of polyphenols and biomaterials may have good potential to reach good bioavailability and controlled release, as well as to give biological signaling properties to the biomaterial surfaces. In this research, conventional solvent extraction was developed for obtaining polyphenols from dry grape skins. The Folin&Ciocalteu method was used to determine the amount of total polyphenols in the extracts. Surface functionalization of two bioactive glasses (SCNA and CEL2) was performed by grafting the extracted polyphenols on their surfaces. The effectiveness of the functionalization was tested by UV spectroscopy, which analyzes the amount of polyphenols in the uptake solution (before and after functionalization) and on solid samples, and XPS, which analyzes the presence of phenols on the material surface.

  8. Biological functioning of PAH-polluted and thermal desorption-treated soils assessed by fauna and microbial bioindicators.

    Science.gov (United States)

    Cébron, Aurélie; Cortet, Jérôme; Criquet, Stéven; Biaz, Asmaa; Calvert, Virgile; Caupert, Cécile; Pernin, Céline; Leyval, Corinne

    2011-11-01

    A large number of soil bioindicators were used to assess biological diversity and activity in soil polluted with polycyclic aromatic hydrocarbons (PAHs) and the same soil after thermal desorption (TD) treatment. Abundance and biodiversity of bacteria, fungi, protozoa, nematodes and microarthropods, as well as functional parameters such as enzymatic activities and soil respiration, were assessed during a two year period of in situ monitoring. We investigated the influence of vegetation (spontaneous vegetation and Medicago sativa) and TD treatment on biological functioning. Multivariate analysis was performed to analyze the whole data set. A principal response curve (PRC) technique was used to evaluate the different treatments (various vegetation and contaminated vs. TD soil) contrasted with control (bare) soil over time. Our results indicated the value of using a number of complementary bioindicators, describing both diversity and functions, to assess the influence of vegetation on soil and discriminate polluted from thermal desorption (TD)-treated soil. Plants had an influence on the abundance and activity of all organisms examined in our study, favoring the whole trophic chain development. However, although TD-treated soil had a high abundance and diversity of microorganisms and fauna, enzymatic activities were weak because of the strong physical and chemical modifications of this soil. PMID:21392572

  9. The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses

    Directory of Open Access Journals (Sweden)

    Larroque Mathieu

    2012-11-01

    provides insight into the evolution and biological roles of CBM1-containing proteins from oomycetes. We show that while CBM1s from fungi and oomycetes are similar, they team up with different protein domains, either in proteins implicated in the degradation of plant cell wall components in the case of fungi or in proteins involved in adhesion to polysaccharidic substrates in the case of oomycetes. This work highlighted the unique role and evolution of CBM1 proteins in oomycete among the Stramenopile lineage.

  10. Self-assembly and stability of double rosette nanostructures with biological functionalities.

    Science.gov (United States)

    ten Cate, Mattijs G J; Omerović, Merdan; Oshovsky, Gennady V; Crego-Calama, Mercedes; Reinhoudt, David N

    2005-10-21

    The syntheses of calix[4]arene dimelamines that are functionalized with alkyl, aminoalkyl, ureido, pyridyl, carbohydrate, amino acid and peptide functionalities, and their self-assembly with barbituric acid or cyanuric acid derivatives into well-defined hydrogen-bonded nanostructures are described. The thermodynamic stability of these hydrogen-bonded assemblies was studied by CD spectroscopy in mixtures of CHCl3 and MeOH. The stability of the assemblies depends on several steric factors and the polarity of the functional groups connected to the assembly components. PMID:16211109

  11. School belongingness and mental health functioning across the primary-secondary transition in a mainstream sample: multi-group cross-lagged analyses.

    Directory of Open Access Journals (Sweden)

    Sharmila Vaz

    Full Text Available The relationship between school belongingness and mental health functioning before and after the primary-secondary school transition has not been previously investigated in students with and without disabilities. This study used a prospective longitudinal design to test the bi-directional relationships between these constructs, by surveying 266 students with and without disabilities and their parents, 6-months before and after the transition to secondary school. Cross-lagged multi-group analyses found student perception of belongingness in the final year of primary school to contribute to change in their mental health functioning a year later. The beneficial longitudinal effects of school belongingness on subsequent mental health functioning were evident in all student subgroups; even after accounting for prior mental health scores and the cross-time stability in mental health functioning and school belongingness scores. Findings of the current study substantiate the role of school contextual influences on early adolescent mental health functioning. They highlight the importance for primary and secondary schools to assess students' school belongingness and mental health functioning and transfer these records as part of the transition process, so that appropriate scaffolds are in place to support those in need. Longer term longitudinal studies are needed to increase the understanding of the temporal sequencing between school belongingness and mental health functioning of all mainstream students.

  12. Differential item functioning in Patient Reported Outcomes Measurement Information System® (PROMIS® Physical Functioning short forms: Analyses across ethnically diverse groups

    Directory of Open Access Journals (Sweden)

    Richard N. Jones

    2016-06-01

    Full Text Available We analyzed physical functioning short form items derived from the PROMIS® item bank (PF16 using data from more than 5,000 recently diagnosed, ethnically diverse cancer patients. Our goal was to determine if the short form items demonstrated evidence of differential item functioning (DIF according to sociodemographic characteristics in this clinical sample. We evaluated respons-es for evidence of unidimensionality, local independence (given a single common factor, differen-tial item functioning, and DIF impact. DIF was evaluated attributable to sex, age (middle aged vs. younger and older, race/ethnicity (White vs. Black or African-American, Asian/Pacific Islander, Hispanic and level of education. We used a multiple group confirmatory factor analysis with covariates approach, a multiple indicators multiple causes (MIMIC model. We confirmed essential unidimensionality but some evidence for multidimensionality is present, particularly for basic activities of daily living items, and many instances of local dependence. The presence of local dependence calls for further review of the meaning and measurement of the physical functioning domain among cancer patients. Nearly every item demonstrated statistically significant DIF. In all group comparisons the impact of DIF was negligible. However, the Hispanic subgroup comparison revealed an impact estimate just below an arbitrary threshold for small impact. Within the limitations of local dependency violations, we conclude that items from a static short form derived from the PROMIS physical functioning item bank displayed trivial and ignorable DIF attributable to sex, race, ethnicity, age, and education among cancer patients.

  13. Biological functions of hCG and hCG-related molecules

    OpenAIRE

    Cole Laurence A

    2010-01-01

    Abstract Background hCG is a term referring to 4 independent molecules, each produced by separate cells and each having completely separate functions. These are hCG produced by villous syncytiotrophoblast cells, hyperglycosylated hCG produced by cytotrophoblast cells, free beta-subunit made by multiple primary non-trophoblastic malignancies, and pituitary hCG made by the gonadotrope cells of the anterior pituitary. Results and discussion hCG has numerous functions. hCG promotes progesterone p...

  14. Load time functions (LTF) for large commercial aircraft based on Riera approach and finite element analyses – a parametric study

    International Nuclear Information System (INIS)

    Conclusions: In cases of a complex geometry of the target structure a careful evaluation of the predefined load time function should be performed. Special attention should be paid on different deceleration of airplane parts and their equivalent load forces. In cases of cylindrical structures with relatively small diameter (in comparison to the airplane wing spread), the impact of the engines should be investigated separately. When auxiliary structures are surrounding the reactor containment, the impact load will be reduced due to initial destruction of part of the airplane in the surrounding auxiliary structures. For the case study, this reduction was found to be non-significant. However if important equipment is situated in surrounding auxiliary buildings, engines may provide higher equivalent forces compared to normal planar target structure

  15. Acclimation, adaptation, traits and trade-offs in plankton functional type models: reconciling terminology for biology and modelling

    DEFF Research Database (Denmark)

    Flynn, Kevin J.; St. John, Michael; Raven, John A.;

    2015-01-01

    ideally only be considered for describing intra-generational interactions; in applications between generations, and certainly between unrelated species, such concepts should be avoided. We suggest that systems biology approaches, through to complex adaptive/acclimative systems modelling, with explicit......We propose definitions in terminology to enhance ongoing collaborations between biologists and modellers on plankton ecology. Organism “functional type” should refer to commonality in ecology not biogeochemistry; the latter is largely an emergent property of the former, while alignment with ecology...

  16. Stability of heroin, 6-monoacetylmorphine, and morphine in biological samples and validation of an LC-MS assay for delayed analyses of pharmacokinetic samples in rats.

    Science.gov (United States)

    Jones, Jessica M; Raleigh, Michael D; Pentel, Paul R; Harmon, Theresa M; Keyler, Daniel E; Remmel, Rory P; Birnbaum, Angela K

    2013-02-23

    Degradation of heroin to 6-monoacetylmorphine (6-MAM) and then morphine happens rapidly in vivo and in vitro. The rates of heroin and 6-MAM degradation depend on the type of biological samples, and the duration and conditions of storage. In order to optimize conditions for measuring heroin and its metabolites in samples collected for pharmacokinetic studies in rats, we investigated the time course of degradation of heroin, 6-MAM, and morphine in four biological matrices: rat blood, rat brain homogenate, bovine serum, and human plasma under various conditions. Analyte concentrations were measured by LC-MS. The goal was to identify conditions that allow maximum flexibility in scheduling sample collection and analysis, as well as gain more information on the stability of heroin in blood and tissue samples. A solid-phase extraction method with ice-cold solvents, sodium fluoride (NaF) and a low pH (3.0) maintained sample stability. Quality controls were within 94.0-105% of the target value. Variability was 4.0-8.9% for all analytes within the range of 5-200 ng/mL for heroin, 5-1000 ng/mL for 6-MAM, and 10-200 ng/mL for morphine. Heroin degradation to 6-MAM was faster in rat whole blood than in plasma, and faster in rat plasma than in rat brain homogenate. Maintaining NaF at 4 mg/mL throughout processing enhanced stability; higher NaF concentrations added to whole blood caused hemolysis. Samples processed through solid phase extraction and stored as dried pellets at 80°C constituted the most stable environment for heroin, and was superior to the storing of samples in solution prior to or after extraction. Nevertheless, post-extraction heroin and 6-MAM levels declined by 6.7-8.3% over one week in rat plasma under these conditions, and by <1-4.7% in bovine serum or human plasma. PMID:23245263

  17. Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0

    Directory of Open Access Journals (Sweden)

    Jing Cong

    2015-09-01

    Full Text Available To examine soil microbial functional gene diversity and causative factors in tropical rainforests, we used a microarray-based metagenomic tool named GeoChip 5.0 to profile it. We found that high microbial functional gene diversity and different soil microbial metabolic potential for biogeochemical processes were considered to exist in tropical rainforest. Soil available nitrogen was the most associated with soil microbial functional gene structure. Here, we mainly describe the experiment design, the data processing, and soil biogeochemical analyses attached to the study in details, which could be published on BMC microbiology Journal in 2015, whose raw data have been deposited in NCBI's Gene Expression Omnibus (accession number GSE69171.

  18. Isolation and functional analyses of a putative floral homeotic C-function gene in a basal eudicot London plane tree (Platanus acerifolia).

    Science.gov (United States)

    Zhang, Jiaqi; Li, Zhineng; Guo, Cong; Liu, Guofeng; Bao, Manzhu

    2013-01-01

    The identification of mutants in model plant species has led to the isolation of the floral homeotic function genes that play crucial roles in flower organ specification. However, floral homeotic C-function genes are rarely studied in basal eudicots. Here, we report the isolation and characterization of the AGAMOUS (AG) orthologous gene (PaAG) from a basal eudicot London plane tree (Platanus acerifolia Willd). Phylogenetic analysis showed that PaAG belongs to the C- clade AG group of genes. PaAG was found to be expressed predominantly in the later developmental stages of male and female inflorescences. Ectopic expression of PaAG-1 in tobacco (Nicotiana tabacum) resulted in morphological alterations of the outer two flower whorls, as well as some defects in vegetative growth. Scanning electron micrographs (SEMs) confirmed homeotic sepal-to-carpel transformation in the transgenic plants. Protein interaction assays in yeast cells indicated that PaAG could interact directly with PaAP3 (a B-class MADS-box protein in P. acerifolia), and also PaSEP1 and PaSEP3 (E-class MADS-box proteins in P. acerifolia). This study performed the functional analysis of AG orthologous genes outside core eudicots and monocots. Our findings demonstrate a conserved functional role of AG homolog in London plane tree, which also represent a contribution towards understanding the molecular mechanisms of flower development in this monoecious tree species. PMID:23691041

  19. Role and Function of MicroRNAs in Extracellular Vesicles in Cardiovascular Biology

    Directory of Open Access Journals (Sweden)

    Philipp Pfeifer

    2015-01-01

    Full Text Available Intercellular communication mediated by extracellular vesicles is crucial for preserving vascular integrity and in the development of cardiovascular disease. Extracellular vesicles consist of apoptotic bodies, microvesicles, and exosomes that can be found in almost every fluid compartment of the body like blood, saliva, and urine. In the recent years, a lot of reports came up suggesting that major cardiovascular and metabolic pathologies like atherogenesis, heart failure, or diabetes are highly influenced by transfer of microRNAs via extracellular vesicles leading to altered protein expression and phenotypes of recipient cells. The following review will summarize the fast developing field of intercellular signaling in cardiovascular biology by microRNA-containing extracellular vesicles.

  20. Translating inter-individual genetic variation to biological function in complex phenotypes

    DEFF Research Database (Denmark)

    Yadav, Rachita

    , Chapter 1 provides an introduction to various methodologies utilised in this thesis work. Subsequently, chapters 2, 3 and 4 in the second section, address finding causal variations in childhood asthma. Chapter 2 focuses on a genome wide association study (GWAS) performed on asthma exacerbation case cohort...... changing proteome and phosphor-proteome in chemotherapy resistant breast cancer cell lines with high TIMP-1 gene expression. In summary, this thesis work demonstrates applications of various omic variations at different levels of complexity and their integration using systems biology based methodologies to...... associate them to multifactorial phenotypes. These studies help in revealing pivotal mechanistic details concerning the phenotypes, which can be further utilized in drug designing and disease management....

  1. Polymeric functional nanostructures for in vivo delivery of biologically active proteins

    International Nuclear Information System (INIS)

    Poly(methyl methacrylate) core-shell particles in the submicron scale range were prepared by dispersion polymerization through an appropriate selection of the experimental parameters. Due to the versatility of this reaction, the macromolecular design can be directed towards the preparation of nano/microspheres with extensively hydrophilic and protein-friendly surfaces with low non-specific interactions. If the steric stabilizer is soluble in physiologic medium, the formation of a core shell structure, constituted by a soft outer shell, made up of long soluble arms able to fix the protein, anchored to an inner hard insoluble core can be envisaged. In the presence of commercial polymeric stabilizers Eudragit L100-55 and Eudragit E100, acid and basic microspheres can be obtained, able to interact with biologically active proteins. (author)

  2. Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes

    DEFF Research Database (Denmark)

    Rohde, Palle Duun; Demontis, Ditte; Castro Dias Cuyabano, Beatriz;

    2016-01-01

    Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited...... power to detect genetic markers with small effects. Instead, aggregating genetic markers based on biological information might increase the power to identify sets of genetic markers of etiological significance. Several set test methods have been proposed: Here we propose a new set test derived from...... among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case–control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism and...

  3. A graphical user interface (GUI) toolkit for the calculation of three-dimensional (3D) multi-phase biological effective dose (BED) distributions including statistical analyses.

    Science.gov (United States)

    Kauweloa, Kevin I; Gutierrez, Alonso N; Stathakis, Sotirios; Papanikolaou, Niko; Mavroidis, Panayiotis

    2016-07-01

    A toolkit has been developed for calculating the 3-dimensional biological effective dose (BED) distributions in multi-phase, external beam radiotherapy treatments such as those applied in liver stereotactic body radiation therapy (SBRT) and in multi-prescription treatments. This toolkit also provides a wide range of statistical results related to dose and BED distributions. MATLAB 2010a, version 7.10 was used to create this GUI toolkit. The input data consist of the dose distribution matrices, organ contour coordinates, and treatment planning parameters from the treatment planning system (TPS). The toolkit has the capability of calculating the multi-phase BED distributions using different formulas (denoted as true and approximate). Following the calculations of the BED distributions, the dose and BED distributions can be viewed in different projections (e.g. coronal, sagittal and transverse). The different elements of this toolkit are presented and the important steps for the execution of its calculations are illustrated. The toolkit is applied on brain, head & neck and prostate cancer patients, who received primary and boost phases in order to demonstrate its capability in calculating BED distributions, as well as measuring the inaccuracy and imprecision of the approximate BED distributions. Finally, the clinical situations in which the use of the present toolkit would have a significant clinical impact are indicated. PMID:27265044

  4. Molecular biology of the kallikrein-kinin system: from structure to function

    Directory of Open Access Journals (Sweden)

    J.B. Pesquero

    1998-09-01

    Full Text Available The participation of the kallikrein-kinin system, comprising the serine proteases kallikreins, the protein substrates kininogens and the effective peptides kinins, in some pathological processes like hypertension and cardiovascular diseases is still a matter of controversy. The use of different experimental set-ups in concert with the development of potent and specific inhibitors and antagonists for the system has highlighted its importance but the results still lack conclusivity. Over the last few years, transgenic and gene-targeting technologies associated with molecular biology tools have provided specific information about the elusive role of the kallikrein-kinin system in the control of blood pressure and electrolyte homeostasis. cDNA and genomic sequences for kinin receptors B2 and B1 from different species were isolated and shown to encode G-protein-coupled receptors and the structure and pharmacology of the receptors were characterized. Transgenic animals expressing an overactive kallikrein-kinin system were established to study the cardiovascular effects of these alterations and the results of these investigations further corroborate the importance of this system in the maintenance of normal blood pressure. Knockout animals for B2 and B1 receptors are available and their analysis also points to the role of these receptors in cardiovascular regulation and inflammatory processes. In this paper the most recent and relevant genetic animal models developed for the study of the kallikrein-kinin system are reviewed, and the advances they brought to the understanding of the biological role of this system are discussed.

  5. Mutation screen in the GWAS derived obesity gene SH2B1 including functional analyses of detected variants

    Directory of Open Access Journals (Sweden)

    Volckmar Anna-Lena

    2012-12-01

    Full Text Available Abstract Background The SH2B1 gene (Src-homology 2B adaptor protein 1 gene is a solid candidate gene for obesity. Large scale GWAS studies depicted markers in the vicinity of the gene; animal models suggest a potential relevance for human body weight regulation. Methods We performed a mutation screen for variants in the SH2B1 coding sequence in 95 extremely obese children and adolescents. Detected variants were genotyped in independent childhood and adult study groups (up to 11,406 obese or overweight individuals and 4,568 controls. Functional implications on STAT3 mediated leptin signalling of the detected variants were analyzed in vitro. Results We identified two new rare mutations and five known SNPs (rs147094247, rs7498665, rs60604881, rs62037368 and rs62037369 in SH2B1. Mutation g.9483C/T leads to a non-synonymous, non-conservative exchange in the beta (βThr656Ile and gamma (γPro674Ser splice variants of SH2B1. It was additionally detected in two of 11,206 (extremely obese or overweight children, adolescents and adults, but not in 4,506 population-based normal-weight or lean controls. The non-coding mutation g.10182C/A at the 3’ end of SH2B1 was only detected in three obese individuals. For the non-synonymous SNP rs7498665 (Thr484Ala we observed nominal over-transmission of the previously described risk allele in 705 obesity trios (nominal p = 0.009, OR = 1.23 and an increased frequency of the same allele in 359 cases compared to 429 controls (nominal p = 0.042, OR = 1.23. The obesity risk-alleles at Thr484Ala and βThr656Ile/γPro674Ser had no effect on STAT3 mediated leptin receptor signalling in splice variants β and γ. Conclusion The rare coding mutation βThr656Ile/γPro674Ser (g.9483C/T in SH2B1 was exclusively detected in overweight or obese individuals. Functional analyzes did not reveal impairments in leptin signalling for the mutated SH2B1.

  6. Functional and genomic analyses of FOXP3-transduced Jurkat-T cells as regulatory T (Treg)-like cells

    International Nuclear Information System (INIS)

    FOXP3, a forkhead transcription factor is essential for the development and function of CD4+CD25+ regulatory T cells (Tregs). In contrast to conversion of murine naive T cells to Tregs by transduction of Foxp3, it is controversial whether ectopic expression of FOXP3 in human CD4+ T cells is sufficient for acquisition of suppressive activity. Here, we show that retroviral transduction of FOXP3 induces a Treg phenotype in human leukemic CD4+ Jurkat-T cells, evidenced by increased expression of Treg-associated cell surface markers as well as inhibition of cytokine production. Furthermore, FOXP3-transduced Jurkat-T cells suppress the proliferation of human CD4+CD25- T cells. Additionally, DNA microarray analysis identifies Treg-related genes regulated by FOXP3. Our study demonstrates that enforced expression of FOXP3 confers Treg-like properties on Jurkat-T cells, which can be a convenient and efficient Treg-like cell model for further study to identify Treg cell surface markers and target genes regulated by FOXP3

  7. Physiological and iTRAQ-Based Proteomic Analyses Reveal the Function of Spermidine on Improving Drought Tolerance in White Clover.

    Science.gov (United States)

    Li, Zhou; Zhang, Yan; Xu, Yi; Zhang, Xinquan; Peng, Yan; Ma, Xiao; Huang, Linkai; Yan, Yanhong

    2016-05-01

    Endogenous spermidine interacting with phytohormones may be involved in the regulation of differentially expressed proteins (DEPs) associated with drought tolerance in white clover. Plants treated with or without spermidine (50 μM) were subjected to 20% PEG 6000 nutrient solution to induce drought stress (50% leaf-relative water content). The results showed that increased endogenous spermidine induced by exogenous spermidine altered endogenous phytohormones in association with improved drought tolerance, as demonstrated by the delay in water-deficit development, improved photosynthesis and water use efficiency, and lower oxidative damage. As compared to untreated plants, Spd-treated plants maintained a higher abundance of DEPs under drought stress involved in (1) protein biosynthesis (ribosomal and chaperone proteins); (2) amino acids synthesis; (3) the carbon and energy metabolism; (4) antioxidant and stress defense (ascorbate peroxidase, glutathione peroxidase, and dehydrins); and (5) GA and ABA signaling pathways (gibberellin receptor GID1, ABA-responsive protein 17, and ABA stress ripening protein). Thus, the findings of proteome could explain the Spd-induced physiological effects associated with drought tolerance. The analysis of functional protein-protein networks further proved that the alteration of endogenous spermidine and phytohormones induced the interaction among ribosome, photosynthesis, carbon metabolism, and amino acid biosynthesis. These differences could contribute to improved drought tolerance. PMID:27030016

  8. Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316.

    Science.gov (United States)

    Guo, Jing; Jing, Xueping; Peng, Wen-Lei; Nie, Qiyu; Zhai, Yile; Shao, Zongze; Zheng, Longyu; Cai, Minmin; Li, Guangyu; Zuo, Huaiyu; Zhang, Zhitao; Wang, Rui-Ru; Huang, Dian; Cheng, Wanli; Yu, Ziniu; Chen, Ling-Ling; Zhang, Jibin

    2016-01-01

    We isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis, and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316. PMID:27384076

  9. Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium.

    Science.gov (United States)

    Iakiviak, Michael; Devendran, Saravanan; Skorupski, Anna; Moon, Young Hwan; Mackie, Roderick I; Cann, Isaac

    2016-01-01

    Ruminococcus albus 8 is a specialist plant cell wall degrading ruminal bacterium capable of utilizing hemicellulose and cellulose. Cellulose degradation requires a suite of enzymes including endoglucanases, exoglucanases, and β-glucosidases. The enzymes employed by R. albus 8 in degrading cellulose are yet to be completely elucidated. Through bioinformatic analysis of a draft genome sequence of R. albus 8, seventeen putatively cellulolytic genes were identified. The genes were heterologously expressed in E. coli, and purified to near homogeneity. On biochemical analysis with cellulosic substrates, seven of the gene products (Ra0185, Ra0259, Ra0325, Ra0903, Ra1831, Ra2461, and Ra2535) were identified as endoglucanases, releasing predominantly cellobiose and cellotriose. Each of the R. albus 8 endoglucanases, except for Ra0259 and Ra0325, bound to the model crystalline cellulose Avicel, confirming functional carbohydrate binding modules (CBMs). The polypeptides for Ra1831 and Ra2535 were found to contain distantly related homologs of CBM65. Mutational analysis of residues within the CBM65 of Ra1831 identified key residues required for binding. Phylogenetic analysis of the endoglucanases revealed three distinct subfamilies of glycoside hydrolase family 5 (GH5). Our results demonstrate that this fibrolytic bacterium uses diverse GH5 catalytic domains appended with different CBMs, including novel forms of CBM65, to degrade cellulose. PMID:27439730

  10. Resurrecting Brinley Plots for a Novel Use: Meta-Analyses of Functional Brain Imaging Data in Older Adults

    Directory of Open Access Journals (Sweden)

    Ann M. Peiffer

    2008-01-01

    Full Text Available By plotting response times of young and older adults across a variety of tasks, Brinley spurred investigation and debate into the theory of general cognitive slowing. Though controversial, Brinley plots can assess between-task differences, the impact of increasing task demand, and the relationship between responses in two groups of subjects. Since a relationship exists between response times and the blood-oxygen level dependent (BOLD signal of functional MRI (fMRI, Brinley's plotting method could be applied as a meta-analysis tool in fMRI studies of aging. Here, fledgling “Peiffer plots” are discussed for their potential impact on understanding general cognitive brain activity in aging. Preliminary results suggest that general cognitive slowing may be localized at the sensorimotor transformation in the precentral gyrus. Although this meta-analysis method is naturally used with imaging studies of aging, theoretically it may be applied to other study pairs (e.g., schizophrenic versus normal or imaging datasets (e.g., PET.

  11. Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316

    Science.gov (United States)

    Guo, Jing; Jing, Xueping; Peng, Wen-Lei; Nie, Qiyu; Zhai, Yile; Shao, Zongze; Zheng, Longyu; Cai, Minmin; Li, Guangyu; Zuo, Huaiyu; Zhang, Zhitao; Wang, Rui-Ru; Huang, Dian; Cheng, Wanli; Yu, Ziniu; Chen, Ling-Ling; Zhang, Jibin

    2016-01-01

    We isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis, and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316. PMID:27384076

  12. Protein variety and functional diversity: Swiss-Prot annotation in its biological context.

    Science.gov (United States)

    Boeckmann, Brigitte; Blatter, Marie-Claude; Famiglietti, Livia; Hinz, Ursula; Lane, Lydie; Roechert, Bernd; Bairoch, Amos

    2005-01-01

    We all know that the dogma 'one gene, one protein' is obsolete. A functional protein and, likewise, a protein's ultimate function depend not only on the underlying genetic information but also on the ongoing conditions of the cellular system. Frequently the transcript, like the polypeptide, is processed in multiple ways, but only one or a few out of a multitude of possible variants are produced at a time. An overview on processes that can lead to sequence variety and structural diversity in eukaryotes is given. The UniProtKB/Swiss-Prot protein knowledgebase provides a wealth of information regarding protein variety, function and associated disorders. Examples for such annotation are shown and further ones are available at http://www.expasy.org/sprot/tutorial/examples_CRB. PMID:16286078

  13. Mechanical properties of lipid bilayers and regulation of mechanosensitive function: from biological to biomimetic channels.

    Science.gov (United States)

    Balleza, Daniel

    2012-01-01

    Material properties of lipid bilayers, including thickness, intrinsic curvature and compressibility regulate the function of mechanosensitive (MS) channels. This regulation is dependent on phospholipid composition, lateral packing and organization within the membrane. Therefore, a more complete framework to understand the functioning of MS channels requires insights into bilayer structure, thermodynamics and phospholipid structure, as well as lipid-protein interactions. Phospholipids and MS channels interact with each other mainly through electrostatic forces and hydrophobic matching, which are also crucial for antimicrobial peptides. They are excellent models for studying the formation and stabilization of membrane pores. Importantly, they perform equivalent responses as MS channels: (1) tilting in response to tension and (2) dissipation of osmotic gradients. Lessons learned from pore forming peptides could enrich our knowledge of mechanisms of action and evolution of these channels. Here, the current state of the art is presented and general principles of membrane regulation of mechanosensitive function are discussed. PMID:22790280

  14. Orphan G protein-coupled receptors (GPCRs):biological functions and potential drug targets

    Institute of Scientific and Technical Information of China (English)

    Xiao-long TANG; Ying WANG; Da-li LI; Jian LUO; Ming-yao LIU

    2012-01-01

    The superfamily of G protein-coupled receptors (GPCRs) includes at least 800 seven-transmembrane receptors that participate in diverse physiological and pathological functions.GPCRs are the most successful targets of modern medicine,and approximately 36%of marketed pharmaceuticals target human GPCRs.However,the endogenous ligands of more than 140 GPCRs remain unidentified,leaving the natural functions of those GPCRs in doubt.These are the so-called orphan GPCRs,a great source of drug targets.This review focuses on the signaling transduction pathways of the Adhesion GPCR family,the LGR subfamily,and the PSGR subfamily,and their potential functions in immunology,development,and cancers.In this review,we present the current approaches and difficulties of orphan GPCR deorphanization and characterization.

  15. Stable Isotope Analyses of Phosphate Oxygen From Micro-samples of Biological Apatite: A new Routine Procedure for Silverphosphate Micro-precipitation and the Removal of Organic Contamination

    Science.gov (United States)

    Wiedemann-Bidlack, F. B.; Colman, A. S.; Fogel, M. L.

    2003-12-01

    Oxygen isotope analyses in bone and teeth of living and fossil animals are widely used for testing hypotheses about variability of diet and habitat. For the analysis of environmental or dietary changes in the past, tooth enamel has become the preferred study material, because its mineral content is higher than bone and dentine, and the relatively large size of the carbonato-apatite crystals of enamel make it more stable against post mortem diagenetic alteration than dentine or bone. Intra-tooth sampling of dental enamel is increasingly used for the investigation of seasonal climate variability, taking advantage of both the high correlation between an animal's drinking water and the δ 18O in its mineralized tissues and the incremental growth pattern of tooth enamel. The different oxygen-containing ions of bioapatite (phosphate, carbonate, and hydroxyl group) incorporate into the mineral lattice at different rates during enamel mineralization, and differ in their susceptibility against post mortem diagenetic alteration. In addition, it is difficult to account for the different reaction chemistries of phosphate, carbonate, and hydroxyl group using isotope analysis techniques that include all oxygen contained in the enamel (e.g., laser ablation). These problems can be addressed analyzing phosphate oxygen only. However, two major factors limit the potential of δ 18O analyses in dental enamel: A) the starting sample size for isotope analyzes often precludes the use of small teeth or the intra-tooth sampling of a given tooth; B) Small amounts of biogenic organic material in tooth enamel (less than 1% by wt) can reduce the precision and lead to anomalous analytical results in δ 18O measurements on Ag3PO4 produced from tooth enamel. A new procedure was developed for the pre-treatment and δ 18O analysis of phosphate from small samples (500 μ g) of tooth enamel containing organic matter. Ag3PO{4} was precipitated quantitatively for analysis of δ 18Ophosphate using a

  16. Integrated ‘omics’, targeted metabolite and single-cell analyses of Arctic snow algae functionality and adaptability

    Directory of Open Access Journals (Sweden)

    Stefanie eLutz

    2015-11-01

    Full Text Available Snow algae are poly-extremophilic microalgae and important primary colonisers and producers on glaciers and snow fields. Depending on their pigmentation they cause green or red mass blooms during the melt season. This decreases surface albedo and thus further enhances snow and ice melting. Although the phenomenon of snow algal blooms has been known for a long time, large aspects of their physiology and ecology sill remain cryptic. This study provides the first in-depth and multi-omics investigation of two very striking adjacent green and red snow fields on a glacier in Svalbard. We have assessed the algal community composition of green and red snow including their associated microbiota, i.e., bacteria and archaea, their metabolic profiles (targeted and non-targeted metabolites on the bulk and single-cell level, and assessed the feedbacks between the algae and their physico-chemical environment including liquid water content, pH, albedo and nutrient availability. We demonstrate that green and red snow clearly vary in their physico-chemical environment, their microbial community composition and their metabolic profiles. For the algae this likely reflects both different stages of their life cycles and their adaptation strategies. Green snow represents a wet, carbon and nutrient rich environment and is dominated by the algae Microglena sp. with a metabolic profile that is characterized by key metabolites involved in growth and proliferation. In contrast, the dry and nutrient poor red snow habitat is colonised by various Chloromonas species with a high abundance of storage and reserve metabolites likely to face upcoming severe conditions. Combining a multitude of techniques we demonstrate the power of such complementary approaches in elucidating the function and ecology of extremophiles such as green and red snow algal blooms, which play crucial roles in glacial ecosystems.

  17. Integrated ‘Omics’, Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability

    Science.gov (United States)

    Lutz, Stefanie; Anesio, Alexandre M.; Field, Katie; Benning, Liane G.

    2015-01-01

    Snow algae are poly-extremophilic microalgae and important primary colonizers and producers on glaciers and snow fields. Depending on their pigmentation they cause green or red mass blooms during the melt season. This decreases surface albedo and thus further enhances snow and ice melting. Although the phenomenon of snow algal blooms has been known for a long time, large aspects of their physiology and ecology sill remain cryptic. This study provides the first in-depth and multi-omics investigation of two very striking adjacent green and red snow fields on a glacier in Svalbard. We have assessed the algal community composition of green and red snow including their associated microbiota, i.e., bacteria and archaea, their metabolic profiles (targeted and non-targeted metabolites) on the bulk and single-cell level, and assessed the feedbacks between the algae and their physico-chemical environment including liquid water content, pH, albedo, and nutrient availability. We demonstrate that green and red snow clearly vary in their physico-chemical environment, their microbial community composition and their metabolic profiles. For the algae this likely reflects both different stages of their life cycles and their adaptation strategies. Green snow represents a wet, carbon and nutrient rich environment and is dominated by the algae Microglena sp. with a metabolic profile that is characterized by key metabolites involved in growth and proliferation. In contrast, the dry and nutrient poor red snow habitat is colonized by various Chloromonas species with a high abundance of storage and reserve metabolites likely to face upcoming severe conditions. Combining a multitude of techniques we demonstrate the power of such complementary approaches in elucidating the function and ecology of extremophiles such as green and red snow algal blooms, which play crucial roles in glacial ecosystems. PMID:26635781

  18. Integrated genomic and functional analyses of histone demethylases identify oncogenic KDM2A isoform in breast cancer.

    Science.gov (United States)

    Liu, Hui; Liu, Lanxin; Holowatyj, Andreana; Jiang, Yuanyuan; Yang, Zeng-Quan

    2016-05-01

    Histone lysine demethylases (KDMs) comprise a large class of enzymes that catalyze site-specific demethylation of lysine residues on histones and other proteins. They play critical roles in controlling transcription, chromatin architecture, and cellular differentiation. However, the genomic landscape and clinical significance of KDMs in breast cancer remain poorly characterized. Here, we conducted a meta-analysis of 24 KDMs in breast cancer and identified associations among recurrent copy number alterations, gene expression, breast cancer subtypes, and clinical outcome. Two KDMs, KDM2A and KDM5B, had the highest frequency of genetic amplification and overexpression. Furthermore, among the 24 KDM genes, KDM2A had the highest correlation between copy number and mRNA expression, and high mRNA levels of KDM2A were significantly associated with shorter survival of breast cancer patients. KDM2A has two isoforms: the long isoform is comprised of a JmjC domain, CXXC-zinc finger, PHD zinc finger, F-box, and the AMN1 protein domain; whereas the short isoform of KDM2A lacks the N-terminal JmjC domain but contains all other motifs. Detailed characterization of KDM2A in breast cancer revealed that the short isoform of KDM2A is more abundant than the long isoform at DNA, mRNA, and protein levels in a subset of breast cancers. Furthermore, our data indicate that the short isoform of KDM2A has oncogenic potential and functions as an oncogenic isoform in a subset of breast cancers. Taken together, our findings suggest that amplification and overexpression of the KDM2A short isoform is critical in breast cancer progression. © 2015 Wiley Periodicals, Inc. PMID:26207617

  19. New MRI technologies. Diffusion MRI and its application to functional neuroimaging and analyses of white matter integrity

    International Nuclear Information System (INIS)

    Described is the technological aspect of MRI, MR diffusion-weighted imaging (MR-DWI), principles of its measurement and application for imaging the cerebral function and for aiding the quantitative diagnosis of brain diseases. The author explains the principle of MR imaging process; diffusion properties of water molecules, MR-DWI based on them and DW-fMRI of the brain; MR-diffusion tensor imaging (MR-DTI), its analysis and color acquisition, and tracking of white matter nerve fibers; analysis of white matter lesions by the tracking; and the new tracking method at the chiasm of nerve fascicles. The usual fMRI reflects the blood oxygen level depending (BOLD) signals whereas recently attracted DW-fMRI, the volume changes of nerve cells concomitant to nerve activation accompanying apparent changes of water diffusion coefficients in and out of cells which occur faster than BOLD signs, resulting in higher resolution of time and space. However, DWI requires the higher intensity of static magnetic field like 3T. MR-DTI acquires the anisotropic diffusion of water molecules using MR-DWI technique with application of 6 or more motion probing gradients, thus makes it possible to track the running directions of nerve fibers and capillary vessels, and is proposed to be a useful mean of specific fiber tracking in the white matter when displayed by 3 different colors exhibiting the directions like the right/left (x axis, red), anterior/posterior (y, green) and upper/lower (z, blue) sides of head. Recently, MR-DWI and MR-DTI have been found usable for pathogenic studies of brain diseases such as dementia. Tensor anisotropy is apparently lowered at the chiasm of nerve fascicles, the cause of tracking error, for which authors have developed a new method using the similarity of directional vector, not of tensor, before and behind the chiasm. As exemplified, MRI technology is further advancing even at present. (T.T.)

  20. Subcellular localization and functional analyses of a PR10 protein gene from Vitis pseudoreticulata in response to Plasmopara viticola infection.

    Science.gov (United States)

    He, Mingyang; Xu, Yan; Cao, Jiangling; Zhu, Ziguo; Jiao, Yuntong; Wang, Yuejin; Guan, Xin; Yang, Yazhou; Xu, Weirong; Fu, Zhenfang

    2013-02-01

    Downy mildew, caused by the oomycete Plasmopara viticola, is a serious fungal disease in the cultivated European grapevines (Vitis vinifera L.). The class 10 of pathogenesis-related (PR) genes in grapevine leaves was reported to be accumulated at mRNA level in response to P. viticola infection. To elucidate the functional roles of PR10 genes during plant-pathogen interactions, a PR10 gene from a fungal-resistant accession of Chinese wild Vitis pseudoreticulata (designated VpPR10.2) was isolated and showed high homology to PR10.2 from susceptible V. vinifera (designated VvPR10.2). Comparative analysis displayed that there were significant differences in the patterns of gene expression between the PR10 genes from the two host species. VpPR10.2 was induced with high level in leaves infected by P. viticola, while VvPR10.2 showed a low response to this inoculation. Recombinant VpPR10.2 protein showed DNase activity against host genomic DNA and RNase activity against yeast total RNA in vitro. Meanwhile, recombinant VpPR10.2 protein inhibited the growth of tobacco fungus Alternaria alternata and over-expression of VpPR10.2 in susceptible V. vinifera enhanced the host resistance to P. viticola. The results from subcellular localization analysis showed that VpPR10.2 proteins were distributed dynamically inside or outside of host cell. Moreover, they were found in haustorium of P. viticola and nucleus of host cell which was associated with a nucleus collapse at 10 days post-inoculation. Taken together, these results suggested that VpPR10.2 might play an important role in host plant defense against P. viticola infection. PMID:22327469

  1. RNase-L control of cellular mRNAs: roles in biologic functions and mechanisms of substrate targeting.

    Science.gov (United States)

    Brennan-Laun, Sarah E; Ezelle, Heather J; Li, Xiao-Ling; Hassel, Bret A

    2014-04-01

    RNase-L is a mediator of type 1 interferon-induced antiviral activity that has diverse and critical cellular roles, including the regulation of cell proliferation, differentiation, senescence and apoptosis, tumorigenesis, and the control of the innate immune response. Although RNase-L was originally shown to mediate the endonucleolytic cleavage of both viral and ribosomal RNAs in response to infection, more recent evidence indicates that RNase-L also functions in the regulation of cellular mRNAs as an important mechanism by which it exerts its diverse biological functions. Despite this growing body of work, many questions remain regarding the roles of mRNAs as RNase-L substrates. This review will survey known and putative mRNA substrates of RNase-L, propose mechanisms by which it may selectively cleave these transcripts, and postulate future clinical applications. PMID:24697205

  2. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

    Science.gov (United States)

    de Brevern, Alexandre G.; Meyniel, Jean-Philippe; Fairhead, Cécile; Neuvéglise, Cécile; Malpertuy, Alain

    2015-01-01

    Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries. PMID:26125026

  3. Cullin 3 Ubiquitin Ligases in Cancer Biology: Functions and Therapeutic Implications

    Science.gov (United States)

    Chen, Hsin-Yi; Chen, Ruey-Hwa

    2016-01-01

    Cullin-RING ubiquitin ligases are the largest E3 ligase family in eukaryotes and are multiprotein complexes. In these complexes, the Cullin protein serves as a scaffold to connect two functional modules of the ligases, the catalytic subunit and substrate-binding subunit. To date, eight members of the Cullin family proteins have been identified. In the Cul3 ubiquitin ligases, Bric-a-brac/Tramtrack/Broad complex (BTB) domain-containing proteins function as a bridge to connect Cul3 and substrates. While the BTB domain is responsible for Cul3 binding, these proteins usually contain an additional domain for substrate interaction, such as MATH, kelch, Zn finger, and PAM, Highwire, and RPM-1 (PHR domain). With the existence of a large number of BTB proteins in human, the Cul3 ubiquitin ligases ubiquitinate a wide range of substrates involving in diverse cellular functions. In this review, we will discuss recent advances on the functions of Cul3 ubiquitin ligases in cancer development, progression, and therapeutic response and the dysregulation of Cul3-mediated ubiquitination events in human malignancies. In particular, we will focus on three Cul3 substrate adaptors, kelch-like ECH-associated protein (Keap1), kelch-like family member 20 (KLHL20), and speckle type BTB/POZ protein (SPOP), with the intent to highlight novel targets in cancer therapy. PMID:27200299

  4. Biological Co-Adaptation of Morphological and Composition Traits Contributes to Mechanical Functionality and Skeletal Fragility

    OpenAIRE

    Tommasini, Steven M.; Nasser, Philip; Hu, Bin; Jepsen, Karl J

    2007-01-01

    A path analysis was conducted to determine whether functional interactions exist among morphological, compositional, and microstructural traits for young adult human tibias. Data provided evidence that bone traits are co-adapted during ontogeny so that the sets of traits together satisfy physiological loading demands. However, certain sets of traits are expected to perform poorly under extreme load conditions.

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

    DEFF Research Database (Denmark)

    Winding, Anne; Rutgers, Michiel; Creamer, Rachel;

    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...

  6. Reproductive biology and functional response of Dineulophus phtorimaeae, a natural enemy of the tomato moth, Tuta absoluta.

    Science.gov (United States)

    Savino, Vivina; Coviella, Carlos E; Luna, María G

    2012-01-01

    The tomato moth, Tuta absoluta (Lepidoptera: Gelechiidae), is a major pest in South America and is at present an important invasive species in the Mediterranean Basin. The larval stadium mines leaves, stems, and fruits, and chemical control is the most used control method in both its original range and the invaded distribution regions. Since current T. absoluta control strategies seem limited, biological control is a prominent tool to be applied abroad. The naturally occurring larval ectoparasitoid in Argentina and Chile Dineulophus phtorimaeae (Hymenoptera: Eulophidae) has been reported to have potential biocontrol efficiency. In this study, the ovigeny strategy of D. phtorimaeae was analyzed throughout the adult female lifetime, and the functional response of females offered a range of 2-15 T. absoluta larvae was measured over a 48-hour period. Mean D. phtorimaeae egg load was 4.15 eggs, and egg production resulted in extremely synovigenic behavior. Meanwhile, a decreasing number of eggs, due to resorption, was found. Proportions of attacked (host-fed and/or parasitized) and only host-fed hosts by the ectoparasitoid were density independent for the tested host range, exhibiting a type I functional response to T. absoluta, with an attack rate of 0.20 host larvae. Meanings of this reproductive strategy in evolutionary time as well as the consequences for augmentative biological control programs are discussed. PMID:23464576

  7. Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation.

    Directory of Open Access Journals (Sweden)

    Xia Wang

    Full Text Available Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ~100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase-LacI expression system was used to replace the σ(54-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ~42% of the nitrogenase activity of the σ(54-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology.

  8. Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746

    Energy Technology Data Exchange (ETDEWEB)

    FRINK, LAURA J. D.; REMPE, SUSAN L.; MEANS, SHAWN A.; STEVENS, MARK J.; CROZIER, PAUL S.; MARTIN, MARCUS G.; SEARS, MARK P.; HJALMARSON, HAROLD P.

    2002-11-01

    This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.

  9. Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal.

    Science.gov (United States)

    Mao, Yanping; Wang, Zhiping; Li, Liguan; Jiang, Xiaotao; Zhang, Xuxiang; Ren, Hongqiang; Zhang, Tong

    2016-01-01

    A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including Candidatus Competibacter phosphatis and Defluviicoccus-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant Candidatus Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively. PMID:27547976

  10. Biological changes in auditory function following training in children with autism spectrum disorders

    Directory of Open Access Journals (Sweden)

    Nicol Trent

    2010-10-01

    Full Text Available Abstract Background Children with pervasive developmental disorders (PDD, such as children with autism spectrum disorders (ASD, often show auditory processing deficits related to their overarching language impairment. Auditory training programs such as Fast ForWord Language may potentially alleviate these deficits through training-induced improvements in auditory processing. Methods To assess the impact of auditory training on auditory function in children with ASD, brainstem and cortical responses to speech sounds presented in quiet and noise were collected from five children with ASD who completed Fast ForWord training. Results Relative to six control children with ASD who did not complete Fast ForWord, training-related changes were found in brainstem response timing (three children and pitch-tracking (one child, and cortical response timing (all five children after Fast ForWord use. Conclusions These results provide an objective indication of the benefit of training on auditory function for some children with ASD.

  11. Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere.

    Science.gov (United States)

    Kai, Marco; Effmert, Uta; Piechulla, Birgit

    2016-01-01

    Rhizobacteria produce an enormous amount of volatile compounds, however, the function of these metabolites is scarcely understood. Investigations evaluating influences on plants performed in various laboratories using individually developed experimental setups revealed different and often contradictory results, e.g., ranging from a significant plant growth promotion to a dramatic suppression of plant development. In addition to these discrepancies, these test systems neglected properties and complexity of the rhizosphere. Therefore, to pursue further investigations of the role of bacterial volatiles in this underground habitat, the applied methods have to simulate its natural characteristics as much as possible. In this review, we will describe and discuss pros and cons of currently used bioassays, give insights into rhizosphere characteristics, and suggest improvements for test systems that would consider in natura conditions and would allow gaining further knowledge of the potential function and significance of rhizobacterial volatiles in plant life. PMID:26903987

  12. Hydrogel-based encapsulation of biological, functional tissue: fundamentals, technologies and applications

    Science.gov (United States)

    Zimmermann, H.; Ehrhart, F.; Zimmermann, D.; Müller, K.; Katsen-Globa, A.; Behringer, M.; Feilen, P. J.; Gessner, P.; Zimmermann, G.; Shirley, S. G.; Weber, M. M.; Metze, J.; Zimmermann, U.

    2007-12-01

    Replacing dysfunctional endocrine cells or tissues (e.g. islets, parathyroid tissue) by functional, foreign material without using immunosuppressives could soon become reality. Immunological reactions are avoided by encapsulating cells/tissues in hydrogel (e.g. alginate) microcapsules, preventing interaction of the enclosed material with the host’s immune system while permitting the unhindered passage of nutrients, oxygen and secreted therapeutic factors. Detailed investigations of the physical, physico-chemical and immunological parameters of alginate-based microcapsules have led recently to the development of a novel class of cell-entrapping microcapsules that meet the demands of biocompatibility, long-term integrity and function. This together with the development of ‘good medical practice’ microfluidic chip technology and of advanced cryopreservation technology for generation and storage of immunoisolated transplants will bring cell-based therapy to clinics and the market.

  13. Prediction of GPCR-G Protein Coupling Specificity Using Features of Sequences and Biological Functions

    Institute of Scientific and Technical Information of China (English)

    Toshihide Ono; Haretsugu Hishigaki

    2006-01-01

    Understanding the coupling specificity between G protein-coupled receptors (GPCRs) and specific classes of G proteins is important for further elucidation of receptor functions within a cell. Increasing information on GPCR sequences and the G protein family would facilitate prediction of the coupling properties of GPCRs. In this study, we describe a novel approach for predicting the coupling specificity between GPCRs and G proteins. This method uses not only GPCR sequences but also the functional knowledge generated by natural language processing, and can achieve 92.2% prediction accuracy by using the C4.5 algorithm.Furthermore, rules related to GPCR-G protein coupling are generated. The combination of sequence analysis and text mining improves the prediction accuracy for GPCR-G protein coupling specificity, and also provides clues for understanding GPCR signaling.

  14. Functionalization of Self-Organized Nanoparticles for Biological Targeting and Active Drug Release

    DEFF Research Database (Denmark)

    Jølck, Rasmus Irming

    and drug delivery. The objective of this PhD thesis was to expand the field of liposomal drug delivery by developing novel methods to efficienctly functionalize and subsequently sensitize liposomes towards internal stimuli, such as matrix metalloproteinases. Initially, we investigated a novel method...... to the importance of the relative position of the reactive functionalities. Surface conjugation reactions of octreotate by Michael addition, Click chemistry, Cu-free Click chemistry or oxime bond formation were investigated. From these studies it was evident that chemical reactions performed directly on the surface...... was significantly higher than for the controlliposomes, which indicated that active targeting can improve tumor-to-muscle contrast, thus, improving bioimaging for diagnostic applications. Finally, a novel drug delivery system based on charge-triggering of matrix metalloproteinase 2/9 sensitive PEGylated...

  15. Statistical properties of coastal long waves analysed through sea-level time-gradient functions: exemplary analysis of the Siracusa, Italy, tide-gauge data

    Science.gov (United States)

    Bressan, L.; Tinti, S.

    2016-01-01

    This study presents a new method to analyse the properties of the sea-level signal recorded by coastal tide gauges in the long wave range that is in a window between wind/storm waves and tides and is typical of several phenomena like local seiches, coastal shelf resonances and tsunamis. The method consists of computing four specific functions based on the time gradient (slope) of the recorded sea level oscillations, namely the instantaneous slope (IS) as well as three more functions based on IS, namely the reconstructed sea level (RSL), the background slope (BS) and the control function (CF). These functions are examined through a traditional spectral fast Fourier transform (FFT) analysis and also through a statistical analysis, showing that they can be characterised by probability distribution functions PDFs such as the Student's t distribution (IS and RSL) and the beta distribution (CF). As an example, the method has been applied to data from the tide-gauge station of Siracusa, Italy.

  16. Synthesis and functionalization of nanoparticles with biogenic amines and their biological application

    OpenAIRE

    Gasiorek, Friederike Britta

    2016-01-01

    This work presents a successful application of newly developed conjugates of bioactive molecule and nanoparticle. A remarkable enhancement of receptor activation was achieved by multivalent presentation of active moieties supported on gold nanoparticles. For this purpose diverse gold nanoparticles were synthesized and functionalized with biogenic amines. Different synthetic approaches were used to obtain gold nanoparticles between 4 nm and 25 nm. Small gold nanoparticles of 4 nm, 6 nm and ...

  17. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

    OpenAIRE

    Ruder, Warren C.; Hsu, Chia-Pei D.; Edelman, Brent D.; Schwartz, Russell; Leduc, Philip R.

    2012-01-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe3O4) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zer...

  18. A Modern Understanding of the Traditional and Nontraditional Biological Functions of Angiotensin-Converting Enzyme

    OpenAIRE

    Bernstein, Kenneth E.; Ong, Frank S.; Blackwell, Wendell-Lamar B.; Shah, Kandarp H.; Giani, Jorge F.; Gonzalez-Villalobos, Romer A.; Shen, Xiao Z.; Fuchs, Sebastien

    2013-01-01

    Angiotensin-converting enzyme (ACE) is a zinc-dependent peptidase responsible for converting angiotensin I into the vasoconstrictor angiotensin II. However, ACE is a relatively nonspecific peptidase that is capable of cleaving a wide range of substrates. Because of this, ACE and its peptide substrates and products affect many physiologic processes, including blood pressure control, hematopoiesis, reproduction, renal development, renal function, and the immune response. The defining feature of...

  19. Biologically Plausible Control of Fast Reaching Movements Using Non-Traditional Cost Functions

    OpenAIRE

    Gamble, Geoffrey

    2016-01-01

    Optimal control has been used as a technique to uncover mathematical principles which are observed regularly in the dynamics of human movement. We present two new models of human reaching movements. While both are rooted in optimal control theory, the models were conceived by questioning basic tenets and typical practices used in optimal control as applied to human movement. In the first model, we use cost functions that measure various control signals via the L_infinity norm as opposed to th...

  20. CNTF variants with increased biological potency and receptor selectivity define a functional site of receptor interaction.

    OpenAIRE

    Saggio, I; Gloaguen, I; Poiana, G; Laufer, R

    1995-01-01

    Human CNTF is a neurocytokine that elicits potent neurotrophic effects by activating a receptor complex composed of the ligand-specific alpha-receptor subunit (CNTFR alpha) and two signal transducing proteins, which together constitute a receptor for leukemia inhibitory factor (LIFR). At high concentrations, CNTF can also activate the LIFR and possibly other cross-reactive cytokine receptors in the absence of CNTFR alpha. To gain a better understanding of its structure-function relationships ...