WorldWideScience

Sample records for biological functional studies

  1. 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.

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

    Science.gov (United States)

    Legrain, Pierre; Rain, Jean-Christophe

    2014-07-31

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

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

    Science.gov (United States)

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

    2013-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Christopher Y Park

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

  5. 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…

  6. 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.

  7. 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…

  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. 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.

  10. Understanding biological functions through molecular networks

    Institute of Scientific and Technical Information of China (English)

    Jing-Dong Jackie Han

    2008-01-01

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

  11. Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology of Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Jörg Soppa

    2011-01-01

    Full Text Available The genome sequence of Haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, RNA modifications, small non-coding RNAs, and ubiquitin-like Small Archaeal Modifier Proteins. The full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. Notably, Hfx. volcanii is together with Halobacterium salinarum the only prokaryotic species for which a translatome analysis has been performed. The results revealed that the fraction of translationally-regulated genes in haloarchaea is as high as in eukaryotes. A highly efficient genetic system has been established that enables the application of libraries as well as the parallel generation of genomic deletion mutants. Facile mutant generation is complemented by the possibility to culture Hfx. volcanii in microtiter plates, allowing the phenotyping of mutant collections. Genetic approaches are currently used to study diverse biological questions–from replication to posttranslational modification—and selected results are discussed. Taken together, the wealth of functional genomic and genetic tools make Hfx. volcanii a bona fide archaeal model species, which has enabled the generation of important results in recent years and will most likely generate further breakthroughs in the future.

  12. Study and reflections on the functional and organizational role of neuromessenger nitric oxide in learning: An artificial and biological approach

    Science.gov (United States)

    Suárez Araujo, C. P.

    2000-05-01

    We present in this work a theoretical and conceptual study and some reflections on a fundamental aspect concerning with the structure and brain function: the Cellular Communication. The main interests of our study are the signal transmission mechanisms and the neuronal mechanisms responsible to learning. We propose the consideration of a new kind of communication mechanisms, different to the synaptic transmission, "Diffusion or Volume Transmission." This new alternative is based on a diffusing messenger as nitric oxide (NO). Our study aims towards the design of a conceptual framework, which covers implications of NO in the artificial neural networks (ANNs), both in neural architecture and learning processing. This conceptual frame might be able to provide possible biological support for many aspects of ANNs and to generate new concepts to improve the structure and operation of them. Some of these new concepts are The Fast Diffusion Neural Propagation (FDNP), the Diffuse Neighborhood (DNB), (1), the Diffusive Hybrid Neuromodulation (DHN), the Virtual Weights. Finally we will propose a new mathematical formulation for the Hebb learning law, taking into account the NO effect. Along the same lines, we will reflect on the possibility of a new formal framework for learning processes in ANNs, which consist of slow and fast learning concerning with co-operation between the classical neurotransmission and FDNP. We will develop this work from a computational neuroscience point of view, proposing a global study framework of diffusion messenger NO (GSFNO), using a hybrid natural/artificial approach. Finally it is important to note that we can consider this paper the first paper of a set of scientific work on nitric oxide (NO) and artificial neural networks (ANNs): NO and ANNs Series. We can say that this paper has a character of search and query on both subjects their implications and co-existence.

  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. 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.

  15. Marine Carotenoids: Biological Functions and Commercial Applications

    Directory of Open Access Journals (Sweden)

    José M. Vega

    2011-03-01

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

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Ye-Rang Yun

    2010-01-01

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

  18. Functional model of biological neural networks.

    Science.gov (United States)

    Lo, James Ting-Ho

    2010-12-01

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

  19. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  20. 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.

  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. 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.)

  3. Biological Function of REE in Plants & Microbes

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

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

  4. 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...

  5. 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.

  6. Case Studies in Biology.

    Science.gov (United States)

    Zeakes, Samuel J.

    1989-01-01

    A case study writing exercise used in a course on parasitology was found to be a powerful learning experience for students because it involved discipline-based technical writing and terminology, brought the students in as evaluators, applied current learning, caused interaction among all students, and simulated real professional activities. (MSE)

  7. Biological Sampling Variability Study

    Energy Technology Data Exchange (ETDEWEB)

    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-11-08

    There are many sources of variability that exist in the sample collection and analysis process. This paper addresses many, but not all, sources of variability. The main focus of this paper was to better understand and estimate variability due to differences between samplers. Variability between days was also studied, as well as random variability within each sampler. Experiments were performed using multiple surface materials (ceramic and stainless steel), multiple contaminant concentrations (10 spores and 100 spores), and with and without the presence of interfering material. All testing was done with sponge sticks using 10-inch by 10-inch coupons. Bacillus atrophaeus was used as the BA surrogate. Spores were deposited using wet deposition. Grime was coated on the coupons which were planned to include the interfering material (Section 3.3). Samples were prepared and analyzed at PNNL using CDC protocol (Section 3.4) and then cultured and counted. Five samplers were trained so that samples were taken using the same protocol. Each sampler randomly sampled eight coupons each day, four coupons with 10 spores deposited and four coupons with 100 spores deposited. Each day consisted of one material being tested. The clean samples (no interfering materials) were run first, followed by the dirty samples (coated with interfering material). There was a significant difference in recovery efficiency between the coupons with 10 spores deposited (mean of 48.9%) and those with 100 spores deposited (mean of 59.8%). There was no general significant difference between the clean and dirty (containing interfering material) coupons or between the two surface materials; however, there was a significant interaction between concentration amount and presence of interfering material. The recovery efficiency was close to the same for coupons with 10 spores deposited, but for the coupons with 100 spores deposited, the recovery efficiency for the dirty samples was significantly larger (65

  8. Dynamics of biomolecules, ligand binding & biological functions

    Science.gov (United States)

    Yi, Myunggi

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

  9. Respiratory function and other biological risk factors for completed suicide: 40 years of follow-up of European cohorts of the Seven Countries Study

    NARCIS (Netherlands)

    Giltay, E.J.; Zitman, F.G.; Menotti, A.; Nissinen, A.; Jacobs, D.R.; Adachi, H.; Kafatos, A.; Kromhout, D.

    2010-01-01

    Background - Prospective cohort studies on biological risk factors of completed suicide are scarce. We aimed to test which biological risk factors independently identify subjects at increased risk of suicidal death. Methods - In the prospective cohort of the Seven Countries Study, 5,321 middle-aged

  10. Flavonoids: Biosynthesis, Biological functions and Biotechnological applications

    Directory of Open Access Journals (Sweden)

    Maria Lorena eFalcone Ferreyra

    2012-09-01

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

  11. Synthesis and Characterisation of Copper(II Complexes with Tridentate NNO Functionalized Ligand: Density Function Theory Study, DNA Binding Mechanism, Optical Properties, and Biological Application

    Directory of Open Access Journals (Sweden)

    Madhumita Hazra

    2014-01-01

    Full Text Available The photo physical properties of two mononuclear pentacoordinated copper(II complexes formulated as [Cu(L(Cl(H2O] (1 and [Cu(L(Br(H2O] (2 HL = (1-[(3-methyl-pyridine-2-ylimino-methyl]-naphthalen-2-ol were synthesized and characterized by elemental, physicochemical, and spectroscopic methods. The density function theory calculations are used to investigate the electronic structures and the electronic properties of ligand and complex. The interactions of copper(II complexes towards calf thymus DNA were examined with the help of absorption, viscosity, and fluorescence spectroscopic techniques at pH 7.40. All spectroscopy's result indicates that complexes show good binding activity to calf thymus DNA through groove binding. The optical absorption and fluorescence emission properties of microwires were characterized by fluorescence microscope. From a spectroscopic viewpoint, all compounds strongly emit green light in the solid state. The microscopy investigation suggested that microwires exhibited optical waveguide behaviour which are applicable as fluorescent nanomaterials and can be used as building blocks for miniaturized photonic devices. Antibacterial study reveals that complexes are better antimicrobial agents than free Schiff base due to bacterial cell penetration by chelation. Moreover, the antioxidant study of the ligand and complexes is evaluated by using 1,1-diphenyl-2-picrylhydrazyl (DPPH free-radical assays, which demonstrate that the complexes are of higher antioxidant activity than free ligand.

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

    NARCIS (Netherlands)

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

    2013-01-01

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

  13. Functionalized Nanodiamonds for Biological and Medical Applications.

    Science.gov (United States)

    Lai, Lin; Barnard, Amanda S

    2015-02-01

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

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

    Science.gov (United States)

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

    2009-03-27

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

  15. 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.

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

    Science.gov (United States)

    Geschwind, Daniel H; Konopka, Genevieve

    2009-10-15

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

  17. 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.

  18. The Structure and Function of Biological Networks

    Science.gov (United States)

    Wu, Daniel Duanqing

    2010-01-01

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

  19. Autofluorescence: Biological functions and technical applications.

    Science.gov (United States)

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

    2015-07-01

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

  20. Space Biology Initiative. Trade Studies, volume 2

    Science.gov (United States)

    1989-01-01

    The six studies which are the subjects of this report are entitled: Design Modularity and Commonality; Modification of Existing Hardware (COTS) vs. New Hardware Build Cost Analysis; Automation Cost vs. Crew Utilization; Hardware Miniaturization versus Cost; Space Station Freedom/Spacelab Modules Compatibility vs. Cost; and Prototype Utilization in the Development of Space Hardware. The product of these six studies was intended to provide a knowledge base and methodology that enables equipment produced for the Space Biology Initiative program to meet specific design and functional requirements in the most efficient and cost effective form consistent with overall mission integration parameters. Each study promulgates rules of thumb, formulas, and matrices that serves as a handbook for the use and guidance of designers and engineers in design, development, and procurement of Space Biology Initiative (SBI) hardware and software.

  1. Space Biology Initiative. Trade Studies, volume 1

    Science.gov (United States)

    1989-01-01

    The six studies which are addressed are entitled: Design Modularity and Commonality; Modification of Existing Hardware (COTS) vs. New Hardware Build Cost Analysis; Automation Cost vs. Crew Utilization; Hardware Miniaturization versus Cost; Space Station Freedom/Spacelab Modules Compatibility vs. Cost; and Prototype Utilization in the Development of Space Hardware. The product of these six studies was intended to provide a knowledge base and methodology that enables equipment produced for the Space Biology Initiative program to meet specific design and functional requirements in the most efficient and cost effective form consistent with overall mission integration parameters. Each study promulgates rules of thumb, formulas, and matrices that serves has a handbook for the use and guidance of designers and engineers in design, development, and procurement of Space Biology Initiative (SBI) hardware and software.

  2. 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.

  3. 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.

  4. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach

    DEFF Research Database (Denmark)

    Adamala, K.; Anella, F.; Wieczorek, R.

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From...... sequences among a vast array of possible ones, the huge "sequence space", leading to the question "why these macromolecules, and not the others?" We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides...

  5. 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

  6. Biological Studies of Posttraumatic Stress Disorder

    Science.gov (United States)

    Pitman, Roger K.; Rasmusson, Ann M.; Koenen, Karestan C.; Shin, Lisa M.; Orr, Scott P.; Gilbertson, Mark W.; Milad, Mohammed R.; Liberzon, Israel

    2016-01-01

    Preface Posttraumatic stress disorder (PTSD) is the only major mental disorder for which a cause is considered to be known, viz., an event that involves threat to the physical integrity of oneself or others and induces a response of intense fear, helplessness, or horror. Although PTSD is still largely regarded as a psychological phenomenon, over the past three decades the growth of the biological PTSD literature has been explosive, and thousands of references now exist. Ultimately, the impact of an environmental event, such as a psychological trauma, must be understood at organic, cellular, and molecular levels. The present review attempts to present the current state of this understanding, based upon psychophysiological, structural and functional neuroimaging, endocrinological, genetic, and molecular biological studies in humans and in animal models. PMID:23047775

  7. Functional Genomics and Cell Biology of the Dolphin (Tursiops runcatus): Establishment of Novel Molecular Tools to Study Marine Mammals in Changing Environments

    OpenAIRE

    Mancia, Annalaura

    2010-01-01

    The dolphin (Tursiops truncatus) is a mammal that is adapted to life in a totally aquatic environment. Despite the popularity and even iconic status of the dolphin, our knowledge of its physiology, its unique adaptations and the effects on it of environmental stressors are limited. One approach to improve this limited understanding is the implementation of established cellular and molecular methods to provide sensitive and insightful information for dolphin biology. We initiated our studi...

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

    Science.gov (United States)

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

    2016-01-11

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

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

    Science.gov (United States)

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

    2014-09-01

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

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

    Science.gov (United States)

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

    2012-04-01

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

  11. Market study: Biological isolation garment

    Science.gov (United States)

    1975-01-01

    The biological isolation garment was originally designed for Apollo astronauts to wear upon their return to earth from the moon to avoid the possibility of their contaminating the environment. The concept has been adapted for medical use to protect certain patients from environmental contamination and the risk of infection. The nature and size of the anticipated market are examined with certain findings and conclusions relative to clinical acceptability and potential commercial viability of the biological isolation garment.

  12. FUNCTION IN BIOLOGY: ETIOLOGICAL AND ORGANIZATIONAL PERSPECTIVES

    Directory of Open Access Journals (Sweden)

    Nunes Neto Nei Freitas Freitas

    2009-12-01

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

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

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

    Science.gov (United States)

    Takeda, K; Kishimoto, T; Akira, S

    1997-05-01

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

  14. 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.

  15. Sucrose metabolism gene families and their biological functions.

    Science.gov (United States)

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

    2015-11-30

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

  16. 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.

  17. Chemical synthesis, docking studies and biological effects of functionalized 1,3-diaryl-2-propen-1-ones on human colon cancer cells

    Directory of Open Access Journals (Sweden)

    Guo-Min Zhu

    2015-03-01

    Full Text Available A series of 1, 3-diaryl-2-propen-1-ones was synthesised in order to obtain a new type of anticancer drug, designed with hybrid features to inhibit colon cancer activated receptor. Based on computational modelling and docking studies, potential inhibitors were synthesised and their biological activity evaluated. The structures of newly synthesized compounds were confirmed by 1HNMR, 13CNMR and Mass spectrometry. All analogues were evaluated for in vitro cytotoxicity against human colon (caco-2 cancer cell lines. Compounds 1b, 1f-1h, and 2i showed significant cytotoxicity. Chalcones 1b, 1f and 1g were identified as the most potent and selective anticancer agents with IC50 values <1 µg/mL and 1.5 µg/mL, against caco-2 cell line, respectively. In conclusion, this finding confirms the suitability of indolyl chalcone analogues as candidates for further investigation towards the management of colon cancer related diseases.

  18. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach.

    Science.gov (United States)

    Adamala, Katarzyna; Anella, Fabrizio; Wieczorek, Rafal; Stano, Pasquale; Chiarabelli, Cristiano; Luisi, Pier Luigi

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the chemical viewpoint, macromolecules are formed by chemical pathways leading to the condensation of building blocks (amino acids, or nucleotides) in long-chain copolymers (proteins and nucleic acids, respectively). The second difficulty deals with a conceptual problem, namely with the emergence of specific sequences among a vast array of possible ones, the huge "sequence space", leading to the question "why these macromolecules, and not the others?" We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called "never born biopolymer" project) with respect to the production of folded structures. Being still far from solved, the main aspects of these "open questions" are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection.

  19. Recent Advances in Studies on Ghrelin and its Biological Functions%生长激素释放肽及其生物学效应

    Institute of Scientific and Technical Information of China (English)

    来景辉; 范红结

    2012-01-01

    Ghrelin, a peptide lying widely in animal bodies, is the endogenous ligand for the growth hormone secretagogue receptor(GHSR). Ghrelin, after binding with GHSR in the hypothalamus and pituitary, not only promotes the GH releasing and increases appetite, but also adjusts the functions of digestive system and energy metabolism. This article mainly reviewed the recent developments on structure, distribution and biological effects of ghrelin as well as its potential applications in animal husbandry, which maybe promotes the further research of ghrelin.%生长激素释放肽(Ghrelin)是一种在动物体内广泛存在的生长激素促分泌素受体(GHSR)的内源性配体,Ghrelin与位于下丘脑的GHSR结合后,具有促进生长激素释放、增加食欲、调节消化系统功能及能量代谢等作用.文章就Ghrelin的结构、分布、生物学效应及在畜牧业上的应用前景等方面进行综述,以期促进Ghrelin的进一步深入研究.

  20. Autofluorescences: Biological functions and technical applications

    Science.gov (United States)

    Fluorescence is the property by which a molecule (fluorophore), excited after the absorption of a photon, is able to de-excite by re-emitting a photon of a longer wavelength. Chlorophylls are the most remarkable examples of plant fluorophores, and their properties have been intensively studied as a ...

  1. 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.

  2. Advanced Functional Nanomaterials for Biological Processes

    Science.gov (United States)

    2014-01-01

    phantom and in animal mode. The expected outcome—the assessment of a patient’s entire blood volume (in adults 5 L)—will provide a significant (100...formation. We hypothesized that such a study could result in a possible vaccine for osteoporosis . 0 0.5 1 1.5 2 2.5 3 3.5 4 Control SW 20 SW40 SWCPE...GCNFs) were produced by a single-step reduction process and used for the growth and differentiation of human adult stem cells. The nanomaterials were

  3. Absent activation in medial prefrontal cortex and temporoparietal junction but not superior temporal sulcus during the perception of biological motion in schizophrenia: a functional MRI study

    Directory of Open Access Journals (Sweden)

    Hashimoto N

    2014-11-01

    Full Text Available Naoki Hashimoto,1,2 Atsuhito Toyomaki,1 Masahiro Hirai,3 Tamaki Miyamoto,1 Hisashi Narita,1 Ryo Okubo,1 Ichiro Kusumi1 1Department of Psychiatry, Graduate School of Medicine, Hokkaido University, Sapporo, Japan; 2Child and Adolescent Psychiatry, Department of Psychiatry, University of California, San Francisco, CA, USA; 3Center for Development of Advanced Medical Technology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi, Japan Background: Patients with schizophrenia show disturbances in both visual perception and social cognition. Perception of biological motion (BM is a higher-level visual process, and is known to be associated with social cognition. BM induces activation in the “social brain network”, including the superior temporal sulcus (STS. Although deficits in the detection of BM and atypical activation in the STS have been reported in patients with schizophrenia, it remains unclear whether other nodes of the “social brain network” are also atypical in patients with schizophrenia.Purpose: We aimed to explore whether brain regions other than STS were involved during BM perception in patients with schizophrenia, using functional magnetic resonance imaging (fMRI.Methods and patients: Seventeen patients with schizophrenia, and 17 age- and sex- matched healthy controls, underwent fMRI scanning during a one-back visual task, containing three experimental conditions: (1 BM, (2 scrambled motion (SM, and (3 static condition. We used one-sample t-tests to examine neural responses selective to BM versus SM within each group, and two-sample t-tests to directly compare neural patterns to BM versus SM in schizophrenics versus controls.Results: We found significant activation in the STS region when BM was contrasted with SM in both groups, with no significant difference between groups. On the contrary, significant activation in the medial prefrontal cortex (MPFC and bilateral temporoparietal junction (TPJ was found only in the

  4. Mimicking biological functionality with polymers for biomedical applications

    Science.gov (United States)

    Green, Jordan J.; Elisseeff, Jennifer H.

    2016-12-01

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

  5. Photonic engineering for biological study

    Science.gov (United States)

    Wu, Fei

    My dissertation focuses on designing and developing prototypes of optical tools in the laboratory that can facilitate practical medical therapies. More specifically, this dissertation examines two novel biophotonic techniques: (1) a frequency multiplexed confocal microscope with the potential to provide rational therapy of congestive heart failure (CHF), and (2) the "optical comb" with the potential to improve results of retina reattachment surgery and accelerate post surgical recovery. Next, I will discuss the background, design and initial experimental results of each study individually. Part I: The Frequency Multiplexed Confocal Microscope. To overcome the limitations of existing confocal microscope technology, this dissertation proposes a non-scanning, real-time, high resolution technique (a multi-point frequency multiplexed confocal microscope) to measure 3-D intracellular calcium ion concentration in a living cardiac myocyte. This method can be also applied to measure the intracellular sodium ion concentration, or other ions in which high quantum-yield fluorescent probes are available. The novelty of the proposed research lies in the introduction of carrier frequency multiplexing techniques which can differentiate fluorescence emitted at different spatial locations in cardiac myocyte by their modulated frequency. It therefore opens the possibility to visualize the transient dynamics of intracellular dynamics at multiple locations in cells simultaneously, which will shine a new light on our understanding of CHF. The procedure for frequency multiplexing proposed is described below. Multiple incident laser beams are focused onto different locations in an isolated rat cardiac myocyte with each beam modulated at a different carrier frequency. The fluorescence emission at each location therefore bears the same modulated frequency as the stimulation laser beam. Each fluorescence signal is sent to the photo multiplier tube (PMT) after being spatially filtered by a

  6. Functionalized nanoparticles for biological imaging and detection applications

    Science.gov (United States)

    Mei, Bing C.

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

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

    Science.gov (United States)

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

    2008-08-05

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

  8. Directing experimental biology: a case study in mitochondrial biogenesis.

    Directory of Open Access Journals (Sweden)

    Matthew A Hibbs

    2009-03-01

    Full Text Available Computational approaches have promised to organize collections of functional genomics data into testable predictions of gene and protein involvement in biological processes and pathways. However, few such predictions have been experimentally validated on a large scale, leaving many bioinformatic methods unproven and underutilized in the biology community. Further, it remains unclear what biological concerns should be taken into account when using computational methods to drive real-world experimental efforts. To investigate these concerns and to establish the utility of computational predictions of gene function, we experimentally tested hundreds of predictions generated from an ensemble of three complementary methods for the process of mitochondrial organization and biogenesis in Saccharomyces cerevisiae. The biological data with respect to the mitochondria are presented in a companion manuscript published in PLoS Genetics (doi:10.1371/journal.pgen.1000407. Here we analyze and explore the results of this study that are broadly applicable for computationalists applying gene function prediction techniques, including a new experimental comparison with 48 genes representing the genomic background. Our study leads to several conclusions that are important to consider when driving laboratory investigations using computational prediction approaches. While most genes in yeast are already known to participate in at least one biological process, we confirm that genes with known functions can still be strong candidates for annotation of additional gene functions. We find that different analysis techniques and different underlying data can both greatly affect the types of functional predictions produced by computational methods. This diversity allows an ensemble of techniques to substantially broaden the biological scope and breadth of predictions. We also find that performing prediction and validation steps iteratively allows us to more completely

  9. 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/.

  10. Study of the structure and dynamics of complex biological networks

    Science.gov (United States)

    Samal, Areejit

    2008-12-01

    In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.

  11. The structure and function of quinones in biological solar energy transduction: a cyclic voltammetry, EPR, and hyperfine sub-level correlation (HYSCORE) spectroscopy study of model naphthoquinones.

    Science.gov (United States)

    Coates, Christopher S; Ziegler, Jessica; Manz, Katherine; Good, Jacob; Kang, Bernard; Milikisiyants, Sergey; Chatterjee, Ruchira; Hao, Sijie; Golbeck, John H; Lakshmi, K V

    2013-06-20

    Quinones function as electron transport cofactors in photosynthesis and cellular respiration. The versatility and functional diversity of quinones is primarily due to the diverse midpoint potentials that are tuned by the substituent effects and interactions with surrounding amino acid residues in the binding site in the protein. In the present study, a library of substituted 1,4-naphthoquinones are analyzed by cyclic voltammetry in both protic and aprotic solvents to determine effects of substituent groups and hydrogen bonds on the midpoint potential. We use continuous-wave electron paramagnetic resonance (EPR) spectroscopy to determine the influence of substituent groups on the electronic properties of the 1,4-naphthoquinone models in an aprotic solvent. The results establish a correlation between the presence of substituent group(s) and the modification of electronic properties and a corresponding shift in the midpoint potential of the naphthoquinone models. Further, we use pulsed EPR spectroscopy to determine the effect of substituent groups on the strength and planarity of the hydrogen bonds of naphthoquinone models in a protic solvent. This study provides support for the tuning of the electronic properties of quinone cofactors by the influence of substituent groups and hydrogen bonding interactions.

  12. 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

  13. Studying cell biology in the skin.

    Science.gov (United States)

    Morrow, Angel; Lechler, Terry

    2015-11-15

    Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists.

  14. Studying cell biology in the skin

    Science.gov (United States)

    Morrow, Angel; Lechler, Terry

    2015-01-01

    Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists. PMID:26564861

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2015-08-01

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

  18. Phytochemical and biological studies of Agave attenuata.

    Science.gov (United States)

    Rizwan, Komal; Zubair, Muhammad; Rasool, Nasir; Riaz, Muhammad; Zia-Ul-Haq, Muhammad; de Feo, Vincenzo

    2012-01-01

    The present study was conducted to examine various biological activities of a methanol extract of Agave attenuata leaves. GC-MS analysis of the n-hexane fraction from the extract revealed the presence of 31 compounds, with mono-2-ethylhexyl phthalate (11.37%), 1,2-benzenedicarboxylic acid (6.33%), n-docosane (6.30%) and eicosane (6.02%) as the major components. The leaves contained appreciable levels of total phenolic contents (10.541-39.35 GAE, mg/100 g) and total flavonoid contents (43.35-304.8 CE, mg/100 g). The extract and some of its fractions showed moderate antimicrobial effects. Leaves extract and fractions also exhibited a good antioxidant potential when measured by DPPH radical scavenging activity and inhibition of lipid peroxidation assays. The hemolytic effect of the plant was found to be in a range of 1.01%-2.64%. From the present study it is concluded that this plant could be used as a source of natural antioxidants and functional food nutraceutical applications.

  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. Biologically active Schiff bases containing thiophene/furan ring and their copper(II) complexes: Synthesis, spectral, nonlinear optical and density functional studies

    Science.gov (United States)

    Gündüzalp, Ayla Balaban; Özsen, İffet; Alyar, Hamit; Alyar, Saliha; Özbek, Neslihan

    2016-09-01

    Schiff bases; 1,8-bis(thiophene-2-carboxaldimine)-p-menthane (L1) and 1,8-bis(furan-2-carboxaldimine)-p-menthane (L2) have been synthesized and characterized by elemental analysis, 1Hsbnd 13C NMR, UV-vis, FT-IR and LC-MS methods. 1H and 13C shielding tensors for L1 and L2 were calculated with GIAO/DFT/B3LYP/6-311++G(d,p) methods in CDCl3. The vibrational band assignments, nonlinear optical (NLO) activities, frontier molecular orbitals (FMOs) and absorption spectrum have been investigated by the same basis set. Schiff base-copper(II) complexes have been synthesized and structurally characterized with spectroscopic methods, magnetic and conductivity measurements. The spectroscopic data suggest that Schiff base ligands coordinate through azomethine-N and thiophene-S/furan-O donors (as SNNS and ONNO chelating systems) to give a tetragonal geometry around the copper(II) ions. Schiff bases and Cu(II) complexes have been screened for their biological activities on different species of pathogenic bacteria, those are, Gram positive bacteria: Bacillus subtitilus, Yersinia enterotica, Bacillus cereus, Listeria monocytogenes, Micrococcus luteus and Gram negative bacteria: Escherichia coli, Pseudomonas aeroginosa, Shigella dysenteriae, Salmonella typhi, Klebsiella pseudomonas by using microdilution technique (MIC values in mM). Biological activity results show that Cu(II) complexes have higher activities than parent ligands and metal chelation may affect significantly the antibacterial behavior of the organic ligands.

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

    Science.gov (United States)

    Ghezzehei, Teamrat; Or, Dani

    2016-04-01

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

  2. Deducing protein function by forensic integrative cell biology.

    Directory of Open Access Journals (Sweden)

    William C Earnshaw

    2013-12-01

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

  3. Deducing protein function by forensic integrative cell biology.

    Science.gov (United States)

    Earnshaw, William C

    2013-12-01

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

  4. Toxicity Studies on "840 Biologic Pesticide"

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    [Objective] "840 Biologic Pesticide" is a very effective biologic pesticide. It consists of Abamectin and celastrus angulatus. Toxicity study was aimed to provide scientific toxicological basis. [Methods] The acute toxicity test,Ames test,micronucleus test and testicle chromosome aberration test were done. [Results] The acute toxicity of single dose of "840 Biologic Pesticide" showed that acute oral LD50 for female and male rats are 4 300 and 4 280 mg/kg,and for female and male mice are 2 330 and 5 110 mg/kg,respectively. The dermal LD50 was >2 000 mg/kg for female and male rats. The mutagenesis studies indicated that Ames test,micronucleus test and testicle chromosome aberration test were negative. [Conclusion] Tested pesticidc belongs to low toticity grade.

  5. OPEN QUESTIONS IN ORIGIN OF LIFE: EXPERIMENTAL STUDIES ON THE ORIGIN OF NUCLEIC ACIDS AND PROTEINS WITH SPECIFIC AND FUNCTIONAL SEQUENCES BY A CHEMICAL SYNTHETIC BIOLOGY APPROACH

    Directory of Open Access Journals (Sweden)

    Katarzyna Adamala

    2014-02-01

    We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called “never born biopolymer” project with respect to the production of folded structures. Being still far from solved, the main aspects of these “open questions” are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection.

  6. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach

    NARCIS (Netherlands)

    Adamala, K.; Anella, F.M.; Wieczorek, R.; Stano, P.; Chiarabelli, C.; Luisi, P.L.

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the c

  7. 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.

  8. Biological properties of extracellular vesicles and their physiological functions

    Science.gov (United States)

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

    2015-01-01

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  10. 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.

  11. II. Biological studies of radiation effects

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, J.H.

    1948-05-24

    With the completion of the 184 inch cyclotron in Berkeley and the successful construction of a deflector system, it was possible to bring the 190 Mev deuteron and the 380 Mev alpha beams out into the air and to begin a study of the effects of high-energy deuteron beams by direct irradiation of biological specimens. The direct biological use of deuteron beams was attempted earlier in Berkeley by Marshak, MacLeish, and Walker in 1940. These and other investigators have been aware for some time of the potential usefulness of high energy particle beams for radio-biological studies and their suitability for biological investigations. R.R. Wilson advanced the idea of using fast proton beams to deliver radiation and intervening tissues. R.E. Zirkle pointed out that such particle beams may be focused or screened until a cross-section of the beam is small enough to study effects of irradiation under the microscope on single cells or on parts of single cells. This article gives an overview of the radiological use of high energy deuteron beams, including the following topics: potential uses of high energy particle beams; experiments on the physical properties of the beam; lethal effect of the deuteron beam on mice.

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

    Science.gov (United States)

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

    2016-06-02

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

  13. Phytochrome from Green Plants: Properties and biological Function

    Energy Technology Data Exchange (ETDEWEB)

    Quail, Peter H.

    2014-07-25

    Plants constantly monitor the light environment for informational light signals used to direct adaptational responses to the prevailing conditions. One major such response, the Shade-Avaoidance Response (SAR), triggered when plants sense the presence of competing neighbors, results in enhanced channeling of photosynthetically-fixed carbon into stem elongation at the expense of deposition in reproductive tissues. This response has been selected against in many modern food crops to ensure maximum edible yield (e.g. seeds). Converse enhancement of the SAR, with consequent increased carbon channeling into vegetative cellulose, could contribute to the generation of crops with improved yield of tissues suitable for cellulosic biofuel production. The signal for this response is light enriched in far-red wavelengths. This signal is produced by sunlight filtered through, or reflected from, neighboring vegetation, as a result of preferential depletion of red photons through chlorophyll absorption. The plant phytochrome (phy) photoreceptor system (predominantly phyB) senses this signal through its capacity to switch reversibly, in milliseconds, between two molecular states: the biologically inactive Pr (red-light-absorbing) and biologically active Pfr (far-red-light-absorbing) conformers. The photoequilibrium established between these two conformers in light-grown plants is determined by the ratio of red-to-far-red wavelengths in the incoming signal. The levels of Pfr then dictate the recipient plant’s growth response: high levels suppress elongation growth; low levels promote elongation growth. Studies on seedling deetiolation have advanced our understanding considerably in recent years, of the mechanism by which the photoactivated phy molecule transduces its signal into cellular growth responses. The data show that a subfamily of phy-interacting bHLH transcription factors (PIFs) promote skotomorphogenic seedling development in post-germinative darkness, but that the phy

  14. Evidence for Alteration in Chemical and Physical Properties of Water and Modulation of its Biological Functions by Sunlight Transmitted through Color Ranges of the Visible Spectrum-A Novel Study

    Directory of Open Access Journals (Sweden)

    M. Rajeswara Rao

    2005-08-01

    Full Text Available We investigated the changes in the properties of water when exposed to sunlight for 40 days. We hypothesize and prove that solar irradiation to water entraps electromagnetic radiation as potential energy, which becomes kinetic energy in various systems. It is postulated that photochemically-induced energy transfers, associated with individual spectral emission of visible spectrum of solar light, exert diverse influences on biological systems. Bottles of distilled water, individually wrapped in spectral-colored cellophane were exposed to sunlight and compared to an unwrapped bottle to determine chemical and physical changes as well as modifications of biological properties. Each bottle of water was named according to the color of cellophane paper with letter E (stands for exposed as a prefix with (E-violet, E-indigo, E-blue, E-green, E-yellow, E-orange, and Ered. E-control (without wrap was exposed to polychromatic sunlight. This study addresses two main issues viz., the chemical and physical changes in E-water and its effect on biological activities. Chemical and physical composition analysis using inductively coupled plasma atomic emission spectrometry; physical conductance by a Wheatstone Bridge type conductivity meter; osmolarity by a vapor pressure osmometer; and, salt solubility profile of 10% sodium bicarbonate were determined. Furthermore, testing the effect of E-waters on human lymphocyte proliferation, mosquito larvae hatching and seed germination determined the functional role of solar radiation through specific spectrum/s of visible light on various biological processes. We found that water exposed to visible spectral emissions of sunlight had an altered elemental composition, electrical conductance, osmolarity and salt-solubility, as well as differences in bio-modulatory effects. A gradual increase in leaching of Boron from Eviolet to E-red was noted. E-indigo showed maximal increase in electrical conductance and maximal salt

  15. 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.

  16. 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.

  17. Advanced femtosecond lasers enable new developments in non-linear imaging and functional studies in neuroscience, biology and medical applications (Conference Presentation)

    Science.gov (United States)

    Arrigoni, Marco; McCoy, Darryl

    2016-03-01

    In the last few years Multiphoton Excitation Microscopy witnessed a mutation from tool for imaging cellular structures in living animals deeper than other high-resolution techniques, into an instrument for monitoring functionality and even stimulating or inhibiting inter-cellular signalling. This paradigm shift has been enabled primarily by the development of genetically encoded probes like Ca indicators (GECI) and Opsins for optogenetics inhibition and stimulation. These developments will hopefully enable the understanding of how local network of hundreds or thousands of neurons operate in response to actual tasks or induced stimuli. Imaging, monitoring signals and activating neurons, all on a millisecond time scale, requires new laser tools providing a combination of wavelengths, higher powers and operating regimes different from the ones traditionally used for classic multiphoton imaging. The other key development in multiphoton techniques relates to potential diagnostic and clinical applications where non-linear imaging could provide all optical marker-free replacement of H and E techniques and even intra-operative guidance for procedures like cancer surgery. These developments will eventually drive the development of specialized laser sources where compact size, ease of use, beam delivery and cost are primary concerns. In this talk we will discuss recent laser product developments targeting the various applications of multiphoton imaging, as fiber lasers and other new type of lasers gradually gain popularity and their own space, side-by-side or as an alternative to conventional titanium sapphire femtosecond lasers.

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

    Science.gov (United States)

    Guseo, Renato

    2016-12-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2015-05-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  2. 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.

  3. 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

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

    Science.gov (United States)

    Lappalainen, Tuuli

    2015-10-01

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

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

    Science.gov (United States)

    Lemmer, Björn

    2009-08-01

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

  6. Linking biological soil crust diversity to ecological functions

    Science.gov (United States)

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

    2016-04-01

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

  7. 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.

  8. 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.

  9. Application of Biolog to Study of Environmental Microbial Function Diversity%Biolog法在环境微生物功能多样性研究中的应用

    Institute of Scientific and Technical Information of China (English)

    田雅楠; 王红旗

    2011-01-01

    微生物是生态系统的重要组成部分,它不仅要受到外界环境的影响,其自身的结构和功能变化也会对环境产生持续的作用,而这种作用主要是通过群落代谢功能差异来实现的,因此研究微生物群落功能多样性更能够揭示微生物与环境间相互作用的内在机制.Biolog法是目前已知的研究微生物代谢功能多样性的很有力的方法.为了使该项技术在更大范围上得以推广,使其为环境微生物群落功能多样性分析更好的服务,为环境工作者进一步剖析环境与微生物间相关关系提供方法,该文从Biolog法应用原理、数据处理、在环境微生物群落功能多样性中的应用及存在的问题几方面对其进行了详细阐述.通过对应用现状的探讨本文得出应引起今后重视的研究方向,主要包括:探讨不同的数据处理方法以寻求更为适宜的数据处理方法、注重方法改进以期早日形成规范的操作流程、注重新领域应用的探索、针对特殊情况形成专用研究微平板等方面.%Microorganism as an important part of the ecosystem is affected by the external environment and its structure and function will have a continuing effect on environment which is mainly achieved by difference among microbial communities,thus the study on microbial communities function diversity can reveal the interaction between microbiology and environment. The method of Biolog is known as one of the most useful analysis of biology function diversity at present. In order to facilitate the technology to a wider extent, to make it serve for analysis of the functional diversity of environmental microbial communities and to provide a method for analysis of the relationship between environment and microorganism, the principle of the Biolog application, data processing, application in functional diversity of environmental microbial community were discussed. The research directions were also proposed

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

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

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

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Sathish ePeriyasamy

    2013-12-01

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

  13. Biosynthesis and biological functions of terpenoids in plants.

    Science.gov (United States)

    Tholl, Dorothea

    2015-01-01

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

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

    OpenAIRE

    Geschwind, Daniel H.; Konopka, Genevieve

    2009-01-01

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

  15. Exosome Function: From Tumor Immunology to Pathogen Biology

    OpenAIRE

    Schorey, Jeffrey S; Bhatnagar, Sanchita

    2008-01-01

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

  16. [The biological reaction of inflammation, methylglyoxal of blood plasma, functional and structural alterations in elastic type arteries at the early stage of hypertension disease].

    Science.gov (United States)

    Titov, V N; Dmitriev, V A; Oshchepkov, E V; Balakhonova, T V; Tripoten', M I; Shiriaeva, Iu K

    2012-08-01

    The article deals with studying of the relationship between biologic reaction of inflammation with glycosylation reaction and content of methylglyoxal in blood serum. The positive correlation between pulse wave velocity and content of methylglyoxal, C-reactive protein in intercellular medium and malleolar brachial index value was established. This data matches the experimental results concerning involvement of biological reaction of inflammation into structural changes of elastic type arteries under hypertension disease, formation of arteries' rigidity and increase of pulse wave velocity. The arterial blood pressure is a biological reaction of hydrodynamic pressure which is used in vivo by several biological functions: biological function of homeostasis, function of endoecology, biological function of adaptation and function of locomotion. The biological reaction of hydrodynamic (hydraulic) pressure is a mode of compensation of derangement of several biological functions which results in the very high rate of hypertension disease in population. As a matter of fact, hypertension disease is a syndrome of lingering pathological compensation by higher arterial blood pressure of the biological functions derangements occurring in the distal section at the level of paracrine cenoses of cells. The arterial blood pressure is a kind of in vivo integral indicator of deranged metabolism. The essential hypertension disease pathogenically is a result of the derangement of three biological functions: biological function of homeostasis, biological function of trophology - nutrition (biological reaction of external feeding - exotrophia) and biological function of endoecology. In case of "littering" of intercellular medium in vivo with nonspecific endogenic flogogens a phylogenetically earlier activation of biological reactions of excretion, inflammation and hydrodynamic arterial blood pressure occur. In case of derangement of biological function of homeostasis, decreasing of

  17. Ag(I), Pb(II) and Hg(II) binding to biomolecules studied by Perturbed Angular Correlation of $\\gamma$-rays (PAC) spectroscopy: Function and toxicity of metal ions in biological systems

    CERN Multimedia

    Metal ions display diverse functions in biological systems and are essential components in both protein structure and function, and in control of biochemical reaction paths and signaling. Similarly, metal ions may be used to control structure and function of synthetic biomolecules, and thus be a tool in the design of molecules with a desired function. In this project we address a variety of questions concerning both the function of metal ions in natural systems, in synthetic biomolecules, and the toxic effect of some metal ions. All projects involve other experimental techniques such as NMR, EXAFS, UV-Vis, fluorescence, and CD spectroscopies providing complementary data, as well as interpretation of the experimental data by quantum mechanical calculations of spectroscopic properties.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ouzounis Christos A

    2011-10-01

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

  20. 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.

  1. 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.

  2. 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.

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

    Science.gov (United States)

    Hou, Nicole Shangming; Taubert, Stefan

    2012-01-01

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

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

    Science.gov (United States)

    Bredt, D S

    1999-12-01

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

  5. Study on Biological Characteristics of Livestock Eperythrozoon

    Institute of Scientific and Technical Information of China (English)

    Peng Haisheng; Xie Minghua; Mu Qionghua

    2015-01-01

    Based on the study of infection and morphological characteristics of 12 kinds of livestock Eperythrozoon,disinfection test by drugs in vitro,disinfection test by ultraviolet light,Eperythrozoon survival test at different times and temperatures,drug sensitivity test and clinical treatment of infected swines were carried out on Eperythrozoon suis and Eperythrozoon wenyonii to further study the biological characteristics. Test results showed that infection level of livestock Eperythrozoon was high,while morbidity was low. Eperythrozoon suis and Eperythrozoon wenyonii could survive for 1 year at 3- 5 ℃,180 d at 16- 26 ℃ and 30 min at- 20 ℃,while which died instantly at 65 ℃. Eperythrozoon was sensitive to general chemical disinfection drugs,while not sensitive to ultraviolet light disinfection. Transmission of Eperythrozoon mainly included contagious transmission and vertical transmission. Results of drug sensitivity test showed that Eperythrozoon was sensitive to Tetracycline and antigen insect drugs. Sizes and shapes of different livestock Eperythrozoon were different. The study provided a scientific basis for the effective prevention and treatment of livestock Eperythrozoonosis.

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

    Science.gov (United States)

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

    2015-11-07

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

  7. Biological studies of post-traumatic stress disorder.

    Science.gov (United States)

    Pitman, Roger K; Rasmusson, Ann M; Koenen, Karestan C; Shin, Lisa M; Orr, Scott P; Gilbertson, Mark W; Milad, Mohammed R; Liberzon, Israel

    2012-11-01

    Post-traumatic stress disorder (PTSD) is the only major mental disorder for which a cause is considered to be known: that is, an event that involves threat to the physical integrity of oneself or others and induces a response of intense fear, helplessness or horror. Although PTSD is still largely regarded as a psychological phenomenon, over the past three decades the growth of the biological PTSD literature has been explosive, and thousands of references now exist. Ultimately, the impact of an environmental event, such as a psychological trauma, must be understood at organic, cellular and molecular levels. This Review attempts to present the current state of this understanding on the basis of psychophysiological, structural and functional neuroimaging, and endocrinological, genetic and molecular biological studies in humans and in animal models.

  8. 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

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

    Science.gov (United States)

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

    2016-01-01

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

  10. 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

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

    Science.gov (United States)

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

    2010-10-01

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

  12. Systems biology strategies to study lipidomes in health and disease.

    Science.gov (United States)

    Hyötyläinen, Tuulia; Orešič, Matej

    2014-07-01

    Lipids are a diverse group of metabolites that have many key biological functions, acting as structural components of cell membranes, energy storage sources and intermediates in signaling pathways. Due to their importance lipids are under tight homeostatic control and exhibit spatial and dynamic complexity at multiple levels. It is thus not surprising that altered lipid metabolism plays important roles in the pathogenesis of most of the common diseases. Lipidomics emerged as a discipline which is dedicated to global study of lipidomes, including pathways and networks of lipids in biological systems. When studying the lipidomes at a systems level, one of the key challenges is how to address the lipid functionality at many physiological levels, from metabolic and signaling pathways to spatial systems such as cellular membranes and lipoprotein particles. Besides the better analytical techniques to study lipids, computational techniques have started to emerge which enable modeling of lipidomes in their spatial and dynamic context. Together, the recent methodological advances in lipidomics have a potential to open novel avenues for predictive and preventive medicine. This review focuses on progress in systems approaches to study lipids in health and disease, with specific emphasis on clinical applications.

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

    Science.gov (United States)

    Her, Minyoung; Kavanaugh, Arthur

    2016-01-01

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

  14. 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.

  15. Study development of PRLs' biological functions and correlation between PRLs and tumors%PRL的生物学功能及与肿瘤关系的研究进展

    Institute of Scientific and Technical Information of China (English)

    郭延林; 朱彦君; 伍青

    2013-01-01

    The phosphatase of regenerating liver(PRL) family contains three subtypes, PRL - 1, PRL - 2, and PRL - 3,they are a new type of protein tyrosine phosphatase. That they have the activity of dual specificity phosphatase, through participating inmitosis and shortening the cell cycle, and can accelerate cell growth, maturity and other physiological functions. In some malignant tumors,such as colorectal cancer,non - small cell lung cancer,the abnormal and ectopic expression of PRLs can affect the proliferation, invasion in tumor cells. It provides a theoretical basis for the potential value for the detection of tumor molecular target, individualized diagnosis and treatment, determining the prognosis in clinical behavior. This article reviews study progress of PRLs about its biological functions and the mechanism of action in tumor occurrence, development and invasion.%肝再生磷酸酶(PRL)家族包含PRL-1、PRL-2、PRL-3三个亚型,是一种新型蛋白酪氨酸磷酸酶.研究表明其具有双特异性磷酸酶活性,通过参与有丝分裂,缩短细胞周期,加快细胞的生长、成熟等生理功能.在大肠癌、非小细胞肺癌等恶性肿瘤中,PRL的异位异常表达可以影响肿瘤细胞的增殖、侵袭、转移等途径,为其在肿瘤的分子靶点检测、个体化诊断治疗、判定预后情况等临床行为中的潜在价值提供了理论依据.现综述PRL的生物学功能及其在肿瘤的发生、转移等过程的研究进展.

  16. Phytochemical and biological studies of bryophytes.

    Science.gov (United States)

    Asakawa, Yoshinori; Ludwiczuk, Agnieszka; Nagashima, Fumihiro

    2013-07-01

    The bryophytes contain the Marchantiophyta (liverworts), Bryophyta (mosses) and Anthocerotophyta (hornworts). Of these, the Marchantiophyta have a cellular oil body which produce a number of mono-, sesqui- and di-terpenoids, aromatic compounds like bibenzyl, bis-bibenzyls and acetogenins. Most sesqui- and di-terpenoids obtained from liverworts are enantiomers of those found in higher plants. Many of these compounds display a characteristic odor, and can have interesting biological activities. These include: allergenic contact dermatitis, antimicrobial, antifungal and antiviral, cytotoxic, insecticidal, insect antifeedant, superoxide anion radical release, 5-lipoxygenase, calmodulin, hyaluronidase, cyclooxygenase, DNA polymerase β, and α-glucosidase and NO production inhibitory, antioxidant, piscicidal, neurotrophic and muscle relaxing activities among others. Each liverwort biosynthesizes unique components, which are valuable for their chemotaxonomic classification. Typical chemical structures and biological activity of the selected liverwort constituents as well as the hemi- and total synthesis of some biologically active compounds are summarized.

  17. Investigating Lebanese Grade Seven Biology Teachers Mathematical Knowledge and Skills: A Case Study

    Science.gov (United States)

    Raad, Nawal Abou; Chatila, Hanadi

    2016-01-01

    This paper investigates Lebanese grade 7 biology teachers' mathematical knowledge and skills, by exploring how they explain a visual representation in an activity depending on the mathematical concept "Function". Twenty Lebanese in-service biology teachers participated in the study, and were interviewed about their explanation for the…

  18. Polyketide stereocontrol: a study in chemical biology

    Science.gov (United States)

    2017-01-01

    The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.

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

    Science.gov (United States)

    Cockcroft, Shamshad; Carvou, Nicolas

    2007-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-10-01

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

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

    Science.gov (United States)

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

    2012-09-01

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

  2. Genome-wide studies of telomere biology in budding yeast

    Directory of Open Access Journals (Sweden)

    Yaniv Harari

    2014-03-01

    Full Text Available Telomeres are specialized DNA-protein structures at the ends of eukaryotic chromosomes. Telomeres are essential for chromosomal stability and integrity, as they prevent chromosome ends from being recognized as double strand breaks. In rapidly proliferating cells, telomeric DNA is synthesized by the enzyme telomerase, which copies a short template sequence within its own RNA moiety, thus helping to solve the “end-replication problem”, in which information is lost at the ends of chromosomes with each DNA replication cycle. The basic mechanisms of telomere length, structure and function maintenance are conserved among eukaryotes. Studies in the yeast Saccharomyces cerevisiae have been instrumental in deciphering the basic aspects of telomere biology. In the last decade, technical advances, such as the availability of mutant collections, have allowed carrying out systematic genome-wide screens for mutants affecting various aspects of telomere biology. In this review we summarize these efforts, and the insights that this Systems Biology approach has produced so far.

  3. Simulation of Interval Censored Data in Medical and Biological Studies

    Science.gov (United States)

    Kiani, Kaveh; Arasan, Jayanthi

    This research looks at the simulation of interval censored data when the survivor function of the survival time is known and attendance probability of the subjects for follow-ups can take any number between 0 to 1. Interval censored data often arise in the medical and biological follow-up studies where the event of interest occurs somewhere between two known times. Regardless of the methods used to analyze these types of data, simulation of interval censored data is an important and challenging step toward model building and prediction of survival time. The simulation itself is rather tedious and very computer intensive due to the interval monitoring of subjects at prescheduled times and subject's incomplete attendance to follow-ups. In this paper the simulated data by the proposed method were assessed using the bias, standard error and root mean square error (RMSE) of the parameter estimates where the survival time T is assumed to follow the Gompertz distribution function.

  4. Missile Studies with a Biological Target

    Science.gov (United States)

    1961-01-23

    Biology and Medicine of the U. S. Atomic Energy Commission and to the Office of Civil Defense and Mobilization (formerly the Federal Civil Defense...None Ear. left, laceration severed a peripheral blood vessel. 4P3A 4 1 Shoulder, left, 14 mm deep to scapular spine with small "nick" fracture

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

    Science.gov (United States)

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

    2016-02-09

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

  6. Peroxisystem: harnessing systems cell biology to study peroxisomes.

    Science.gov (United States)

    Schuldiner, Maya; Zalckvar, Einat

    2015-04-01

    In recent years, high-throughput experimentation with quantitative analysis and modelling of cells, recently dubbed systems cell biology, has been harnessed to study the organisation and dynamics of simple biological systems. Here, we suggest that the peroxisome, a fascinating dynamic organelle, can be used as a good candidate for studying a complete biological system. We discuss several aspects of peroxisomes that can be studied using high-throughput systematic approaches and be integrated into a predictive model. Such approaches can be used in the future to study and understand how a more complex biological system, like a cell and maybe even ultimately a whole organism, works.

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

    NARCIS (Netherlands)

    Gadella, B.M.; Luna, C.

    2014-01-01

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

  8. Design of Functional Polyesters for Electronic and Biological Applications

    OpenAIRE

    Nelson, Ashley Marie

    2015-01-01

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

  9. Oxidative metabolites of lycopene and their biological functions

    Science.gov (United States)

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

  10. 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.

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

    Institute of Scientific and Technical Information of China (English)

    原素梅; 徐超; 张煦; 王源; 谢冰玉; 熊庆; 彭宜红

    2016-01-01

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

  12. Novel nuclear magnetic resonance techniques for studying biological molecules

    Energy Technology Data Exchange (ETDEWEB)

    Laws, David D.

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone ({phi}/{psi}) dihedral angles by comparing experimentally determined {sup 13}C{sub a}, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of {alpha}-helical and {beta}-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly {beta}-sheet.

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

    Directory of Open Access Journals (Sweden)

    Timothy G Bromage

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  16. In search of lipid translocases and their biological functions

    NARCIS (Netherlands)

    Hoekstra, D; van Ijzendoorn, SCD

    2003-01-01

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

  17. Chemical approaches to studying stem cell biology

    Institute of Scientific and Technical Information of China (English)

    Wenlin Li; Kai Jiang; Wanguo Wei; Yan Shi; Sheng Ding

    2013-01-01

    Stem cells,including both pluripotent stem cells and multipotent somatic stem cells,hold great potential for interrogating the mechanisms of tissue development,homeostasis and pathology,and for treating numerous devastating diseases.Establishment of in vitro platforms to faithfully maintain and precisely manipulate stem cell fates is essential to understand the basic mechanisms of stem cell biology,and to translate stem cells into regenerative medicine.Chemical approaches have recently provided a number of small molecules that can be used to control cell selfrenewal,lineage differentiation,reprogramming and regeneration.These chemical modulators have been proven to be versatile tools for probing stem cell biology and manipulating cell fates toward desired outcomes.Ultimately,this strategy is promising to be a new frontier for drug development aimed at endogenous stem cell modulation.

  18. Chemical Biology Studies on Molecular Diversity of Annonaceous Acetogenins

    Institute of Scientific and Technical Information of China (English)

    Yao Zhu-Jun

    2004-01-01

    Annonaceous acetogenins, isolated from the Annonaceae plants, have been attracting worldwide attention in recent years due to their biological activities, especially as growth inhibitors of certain tumor ceils [ 1 ]. They have been shown to function by blocking complex I in mitochondria [2] as well as ubiquinone-linked NADPH oxidase in the cells of specific tumor cell lines, including some multidrug-resistant ones [3]. These features make these acetogenins excellent leads for the new antitumor agents. In our previous work, the compounds 1a to 1d (Figure 1), which relies on structure simplification while maintaining all essential functionalities of the acetogenins, was in vitro tested against several human solid tumor cell lines and showed interesting cell selectivity [4]. All four analogues show remarkable activity against the HCT-8 and HT-29 cell lines, while compound 1c was found the best [4bi. In order to further investigate the effects of key structural features, a convergent parallel fragments assembly strategy was developed [4e]. In addition, the biological relevancies of typical annonaceous acetogenin mimetics were also studied [4f].

  19. Bayesian networks: a powerful tool for systems biology study

    Institute of Scientific and Technical Information of China (English)

    Xiu-Jie WANG

    2010-01-01

    @@ Higher Education Press and Springer-Verlag Berlin Heidelberg 2010The wide application of omics research approaches caused a burst of biological data in the past decade, and also promoted the growth of systems biology, a research field that studies biological questions from a genome-wide point of view. One feature of systems biology study is to integrate and identify. Not only experiments are carried out at whole-genome scales, but also data from various resources, such as genomics, transcriptomics, proteomics,and metabolics data, need to be integrated to identify correlations among targeted entities. Therefore, plenty amounts of experimental data, robust statistical methods, and reliable network construction models are indispensable for systems biology study. Among the available network construction models, Bayesian network is considered as one of the most effective methods available so far for biological network predictions (Pe'er, 2005).

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

    Science.gov (United States)

    Pankov, Y A

    2016-01-01

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

  1. 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.

  2. New advances in pollination biology and the studies in China

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Pollination biology is the study of the various biological features in relation to the event of pollen transfer. It is one of the central concerns of plant reproductive ecology and evolutionary biology. In this paper, we attempt to introduce the main advances and some new interests in pollination biology and make a brief review of the research work that has been done in China in recent years. We also give some insights into the study that we intend to carry out in this field in the future.

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

    Directory of Open Access Journals (Sweden)

    Filimon eAntonakis

    2016-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Qi Ying

    2015-11-01

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

  5. 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.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Werner Mark

    2008-08-01

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

  8. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...

  9. Mimicking/extracting structure and functions of natural products: synthetic approaches that address unexplored needs in chemical biology.

    Science.gov (United States)

    Hirai, Go

    2015-04-01

    Natural products are often attractive and challenging targets for synthetic chemists, and many have interesting biological activities. However, synthetic chemists need to be more than simply suppliers of compounds to biologists. Therefore, we have been seeking ways to actively apply organic synthetic methods to chemical biology studies of natural products and their activities. In this personal review, I would like to introduce our work on the development of new biologically active compounds inspired by, or extracted from, the structures of natural products, focusing on enhancement of functional activity and specificity and overcoming various drawbacks of the parent natural products.

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

    Science.gov (United States)

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

    2009-10-14

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

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

    Science.gov (United States)

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

    2009-03-01

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

  12. Phytochemical and biological studies of Ochna species.

    Science.gov (United States)

    Bandi, Anil Kumar Reddy; Lee, Dong-Ung; Tih, Raphaël Ghogomu; Gunasekar, Duvvuru; Bodo, Bernard

    2012-02-01

    The genus Ochna L. (Gr, Ochne; wild pear), belonging to the Ochnaceae family, includes ca. 85 species of evergreen trees, shrubs, and shrublets, distributed in tropical Asia, Africa, and America. Several members of this genus have long been used in folk medicine for treatment of various ailments, such as asthma, dysentery, epilepsy, gastric disorders, menstrual complaints, lumbago, ulcers, as an abortifacient, and as antidote against snake bites. Up to now, ca. 111 constituents, viz. flavonoids (including bi-, tri-, and pentaflavonoids), anthranoids, triterpenes, steroids, fatty acids, and a few others have been identified in the genus. Crude extracts and isolated compounds have been found to exhibit analgesic, anti-HIV-1, anti-inflammatory, antimalarial, antimicrobial, and cytotoxic activities, lending support to the rationale behind several of its traditional uses. The present review compiles the informations concerning the traditional uses, phytochemistry, and biological activities of Ochna.

  13. ALOUD biological: Adult Learning Open University Determinants study - Association of biological determinants with study success in formal lifelong learners

    NARCIS (Netherlands)

    Gijselaers, Jérôme; De Groot, Renate; Kirschner, Paul A.

    2012-01-01

    Gijselaers, H. J. M., De Groot, R. H. M., & Kirschner, P. A. (2012, 15 March). ALOUD biological: Adult Learning Open University Determinants study - Association of biological determinants with study success in formal lifelong learners. Presentation given at the plenary meeting of Learning & Cognitio

  14. Systems biology studies of Aspergilli - from sequence to science

    DEFF Research Database (Denmark)

    Andersen, Mikael Rørdam

    2008-01-01

    The recent dawn of the new biological mindset called systems biology has put forth a new way of analyzing and understanding biology. Carried by the notion that no element of a cell is an island, systems biology takes a holistic approach, and attempts to understand life as systems that have co...... a few. The recent publication of the genome sequences of several filamentous fungi of the Aspergillus species (Aspergilli), has, along with the accumulation of years of reductionist studies, been a catalyst for the application of systems biology to this interesting group of fungi. Among the genome...... biology approach has been applied to a wide range of issues. These tools include the compilation of data from literature on A. niger enzymes to form a re-constructed metabolic network and model of metabolism, allowing assessment of the industrial production potential of metabolites from this fungus. Based...

  15. 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...

  16. 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.

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

    Science.gov (United States)

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

    2014-07-01

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

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

    Science.gov (United States)

    Campsteijn, Coen; Vietri, Marina; Stenmark, Harald

    2016-08-01

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

  19. 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.

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

    NARCIS (Netherlands)

    Mazereeuw, M.

    2013-01-01

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

  1. Microbubble generation by piezotransducer for biological studies

    Science.gov (United States)

    Zhu, W.; Alkhazal, M.; Cho, M.; Xiao, S.

    2015-12-01

    Bubbles induced by blast waves or shocks are speculated to be the major cause of damages in biological cells in mild traumatic brain injuries. Microbubble collapse was found to induce noticeable cell detachment from the cell substrate, changes in focal adhesion and biomechanics. To better understand the bubble mechanism, we would like to construct a system, which allows us to clearly differentiate the impact of bubbles from that of shocks. Such a generator needs to be low profile in order to place under a microscope. A piezoelectric transducer system was designed to meet the need. The system uses either a flat or a spherical focusing piezoelectric transducer to produce microbubbles in a cuvette loaded with cell-culture medium. The transducer is placed on the side of the cuvette with its axis lining horizontally. A cover slip is placed on the top of the cuvette. The impact of the waves to the cells is minimized as the cover slip is parallel to the direction of the wave. Only bubbles from the medium reach the cover slip and interact with cells. The effect of bubbles therefore can be separated that of pressure waves. The bubbles collected on a cover slip range in size from 100 μm to 10 μm in radius, but the dominant size is 20-30 μm.

  2. Teaching Biochemestry in Biology and Microbiology in the Faculty of Biology, University of Havana, in Studies Plan D

    Directory of Open Access Journals (Sweden)

    Jorge Oscar González Bacerio

    2014-04-01

    Full Text Available In this work, a review of the contents traditionally studied on Biochemistry I and II courses for Biology and Microbiology careers, at the Faculty of Biology, University of Havana, is realized. This analysis was done taking into account the agreement of contents with the Knowledge and Skills Systems recognized in the current Study Plan D. From this analysis, compa-rative with the equivalent courses on Biochemistry and Molecular Biology career, a redesign of the studied contents is presented. According to this, these con-tents were displaced, when was possible and conve-nient, from the classical mammal model to the study objects of these professionals: the living world in all its diversity, for biologists, and microorganisms and viru-ses, for microbiologists. In this manner, we use on Bio-chemistry I lectures specific examples of structure-function relationship of biomolecules from models of organisms more appropriated for the two careers. Similarly, we exploit on Biochemistry II the extraordi-nary metabolic diversity that is present in different groups of living organisms, as well as we introduced the teaching of other metabolic routes, characteristic of each group or which constitute variations of classi-cal mammalian pathways. These modifications could make easier the teaching and learning of Biochemistry for biologists and microbiologists, as well as could increase the contribution of these courses to the for-mation of professionals in these domains of Biological Sciences.

  3. Functional MRI studies in disruptive behaviour disorders.

    Science.gov (United States)

    Bellani, M; Garzitto, M; Brambilla, P

    2012-03-01

    Aggressive or antisocial behaviours with violations of social rules are the main features of disruptive behaviour disorders (DBDs), which are developmental diseases and include conduct disorder and oppositional defiant disorder. In the last decade, several efforts have been made to shed light on the biological underpinnings of DBDs. In this context, the main findings of functional magnetic resonance imaging studies in DBD are reported here. There are indications of neural dysfunctions in response to affective stimuli, especially regarding medial and orbitofrontal prefrontal cortex and connected subcortical structures.

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

    Science.gov (United States)

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

    2016-01-01

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

  5. 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.

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

    Science.gov (United States)

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

    2014-03-13

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

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

    Directory of Open Access Journals (Sweden)

    Yang Bai

    2014-04-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    Niwa, Ryusuke; Niwa, Yuko S

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-04-15

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

  11. Novel nuclear magnetic resonance techniques for studying biological molecules

    Energy Technology Data Exchange (ETDEWEB)

    Laws, David Douglas [Univ. of California, Berkeley, CA (United States)

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (Φ/Ψ) dihedral angles by comparing experimentally determined 13Ca, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.

  12. Biologic Discontinuations Studies: A Systematic Review of Methods

    Science.gov (United States)

    Yoshida, Kazuki; Sung, Yoon-Kyoung; Kavanaugh, Arthur; Bae, Sang-Cheol; Weinblatt, Michael E.; Kishimoto, Mitsumasa; Matsui, Kazuo; Tohma, Shigeto; Solomon, Daniel H.

    2016-01-01

    Objectives We conducted a systematic review to assess the design and “failure definition” in studies of biologic discontinuation in rheumatoid arthritis (RA). Methods We found 403 studies on PubMed, and included 9 published papers and 5 abstracts from scientific meetings. We used a structured extraction form to collect information regarding study design and outcome (failure) definition. Results Three types of studies were found: randomized controlled trials, long-term extension studies of clinical trials, and prospective discontinuation studies. The largest study had 196 subjects in the discontinuation arm. Most studies allowed concomitant use of non-biologic drugs at biologic discontinuation. Heterogeneity was also found in the failure definition. Although all studies used measures of disease activity, the threshold for failure and the time point of assessment differed among studies. Few studies incorporated changing use of non-biologic drugs or glucocorticoids into the failure definition. Conclusions Although many studies have examined the outcome of biologic discontinuation, they have all been relatively small. Typical practice studies from registries may add important information, but will likely need to rely on a broader failure definition. PMID:23723316

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

    Science.gov (United States)

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

    2013-05-01

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

  14. In vitro study of biofilm growth on biologic prosthetics.

    Science.gov (United States)

    Bellows, Charles; Smith, Alison

    2014-01-01

    Biologic prosthetics are increasingly used for the repair of abdominal wall hernia defects but can become infected as a result of peri- or early post-operative bacterial contamination. Data evaluating biofilm formation on biologic prosthetics is lacking. The aim of this study was to investigate the influence of different biologic prosthetics on the growth behavior of two different bacterial species and their ability to form biofilms. Methicillin resistant Staphylococcus aureus (MRSA) or Pseudomrnonas aeruginosa were incubated on disks of two biologic prosthetics-human acellular dermis (ADM), and porcine small intestinal submucosa (SIS). The bacteria were allowed to attach to the prosthetics and propagate into mature biofilms for 24 hours at 370C. Images of biofilms were obtained using confocal microscopy and scanning electron microscopy (SEM). The number of viable cells and the biofilm biomass were quantified by colony forming units (CFUs) and crystal violet staining respectively. Analysis of variance was performed to compare the mean values for the different prosthetics. Each biologic matrix had a distinct surface characteristic. SEM visualized mature biofilms characterized by highly organized multi-cellular structures on surface of both biologic prosthetics. Quantification of bacterial growth over time showed that ADM had the lowest CFUs and biofilm biomass at 24 hours post-inoculation compared to SIS for both bacterial strains. MRSA and P. aeruginosa can form mature biofilms on biologic prosthetics but the relative abundance of the biofilm varies on different prosthetic constructs. Biologic material composition and manufacturing methods may influence bacterial adherence.

  15. Biological - Elwha River Dam Removal Study

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This study examines the ecosystem response of the Elwha River to the removal of the Elwha River dams. We will measure the following attributes of ecosystem response:...

  16. 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.

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Sri Kripa Balakrishnan

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

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

    Science.gov (United States)

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

    2015-07-06

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

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

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  1. How biological soil crusts became recognized as a functional unit: a selective history

    Science.gov (United States)

    Lange, Otto L.; Belnap, Jayne

    2016-01-01

    It is surprising that despite the world-wide distribution and general importance of biological soil crusts (biocrusts), scientific recognition and functional analysis of these communities is a relatively young field of science. In this chapter, we sketch the historical lines that led to the recognition of biocrusts as a community with important ecosystem functions. The idea of biocrusts as a functional ecological community has come from two main scientific branches: botany and soil science. For centuries, botanists have long recognized that multiple organisms colonize the soil surface in the open and often dry areas occurring between vascular plants. Much later, after the initial taxonomic and phyto-sociological descriptions were made, soil scientists and agronomists observed that these surface organisms interacted with soils in ways that changed the soil structure. In the 1970’s, research on these communities as ecological units that played an important functional role in drylands began in earnest, and these studies have continued to this day. Here, we trace the history of these studies from the distant past until 1990, when biocrusts became well-known to scientists and the public.

  2. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  4. 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...

  5. In Vivo Models to Study Chemokine Biology.

    Science.gov (United States)

    Amaral, F A; Boff, D; Teixeira, M M

    2016-01-01

    Chemokines are essential mediators of leukocyte movement in vivo. In vitro assays of leukocyte migration cannot mimic the complex interactions with other cell types and matrix needed for cells to extravasate and migrate into tissues. Therefore, in vivo strategies to study the effects and potential relevance of chemokines for the migration of particular leukocyte subsets are necessary. Here, we describe methods to study the effects and endogenous role of chemokine in mice. Advantages and pitfalls of particular models are discussed and we focus on description in model's joint and pleural cavity inflammation and the effects and relevance of CXCR2 and CCR2 ligands on cell migration.

  6. Dynamical model for biological functions of DNA molecules

    Institute of Scientific and Technical Information of China (English)

    PANGXiao-fengI; YANGYao

    2004-01-01

    We proposed a dynamic model of DNA to study its nonlinear excitation and duplication and transcription in the basis of molecular structure and changes of conformation of DNA under influence of bioenergy.

  7. 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

  8. Experimental genomics: The application of DNA microarrays in cellular and molecular biology studies

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The genome sequence information in combination with DNA microarrays promises to revolutionize the way of cellular and molecular biological research by allowing complex mixtures of RNA and DNA to interrogated in a parallel and quant itative fashion. DNA microarrays can be used to measure levels of gene expressio n for tens of thousands of gene simultaneously and take advantage of all availab le sequence information for experimental design and data interpretation in pursu it of biological understanding. Recent progress in experimental genomics allows DNA microarrays not simply to provide a catalogue of all the genes and informati on about their function, but to understand how the components work together to comprise functioning cells and organisms. This brief review gives a survey of DNA microarrays technology and its applications in genome and gene function analysis, gene expression studies, biological signal and defense system, cell cyclereg ulation, mechanism of transcriptional regulation, proteomics, and the functional ity of food component.

  9. 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.

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

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-feng

    2001-01-01

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

  11. 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.

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

    Science.gov (United States)

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

    2016-10-20

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

  13. Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.

    Science.gov (United States)

    Chen, Z; Lönnberg, T; Lahesmaa, R

    2013-08-01

    Current knowledge of helper T cell differentiation largely relies on data generated from mouse studies. To develop therapeutical strategies combating human diseases, understanding the molecular mechanisms how human naïve T cells differentiate to functionally distinct T helper (Th) subsets as well as studies on human differentiated Th cell subsets is particularly valuable. Systems biology approaches provide a holistic view of the processes of T helper differentiation, enable discovery of new factors and pathways involved and generation of new hypotheses to be tested to improve our understanding of human Th cell differentiation and immune-mediated diseases. Here, we summarize studies where high-throughput systems biology approaches have been exploited to human primary T cells. These studies reveal new factors and signalling pathways influencing T cell differentiation towards distinct subsets, important for immune regulation. Such information provides new insights into T cell biology and into targeting immune system for therapeutic interventions.

  14. Biological Sensors Using DNA Functionalized Multiwalled Carbon Nanotubes

    Science.gov (United States)

    2009-10-01

    out using potassium ferro cyanide as the redox electrolyte. Cyclic voltammetry gave well-defined quasi-reversible voltammetric responses, flat and...performance studies have been carried out using potassium ferro cyanide as the redox electrolyte and DNA-MWNT film electrode and results have been discussed...for the synthesis of MWNT in large quantities using Mischmetal (Bharat Rare Earths Metals, India; composition:- Ce 50%, La 35%, Pr 8 %, Nd 5%, Fe

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

    Directory of Open Access Journals (Sweden)

    A M Botelho

    2012-01-01

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

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

    Science.gov (United States)

    Singh, Arashdeep; Sharma, Savita

    2015-10-14

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

  17. 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.

  18. Biowaste resistojet propellant system biological and functional analysis, task 3

    Science.gov (United States)

    1972-01-01

    Exhaust flow contamination aspects of the biowaste resistojet are studied by evaluating effects of operating pressure, temperature and composition. Biowaste propellant mixtures considered are comprised of: (1) The Sabatier reactor effluent; (2) the effluent of the cabin carbon dioxide molecular sieve; and (3) water and water vapor from various sources. Results show that plume shapes of resistojet thrusters in the 25 to 100 mlb range exhibit greater apex angles for a given density contour than a scaled inviscid jet. Operation at low thrust, low pressure and high temperature accentuates this pluming due to viscous effects in the nozzle flow. Since the biowaste resistojet effluent is traveling at high velocity in the plume away from the aircraft it is found to be a superior method of damping than the ambient venting.

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

    Science.gov (United States)

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

    2013-05-01

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

  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...... 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. Phenolic Phytoalexins in Rice: Biological Functions and Biosynthesis

    Directory of Open Access Journals (Sweden)

    Man-Ho Cho

    2015-12-01

    Full Text Available Phytoalexins are inducible secondary metabolites possessing antimicrobial activity against phytopathogens. Rice produces a wide array of phytoalexins in response to pathogen attacks and environmental stresses. With few exceptions, most phytoalexins identified in rice are diterpenoid compounds. Until very recently, flavonoid sakuranetin was the only known phenolic phytoalexin in rice. However, recent studies have shown that phenylamides are involved in defense against pathogen attacks in rice. Phenylamides are amine-conjugated phenolic acids that are induced by pathogen infections and abiotic stresses including ultra violet (UV radiation in rice. Stress-induced phenylamides, such as N-trans-cinnamoyltryptamine, N-p-coumaroylserotonin and N-cinnamoyltyramine, have been reported to possess antimicrobial activities against rice bacterial and fungal pathogens, an indication of their direct inhibitory roles against invading pathogens. This finding suggests that phenylamides act as phytoalexins in rice and belong to phenolic phytoalexins along with sakuranetin. Phenylamides also have been implicated in cell wall reinforcement for disease resistance and allelopathy of rice. Synthesis of phenolic phytoalexins is stimulated by phytopathogen attacks and abiotic challenges including UV radiation. Accumulating evidence has demonstrated that biosynthetic pathways including the shikimate, phenylpropanoid and arylmonoamine pathways are coordinately activated for phenolic phytoalexin synthesis, and related genes are induced by biotic and abiotic stresses in rice.

  2. Candida albicans mannoprotein influences the biological function of dendritic cells.

    Science.gov (United States)

    Pietrella, Donatella; Bistoni, Giovanni; Corbucci, Cristina; Perito, Stefano; Vecchiarelli, Anna

    2006-04-01

    Cell wall components of fungi involved in induction of host immune response are predominantly proteins and glycoproteins, the latter being mainly mannoproteins (MP). In this study we analyse the interaction of the MP from Candida albicans (MP65) with dendritic cells (DC) and demonstrate that MP65 stimulates DC and induces the release of TNF-alpha, IL-6 and the activation of IL-12 gene, with maximal value 6 h post treatment. MP65 induces DC maturation by increasing costimulatory molecules and decreasing CD14 and FcgammaR molecule expression. The latter effect is partly mediated by toll-like receptor 2 (TLR2) and TLR4, and the MyD88-dependent pathway is involved in the process. MP65 enables DC to activate T cell response, its protein core is essential for induction of T cell activation, while its glycosylated portion primarily promotes cytokine production. The mechanisms involved in induction of protective response against C. albicans could be mediated by the MP65 antigen, suggesting that MP65 may be a suitable candidate vaccine.

  3. 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

  4. 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.

  5. N-Hexyl-4-aminobutyl glycosides for investigating structures and biological functions of carbohydrates.

    Science.gov (United States)

    Suzuki, Katsuhiko; Tobe, Akifumi; Adachi, Shin; Daikoku, Shusaku; Hasegawa, Yasuko; Shioiri, Yuki; Kobayashi, Mariko; Kanie, Osamu

    2009-11-21

    The potential applications of N-hexyl-4-aminobutyl glycosides in the mass spectrometric investigation of glycan structure and in the investigation of glycan functions were studied. Under collision-induced dissociation (CID) conditions, sodiated glycosides carrying N-hexyl-4-aminobutyl groups effectively produced a hemiacetal species (C-ions), which is important in mass-spectrometry-based structural investigation. The usefulness of N-hexyl-4-aminobutyl glycosides in biological analysis was also confirmed by obtaining a binding constant for the binding of dipyrrometheneboron difluoride C3-labeled N-hexyl-4-aminobutyl beta-lactoside with an Erythrina cristagalli lectin, and by visualizing cellular organelles using a more hydrophobic BODIPY-labeled compound.

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

    Science.gov (United States)

    Rouleau, Nicolas; Dotta, Blake T

    2014-01-01

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

  7. Restoration of voice function by using biological feedback in laryngeal and hypopharyngeal carcinoma patients

    Science.gov (United States)

    Choinzonov, E. L.; Balatskaya, L. N.; Chizhevskaya, S. Yu.; Meshcheryakov, R. V.; Kostyuchenko, E. Yu.; Ivanova, T. A.

    2016-08-01

    The aim of the research is to develop and introduce a new technique of post-laryngectomy voice rehabilitation of laryngeal and hypopharyngeal carcinoma patients. The study involves comparing and analyzing 82 cases of voice function restoration by using biological feedback based on mathematical modeling of voice production. The advantage of the modern technology-based method in comparison with the conventional one is proved. Restoration of voice function using biofeedback allows taking into account patient's abilities, adjusting parameters of voice trainings, and controlling their efficiency in real-time mode. The data obtained indicate that the new method contributes to the rapid inclusion of self-regulation mechanisms of the body and results in the overall success rate of voice rehabilitation in totally laryngectomized patients reaching 92%, which reduces the rehabilitation period to 18 days, compared to 86% and 38 days in the control group, respectively. Restoration of disturbed functions after successful treatment is an important task of rehabilitation and is crucial in terms of the quality of cancer patients' lives. To assess life quality of laryngeal cancer patients, the EORTC Quality of Life Core Questionnaire (QLQ-C30), and head and neck module (QLQ-H&N35) were used. The analyzed results proved that the technique of biofeedback voice restoration significantly improves the quality of life of laryngectomized patients. It allows reducing the number of disabled people, restoring patients' ability to work-related activities, and significantly improving social adaptation of these patients.

  8. Psychological and biological foundations of time preference: evidence from a day reconstruction study with biological tracking

    OpenAIRE

    Daly, Michael; Delaney, Liam; Harmon, Colm

    2008-01-01

    This paper considers the relationship between the economic concept of time preference and relevant concepts from psychology and biology. Using novel data from a time diary study conducted in Ireland that combined detailed psychometric testing with medical testing and real-time bio-tracking, we examine the distribution of a number of psychometric measures linked to the economic concept of time preferences and test the extent to which these measures form coherent clusters and the degree to whic...

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

    Science.gov (United States)

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

    2011-07-01

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

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

    Science.gov (United States)

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

    2015-05-01

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

  11. 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...

  12. Organic Composition and Morphology of Sea Spray Aerosols as a Function of Biological Life during IMPACTS

    Science.gov (United States)

    Pham, D.; Moffet, R.; Fraund, M. W.; O'Brien, R.; Laskina, O.; Prather, K. A.; Grassian, V. H.; Beall, C.; Wang, X.; Forestieri, S.; Cappa, C. D.

    2015-12-01

    Aerosols influence climate by directly reflecting or absorbing sunlight, or indirectly by affecting clouds. A major source of aerosols is from oceanic wave breaking. Due to their complexity, the effects of marine aerosol on climate are uncertain. To provide more detailed measurements of the chemical composition of marine aerosols, Scanning Transmission X-Ray Microscopy coupled with Near Edge X-Ray Absorption Fine Structure (SXTM-NEXAFS) was used to give spatially resolved molecular information for carbon and oxygen. Application of STXM/NEXAFS to particles collected during a mesocosm study using a unique wave channel facility to generate aerosols shows that the organic volume fraction of aerosols at the aerodynamic diameter size range of 0.18-0.32 μm are a direct function of the biological activity in the sea water. Aerosol organic volume fraction increased from 0.32 for particles generated from seawater containing low biolife to 0.49 and 0.40 for particles produced during phytoplankton blooms. However, the organic volume fraction of aerosols at the aerodynamic diameter size range of 0.56-1 μm did not change with biological activity. Measurements also show that different types of organics can concentrate into aerosols depending on the enzyme activity expressed at the time. Enhanced spectral signatures for aliphatic hydrocarbons were observed during the first phytoplankton bloom compared to a second phytoplankton bloom occurring directly thereafter. The decreased signature of aliphatic organics in the second phytoplankton bloom was correlated with increased lipase activity from heterobacteria. Organic aggregates having similar morphology also differ in composition from their carbon spectra from the two blooms. For July 17, organic aggregates were much richer in hydrocarbons, which showed a remarkably intense C-H absorbance and a broad C-C absorbance. Organic aggregates observed for July 26-27, did not have the C-H and C-C signatures, but contained more polar

  13. Subject Didactic Studies of Research Training in Biology and Physics.

    Science.gov (United States)

    Lybeck, Leif

    1984-01-01

    The objectives and design of a 3-year study of research training and supervision in biology and physics are discussed. Scientific problems arising from work on the thesis will be a focus for the postgraduate students and their supervisors. Attention will be focused on supervisors' and students' conceptions of science, subject range, research,…

  14. Vitamin D biology and heart failure : Clinical and experimental studies

    NARCIS (Netherlands)

    Meems, Laura

    2015-01-01

    In the last decade, vitamin D biology has been studied more extensively than ever before.. The use of vitamin D supplements is common, and so is determination of plasma vitamin D status. Besides its role in bone homeostasis, vitamin D is thought to be an important player in the development and treat

  15. Considerations for clinical pharmacology studies for biologics in emerging markets.

    Science.gov (United States)

    Damle, Bharat; White, Robert; Wang, Huifen Faye

    2015-03-01

    Registration of innovative biologics in Emerging Markets (EMs) poses many opportunities and challenges. The BRIC-MT countries (Brazil, Russia, India, China, Mexico, and Turkey) that are the fastest growing markets and regulators in these countries have imposed certain requirements, including the need for local clinical studies, for registration of biologics. The regulatory landscape in these countries is rapidly evolving, which necessitates an up-to-date understanding of such requirements. There is growing evidence which suggests that race, after accounting for body weight differences, may not influence the pharmacokinetics of biologics to the same extent that it does for small molecules. Thus, the requirements for clinical pharmacology trials in EMs are driven mainly by regulatory needs set forth by local Ministry of Health. In addition to the clinical Phase I to III studies done in the global program that supports registration in large geographies, countries such as China require local single and multiple dose Phase I studies. Participating in global studies with clinical sites within their country may be sufficient for some markets, while other regulators may be satisfied with a Certificate of Pharmaceutical Product. This paper discusses the current requirements for registration of innovative biologics in key EMs.

  16. Learning Experiences of University Biology Faculty: A Qualitative Pilot Study

    Science.gov (United States)

    Kusch, Jennifer

    2016-01-01

    The study described in this article incorporates qualitative research through in-depth, individual, structured interviews with 12 biology faculty from two Midwestern universities to explore perceptions about how they have learned to teach and how they work to improve their skills.

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

    Science.gov (United States)

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

    2016-04-20

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

  18. Case studies of community college non-science majors: Effects of self-regulatory interventions on biology self-efficacy and biological literacy

    Science.gov (United States)

    Maurer, Matthew J.

    Science literacy has been at the heart of current reform efforts in science education. The focus on developing essential skills needed for individual ability to be literate in science has been at the forefront of most K--12 science curricula. Reform efforts have begun to stretch into the postsecondary arena as well, with an ever increasing dialogue regarding the need for attention to science literacy by college students, especially non-science majors. This study set out to investigate how the use of self-regulatory interventions (specifically, goal setting, concept mapping, and reflective writing) affected student biology self-efficacy and biological literacy. This study employed a qualitative research design, analyzing three case studies. Participants in the study received ten self-regulatory interventions as a set of portfolio assignments. Portfolio work was qualitatively analyzed and coded for self-efficacy, as well as evidence of biological literacy. A biology self-efficacy survey was administered pre- and post- to provide a means of self-efficacy data triangulation. Literacy data was supported via a biological literacy rubric, constructed specifically for this study. Results indicated that mastery experiences were the source of biology self-efficacy. Self-efficacy for specific tasks increased over time, and changes in self-efficacy were corroborated by the self-efficacy survey. Students were found to express biological literacy at nominal, functional, or conceptual levels depending on the specific task. This was supported by data from the biological literacy rubric scores. Final conclusions and implications for the study indicated the need for further research with more samples of students in similar and different contexts. Given the fact that the literature in this area is sparse, the results obtained here have only begun to delve into this area of research. Generalization to other biology courses or contexts outside of the one presented in this study was

  19. Pegylation of fibronectin and its functional domains: Effect on stability and biological activity

    Science.gov (United States)

    Zhang, Chen

    Delayed wound healing in many chronic wounds has been linked to the lack of extracellular matrix (ECM) support and the degradation of fibronectin (FN) by an abnormally high protease level. The ECM provides physical and chemical cues that direct tissue growth and development while FN is a key ECM protein that attracts and binds different molecules and cells. The goal of my study is creating an ECM analogue based on a composite of polyethylene glycol (PEG) hydrogels and FN binding domains and stabilizing FN against proteolytic degradation by conjugating it to PEG. The work presented here shows a two-prong approach by which the problem of ECM degradation and deficiency chronic wound healing can be addressed. The first approach for addressing ECM deficiency is through a scaffold design methodology. The novelty of the scaffold approach is that it uses the cell-binding domains of FN instead of the often-used RGD peptide. I demonstrate that a PEG hydrogel with the cell-binding domain produces a more robust biological response in cells than a PEG hydrogel with the RGD peptide. I also demonstrate that varying different functional domains of FN can be used to controllably stimulate multiple biological responses. The second approach demonstrates a method by which FN, a key ECM protein, is stabilized against proteolytic degradation without perturbing its activity. These studies of creating PEG-FN conjugates are the first of their kind. Collectively, the data that I present in this thesis will lead to novel therapeutic methods for treating chronic wounds.

  20. 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....

  1. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    Science.gov (United States)

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  2. 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.

  3. Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea

    Science.gov (United States)

    Díaz-Pérez, Leopoldo; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D.; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María del Carmen

    2016-01-01

    This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea. PMID:27579575

  4. 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.

  5. Models to Study NK Cell Biology and Possible Clinical Application.

    Science.gov (United States)

    Zamora, Anthony E; Grossenbacher, Steven K; Aguilar, Ethan G; Murphy, William J

    2015-08-03

    Natural killer (NK) cells are large granular lymphocytes of the innate immune system, responsible for direct targeting and killing of both virally infected and transformed cells. NK cells rapidly recognize and respond to abnormal cells in the absence of prior sensitization due to their wide array of germline-encoded inhibitory and activating receptors, which differs from the receptor diversity found in B and T lymphocytes that is due to the use of recombination-activation gene (RAG) enzymes. Although NK cells have traditionally been described as natural killers that provide a first line of defense prior to the induction of adaptive immunity, a more complex view of NK cells is beginning to emerge, indicating they may also function in various immunoregulatory roles and have the capacity to shape adaptive immune responses. With the growing appreciation for the diverse functions of NK cells, and recent technological advancements that allow for a more in-depth understanding of NK cell biology, we can now begin to explore new ways to manipulate NK cells to increase their clinical utility. In this overview unit, we introduce the reader to various aspects of NK cell biology by reviewing topics ranging from NK cell diversity and function, mouse models, and the roles of NK cells in health and disease, to potential clinical applications. © 2015 by John Wiley & Sons, Inc.

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

    Science.gov (United States)

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

    2006-03-01

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

  7. Study of complex molecules of biological interest with synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Prince, K.C. [Elettra-Sincrotrone Trieste, Strada Statale 14–km 163,5 in AREA Science Park, I-34149 Trieste (Italy); Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, in Area Science Park, I-34149 Trieste (Italy); Molecular Model Discovery Laboratory, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Melbourne, Victoria, 3122 (Australia); Bolognesi, P., E-mail: paola.bolognesi@cnr.it [CNR-ISM, Area della Ricerca di Roma 1, Via Salaria Km. 29,300, Monterotondo (Roma) (Italy); Feyer, V. [Elettra-Sincrotrone Trieste, Strada Statale 14–km 163,5 in AREA Science Park, I-34149 Trieste (Italy); Research Center Jülich, Peter Grünberg Institute (PGI-6), 52425 Jülich (Germany); Plekan, O. [Elettra-Sincrotrone Trieste, Strada Statale 14–km 163,5 in AREA Science Park, I-34149 Trieste (Italy); Avaldi, L. [CNR-ISM, Area della Ricerca di Roma 1, Via Salaria Km. 29,300, Monterotondo (Roma) (Italy)

    2015-10-15

    Synchrotron radiation and synchrotron based spectroscopic techniques have found important applications in the study of isolated molecular species of biological interest. In this paper, some examples of spectroscopic and dynamic studies of amino acids and small peptides, nucleobases and pharmaceuticals are reviewed. Opportunities offered by the advent of new radiation sources combined with novel methods for the production of beams of these molecules are also discussed.

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

    DEFF Research Database (Denmark)

    Petersen, Anders; Andersen, Tobias

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

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

    Science.gov (United States)

    Emmeche, C

    2000-01-01

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

  10. Relationship between chemical composition and biological function of Pseudomonas aeruginosa lipopolysaccharide: effect on human neutrophil chemotaxis and oxidative burst

    DEFF Research Database (Denmark)

    Kharazmi, A; Fomsgaard, A; Conrad, R S;

    1991-01-01

    There are conflicting data on the effect of bacterial lipopolysaccharides (LPS) on the function of human neutrophils. The present study was designed to examine the relationship between chemical composition and the modulatory effect of LPS on human neutrophil function. LPS was extracted from five ...... composition of the LPS molecule may play an important role in biological activity of LPS.......There are conflicting data on the effect of bacterial lipopolysaccharides (LPS) on the function of human neutrophils. The present study was designed to examine the relationship between chemical composition and the modulatory effect of LPS on human neutrophil function. LPS was extracted from five...... no effect on neutrophil chemotaxis and a slight effect on chemiluminescence. The major differences in chemical composition of the LPS from these two strains are in the rhamnose and heptose content of the O side chain and in the alanine content of the core region. These data indicate that chemical...

  11. 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.

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

    Science.gov (United States)

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

    2014-12-03

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

  13. Improved normal tissue sparing in head and neck radiotherapy using biological cost function based-IMRT.

    Science.gov (United States)

    Anderson, N; Lawford, C; Khoo, V; Rolfo, M; Joon, D L; Wada, M

    2011-12-01

    Intensity-modulated radiotherapy (IMRT) has reduced the impact of acute and late toxicities associated with head and neck radiotherapy. Treatment planning system (TPS) advances in biological cost function based optimization (BBO) and improved segmentation techniques have increased organ at risk (OAR) sparing compared to conventional dose-based optimization (DBO). A planning study was undertaken to compare OAR avoidance in DBO and BBO treatment planning. Simultaneous integrated boost treatment plans were produced for 10 head and neck patients using both planning systems. Plans were compared for tar get coverage and OAR avoidance. Comparisons were made using the BBO TPS Monte Carlo dose engine to eliminate differences due to inherent algorithms. Target coverage (V95%) was maintained for both solutions. BBO produced lower OAR doses, with statistically significant improvement to left (12.3%, p = 0.005) and right parotid mean dose (16.9%, p = 0.004), larynx V50_Gy (71.0%, p = 0.005), spinal cord (21.9%, p < 0.001) and brain stem dose maximums (31.5%, p = 0.002). This study observed improved OAR avoidance with BBO planning. Further investigations will be undertaken to review any clinical benefit of this improved planned dosimetry.

  14. Soft robotic arm inspired by the octopus: I. From biological functions to artificial requirements.

    Science.gov (United States)

    Margheri, L; Laschi, C; Mazzolai, B

    2012-06-01

    Octopuses are molluscs that belong to the group Cephalopoda. They lack joints and rigid links, and as a result, their arms possess virtually limitless freedom of movement. These flexible appendages exhibit peculiar biomechanical features such as stiffness control, compliance, and high flexibility and dexterity. Studying the capabilities of the octopus arm is a complex task that presents a challenge for both biologists and roboticists, the latter of whom draw inspiration from the octopus in designing novel technologies within soft robotics. With this idea in mind, in this study, we used new, purposively developed methods of analysing the octopus arm in vivo to create new biologically inspired design concepts. Our measurements showed that the octopus arm can elongate by 70% in tandem with a 23% diameter reduction and exhibits an average pulling force of 40 N. The arm also exhibited a 20% mean shortening at a rate of 17.1 mm s(-1) and a longitudinal stiffening rate as high as 2 N (mm s)(-1). Using histology and ultrasounds, we investigated the functional morphology of the internal tissues, including the sinusoidal arrangement of the nerve cord and the local insertion points of the longitudinal and transverse muscle fibres. The resulting information was used to create novel design principles and specifications that can in turn be used in developing a new soft robotic arm.

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

    Science.gov (United States)

    Kalay, Ziya

    2011-08-01

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

  16. Perception of biological motion in schizophrenia and healthy individuals: a behavioral and FMRI study.

    Directory of Open Access Journals (Sweden)

    Jejoong Kim

    Full Text Available BACKGROUND: Anomalous visual perception is a common feature of schizophrenia plausibly associated with impaired social cognition that, in turn, could affect social behavior. Past research suggests impairment in biological motion perception in schizophrenia. Behavioral and functional magnetic resonance imaging (fMRI experiments were conducted to verify the existence of this impairment, to clarify its perceptual basis, and to identify accompanying neural concomitants of those deficits. METHODOLOGY/FINDINGS: In Experiment 1, we measured ability to detect biological motion portrayed by point-light animations embedded within masking noise. Experiment 2 measured discrimination accuracy for pairs of point-light biological motion sequences differing in the degree of perturbation of the kinematics portrayed in those sequences. Experiment 3 measured BOLD signals using event-related fMRI during a biological motion categorization task. Compared to healthy individuals, schizophrenia patients performed significantly worse on both the detection (Experiment 1 and discrimination (Experiment 2 tasks. Consistent with the behavioral results, the fMRI study revealed that healthy individuals exhibited strong activation to biological motion, but not to scrambled motion in the posterior portion of the superior temporal sulcus (STSp. Interestingly, strong STSp activation was also observed for scrambled or partially scrambled motion when the healthy participants perceived it as normal biological motion. On the other hand, STSp activation in schizophrenia patients was not selective to biological or scrambled motion. CONCLUSION: Schizophrenia is accompanied by difficulties discriminating biological from non-biological motion, and associated with those difficulties are altered patterns of neural responses within brain area STSp. The perceptual deficits exhibited by schizophrenia patients may be an exaggerated manifestation of neural events within STSp associated with

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

    Science.gov (United States)

    Chalkidis, Georgios; Nagasaki, Masao; Miyano, Satoru

    2011-01-01

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

  18. 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.

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

    Science.gov (United States)

    Ludwig, David

    2013-01-01

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

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

    Science.gov (United States)

    Podder, Avijit; Jatana, Nidhi; Latha, N

    2014-09-21

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

  1. A Density Functional Theory Study

    KAUST Repository

    Lim, XiaoZhi

    2011-12-11

    Complexes with pincer ligand moieties have garnered much attention in the past few decades. They have been shown to be highly active catalysts in several known transition metal-catalyzed organic reactions as well as some unprecedented organic transformations. At the same time, the use of computational organometallic chemistry to aid in the understanding of the mechanisms in organometallic catalysis for the development of improved catalysts is on the rise. While it was common in earlier studies to reduce computational cost by truncating donor group substituents on complexes such as tertbutyl or isopropyl groups to hydrogen or methyl groups, recent advancements in the processing capabilities of computer clusters and codes have streamlined the time required for calculations. As the full modeling of complexes become increasingly popular, a commonly overlooked aspect, especially in the case of complexes bearing isopropyl substituents, is the conformational analysis of complexes. Isopropyl groups generate a different conformer with each 120 ° rotation (rotamer), and it has been found that each rotamer typically resides in its own potential energy well in density functional theory studies. As a result, it can be challenging to select the most appropriate structure for a theoretical study, as the adjustment of isopropyl substituents from a higher-energy rotamer to the lowest-energy rotamer usually does not occur during structure optimization. In this report, the influence of the arrangement of isopropyl substituents in pincer complexes on calculated complex structure energies as well as a case study on the mechanism of the isomerization of an iPrPCP-Fe complex is covered. It was found that as many as 324 rotamers can be generated for a single complex, as in the case of an iPrPCP-Ni formato complex, with the energy difference between the global minimum and the highest local minimum being as large as 16.5 kcalmol-1. In the isomerization of a iPrPCP-Fe complex, it was found

  2. 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...

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

    OpenAIRE

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

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2014-03-01

    Resilience in executive functioning (EF) is characterized by high EF measured by neuropsychological test performance despite structural brain damage from neurodegenerative conditions. We previously reported single nucleotide polymorphism (SNP) genome-wide association study (GWAS) results for EF resilience. Here, we report gene- and pathway-based analyses of the same resilience phenotype, using an optimal SNP-set (Sequence) Kernel Association Test (SKAT) for gene-based analyses (conservative threshold for genome-wide significance = 0.05/18,123 = 2.8 × 10(-6)) and the gene-set enrichment package GSA-SNP for biological pathway analyses (False discovery rate (FDR) resilience (p = 1.33 × 10(-7)). Genetic pathways involved with dendritic/neuron spine, presynaptic membrane, postsynaptic density, etc., were enriched with association to EF resilience. Although replication of these results is necessary, our findings indicate the potential value of gene- and pathway-based analyses in research on determinants of cognitive resilience.

  7. Structural changes in PVDF fibers due to electrospinning and its effect on biological function.

    Science.gov (United States)

    Damaraju, Sita M; Wu, Siliang; Jaffe, Michael; Arinzeh, Treena Livingston

    2013-08-01

    Polyvinylidine fluoride (PVDF) is being investigated as a potential scaffold for bone tissue engineering because of its proven biocompatibility and piezoelectric property, wherein it can generate electrical activity when mechanically deformed. In this study, PVDF scaffolds were prepared by electrospinning using different voltages (12-30 kV), evaluated for the presence of the piezoelectric β-crystal phase and its effect on biological function. Electrospun PVDF was compared with unprocessed/raw PVDF, films and melt-spun fibers for the presence of the piezoelectric β-phase using differential scanning calorimetry, Fourier transform infrared spectroscopy and x-ray diffraction. The osteogenic differentiation of human mesenchymal stem cells (MSCs) was evaluated on scaffolds electrospun at 12 and 25 kV (PVDF-12 kV and PVDF-25 kV, respectively) and compared to tissue culture polystyrene (TCP). Electrospinning PVDF resulted in the formation of the piezoelectric β-phase with the highest β-phase fraction of 72% for electrospun PVDF at 25 kV. MSCs cultured on both the scaffolds were well attached as indicated by a spread morphology. Cells on PVDF-25 kV scaffolds had the greatest alkaline phosphatase activity and early mineralization by day 10 as compared to TCP and PVDF-12 kV. The results demonstrate the potential for the use of PVDF scaffolds for bone tissue engineering applications.

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

    Science.gov (United States)

    Goncharenko, Anatoliy V; Chang, Yia-Chung

    2009-07-23

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

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

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

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

  10. Studies about space radiation promote new fields in radiation biology.

    Science.gov (United States)

    Ohnishi, Takeo; Takahashi, Akihisa; Ohnishi, Ken

    2002-12-01

    Astronauts are constantly exposed to space radiation of various types of energy with a low dose-rate during long-term stays in space. Therefore, it is important to determine correctly the biological effects of space radiation on human health. Studies about biological the effects at a low dose and a low dose-rate include various aspects of microbeams, bystander effects, radioadaptive responses and hormesis which are important fields in radiation biology. In addition, space radiations contain high linear energy transfer (LET) particles. In particular, neutrons may cause reverse effectiveness at a low dose-rate in comparison to ionizing radiation. We are also interested in p53-centered signal transduction pathways involved in the cell cycle, DNA repair and apoptosis induced by space radiations. We must also study whether the relative biological effectiveness (RBE) of space radiation is affected by microgravity which is another typical component in space. To confirm this, we must prepare centrifuge systems in an International Space Station (ISS). In addition, we must prepare many types of equipment for space experiments in an ISS, because we cannot use conventional equipment from our laboratories. Furthermore, the research for space radiation might give us valuable information about the birth and evolution of life on the Earth. We can also realize the importance of preventing the ozone layer from depletion by the use of exposure equipment to sunlight in an ISS. For these reasons, we desire to educate space researchers of the next generation based on the consideration of the preservation of the Earth from research about space radiation.

  11. Study on the biological characteristics of Homalotglus flaminus

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Homalotglus flaminus (Dalman) is an important natural enemy of the Chilocorus kuwanae. Its biological characteristic, life history, the action style on hosts were studied at Hongqi Forest Farm, Daqing City, Heilongjiang Province from June 1998 to October 2000, in order to control H. flaminus and raise the control ability of Chilocorus kuwanae to Quadraspidiotus gigas pest. The observed results indicated that H. flaminus has two generation one year in study area, the pupating span is 12.7 d, life span of females and males is 17.6 d and 10.8 d respectively, egg span is 10 d, and the sex ratio of females to males is 1:3.

  12. Algebraic Systems Biology: A Case Study for the Wnt Pathway.

    Science.gov (United States)

    Gross, Elizabeth; Harrington, Heather A; Rosen, Zvi; Sturmfels, Bernd

    2016-01-01

    Steady-state analysis of dynamical systems for biological networks gives rise to algebraic varieties in high-dimensional spaces whose study is of interest in their own right. We demonstrate this for the shuttle model of the Wnt signaling pathway. Here, the variety is described by a polynomial system in 19 unknowns and 36 parameters. It has degree 9 over the parameter space. This case study explores multistationarity, model comparison, dynamics within regions of the state space, identifiability, and parameter estimation, from a geometric point of view. We employ current methods from computational algebraic geometry, polyhedral geometry, and combinatorics.

  13. Morphological and Biological Study of Sanguisorba Officinalis Germination

    Directory of Open Access Journals (Sweden)

    Alexandra Sh. Dodonova

    2013-01-01

    Full Text Available This work deals with the study of influence of terms and storage conditions on Sanguisorba officinalis seed material quality, put into various containers (paper, plastic, fabric, glass, in the different temperature conditions, light and dark grown. The morphology, biology of Sanguisorba officinalis seeds was described and experiments on cryopreservation were made. Basing on the study, we recommend to store Sanguisorba officinalis seed material within 3 months at a temperature of +4˚С in glass container, use plastic container for cryopreservation and to defreeze seeds by double boiling.

  14. Caenorhabditis elegans - A model system for space biology studies

    Science.gov (United States)

    Johnson, Thomas E.; Nelson, Gregory A.

    1991-01-01

    The utility of the nematode Caenorhabditis elegans in studies spanning aspects of development, aging, and radiobiology is reviewed. These topics are interrelated via cellular and DNA repair processes especially in the context of oxidative stress and free-radical metabolism. The relevance of these research topics to problems in space biology is discussed and properties of the space environment are outlined. Exposure to the space-flight environment can induce rapid changes in living systems that are similar to changes occurring during aging; manipulation of these environmental parameters may represent an experimental strategy for studies of development and senescence. The current and future opportunities for such space-flight experimentation are presented.

  15. Biological conversion of synthesis gas. Topical report: Bioreactor studies

    Energy Technology Data Exchange (ETDEWEB)

    Basu, R.; Klasson, K.T.; Clausen, E.C.; Gaddy, J.L.

    1993-09-01

    The purpose of the proposed research is to develop a technically and economically feasible process for biologically producing H{sub 2} from synthesis gas while, at the same time, removing harmful sulfur gas compounds. Six major tasks are being studied: culture development, where the best cultures are selected and conditions optimized for simultaneous hydrogen production and sulfur gas removal; mass transfer and kinetic studies in which equations necessary for process design are developed; bioreactor design studies, where the cultures chosen in Task 1 are utilized in continuous reaction vessels to demonstrate process feasibility and define operating conditions; evaluation of biological synthesis gas conversion under limiting conditions in preparation for industrial demonstration studies; process scale-up where laboratory data are scaled to larger-size units in preparation for process demonstration in a pilot-scale unit; and economic evaluation, where process simulations are used to project process economics and identify high cost areas during sensitivity analyses. The purpose of this report is to present results from bioreactor studies involving H{sub 2} production by water gas shift and H{sub 2}S removal to produce elemental sulfur. Many of the results for H{sub 2} production by Rhodospirillum rubrum have been presented during earlier contracts. Thus, this report concentrates mainly on H{sub 2}S conversion to elemental sulfur by R. rubrum.

  16. Adult Learning Open University Determinants study (ALOUD): Biological lifestyle factors associated with study success

    NARCIS (Netherlands)

    Gijselaers, Jérôme; De Groot, Renate; Kirschner, Paul A.

    2012-01-01

    Gijselaers, H. J. M., De Groot, R. H. M., & Kirschner, P. A. (2012, 7 November). Adult Learning Open University Determinants study (ALOUD): Biological lifestyle factors associated with study success. Poster presentation at the International ICO Fall School, Girona, Spain.

  17. Computational Biology Study of S100 Family with Suggestions for Crystallization

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The S100 family is a class of calcium-regulated proteins with EF-hand. They are widely distributed and are implicated in diverse intracellular and extracellular physiological processes. A study of the S100 family using computational biology methods such as multiple sequence alignment, structural alignment and the construction of an evolutionary tree will promote understanding of S100 protein structures and their function, and could provide suggestions for crystallization.

  18. 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.

  19. Biological oscillations for learning walking coordination: dynamic recurrent neural network functionally models physiological central pattern generator.

    Science.gov (United States)

    Hoellinger, Thomas; Petieau, Mathieu; Duvinage, Matthieu; Castermans, Thierry; Seetharaman, Karthik; Cebolla, Ana-Maria; Bengoetxea, Ana; Ivanenko, Yuri; Dan, Bernard; Cheron, Guy

    2013-01-01

    The existence of dedicated neuronal modules such as those organized in the cerebral cortex, thalamus, basal ganglia, cerebellum, or spinal cord raises the question of how these functional modules are coordinated for appropriate motor behavior. Study of human locomotion offers an interesting field for addressing this central question. The coordination of the elevation of the 3 leg segments under a planar covariation rule (Borghese et al., 1996) was recently modeled (Barliya et al., 2009) by phase-adjusted simple oscillators shedding new light on the understanding of the central pattern generator (CPG) processing relevant oscillation signals. We describe the use of a dynamic recurrent neural network (DRNN) mimicking the natural oscillatory behavior of human locomotion for reproducing the planar covariation rule in both legs at different walking speeds. Neural network learning was based on sinusoid signals integrating frequency and amplitude features of the first three harmonics of the sagittal elevation angles of the thigh, shank, and foot of each lower limb. We verified the biological plausibility of the neural networks. Best results were obtained with oscillations extracted from the first three harmonics in comparison to oscillations outside the harmonic frequency peaks. Physiological replication steadily increased with the number of neuronal units from 1 to 80, where similarity index reached 0.99. Analysis of synaptic weighting showed that the proportion of inhibitory connections consistently increased with the number of neuronal units in the DRNN. This emerging property in the artificial neural networks resonates with recent advances in neurophysiology of inhibitory neurons that are involved in central nervous system oscillatory activities. The main message of this study is that this type of DRNN may offer a useful model of physiological central pattern generator for gaining insights in basic research and developing clinical applications.

  20. Biological oscillations for learning walking coordination: dynamic recurrent neural network functionally models physiological central pattern generator

    Directory of Open Access Journals (Sweden)

    Thomas eHoellinger

    2013-05-01

    Full Text Available The existence of dedicated neuronal modules such as those organized in the cerebral cortex, thalamus, basal ganglia, cerebellum or spinal cord raises the question of how these functional modules are coordinated for appropriate motor behavior. Study of human locomotion offers an interesting field for addressing this central question. The coordination of the elevation of the 3 leg segments under a planar covariation rule (Borghese et al., 1996 was recently modeled (Barliya et al., 2009 by phase-adjusted simple oscillators shedding new light on the understanding of the central pattern generator processing relevant oscillation signals. We describe the use of a dynamic recurrent neural network (DRNN mimicking the natural oscillatory behavior of human locomotion for reproducing the planar covariation rule in both legs at different walking speeds. Neural network learning was based on sinusoid signals integrating frequency and amplitude features of the first three harmonics of the sagittal elevation angles of the thigh, shank and foot of each lower limb. We verified the biological plausibility of the neural networks. Best results were obtained with oscillations extracted from the first three harmonics in comparison to oscillations outside the harmonic frequency peaks. Physiological replication steadily increased with the number of neuronal units from 1 to 80, where similarity index reached 0.99. Analysis of synaptic weighting showed that the proportion of inhibitory connections consistently increased with the number of neuronal units in the DRNN. This emerging property in the artificial neural networks resonates with recent advances in neurophysiology of inhibitory neurons that are involved in central nervous system oscillatory activities. The main message of this study is that this type of DRNN may offer a useful model of physiological central pattern generator for gaining insights in basic research and developing clinical applications.

  1. Biological function of hpsh4590 localized in the plasticity zone of Helicobacter pylori.

    Science.gov (United States)

    Gu, Yu-feng; Li, Yu; Song, Yu; Chang, Xin; Qu, Ye-Min; Wang, Ming-Yi; Gao, Xiao-Zhong

    2016-04-01

    The aim of this study was to determine the biological function of hpsh4590 in Helicobacter pylori. After Hpsh4590 was expressed using a prokaryotic expression system, the cytotoxic effects and IL-8 production of Hpsh4590 were analyzed by co-culturing with GES-1 cells. Meanwhile, the antibody of rHpsh4590, produced by immunizing rabbit, was used for localization and protein interaction studies. Hpsh4590 fusion protein was expressed successfully in Escherichia coli Rosetta (DE3), and the polyclonal antibody was produced at high titers. The MTT assay showed that the inhibition ratio of GES-1 cells cultured with 0.1 μg/mL rHpsh4590 (3.02% ± 0.02%) was significantly lower than that of 20 μg/mL rHpsh4590 (57.57% ± 0.03%, p < 0.01), while DAPI staining showed the cytotoxic effects of rHpsh4590 for GES-1 cells. The up-regulation of cleaved caspase-3 and cleaved PARP was observed after GES-1 cells co-cultured with rHpsh4590 by Western blot. Co-culturing of GES-1 cells with rHpsh0459 (20 μg/mL) led to significant production of IL-8 at 12 h(1097.74 ± 212.37 pg/mL) and 24 h (1379.55 ± 209.58 pg/mL) then at 6 h(134.68 ± 14.64 pg/mL, p < 0.01). These observations suggest that the cytotoxicity of Hpsh4590 occurred in a concentration dependent manner, which is related with IL-8 secretion from gastric mucosal epithelial cells. Hpsh4590 was found localized in the membrane and the periplasm of H. pylori, interacted with zinc finger protein and methionine ABC transporter ATP-binding protein, and potentially regulates DNA uptake or transfer.

  2. 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

  3. Use of a new glass microfibre histamine release method to study the modulation of the host response in human schistosomiasis mansoni. Individuals with different degrees of exposure to the disease show differing antibody biological function

    DEFF Research Database (Denmark)

    Satti, M.Z.; Ebbesen, F.; Vennervald, B.;

    1996-01-01

    A new glass microfibre histamine release method was used to study the modulation of the host response in human schistosomiasis mansoni to improve our understanding of the role of basophils in the development of immunity in schistosomiasis mansoni. The histamine release from umbilical cord blood b...... basophils sensitized with sera from Sudanese individuals infected with Schistosoma mansoni was measured. Schistosomiasis sera (n=113) were able to passively sensitize basophils and induce a positive histamine release in response to whole worm homogenate (WWH)(chi(2)=40.5, P......A new glass microfibre histamine release method was used to study the modulation of the host response in human schistosomiasis mansoni to improve our understanding of the role of basophils in the development of immunity in schistosomiasis mansoni. The histamine release from umbilical cord blood...

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

    Science.gov (United States)

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

    2011-01-01

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

  5. Pig Brain Mitochondria as a Biological Model for Study of Mitochondrial Respiration.

    Science.gov (United States)

    Fišar, Z; Hroudová, J

    2016-01-01

    Oxidative phosphorylation is a key process of intracellular energy transfer by which mitochondria produce ATP. Isolated mitochondria serve as a biological model for understanding the mitochondrial respiration control, effects of various biologically active substances, and pathophysiology of mitochondrial diseases. The aim of our study was to evaluate pig brain mitochondria as a proper biological model for investigation of activity of the mitochondrial electron transport chain. Oxygen consumption rates of isolated pig brain mitochondria were measured using high-resolution respirometry. Mitochondrial respiration of crude mitochondrial fraction, mitochondria purified in sucrose gradient, and mitochondria purified in Percoll gradient were assayed as a function of storage time. Oxygen flux and various mitochondrial respiratory control ratios were not changed within two days of mitochondria storage on ice. Leak respiration was found higher and Complex I-linked respiration lower in purified mitochondria compared to the crude mitochondrial fraction. Damage to both outer and inner mitochondrial membrane caused by the isolation procedure was the greatest after purification in a sucrose gradient. We confirmed that pig brain mitochondria can serve as a biological model for investigation of mitochondrial respiration. The advantage of this biological model is the stability of respiratory parameters for more than 48 h and the possibility to isolate large amounts of mitochondria from specific brain areas without the need to kill laboratory animals. We suggest the use of high-resolution respirometry of pig brain mitochondria for research of the neuroprotective effects and/or mitochondrial toxicity of new medical drugs.

  6. 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 Tfat globules during processing and digestion.

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

    Science.gov (United States)

    Pandit, Sunil D; Li, King C P

    2004-04-01

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

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

    Science.gov (United States)

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

    2015-02-01

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

  9. 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.

  10. 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.

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

    Science.gov (United States)

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

    2014-05-05

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

  12. Density functional theory study on the molecular structure of loganin

    OpenAIRE

    Pandey, Anoop Kumar; Siddiqui, Shamoon Ahmad; Dwivedi, Apoorva; Raj, Kanwal; Misra, Neeraj

    2011-01-01

    The computational Quantum Chemistry (QC) has been used for different types of problems, for example: structural biology, surface phenomena and liquid phase. In this paper we have employed the density functional method for the study of molecular structure of loganin. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by B3LYP/6-311G (d, p) method and basis set combinations. It was found that the optimized parameters obtained by the DFT/B3LYP met...

  13. Applying functional genomics research to the study of pig reproduction.

    Science.gov (United States)

    Pomp, D; Caetano, A R; Bertani, G R; Gladney, C D; Johnson, R K

    2001-01-01

    Functional genomics is an experimental approach that incorporates genome-wide or system-wide experimentation, expanding the scope of biological investigation from studying single genes to studying potentially all genes at once in a systematic manner. This technology is highly appealing because of its high throughput and relatively low cost. Furthermore, analysis of gene expression using microarrays is likely to be more biologically relevant than the conventional paradigm of reductionism, because it has the potential to uncover new biological connections between genes and biochemical pathways. However, functional genomics is still in its infancy, especially with regard to the study of pig reproduction. Currently, efforts are centred on developing the necessary resources to enable high throughput evaluation and comparison of gene expression. However, it is clear that in the near future functional genomics will be applied on a large scale to study the biology and physiology of reproduction in pigs, and to understand better the complex nature of genetic control over polygenic characteristics, such as ovulation rate and litter size. We can look forward to generating a significant amount of new data on differences in gene expression between genotypes, treatments, or at various temporal and spatial coordinates within a variety of reproductively relevant systems. Along with this capability will be the challenge of collating, analysing and interpreting datasets that are orders of magnitude more extensive and complex than those currently used. Furthermore, integration of functional genomics with traditional genetic approaches and with detailed analysis of the proteome and relevant whole animal phenotypes will be required to make full use of this powerful new experimental paradigm as a beneficial research tool.

  14. 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

  15. 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

  16. Electron crystallography for structural and functional studies of membrane proteins.

    Science.gov (United States)

    Fujiyoshi, Yoshinori

    2011-01-01

    Membrane proteins are important research targets for basic biological sciences and drug design, but studies of their structure and function are considered difficult to perform. Studies of membrane structures have been greatly facilitated by technological and instrumental advancements in electron microscopy together with methodological advancements in biology. Electron crystallography is especially useful in studying the structure and function of membrane proteins. Electron crystallography is now an established method of analyzing the structures of membrane proteins in lipid bilayers, which resembles their natural biological environment. To better understand the neural system function from a structural point of view, we developed the cryo-electron microscope with a helium-cooled specimen stage, which allows for analysis of the structures of membrane proteins at a resolution higher than 3 Å. This review introduces recent instrumental advances in cryo-electron microscopy and presents some examples of structure analyses of membrane proteins, such as bacteriorhodopsin, water channels and gap junction channels. This review has two objectives: first, to provide a personal historical background to describe how we came to develop the cryo-electron microscope and second, to discuss some of the technology required for the structural analysis of membrane proteins based on cryo-electron microscopy.

  17. Pilot study of sexual dysfunction in patients with psoriasis: Influence of biologic therapy

    Directory of Open Access Journals (Sweden)

    Ricardo Ruiz-Villaverde

    2011-01-01

    Full Text Available Background: Psoriasis is a chronic skin disease that affects 1 to 3% of the population in most industrialized countries. It is commonly associated with a variety of psychological problems including low self-esteem, depression, suicidal thoughts, and sexual dysfunction. Materials and Methods : We have performed a pilot study in which we have tried to assess the impact on sexual dysfunction in patients with psoriasis who have started treatment with biological therapy using validated indexes in Spanish: International Index of Erectile Function for men and female sexual function index in women. Results : Considering the men and women from our study, an improvement in FSFI by an average of 9.5 and 6.3 points is observed, respectively. Conclusion: We considered our series as a first step for a more detailed approach to the study of sexual function in patients with psoriasis.

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

    Science.gov (United States)

    Price, S A; Schmitz, L

    2016-04-05

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

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

    Directory of Open Access Journals (Sweden)

    Baumann Ute

    2005-11-01

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

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

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

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

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

    Science.gov (United States)

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

    2011-04-01

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

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

    Science.gov (United States)

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

    2014-12-16

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

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

    Science.gov (United States)

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

    2005-12-01

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

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

    Science.gov (United States)

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

    2001-01-01

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

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

    Science.gov (United States)

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

    2011-04-01

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

  6. A snapshot of functional genetic studies in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Yun Kang

    2016-08-01

    Full Text Available In the current context of food security, increase of plant protein production in a sustainable manner represents one of the major challenges of agronomic research, which could be partially resolved by increased cultivation of legume crops. Medicago truncatula is now a well-established model for legume genomic and genetic studies. With the establishment of genomics tools and mutant populations in M. truncatula, it has become an important resource to answer some of the basic biological questions related to plant development and stress tolerance. This review has an objective to overview a decade of genetic studies in this model plant from generation of mutant populations to nowadays. To date, the three biological fields, which have been extensively studied in M. truncatula, are the symbiotic nitrogen fixation, the seed development, and the abiotic stress tolerance, due to their significant agronomic impacts. In this review, we summarize functional genetic studies related to these three major biological fields. We integrated analyses of a nearly exhaustive list of genes into their biological contexts in order to provide an overview of the forefront research advances in this important legume model plant.

  7. MODERN TECHNOLOGIES AND APPROACHES TO APOPTOSIS STUDIES IN EXPERIMENTAL BIOLOGY

    Directory of Open Access Journals (Sweden)

    I. V. Kudriavtsev

    2012-01-01

    Full Text Available Abstract. This review is focused on analysis of currently used flow cytometric methods designed foridentifying apoptotic cells in various invertebrate and vertebrate species. Apoptosis can be characterized by stage-specific morphological and biochemical changes that are typical to all kinds of eukaryotic cells. In this article, we consider different techniques of apoptosis detection based on assessment of cellular morphology and plasma membrane alterations, activation of intracellular enzymes and components of a caspase cascade, as well as DNA fragmentation and failure of mitochondrial transmembrane potential, as assessed in various animal groups. Apoptosis recognized as a key mechanism aiming at maintenance of cellular homeostasis in multicellular organisms, and such investigations represent a necessary component of fundamental and applied studies in diverse fields of experimental biology and immunology. A broad spectrum of apoptosis markers isused, and the preference is given to optimal approaches, as determined by experimental tasks, and technical opportunities of the laboratory.

  8. Using Femtosecond Laser Subcellular Surgery as a Tool to Study Cell Biology

    Energy Technology Data Exchange (ETDEWEB)

    Shen, N; Colvin, M E; Huser, T

    2007-02-27

    Research on cellular function and regulation would be greatly advanced by new instrumentation using methods to alter cellular processes with spatial discrimination on the nanometer-scale. We present a novel technique for targeting submicrometer sized organelles or other biologically important regions in living cells using femtosecond laser pulses. By tightly focusing these pulses beneath the cell membrane, we can vaporize cellular material inside the cell through nonlinear optical processes. This technique enables non-invasive manipulation of the physical structure of a cell with sub-micrometer resolution. We propose to study the role mitochondria play in cell proliferation and apoptosis. Our technique provides a unique tool for the study of cell biology.

  9. [The importance of model organisms to study cilia and flagella biology].

    Science.gov (United States)

    Vincensini, Laetitia; Blisnick, Thierry; Bastin, Philippe

    2011-01-01

    Cilia and flagella are ubiquitous organelles that protrude from the surfaces of many cells, and whose architecture is highly conserved from protists to humans. These complex organelles, composed of over 500 proteins, can be either immotile or motile. They are involved in a myriad of biological processes, including sensing (non-motile cilia) and/or cell motility or movement of extracellular fluids (motile cilia). The ever-expanding list of human diseases linked to defective cilia illustrates the functional importance of cilia and flagella. These ciliopathies are characterised by an impressive diversity of symptoms and an often complex genetic etiology. A precise knowledge of cilia and flagella biology is thus critical to better understand these pathologies. However, multi-ciliated cells are terminally differentiated and difficult to manipulate, and a primary cilium is assembled only when the cell exits from the cell cycle. In this context the use of model organisms, that relies on the high degree of structural but also of molecular conservation of these organelles across evolution, is instrumental to decipher the many facets of cilia and flagella biology. In this review, we highlight the specific strengths of the main model organisms to investigate the molecular composition, mode of assembly, sensing and motility mechanisms and functions of cilia and flagella. Pioneering studies carried out in the green alga Chlamydomonas established the link between cilia and several genetic diseases. Moreover, multicellular organisms such as mouse, zebrafish, Xenopus, C. elegans or Drosophila, and protists like Paramecium, Tetrahymena and Trypanosoma or Leishmania each bring specific advantages to the study of cilium biology. For example, the function of genes involved in primary ciliary dyskinesia (due to defects in ciliary motility) can be efficiently assessed in trypanosomes.

  10. Extraction, characterization and biological studies of phytochemicals from Mammea suriga

    Directory of Open Access Journals (Sweden)

    Mahesha M. Poojary

    2015-06-01

    Full Text Available The present work involves extraction of phytochemicals from the root bark of a well-known Indian traditional medicinal plant, viz. Mammea suriga, with various solvents and evaluation of their in vitro antimicrobial and antioxidant activities using standard methods. The phytochemical analysis indicates the presence of some interesting secondary metabolites like flavonoids, cardiac glycosides, alkaloids, saponins and tannins in the extracts. Also, the solvent extracts displayed promising antimicrobial activity against Staphylococcus aureus, Bacillus subtilis and Cryptococcus neoformans with inhibition zone in a range of 20–33 mm. Further, results of their antioxidant screening revealed that aqueous extract (with IC50 values of 111.51±1.03 and 31.05±0.92 μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively and ethanolic extract (with IC50 values of 128.00±1.01 and 33.25±0.89 μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively were better antioxidants than standard ascorbic acid. Interestingly, FT-IR analysis of each extract established the presence of various biologically active functional groups in it.

  11. Extraction, characterization and biological studies of phytochemicals from Mammea suriga

    Institute of Scientific and Technical Information of China (English)

    Mahesha M. Poojary; Kanivebagilu A.Vishnumurthy; Airody Vasudeva Adhikari

    2015-01-01

    The present work involves extraction of phytochemicals from the root bark of a well-known Indian traditional medicinal plant, viz. Mammea suriga, with various solvents and evaluation of their in vitro antimicrobial and antioxidant activities using standard methods. The phytochemical analysis indicates the presence of some interesting secondary metabolites like flavonoids, cardiac glycosides, alkaloids, saponins and tannins in the extracts. Also, the solvent extracts displayed promising anti-microbial activity against Staphylococcus aureus, Bacillus subtilis and Cryptococcus neoformans with inhibition zone in a range of 20–33 mm. Further, results of their antioxidant screening revealed that aqueous extract (with IC50 values of 111.51±1.03 and 31.05±0.92μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively) and ethanolic extract (with IC50 values of 128.00±1.01 and 33.25±0.89μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively) were better antioxidants than standard ascorbic acid. Interestingly, FT-IR analysis of each extract established the presence of various biologically active functional groups in it.

  12. Biological control of harmful algal blooms: A modelling study

    Science.gov (United States)

    Solé, Jordi; Estrada, Marta; Garcia-Ladona, Emilio

    2006-07-01

    A multispecies dynamic simulation model (ERSEM) was used to examine the influence of allelopathic and trophic interactions causing feeding avoidance by predators, on the formation of harmful algal blooms, under environmental scenarios typical of a Mediterranean harbour (Barcelona). The biological state variables of the model included four functional groups of phytoplankton (diatoms, toxic and non-toxic flagellates and picophytoplankton), heterotrophic flagellates, micro- and mesozooplankton and bacteria. The physical-chemical forcing (irradiance, temperature and major nutrient concentrations) was based on an actual series of measurements taken along a year cycle in the Barcelona harbour. In order to evaluate potential effects of advection, some runs were repeated after introducing a biomass loss term. Numerical simulations showed that allelopathic effects of a toxic alga on a non-toxic but otherwise similar competitor did not have appreciable influence on the dynamics of the system. However, induction of avoidance of the toxic alga by predators, which resulted on increased predation pressure on other algal groups had a significant effect on the development of algal and predator populations. The presence of advection overrided the effect of these interactions and only allowed organisms with sufficiently high potential growth rates to thrive.

  13. Synthesis, characterization and functionalization of silicon nanoparticle based hybrid nanomaterials for photovoltaic and biological applications

    Science.gov (United States)

    Xu, Zejing

    Silicon nanoparticles are attractive candidates for biological, photovoltaic and energy storage applications due to their size dependent optoelectronic properties. These include tunable light emission, high brightness, and stability against photo-bleaching relative to organic dyes (see Chapter 1). The preparation and characterization of silicon nanoparticle based hybrid nanomaterials and their relevance to photovoltaic and biological applications are described. The surface-passivated silicon nanoparticles were produced in one step from the reactive high-energy ball milling (RHEBM) of silicon wafers with various organic ligands. The surface structure and optical properties of the passivated silicon nanoparticles were systematically characterized. Fast approaches for purifying and at the same time size separating the silicon nanoparticles using a gravity GPC column were developed. The hydrodynamic diameter and size distribution of these size-separated silicon nanoparticles were determined using GPC and Diffusion Ordered NMR Spectroscopy (DOSY) as fast, reliable alternative approaches to TEM. Water soluble silicon nanoparticles were synthesized by grafting PEG polymers onto functionalized silicon nanoparticles with distal alkyne or azide moieties. The surface-functionalized silicon nanoparticles were produced from the reactive high-energy ball milling (RHEBM) of silicon wafers with a mixture of either 5-chloro-1-pentyne in 1-pentyne or 1,7 octadiyne in 1-hexyne to afford air and water stable chloroalkyl or alkynyl terminated nanoparticles, respectively. Nanoparticles with the ω-chloroalkyl substituents were easily converted to ω-azidoalkyl groups through the reaction of the silicon nanoparticles with sodium azide in DMF. The azido terminated nanoparticles were then grafted with monoalkynyl-PEG polymers using a copper catalyzed alkyne-azide cycloaddition (CuAAC) reaction to afford core-shell silicon nanoparticles with a covalently attached PEG shell. Covalently

  14. Systems biology studies of Aspergilli - from sequence to science

    OpenAIRE

    Andersen, Mikael Rørdam; Nielsen, Jens; Nielsen, Michael Lynge

    2008-01-01

    The recent dawn of the new biological mindset called systems biology has put forth a new way of analyzing and understanding biology. Carried by the notion that no element of a cell is an island, systems biology takes a holistic approach, and attempts to understand life as systems that have co-evolved and not as a haphazardly compiled list of parts. This has been made possible by the socalled genomic revolution — the sequencing of the genomic DNA of a rapidly increasing number of organisms — a...

  15. Bioorthogonal chemistry:a covalent strategy for the study of biological systems

    Institute of Scientific and Technical Information of China (English)

    LIM; Reyna; K.V.

    2010-01-01

    The development of genetically encoded,wavelength-tunable fluorescent proteins has provided a powerful imaging tool to the study of protein dynamics and functions in cellular and organismal biology.However,many biological functions are not directly encoded in the protein primary sequence,e.g.,dynamic regulation afforded by protein posttranslational modifications such as phosphorylation.To meet this challenge,an emerging field of bioorthogonal chemistry has promised to offer a versatile strategy to selectively label a biomolecule of interest and track their dynamic regulations in its native habitat.This strategy has been successfully applied to the studies of all classes of biomolecules in living systems,including proteins,nucleic acids,carbohydrates,and lipids.Whereas the incorporation of a bioorthogonal reporter site-selectively into a biomolecule through either genetic or metabolic approaches has been well established,the development of bioorthogonal reactions that allow fast ligation of exogenous chemical probes with the bioorthogonal reporter in living systems remains in its early stage.Here,we review the recent development of bioorthogonal reactions and their applications in various biological systems,with a detailed discussion about our own work―the development of the tetrazole-based,photoinducible 1,3-dipolar cycloaddition reaction.

  16. Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).

    Science.gov (United States)

    Warshel, Arieh

    2014-09-15

    A detailed understanding of the action of biological molecules is a pre-requisite for rational advances in health sciences and related fields. Here, the challenge is to move from available structural information to a clear understanding of the underlying function of the system. In light of the complexity of macromolecular complexes, it is essential to use computer simulations to describe how the molecular forces are related to a given function. However, using a full and reliable quantum mechanical representation of large molecular systems has been practically impossible. The solution to this (and related) problems has emerged from the realization that large systems can be spatially divided into a region where the quantum mechanical description is essential (e.g. a region where bonds are being broken), with the remainder of the system being represented on a simpler level by empirical force fields. This idea has been particularly effective in the development of the combined quantum mechanics/molecular mechanics (QM/MM) models. Here, the coupling between the electrostatic effects of the quantum and classical subsystems has been a key to the advances in describing the functions of enzymes and other biological molecules. The same idea of representing complex systems in different resolutions in both time and length scales has been found to be very useful in modeling the action of complex systems. In such cases, starting with coarse grained (CG) representations that were originally found to be very useful in simulating protein folding, and augmenting them with a focus on electrostatic energies, has led to models that are particularly effective in probing the action of molecular machines. The same multiscale idea is likely to play a major role in modeling of even more complex systems, including cells and collections of cells.

  17. Recombinant human thrombopoietin: basic biology and evaluation of clinical studies.

    Science.gov (United States)

    Kuter, David J; Begley, C Glenn

    2002-11-15

    Thrombocytopenia is a common medical problem for which the main treatment is platelet transfusion. Given the increasing use of platelets and the declining donor population, identification of a safe and effective platelet growth factor could improve the management of thrombocytopenia. Thrombopoietin (TPO), the c-Mpl ligand, is the primary physiologic regulator of megakaryocyte and platelet development. Since the purification of TPO in 1994, 2 recombinant forms of the c-Mpl ligand--recombinant human thrombopoietin (rhTPO) and pegylated recombinant human megakaryocyte growth and development factor (PEG-rHuMGDF)--have undergone extensive clinical investigation. Both have been shown to be potent stimulators of megakaryocyte growth and platelet production and are biologically active in reducing the thrombocytopenia of nonmyeloablative chemotherapy. However, neither TPO has demonstrated benefit in stem cell transplantation or leukemia chemotherapy. Other clinical studies have investigated the use of TPO in treating chronic nonchemotherapy-induced thrombocytopenia associated with myelodysplastic syndromes, idiopathic thrombocytopenic purpura, thrombocytopenia due to human immunodeficiency virus, and liver disease. Based solely on animal studies, TPO may be effective in reducing surgical thrombocytopenia and bleeding, ex vivo expansion of pluripotent stem cells, and as a radioprotectant. Ongoing and future studies will help define the clinical role of recombinant TPO and TPO mimetics in the treatment of chemotherapy- and nonchemotherapy-induced thrombocytopenia.

  18. Using CAVE technology for functional genomics studies.

    Science.gov (United States)

    Sensen, Christoph W

    2002-01-01

    We have established the first Java 3D-enabled CAVE (CAVE automated virtual environment). The Java application programming interface allows the complete separation of the program development from the program execution, opening new application domains for the CAVE technology. Programs can be developed on any Java-enabled computer platform, including Windows, Macintosh, and Linux workstations, and executed in the CAVE without modification. The introduction of Java, one of the major programming environments for bioinformatics, into the CAVE environment allows the rapid development applications for genome research, especially for the analysis of the spatial and temporal data that are being produced by functional genomics experiments. The CAVE technology will play a major role in the modeling of biological systems that is necessary to understand how these systems are organized and how they function.

  19. The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions.

    Science.gov (United States)

    Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

    2011-03-04

    Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion.

  20. 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.

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

    Science.gov (United States)

    Hoehndorf, Robert; Schofield, Paul N; Gkoutos, Georgios V

    2015-11-01

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  2. Identification of distinct biological functions for four 3′-5′ RNA polymerases

    Science.gov (United States)

    Long, Yicheng; Abad, Maria G.; Olson, Erik D.; Carrillo, Elisabeth Y.; Jackman, Jane E.

    2016-01-01

    The superfamily of 3′-5′ polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNAHis guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNAHis maturation reaction, which is distinct from the tRNAHis maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5′-editing in vivo and in vitro, establishing template-dependent 3′-5′ polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3′-5′ polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3′-5′ polymerases in eukaryotes. PMID:27484477

  3. Identification of distinct biological functions for four 3'-5' RNA polymerases.

    Science.gov (United States)

    Long, Yicheng; Abad, Maria G; Olson, Erik D; Carrillo, Elisabeth Y; Jackman, Jane E

    2016-09-30

    The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNA(His) maturation reaction, which is distinct from the tRNA(His) maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5'-editing in vivo and in vitro, establishing template-dependent 3'-5' polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3'-5' polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3'-5' polymerases in eukaryotes.

  4. 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.

  5. Acceleration of cardiovascular-biological age by amphetamine exposure is a power function of chronological age

    Science.gov (United States)

    Norman, Amanda; Hulse, Gary Kenneth

    2017-01-01

    Background Amphetamine abuse is becoming more widespread internationally. The possibility that its many cardiovascular complications are associated with a prematurely aged cardiovascular system, and indeed biological organism systemically, has not been addressed. Methods Radial arterial pulse tonometry was performed using the SphygmoCor system (Sydney). 55 amphetamine exposed patients were compared with 107 tobacco smokers, 483 non-smokers and 68 methadone patients (total=713 patients) from 2006 to 2011. A cardiovascular-biological age (VA) was determined. Results The age of the patient groups was 30.03±0.51–40.45±1.15 years. This was controlled for with linear regression. The sex ratio was the same in all groups. 94% of amphetamine exposed patients had used amphetamine in the previous week. When the (log) VA was regressed against the chronological age (CA) and a substance-type group in both cross-sectional and longitudinal models, models quadratic in CA were superior to linear models (both pamphetamine exposure persisted after adjustment for all known cardiovascular risk factors (pamphetamines is associated with an advancement of cardiovascular-organismal age both over age and over time, and is robust to adjustment. That this is associated with power functions of age implies a feed-forward positively reinforcing exacerbation of the underlying ageing process. PMID:28243315

  6. 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.

  7. Free-falling Crystals: Biological Macromolecular Crystal Growth Studies in Low Earth Orbit

    Science.gov (United States)

    Judge, Russell A.; Snell, E. H.; Pusey, M. L.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Spacecraft orbiting the earth experience a reduced acceleration environment due to being in a state of continuous free-fall. This state colloquially termed microgravity, has produced improved X-ray diffraction quality crystals of biological macromolecules. Improvements in X-ray diffraction resolution (detail) or signal to noise, provide greater detail in the three-dimensional molecular structure providing information about the molecule, how it works, how to improve its function or how to impede it. Greater molecular detail obtained by crystallization in microgravity, has important implications for structural biology. In this article we examine the theories behind macromolecule crystal quality improvement in microgravity using results obtained from studies with the model protein, chicken egg white lysozyme.

  8. Generation of structurally novel short carotenoids and study of their biological activity

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Kim, Moon S.; Lee, Bun Y.

    2016-01-01

    Recent research interest in phytochemicals has consistently driven the efforts in the metabolic engineering field toward microbial production of various carotenoids. In spite of systematic studies, the possibility of using C30 carotenoids as biologically functional compounds has not been explored...... thus far. Here, we generated 13 novel structures of C30 carotenoids and one C35 carotenoid, including acyclic, monocyclic, and bicyclic structures, through directed evolution and combinatorial biosynthesis, in Escherichia coli. Measurement of radical scavenging activity of various C30 carotenoid...... structures revealed that acyclic C30 carotenoids showed higher radical scavenging activity than did DL-atocopherol. We could assume high potential biological activity of the novel structures of C30 carotenoids as well, based on the neuronal differentiation activity observed for the monocyclic C30 carotenoid...

  9. The effect of teaching methods on cognitive achievement, retention, and attitude among in biology studying

    Directory of Open Access Journals (Sweden)

    Snezana Stavrova Veselinovskaa

    2011-12-01

    Full Text Available The purpose of this paper is to determine the effects of usage of sequential teaching method on the academic achievement and retention level of students. Three student groups of biology students in University “Goce Delcev”, Faculty of Natural and Technical Sciences, Institute of Biology, - Stip, R. Macedonia were offered a topic on general characteristics of Proteins: Their Biological Functions and Primary Structure with different sequences of 3 teaching methods. The teaching methods were Laboratory method (student experiment, slide demonstration and lecture method. The first group started to course with experiments in the laboratory, then the relevant theory of proteins was given lecture method, and then the slides was shown (Group I. The sequence of these three teaching methods used in the first group was changed in both second and third group as follow: The lecture methods, slide show and experiment in Group II, and slide show, experiment and lecture method in Group III, respectively. Laboratory method used in the study was focused on the topic of this diversity and abundance reflect the central role of proteins in virtually all aspects of cell structure and function. Achievement test contained 20 questions, testing the knowledge of facts as well as the ability to transfer the knowledge and problem solving ability. This test was used as pre-test before methods’ application, post-test after the methods’ application and retention test after 30 days from methods’ applied.

  10. Distinguishing Pattern Formation Phenotypes: Applying Minkowski Functionals to Cell Biology Systems

    Science.gov (United States)

    Rericha, Erin; Guven, Can; Parent, Carole; Losert, Wolfgang

    2011-03-01

    Spatial Clustering of proteins within cells or cells themselves frequently occur in cell biology systems. However quantifying the underlying order and determining the regulators of these cluster patterns have proved difficult due to the inherent high noise levels in the systems. For instance the patterns formed by wild type and cyclic-AMP regulatory mutant Dictyostelium cells are visually distinctive, yet the large error bars in measurements of the fractal number, area, Euler number, eccentricity, and wavelength making it difficult to quantitatively distinguish between the patterns. We apply a spatial analysis technique based on Minkowski functionals and develop metrics which clearly separate wild type and mutant cell lines into distinct categories. Having such a metric facilitated the development of a computational model for cellular aggregation and its regulators. Supported by NIH-NGHS Nanotechnology (R01GM085574) and the Burroughs Wellcome Fund.

  11. 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.

  12. Function of parotid gland following irradiation and its relation to biological parameters

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, T. (Tohoku Univ., Sendai, Japan); Yamamoto, M.; Takeda, M.

    1980-09-01

    The function of the parotid gland in the mouse (synthesis and secretion of ..cap alpha..-amylase) following X irradiation was analyzed in relation to the parameters of surviving acinar cell fraction, DNA or protein content, and wet weight of the gland. Both synthesis and secretion of amylase in parotid were essentially unchanged when mice were irradiated with a dose of up to 3000 rad. When mice were irradiated and then given a proliferative stimulus of isoproterenol, latent lethal damage in the acinar cell population was expressed and resulted in cell degeneration in a dose-dependent manner. The mean value of amylase activity per gland in similarly treated parotids was, however, totally unaffected. The relationship between amylase activity per gland and the other biological parameters was analyzed by regression analysis. The results indicate that amylase activity per surviving acinar cell increased proportionately to compensate for the loss of acinar cells.

  13. The Evolution of Human Basophil Biology from Neglect towards Understanding of Their Immune Functions

    Science.gov (United States)

    Steiner, Markus; Huber, Sara; Harrer, Andrea

    2016-01-01

    Being discovered long ago basophils have been neglected for more than a century. During the past decade evidence emerged that basophils share features of innate and adaptive immunity. Nowadays, basophils are best known for their striking effector role in the allergic reaction. They hence have been used for establishing new diagnostic tests and therapeutic approaches and for characterizing natural and recombinant allergens as well as hypoallergens, which display lower or diminished IgE-binding activity. However, it was a long way from discovery in 1879 until identification of their function in hypersensitivity reactions, including adverse drug reactions. Starting with a historical background, this review highlights the modern view on basophil biology. PMID:28078302

  14. Perspectives in the biological function and the technological application of polygalacturonases.

    Science.gov (United States)

    Lang, C; Dörnenburg, H

    2000-04-01

    Polygalacturonases (PG) have evolved in the past years from a pectinase "simply" being used for food processing to an important parameter in plant-fungal interaction. PG-inhibiting proteins (PGIP) that are synthesised in plants as a specific response to PGs of pathogenic fungi, have become a focus as a possible target in resistance breeding, and PGIPs are also a concern as an inhibiting factor in food processing. Plant PGs have been identified as a major factor in fruit ripening, and PG-deficient transgenic plants have been bred. Mainly fungal PGs are used in industrial processes for juice clarification and the range of enzymes is being extended through new recombinant and non-recombinant fungal strains. Finally, novel fields of application can be envisaged for PGs in the production of oligogalacturonides as functional food components. Here we aim to highlight the various fields where PGs are encountered and where they are of biological or technological importance.

  15. Stereoelectronic effects dictate molecular conformation and biological function of heterocyclic amides.

    Science.gov (United States)

    Reid, Robert C; Yau, Mei-Kwan; Singh, Ranee; Lim, Junxian; Fairlie, David P

    2014-08-27

    Heterocycles adjacent to amides can have important influences on molecular conformation due to stereoelectronic effects exerted by the heteroatom. This was shown for imidazole- and thiazole-amides by comparing low energy conformations (ab initio MP2 and DFT calculations), charge distribution, dipole moments, and known crystal structures which support a general principle. Switching a heteroatom from nitrogen to sulfur altered the amide conformation, producing different three-dimensional electrostatic surfaces. Differences were attributed to different dipole and orbital alignments and spectacularly translated into opposing agonist vs antagonist functions in modulating a G-protein coupled receptor for inflammatory protein complement C3a on human macrophages. Influences of the heteroatom were confirmed by locking the amide conformation using fused bicyclic rings. These findings show that stereoelectronic effects of heterocycles modulate molecular conformation and can impart strikingly different biological properties.

  16. Applications of nonlinear microscopy for studying the structure and dynamics in biological systems

    Science.gov (United States)

    Prent, Nicole; Cisek, Richard; Greenhalgh, Catherine; Sparrow, Raymond; Rohitlall, Neeresh; Milkereit, Maike-Svenja; Green, Chantal; Barzda, Virginijus

    2005-09-01

    Laser scanning nonlinear optical microscopy is used to study structure and dynamics of cellular and sub-cellular structures in vivo. Under tight focusing conditions with a high numerical aperture objective, nonlinear optical signals such as third harmonic generation (THG), second harmonic generation (SHG), and multiphoton excitation fluorescence (MPF) are simultaneously produced. MPF is extensively used in biological imaging. Unfortunately, fluorescence is accompanied by heat dissipation in the sample and photobleaching effects. On the other hand, parametric processes such as SHG and THG are free of photobleaching since they involve only virtual electronic states where there is no transfer of energy into the medium. There are many naturally occurring structures that exhibit harmonic generation effects, and hence, do not require dyes that can potentially disrupt the normal functionality of the system. SHG is efficiently generated in non-centrosymmetric media, such as chiral structures and interfaces. The THG signal is generated due to a break in symmetry at interfaces and can be enhanced by the presence of multilamellar structures, as in the mitochondria or chloroplasts. Many interesting biological processes, such as signal transduction in neurons or ATP synthesis in mitochondria, involve the movement of ions across membranes. THG and SHG are sensitive to changing electric potential gradients, and hence are ideally suited for dynamical investigations of these biological processes. The present work will expose the structural factors and conditions that influence THG and SHG generation efficiencies in biological samples. Examples of visualizing chloroplasts and mitochondria will illustrate the advantages of harmonic generation microscopy for studying structural and functional properties of the in vivo systems.

  17. Functional genomics studies on the innate immunity of disease vectors

    Institute of Scientific and Technical Information of China (English)

    Luke A. Baton; Lindsey Garver; Zhiyong Xi; George Dimopoulos

    2008-01-01

    The increasing availability of genome sequences and the development of high-throughput techniques for gene expression profiling and functional characterization are transforming the study of innate immunity and other areas of insect biology. Already,functional genomic approaches have enabled a quantum advance in the characterization of mosquito immune responses to malaria parasite infection, and similar high-throughput functional genomic studies of other vector-pathogen interactions can be expected in the near future. The application of microarray-based and other expression analyses provide genomewide transcriptional profiles that can be used to identify insect immune system components that are differentially regulated upon exposure to various classes of pathogens, including many important etiologic agents of human and animal diseases. The role of infection-responsive or other candidate immune genes identified through comparative genomic approaches can then be functionally characterized, either in vivo, for instance in adult mosquitoes, or in vitro using cell lines. In most insect vectors of human pathogens, germ-line transgenesis is still technically difficult and maintenance of multiple transgenic lines logistically demanding.Consequently, transient RNA interference (RNAi)-mediated gene-silencing has rapidly become the method of choice for functional characterization of candidate innate immune genes. The powerful combination of transcriptional profiling in conjunction with assays using RNAi to determine gene function, and identify regulatory pathways, together with downstream cell biological approaches to determine protein localization and interactions,will continue to provide novel insights into the role of insect innate immunity in a variety of vector-pathogen interactions. Here we review advances in functional genomics studies of innate immunity in the insect disease vectors, over the past decade, with a particular focus on the Anopheles mosquito and its

  18. A human haploid gene trap collection to study lncRNAs with unusual RNA biology.

    Science.gov (United States)

    Kornienko, Aleksandra E; Vlatkovic, Irena; Neesen, Jürgen; Barlow, Denise P; Pauler, Florian M

    2016-01-01

    Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. Here we use the uncharacterized LOC100288798 lncRNA as a model to answer this question. Using public RNA-seq data we show that LOC100288798 is ubiquitously expressed, but inefficiently spliced. The minor spliced LOC100288798 isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. This shows that LOC100288798 RNA biology differs markedly from typical mRNAs. De novo assembly from RNA-seq data suggests that LOC100288798 extends 289kb beyond its annotated 3' end and overlaps the downstream SLC38A4 gene. Three cell lines with independent gene trap insertions in LOC100288798 were available from the KBM7 gene trap collection. RT-qPCR and RNA-seq confirmed successful lncRNA truncation and its extended length. Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon LOC100288798 truncation. Our data shows that gene trap collections in human haploid cell lines are useful tools to study lncRNAs, and identifies the previously uncharacterized LOC100288798 as a potential gene regulator.

  19. The Role of Soil Biological Function in Regulating Agroecosystem Services and Sustainability in the Quesungual Agroforestry System

    Science.gov (United States)

    Fonte, S.; Pauli, N.; Rousseau, L.; SIX, J. W. U. A.; Barrios, E.

    2014-12-01

    The Quesungual agroforestry system from western Honduras has been increasingly promoted as a promising alternative to traditional slash-and-burn agriculture in tropical dry forest regions of the Americas. Improved residue management and the lack of burning in this system can greatly impact soil biological functioning and a number of key soil-based ecosystem services, yet our understanding of these processes has not been thoroughly integrated to understand system functionality as a whole that can guide improved management. To address this gap, we present a synthesis of various field studies conducted in Central America aimed at: 1) quantifying the influence of the Quesungual agroforestry practices on soil macrofauna abundance and diversity, and 2) understanding how these organisms influence key soil-based ecosystem services that ultimately drive the success of this system. A first set of studies examined the impact of agroecosystem management on soil macrofauna populations, soil fertility and key soil processes. Results suggest that residue inputs (derived from tree biomass pruning), a lack of burning, and high tree densities, lead to conditions that support abundant, diverse soil macrofauna communities under agroforestry, with soil organic carbon content comparable to adjacent forest. Additionally, there is great potential in working with farmers to develop refined soil quality indicators for improved land management. A second line of research explored interactions between residue management and earthworms in the regulation of soil-based ecosystem services. Earthworms are the most prominent ecosystem engineers in these soils. We found that earthworms are key drivers of soil structure maintenance and the stabilization of soil organic matter within soil aggregates, and also had notable impacts on soil nutrient dynamics. However, the impact of earthworms appears to depend on residue management practices, thus indicating the need for an integrated approach for

  20. Spectroscopic studies of silica nanoparticles: Magnetic resonance and nanomaterial-biological interactions

    Science.gov (United States)

    Lehman, Sean E.

    Primarily concerned with manipulation and study of matter at the nanoscale, the concept of nanoscience encompasses ideas such as nanomaterial synthesis, characterization, and applications to modern scientific and societal problems. These problems encompass a broad range of issues such as energy storage and conversion, medical diagnostics and treatment, environmental remediation and detection, carbon economy and as well as many others. Silica nanoparticles of porous morphology have broad application to many of these issues. In particular, the utility of silica nanoparticles is facilitated by their large intrinsic surface area, tunable surface chemistry, and synthetic variability in both their size and morphology. This facilitates applications to these problems. However, extensive characterization and deeper understanding is needed before full implementation in key applications can be realized. The work described in this thesis aims to explore fundamental and applied characterization of silica nanoparticles that might be used in biomedical and environmental applications. Fundamental studies of functionalized nanomaterials using NMR spectroscopy reveal complex, dynamic phenomena related to-and ultimately deriving from-the intrinsic and/or modified surface chemistry. Applied studies of nanomaterial-biological interfaces demonstrate free radical chemistry as dominating the toxic response of the materials when exposed to biological systems of interest. Characterization of protein adsorbed on the interface reinforces the ubiquitous nature of protein adsorption on nanomaterial surface in biological and environmental media. Overall, this work illuminates and highlights complex changes that take place in aqueous solution for silica nanoparticles of varied morphology and surface chemistry.

  1. Application of Bioinformatics and Systems Biology in Medicinal Plant Studies

    Institute of Scientific and Technical Information of China (English)

    DENG You-ping; AI Jun-mei; XIAO Pei-gen

    2010-01-01

    One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds.Genome wide high throughput technologies such as genomics,transcriptomics,proteomics and metabolomics can help reach that goal.Such technologies can produce a vast amount of data which desperately need bioinformatics and systems biology to process,manage,distribute and understand these data.By dealing with the"omics"data,bioinformatics and systems biology can also help improve the quality of traditional medicinal materials,develop new approaches for the classification and authentication of medicinal plants,identify new active compounds,and cultivate medicinal plant species that tolerate harsh environmental conditions.In this review,the application of bioinformatics and systems biology in medicinal plants is briefly introduced.

  2. Cahaba River: Biological and Water Quality Studies, Birmingham, AL,

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Excessive sedimentation and nutrient enrichment are affecting the biology of the Cahaba Riverwatershed. Deleterious effects of sediment deposition on the fish and...

  3. Genetic studies of body mass index yield new insights for obesity biology.

    Science.gov (United States)

    Locke, Adam E; Kahali, Bratati; Berndt, Sonja I; Justice, Anne E; Pers, Tune H; Day, Felix R; Powell, Corey; Vedantam, Sailaja; Buchkovich, Martin L; Yang, Jian; Croteau-Chonka, Damien C; Esko, Tonu; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Kutalik, Zoltán; Luan, Jian'an; Mägi, Reedik; Randall, Joshua C; Winkler, Thomas W; Wood, Andrew R; Workalemahu, Tsegaselassie; Faul, Jessica D; Smith, Jennifer A; Hua Zhao, Jing; Zhao, Wei; Chen, Jin; Fehrmann, Rudolf; Hedman, Åsa K; Karjalainen, Juha; Schmidt, Ellen M; Absher, Devin; Amin, Najaf; Anderson, Denise; Beekman, Marian; Bolton, Jennifer L; Bragg-Gresham, Jennifer L; Buyske, Steven; Demirkan, Ayse; Deng, Guohong; Ehret, Georg B; Feenstra, Bjarke; Feitosa, Mary F; Fischer, Krista; Goel, Anuj; Gong, Jian; Jackson, Anne U; Kanoni, Stavroula; Kleber, Marcus E; Kristiansson, Kati; Lim, Unhee; Lotay, Vaneet; Mangino, Massimo; Mateo Leach, Irene; Medina-Gomez, Carolina; Medland, Sarah E; Nalls, Michael A; Palmer, Cameron D; Pasko, Dorota; Pechlivanis, Sonali; Peters, Marjolein J; Prokopenko, Inga; Shungin, Dmitry; Stančáková, Alena; Strawbridge, Rona J; Ju Sung, Yun; Tanaka, Toshiko; Teumer, Alexander; Trompet, Stella; van der Laan, Sander W; van Setten, Jessica; Van Vliet-Ostaptchouk, Jana V; Wang, Zhaoming; Yengo, Loïc; Zhang, Weihua; Isaacs, Aaron; Albrecht, Eva; Ärnlöv, Johan; Arscott, Gillian M; Attwood, Antony P; Bandinelli, Stefania; Barrett, Amy; Bas, Isabelita N; Bellis, Claire; Bennett, Amanda J; Berne, Christian; Blagieva, Roza; Blüher, Matthias; Böhringer, Stefan; Bonnycastle, Lori L; Böttcher, Yvonne; Boyd, Heather A; Bruinenberg, Marcel; Caspersen, Ida H; Ida Chen, Yii-Der; Clarke, Robert; Daw, E Warwick; de Craen, Anton J M; Delgado, Graciela; Dimitriou, Maria; Doney, Alex S F; Eklund, Niina; Estrada, Karol; Eury, Elodie; Folkersen, Lasse; Fraser, Ross M; Garcia, Melissa E; Geller, Frank; Giedraitis, Vilmantas; Gigante, Bruna; Go, Alan S; Golay, Alain; Goodall, Alison H; Gordon, Scott D; Gorski, Mathias; Grabe, Hans-Jörgen; Grallert, Harald; Grammer, Tanja B; Gräßler, Jürgen; Grönberg, Henrik; Groves, Christopher J; Gusto, Gaëlle; Haessler, Jeffrey; Hall, Per; Haller, Toomas; Hallmans, Goran; Hartman, Catharina A; Hassinen, Maija; Hayward, Caroline; Heard-Costa, Nancy L; Helmer, Quinta; Hengstenberg, Christian; Holmen, Oddgeir; Hottenga, Jouke-Jan; James, Alan L; Jeff, Janina M; Johansson, Åsa; Jolley, Jennifer; Juliusdottir, Thorhildur; Kinnunen, Leena; Koenig, Wolfgang; Koskenvuo, Markku; Kratzer, Wolfgang; Laitinen, Jaana; Lamina, Claudia; Leander, Karin; Lee, Nanette R; Lichtner, Peter; Lind, Lars; Lindström, Jaana; Sin Lo, Ken; Lobbens, Stéphane; Lorbeer, Roberto; Lu, Yingchang; Mach, François; Magnusson, Patrik K E; Mahajan, Anubha; McArdle, Wendy L; McLachlan, Stela; Menni, Cristina; Merger, Sigrun; Mihailov, Evelin; Milani, Lili; Moayyeri, Alireza; Monda, Keri L; Morken, Mario A; Mulas, Antonella; Müller, Gabriele; Müller-Nurasyid, Martina; Musk, Arthur W; Nagaraja, Ramaiah; Nöthen, Markus M; Nolte, Ilja M; Pilz, Stefan; Rayner, Nigel W; Renstrom, Frida; Rettig, Rainer; Ried, Janina S; Ripke, Stephan; Robertson, Neil R; Rose, Lynda M; Sanna, Serena; Scharnagl, Hubert; Scholtens, Salome; Schumacher, Fredrick R; Scott, William R; Seufferlein, Thomas; Shi, Jianxin; Vernon Smith, Albert; Smolonska, Joanna; Stanton, Alice V; Steinthorsdottir, Valgerdur; Stirrups, Kathleen; Stringham, Heather M; Sundström, Johan; Swertz, Morris A; Swift, Amy J; Syvänen, Ann-Christine; Tan, Sian-Tsung; Tayo, Bamidele O; Thorand, Barbara; Thorleifsson, Gudmar; Tyrer, Jonathan P; Uh, Hae-Won; Vandenput, Liesbeth; Verhulst, Frank C; Vermeulen, Sita H; Verweij, Niek; Vonk, Judith M; Waite, Lindsay L; Warren, Helen R; Waterworth, Dawn; Weedon, Michael N; Wilkens, Lynne R; Willenborg, Christina; Wilsgaard, Tom; Wojczynski, Mary K; Wong, Andrew; Wright, Alan F; Zhang, Qunyuan; Brennan, Eoin P; Choi, Murim; Dastani, Zari; Drong, Alexander W; Eriksson, Per; Franco-Cereceda, Anders; Gådin, Jesper R; Gharavi, Ali G; Goddard, Michael E; Handsaker, Robert E; Huang, Jinyan; Karpe, Fredrik; Kathiresan, Sekar; Keildson, Sarah; Kiryluk, Krzysztof; Kubo, Michiaki; Lee, Jong-Young; Liang, Liming; Lifton, Richard P; Ma, Baoshan; McCarroll, Steven A; McKnight, Amy J; Min, Josine L; Moffatt, Miriam F; Montgomery, Grant W; Murabito, Joanne M; Nicholson, George; Nyholt, Dale R; Okada, Yukinori; Perry, John R B; Dorajoo, Rajkumar; Reinmaa, Eva; Salem, Rany M; Sandholm, Niina; Scott, Robert A; Stolk, Lisette; Takahashi, Atsushi; Tanaka, Toshihiro; Van't Hooft, Ferdinand M; Vinkhuyzen, Anna A E; Westra, Harm-Jan; Zheng, Wei; Zondervan, Krina T; Heath, Andrew C; Arveiler, Dominique; Bakker, Stephan J L; Beilby, John; Bergman, Richard N; Blangero, John; Bovet, Pascal; Campbell, Harry; Caulfield, Mark J; Cesana, Giancarlo; Chakravarti, Aravinda; Chasman, Daniel I; Chines, Peter S; Collins, Francis S; Crawford, Dana C; Cupples, L Adrienne; Cusi, Daniele; Danesh, John; de Faire, Ulf; den Ruijter, Hester M; Dominiczak, Anna F; Erbel, Raimund; Erdmann, Jeanette; Eriksson, Johan G; Farrall, Martin; Felix, Stephan B; Ferrannini, Ele; Ferrières, Jean; Ford, Ian; Forouhi, Nita G; Forrester, Terrence; Franco, Oscar H; Gansevoort, Ron T; Gejman, Pablo V; Gieger, Christian; Gottesman, Omri; Gudnason, Vilmundur; Gyllensten, Ulf; Hall, Alistair S; Harris, Tamara B; Hattersley, Andrew T; Hicks, Andrew A; Hindorff, Lucia A; Hingorani, Aroon D; Hofman, Albert; Homuth, Georg; Hovingh, G Kees; Humphries, Steve E; Hunt, Steven C; Hyppönen, Elina; Illig, Thomas; Jacobs, Kevin B; Jarvelin, Marjo-Riitta; Jöckel, Karl-Heinz; Johansen, Berit; Jousilahti, Pekka; Jukema, J Wouter; Jula, Antti M; Kaprio, Jaakko; Kastelein, John J P; Keinanen-Kiukaanniemi, Sirkka M; Kiemeney, Lambertus A; Knekt, Paul; Kooner, Jaspal S; Kooperberg, Charles; Kovacs, Peter; Kraja, Aldi T; Kumari, Meena; Kuusisto, Johanna; Lakka, Timo A; Langenberg, Claudia; Le Marchand, Loic; Lehtimäki, Terho; Lyssenko, Valeriya; Männistö, Satu; Marette, André; Matise, Tara C; McKenzie, Colin A; McKnight, Barbara; Moll, Frans L; Morris, Andrew D; Morris, Andrew P; Murray, Jeffrey C; Nelis, Mari; Ohlsson, Claes; Oldehinkel, Albertine J; Ong, Ken K; Madden, Pamela A F; Pasterkamp, Gerard; Peden, John F; Peters, Annette; Postma, Dirkje S; Pramstaller, Peter P; Price, Jackie F; Qi, Lu; Raitakari, Olli T; Rankinen, Tuomo; Rao, D C; Rice, Treva K; Ridker, Paul M; Rioux, John D; Ritchie, Marylyn D; Rudan, Igor; Salomaa, Veikko; Samani, Nilesh J; Saramies, Jouko; Sarzynski, Mark A; Schunkert, Heribert; Schwarz, Peter E H; Sever, Peter; Shuldiner, Alan R; Sinisalo, Juha; Stolk, Ronald P; Strauch, Konstantin; Tönjes, Anke; Trégouët, David-Alexandre; Tremblay, Angelo; Tremoli, Elena; Virtamo, Jarmo; Vohl, Marie-Claude; Völker, Uwe; Waeber, Gérard; Willemsen, Gonneke; Witteman, Jacqueline C; Zillikens, M Carola; Adair, Linda S; Amouyel, Philippe; Asselbergs, Folkert W; Assimes, Themistocles L; Bochud, Murielle; Boehm, Bernhard O; Boerwinkle, Eric; Bornstein, Stefan R; Bottinger, Erwin P; Bouchard, Claude; Cauchi, Stéphane; Chambers, John C; Chanock, Stephen J; Cooper, Richard S; de Bakker, Paul I W; Dedoussis, George; Ferrucci, Luigi; Franks, Paul W; Froguel, Philippe; Groop, Leif C; Haiman, Christopher A; Hamsten, Anders; Hui, Jennie; Hunter, David J; Hveem, Kristian; Kaplan, Robert C; Kivimaki, Mika; Kuh, Diana; Laakso, Markku; Liu, Yongmei; Martin, Nicholas G; März, Winfried; Melbye, Mads; Metspalu, Andres; Moebus, Susanne; Munroe, Patricia B; Njølstad, Inger; Oostra, Ben A; Palmer, Colin N A; Pedersen, Nancy L; Perola, Markus; Pérusse, Louis; Peters, Ulrike; Power, Chris; Quertermous, Thomas; Rauramaa, Rainer; Rivadeneira, Fernando; Saaristo, Timo E; Saleheen, Danish; Sattar, Naveed; Schadt, Eric E; Schlessinger, David; Slagboom, P Eline; Snieder, Harold; Spector, Tim D; Thorsteinsdottir, Unnur; Stumvoll, Michael; Tuomilehto, Jaakko; Uitterlinden, André G; Uusitupa, Matti; van der Harst, Pim; Walker, Mark; Wallaschofski, Henri; Wareham, Nicholas J; Watkins, Hugh; Weir, David R; Wichmann, H-Erich; Wilson, James F; Zanen, Pieter; Borecki, Ingrid B; Deloukas, Panos; Fox, Caroline S; Heid, Iris M; O'Connell, Jeffrey R; Strachan, David P; Stefansson, Kari; van Duijn, Cornelia M; Abecasis, Gonçalo R; Franke, Lude; Frayling, Timothy M; McCarthy, Mark I; Visscher, Peter M; Scherag, André; Willer, Cristen J; Boehnke, Michael; Mohlke, Karen L; Lindgren, Cecilia M; Beckmann, Jacques S; Barroso, Inês; North, Kari E; Ingelsson, Erik; Hirschhorn, Joel N; Loos, Ruth J F; Speliotes, Elizabeth K

    2015-02-12

    Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P 20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.

  4. LASER BIOLOGY AND MEDICINE: Light scattering study of rheumatoid arthritis

    Science.gov (United States)

    Beuthan, J.; Netz, U.; Minet, O.; Klose, Annerose D.; Hielscher, A. H.; Scheel, A.; Henniger, J.; Müller, G.

    2002-11-01

    The distribution of light scattered by finger joints is studied in the near-IR region. It is shown that variations in the optical parameters of the tissue (scattering coefficient μs, absorption coefficient μa, and anisotropy factor g) depend on the presence of the rheumatoid arthritis (RA). At the first stage, the distribution of scattered light was measured in diaphanoscopic experiments. The convolution of a Gaussian error function with the scattering phase function proved to be a good approximation of the data obtained. Then, a new method was developed for the reconstruction of distribution of optical parameters in the finger cross section. Model tests of the quality of this reconstruction method show good results.

  5. Gold complexes with benzimidazole derivatives: synthesis, characterization and biological studies.

    Science.gov (United States)

    Mota, Vinicius Zamprogno; de Carvalho, Gustavo Senra Gonçalves; da Silva, Adilson David; Costa, Luiz Antônio Sodré; de Almeida Machado, Patrícia; Coimbra, Elaine Soares; Ferreira, Carmen Veríssima; Shishido, Silvia Mika; Cuin, Alexandre

    2014-02-01

    Synthesis, characterization, DFT studies and biological assays of new gold(I) and gold(III) complexes of benzimidazole are reported. Molecular and structural characterizations of the compounds were based on elemental (C, H and N) and thermal (TG-DTA) analyses, and FT-IR and UV-Visible spectroscopic measurements. The structures of complexes were proposed based DFT calculations. The benzimidazole compounds (Lig1 and Lig2) and the gold complexes were tested against three Leishmania species related to cutaneous manifestations of leishmaniasis. The free benzimidazole compounds showed no leishmanicidal activity. On the other hand, the gold(I and III) complexes have shown to possess significant activity against Leishmania in both stages of parasite, and the gold(III) complex with Lig2 exhibited expressive leishmanicidal activity with IC50 values below 5.7 μM. Also, the gold complexes showed high leishmania selectivity. The gold(I) complex with Lig1, for example, is almost 50 times more toxic for the parasite than for macrophages. Besides the leishmanicidal activity, all complexes exhibited toxic effect against SK-Mel 103 and Balb/c 3T3, cancer cells.

  6. Biological conversion of synthesis gas. Mass transfer/kinetic studies

    Energy Technology Data Exchange (ETDEWEB)

    Klasson, K.T.; Basu, R.; Johnson, E.R.; Clausen, E.C.; Gaddy, J.L.

    1992-03-01

    Mass transfer and kinetic studies were carried out for the Rhodospirillum rubrum and Chlorobium thiosulfatophilum bacterial systems. R. rubrum is a photosynthetic anaerobic bacterium which catalyzes the biological water gas shift reaction: CO + H{sub 2}0 {yields} CO{sub 2} + H{sub 2}. C. thiosulfatophilum is also a H{sub 2}S and COS to elemental sulfur. The growth of R. rubrum may be satisfactorily carried out at 25{degree} and 30{degree}C, while CO uptake and thus the conversion of CO best occurs at temperatures of either 30{degree}, 32{degree} or 34{degree}C. The rate of conversion of COs and H{sub 2}O to CO{sub 2} and H{sub 2}S may be modeled by a first order rate expression. The rate constant at 30{degree}C was found to be 0.243 h{sup {minus}1}. The growth of C. thiosulfatophilum may be modeled in terms of incoming light intensity using a Monod equation: {mu} = {sub 351} + I{sub o}/{sup 0.152}I{sub o}. Comparisons of the growth of R. rubrum and C. thiosulfatophilum shows that the specific growth rate of C. thiosulfatophilum is much higher at a given light intensity.

  7. Mammalian Exo1 encodes both structural and catalytic functions that play distinct roles in essential biological processes.

    Science.gov (United States)

    Schaetzlein, Sonja; Chahwan, Richard; Avdievich, Elena; Roa, Sergio; Wei, Kaichun; Eoff, Robert L; Sellers, Rani S; Clark, Alan B; Kunkel, Thomas A; Scharff, Matthew D; Edelmann, Winfried

    2013-07-02

    Mammalian Exonuclease 1 (EXO1) is an evolutionarily conserved, multifunctional exonuclease involved in DNA damage repair, replication, immunoglobulin diversity, meiosis, and telomere maintenance. It has been assumed that EXO1 participates in these processes primarily through its exonuclease activity, but recent studies also suggest that EXO1 has a structural function in the assembly of higher-order protein complexes. To dissect the enzymatic and nonenzymatic roles of EXO1 in the different biological processes in vivo, we generated an EXO1-E109K knockin (Exo1(EK)) mouse expressing a stable exonuclease-deficient protein and, for comparison, a fully EXO1-deficient (Exo1(null)) mouse. In contrast to Exo1(null/null) mice, Exo1(EK/EK) mice retained mismatch repair activity and displayed normal class switch recombination and meiosis. However, both Exo1-mutant lines showed defects in DNA damage response including DNA double-strand break repair (DSBR) through DNA end resection, chromosomal stability, and tumor suppression, indicating that the enzymatic function is required for those processes. On a transformation-related protein 53 (Trp53)-null background, the DSBR defect caused by the E109K mutation altered the tumor spectrum but did not affect the overall survival as compared with p53-Exo1(null) mice, whose defects in both DSBR and mismatch repair also compromised survival. The separation of these functions demonstrates the differential requirement for the structural function and nuclease activity of mammalian EXO1 in distinct DNA repair processes and tumorigenesis in vivo.

  8. [The hyperiricosuria as an indicator of derangement of biologic functions of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension].

    Science.gov (United States)

    Titov, V N; Oshchepkova, E V; Dmitriev, V A; Gushchina, O V; Shiriaeva, Iu K; Iashin, A Ia

    2012-04-01

    During millions years in all animals allantoine (oxidized by uricase uric acid) was catabolite of purines and ascorbic acid was an acceptor of active forms of oxygen. The proximal tubules of nephron reabsorbed the trace amounts of uric acid Then during phylogenesis the primates had a mutation of ascorbic acid gen minus. Later on occurred a second spontaneous mutation and uricase gen minus and uric acid became catabolites of purines. In absence of ascorbic acid synthesis ions of urates became a major capturers of active forms of oxygen and all uric acid as before underwent the reabsorption. Later the carriers were formed which began in epithelium of proximal tubules to secrete all uric acid into urine. At every incident of "littering" of intercellular medium with endogenic flogogens (impairment of biologic function of endoecology) under compensatory development of biologic reaction of inflammation the need in inactivation of active forms of oxygen increases. Hence later on in phylogenesis one more stage was formed--post secretory reabsorption of uric acid In the biologic reaction of inflammation epithelium of proximal tubules initiates retentional hyperiricosuria. The general antioxidant activity of human blood plasma in 60% is presented by urates' ions. The excretion of uric acid includes 4 stages: filtration, full reabsorption, secretion and post secretory reabsorption. In phylogenesis these stages formed in sequence. The mild hyperiricosuria is most frequently considered as a non-specific indicator of activation of biologic reaction of inflammation. The productive hyperiricosuria develops more infrequently under surplus of meat food and cytolysis syndrome (intensification of cell loss in vivo). Under concentration of uric acid more than 400 mkmol/l part of urates circulates in intercellular medium in the form of crystals. The microcrystals of uric acid (biologic "litter") initiate the syndrome of systemic inflammatory response as an endogenic flogogen

  9. Recent Studies in Functional Analytic Psychotherapy

    Science.gov (United States)

    Garcia, Rafael Ferro

    2008-01-01

    Functional Analytic Psychotherapy (FAP), based on the principles of radical behaviorism, emphasizes the impact of eventualities that occur during therapeutic sessions, the therapist-client interaction context, functional equivalence between environments, natural reinforcement and shaping by the therapist. This paper reviews recent studies of FAP…

  10. A study of a curious arithmetic function

    CERN Document Server

    Farhi, Bakir

    2010-01-01

    In this note, we study the arithmetic function $f : \\mathbb{Z}_+^* \\to \\mathbb{Q}_+^*$ defined by $f(2^k \\ell) = \\ell^{1 - k}$ ($\\forall k, \\ell \\in \\mathbb{N}$, $\\ell$ odd). We show several important properties about that function and then we use them to obtain some curious results involving the 2-adic valuation.

  11. Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton

    Science.gov (United States)

    Sattlegger, Evelyn; Chernova, Tatiana A.; Gogoi, Neeku M.; Pillai, Indu V.; Chernoff, Yury O.; Munn, Alan L.

    2014-01-01

    Classic functions of the actin cytoskeleton include control of cell size and shape and the internal organisation of cells. These functions are manifest in cellular processes of fundamental importance throughout biology such as the generation of cell polarity, cell migration, cell adhesion and cell division. However, studies in the unicellular model eukaryote Saccharomyces cerevisiae (Baker's yeast) are giving insights into other functions in which the actin cytoskeleton plays a critical role. These include endocytosis, control of protein translation and determination of protein 3-dimensional shape (especially conversion of normal cellular proteins into prions). Here we present a concise overview of these new "moonlighting" roles for the actin cytoskeleton and how some of these roles might lie at the heart of important molecular switches. This is an exciting time for researchers interested in the actin cytoskeleton. We show here how studies of actin are leading us into many new and exciting realms at the interface of genetics, biochemistry and cell biology. While many of the pioneering studies have been conducted using yeast, the conservation of the actin cytoskeleton and its component proteins throughout eukaryotes suggests that these new roles for the actin cytoskeleton may not be restricted to yeast cells but rather may reflect new roles for the actin cytoskeleton of all eukaryotes. PMID:25138357

  12. Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function

    Energy Technology Data Exchange (ETDEWEB)

    Alfano, Robert R.; Yang, Yuanlong

    2003-09-02

    Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

  13. SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function.

    Science.gov (United States)

    Tomer, Raju; Lovett-Barron, Matthew; Kauvar, Isaac; Andalman, Aaron; Burns, Vanessa M; Sankaran, Sethuraman; Grosenick, Logan; Broxton, Michael; Yang, Samuel; Deisseroth, Karl

    2015-12-17

    The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca(2+) imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function.

  14. Biology of Bone Tissue: Structure, Function, and Factors That Influence Bone Cells.

    Science.gov (United States)

    Florencio-Silva, Rinaldo; Sasso, Gisela Rodrigues da Silva; Sasso-Cerri, Estela; Simões, Manuel Jesus; Cerri, Paulo Sérgio

    2015-01-01

    Bone tissue is continuously remodeled through the concerted actions of bone cells, which include bone resorption by osteoclasts and bone formation by osteoblasts, whereas osteocytes act as mechanosensors and orchestrators of the bone remodeling process. This process is under the control of local (e.g., growth factors and cytokines) and systemic (e.g., calcitonin and estrogens) factors that all together contribute for bone homeostasis. An imbalance between bone resorption and formation can result in bone diseases including osteoporosis. Recently, it has been recognized that, during bone remodeling, there are an intricate communication among bone cells. For instance, the coupling from bone resorption to bone formation is achieved by interaction between osteoclasts and osteoblasts. Moreover, osteocytes produce factors that influence osteoblast and osteoclast activities, whereas osteocyte apoptosis is followed by osteoclastic bone resorption. The increasing knowledge about the structure and functions of bone cells contributed to a better understanding of bone biology. It has been suggested that there is a complex communication between bone cells and other organs, indicating the dynamic nature of bone tissue. In this review, we discuss the current data about the structure and functions of bone cells and the factors that influence bone remodeling.

  15. The schizophrenia risk gene ZNF804A: clinical associations, biological mechanisms and neuronal functions.

    Science.gov (United States)

    Chang, H; Xiao, X; Li, M

    2017-03-14

    ZNF804A (zinc-finger protein 804A) has been recognized as a schizophrenia risk gene across multiple world populations. Its intronic single-nucleotide polymorphism (SNP) rs1344706 is among one of the strongest susceptibility variants that have achieved genome-wide significance in genome-wide association studies (GWAS) for schizophrenia and has been widely and intensively studied. To elucidate the biological mechanisms underlying the genetic risk conferred by rs1344706, we retrospectively analyzed the progresses in brain gene expression quantitative trait loci (eQTL) analyses, ZNF804A-induced pathway alterations in neural cells and changes in synaptic phenotypes associated with ZNF804A expression. Based on these data, we hypothesize a potential biological mechanism for a genetic risk allele of ZNF804A in schizophrenia pathogenesis. We also review the efforts being made to characterize the affected intermediate phenotypes using neuroimaging and neuropsychological approaches. We then discuss additional common and rare ZNF804A variants in schizophrenia susceptibility and the potential genetic heterogeneity of these genomic loci between Europeans and Asians. This review for we believe the first time systematically presents the evidence for ZNF804A, describing its discovery and likely roles in brain development and schizophrenia pathogenesis. We believe that this work has summarized this information with a systemic and broad assessment of recent findings.Molecular Psychiatry advance online publication, 14 March 2017; doi:10.1038/mp.2017.19.

  16. Rate-dependence of 'wet' biological adhesives and the function of the pad secretion in insects.

    Science.gov (United States)

    Labonte, David; Federle, Walter

    2015-11-28

    Many insects use soft adhesive footpads for climbing. The surface contact of these organs is mediated by small volumes of a liquid secretion, which forms thin films in the contact zone. Here, we investigate the role of viscous dissipation by this secretion and the 'bulk' pad cuticle by quantifying the rate-dependence of the adhesive force of individual pads. Adhesion increased with retraction speed, but this effect was independent of the amount of pad secretion present in the contact zone, suggesting that the secretion's viscosity did not play a significant role. Instead, the rate-dependence can be explained by relating the strain energy release rate to the speed of crack propagation, using an established empirical power law. The 'wet' pads' behaviour was akin to that of 'dry' elastomers, with an equilibrium energy release rate close to that of dry van-der-Waals contacts. We suggest that the secretion mainly serves as a 'release layer', minimising viscous dissipation and thereby reducing the time- and 'loading-history'-dependence of the adhesive pads. In contrast to many commercial adhesives which derive much of their strength from viscous dissipation, we show that the major modulator of adhesive strength in 'wet' biological adhesive pads is friction, exhibiting a much larger effect than retraction speed. A comparison between 'wet' and 'dry' biological adhesives, using both results from this study and the literature, revealed a striking lack of differences in attachment performance under varying experimental conditions. Together, these results suggest that 'wet' and 'dry' biological adhesives may be more similar than previously thought.

  17. Biology, literacy, and the African American voice: A case study of meaningful learning in the biology classroom

    Science.gov (United States)

    Reese, Keturah

    Under the direction of Sharon Murphy Augustine, Ph.D./Ph.D Curriculum and Instruction There was a substantial performance gap among African Americans and other ethnic groups. Additionally, African American students in a Title I school were at a significantly high risk of not meeting or exceeding on performance tests in science. Past reports have shown average gains in some subject areas, and declines in others (NCES, 2011; GADOE, 2012). Current instructional strategies and the lack of literacy within the biology classroom created a problem for African American high school students on national and state assessments. The purpose of this study was to examine the perceptions of African American students and teachers in the context of literacy and biology through the incorporation of an interactive notebook and other literacy strategies. The data was collected three ways: field notes for a two week observation period within the biology classroom, student and teacher interviews, and student work samples. During the observations, student work collection, and interviews, I looked for the following codes: active learning, constructive learning, collaborative learning, authentic learning, and intentional learning. In the process of coding for the pre-determined codes, three more codes emerged. The three codes that emerged were organization, studying/student ownership, and student teacher relationships. Students and teachers both solidified the notion that literacy and biology worked well together. The implemented literacy strategies were something that both teachers and students appreciated in their learning of biology. Overall students and teachers perceived that the interactive notebook along Cornell notes, Thinking maps, close reads, writing, lab experiments, and group work created meaningful learning experiences within the biology classroom.

  18. Decreased functional diversity and biological pest control in conventional compared to organic crop fields.

    Science.gov (United States)

    Krauss, Jochen; Gallenberger, Iris; Steffan-Dewenter, Ingolf

    2011-01-01

    Organic farming is one of the most successful agri-environmental schemes, as humans benefit from high quality food, farmers from higher prices for their products and it often successfully protects biodiversity. However there is little knowledge if organic farming also increases ecosystem services like pest control. We assessed 30 triticale fields (15 organic vs. 15 conventional) and recorded vascular plants, pollinators, aphids and their predators. Further, five conventional fields which were treated with insecticides were compared with 10 non-treated conventional fields. Organic fields had five times higher plant species richness and about twenty times higher pollinator species richness compared to conventional fields. Abundance of pollinators was even more than one-hundred times higher on organic fields. In contrast, the abundance of cereal aphids was five times lower in organic fields, while predator abundances were three times higher and predator-prey ratios twenty times higher in organic fields, indicating a significantly higher potential for biological pest control in organic fields. Insecticide treatment in conventional fields had only a short-term effect on aphid densities while later in the season aphid abundances were even higher and predator abundances lower in treated compared to untreated conventional fields. Our data indicate that insecticide treatment kept aphid predators at low abundances throughout the season, thereby significantly reducing top-down control of aphid populations. Plant and pollinator species richness as well as predator abundances and predator-prey ratios were higher at field edges compared to field centres, highlighting the importance of field edges for ecosystem services. In conclusion organic farming increases biodiversity, including important functional groups like plants, pollinators and predators which enhance natural pest control. Preventative insecticide application in conventional fields has only short-term effects on aphid

  19. Metalloproteinases: A parade of functions in matrix biology and an outlook for the future.

    Science.gov (United States)

    Apte, Suneel S; Parks, William C

    2015-01-01

    This issue of Matrix Biology is devoted to exploring how metalloproteinases - here inclusive of related families of extracellular proteinases - act on extracellular matrix (ECM) proteins to influence an astonishing diversity of biological systems and diseases. Since their discovery in the 1960's, matrix metalloproteinases (MMPs) have oft and widely been considered as the principal mediators of ECM destruction. However, as becomes clear from several articles in this issue, MMPs affect processes that both promote and limit ECM assembly, structure, and quantity. Furthermore, it has become increasingly apparent that ECM proteolysis is neither the exclusive function of MMPs nor their only sphere of influence. Thus, other enzymes may be important participants in ECM proteolysis, and indeed they are. The ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type 1 repeat) proteinases, BMP/tolloid proteases, and meprins have all emerged as major mechanisms of ECM proteolysis. An aggregate view of proteolysis as an exquisitely specific and crucial post-translational modification of secreted proteins emerges from these reviews. The cumulative evidence strongly suggests that although some MMPs can and do cleave ECM components, notably fibrillar collagens, the majority of these proteinases are not key physiological participants in morphogenesis nor in control of matrix metabolism in homeostasis or disease. In contrast, deficiency of ADAMTS proteases leads to a remarkable array of morphogenetic defects and connective tissue disorders consistent with a specialized role in turnover of the embryonic provisional ECM and in ECM assembly. Astacin-related proteases emerge into crucial positions in ECM assembly and turnover, although they also have numerous roles related to morphogen and growth factor regulation. To further turn the traditional view on its head, it is clear that many MMPs are key participants in many, diverse immune and inflammation processes

  20. 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.

  1. The biological function and clinical utilization of CD147 in human diseases: a review of the current scientific literature.

    Science.gov (United States)

    Xiong, Lijuan; Edwards, Carl K; Zhou, Lijun

    2014-09-29

    CD147 or EMMPRIN is a member of the immunoglobulin superfamily in humans. It is widely expressed in human tumors and plays a central role in the progression of many cancers by stimulating the secretion of matrix metalloproteinases (MMPs) and cytokines. CD147 regulates cell proliferation, apoptosis, and tumor cell migration, metastasis and differentiation, especially under hypoxic conditions. CD147 is also important to many organ systems. This review will provide a detailed overview of the discovery, characterization, molecular structure, diverse biological functions and regulatory mechanisms of CD147 in human physiological and pathological processes. In particular, recent studies have demonstrated the potential application of CD147 not only as a phenotypic marker of activated regulatory T cells but also as a potential diagnostic marker for early-stage disease. Moreover, CD147 is recognized as an effective therapeutic target for hepatocellular carcinoma (HCC) and other cancers, and exciting clinical progress has been made in HCC treatment using CD147-directed monoclonal antibodies.

  2. Study of structural model of biological membranes by synchrotron radiation

    CERN Document Server

    Cavalcanti, L P

    2001-01-01

    The objective of this work has been to study, from the structural point of view, the process of incorporation of various types of hydrophobic compounds into the lamellar phase of liposomes and multilayers of the zwitterionic phospholipid DPPC. X-ray diffraction and scattering techniques using synchrotron radiation, have been used to monitor changes of several bilayer systems. Thermotropic phase transitions as well as the order of the lamellar packing were studied in situ experiments. The behavior of the L beta' and L alpha phases was followed as a function of the water content in dispersions of DPPC multi lamellar vesicles with the addition of the alkaloid Ellipticine in several concentrations. The results showed a decrease in the temperature of the pre-transition as well as that of the main transition (P beta' ->L alpha). The decrease of the lamellar spacing as a function of temperature in the liquid crystalline phase leads to the description of the thermal compression coefficient in the L alpha phase. It wa...

  3. New perspectives of studying gastrointestinal muscle function

    Institute of Scientific and Technical Information of China (English)

    Hans Gregersen; Donghua Liao

    2006-01-01

    The motor function of the gastrointestinal tract has primarily been studied using manometry and radiography,though more indirect tests have also been applied. Manometry and radiography do not provide detailed information about the muscle properties as can be assessed from studies of muscle properties in muscle strips in vitro. In recent years a technique based on impedance planimetric mEasurement of pressure-cross-sectional area relations in a distending bag has proven to provide more detailed information about the muscle function in vivo. This review shows examples of new muscle function analysis such as length-tension diagrams, forcevelocity curves and preload-afterload diagrams.

  4. International Biological Engagement Programs Facilitate Newcastle Disease Epidemiological Studies

    Science.gov (United States)

    Miller, Patti J.; Dimitrov, Kiril M.; Williams-Coplin, Dawn; Peterson, Melanie P.; Pantin-Jackwood, Mary J.; Swayne, David E.; Suarez, David L.; Afonso, Claudio L.

    2015-01-01

    Infections of poultry species with virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), one of the most economically significant and devastating diseases for poultry producers worldwide. Biological engagement programs between the Southeast Poultry Research Laboratory (SEPRL) of the United States Department of Agriculture and laboratories from Russia, Pakistan, Ukraine, Kazakhstan, and Indonesia collectively have produced a better understanding of the genetic diversity and evolution of the viruses responsible for ND, which is crucial for the control of the disease. The data from Kazakhstan, Russia, and Ukraine identified possible migratory routes for birds that may carry both virulent NDV (vNDV) and NDV of low virulence into Europe. In addition, related NDV strains were isolated from wild birds in Ukraine and Nigeria, and from birds in continental USA, Alaska, Russia, and Japan, identifying wild birds as a possible mechanism of intercontinental spread of NDV of low virulence. More recently, the detection of new sub-genotypes of vNDV suggests that a new, fifth, panzootic of ND has already originated in Southeast Asia, extended to the Middle East, and is now entering into Eastern Europe. Despite expected challenges when multiple independent laboratories interact, many scientists from the collaborating countries have successfully been trained by SEPRL on molecular diagnostics, best laboratory practices, and critical biosecurity protocols, providing our partners the capacity to further train other employes and to identify locally the viruses that cause this OIE listed disease. These and other collaborations with partners in Mexico, Bulgaria, Israel, and Tanzania have allowed SEPRL scientists to engage in field studies, to elucidate more aspects of ND epidemiology in endemic countries, and to understand the challenges that the scientists and field veterinarians in these countries face on a daily basis. Finally, new viral characterization tools

  5. [Studies on acetylspiramycin. II. Biological activities of spiramycin components].

    Science.gov (United States)

    Kondo, A; Sato, K; Shuto, K; Yamashita, K; Ichikawa, S; Takahashi, K; Kita, K; Nishiie, Y; Sano, H; Yamaguchi, K

    1990-09-01

    Acetylspiramycin (ASPM) was fractionated using high performance liquid chromatography (HPLC). The peak fractions were named F1 to F7 successively in order of increasing retention times (Rt), i.e., increasing hydrophobicity, and studied for 1) antibacterial activities (MIC), 2) antibacterial potency against Bacillus subtilis ATCC 6633, 3) therapeutic effect on mice infected with Streptococcus pneumoniae III, Staphylococcus aureus Smith, 4) acute toxicity by i.p. administration to mice (LD50) and 5) cytotoxicities to fibroblasts derived from Chinese-hamster lung (CHL), cow pulmonary artery endothelial cells (CPAE) and rat hepatic cells. The results obtained are summarized below. 1. Components F1 and 4'-acetylspiramycin F2 had significantly different biological activities from those of other components: F1 showed the lowest antibacterial potency of 492 micrograms (potency)/mg, F2 showed the highest antibacterial potency of 2,040 micrograms (potency)/mg and correspondingly the lowest LD50 value of 692 mg/kg (the highest toxicity). The therapeutic effect of F2 on infections in mice was found to be the second smallest and was superior only to that of F1. The LD50 value of F1 was 1,200 mg/kg and similar to that of ASPM. 2. Antibacterial potencies of F3, F4, F5 and F6 were 1,165, 1,266, 1,374 and 1,530 micrograms (potency)/mg, respectively; fraction with the higher antibacterial activities corresponded to the longer retention times, i.e., the greater hydrophobicities. The most hydrophobic component, F7, 3-propionyl-3",4"-diacetylspiramycin, however, showed a low antibacterial potency of 1,085 micrograms (potency)/mg, next to the lowest one, F1, a fact which was in contradiction to with the sequential relation between hydrophobicities and potencies from F3 to F6.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Recruitment of SH-containing peptides to lipid and biological membranes through the use of a palmitic acid functionalized with a maleimide group.

    Science.gov (United States)

    Haralampiev, Ivan; Mertens, Monique; Schwarzer, Roland; Herrmann, Andreas; Volkmer, Rudolf; Wessig, Pablo; Müller, Peter

    2015-01-02

    This study presents a novel and easily applicable approach to recruit sulfhydryl-containing biomolecules to membranes by using a palmitic acid which is functionalized with a maleimide group. Notably, this strategy can also be employed with preformed (biological) membranes. The applicability of the assay is demonstrated by characterizing the binding of a Rhodamine-labeled peptide to lipid and cellular membranes using methods of fluorescence spectroscopy, lifetime measurement, and microscopy. Our approach offers new possibilities for preparing biologically active liposomes and manipulating living cells.

  7. Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin.

    Science.gov (United States)

    Higdon, Charles W; Mitra, Robi D; Johnson, Stephen L

    2013-01-01

    In order to facilitate understanding of pigment cell biology, we developed a method to concomitantly purify melanocytes, iridophores, and retinal pigmented epithelium from zebrafish, and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co-enrichment in melanocytes and retinal pigmented epithelium, as well as in melanocytes and iridophores. We found 214 genes co-enriched in melanocytes and retinal pigmented epithelium, indicating the shared functions of melanin-producing cells. We found 62 genes significantly co-enriched in melanocytes and iridophores, illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine-based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate-limiting substrate for purine synthesis, phosphoribosyl pyrophosphate, thus constituting a guanine cycle. The purification procedure and expression analysis described here, along with the accompanying transcriptome-wide expression data, provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types, and will be a useful resource for further studies of pigment cell biology.

  8. Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin.

    Directory of Open Access Journals (Sweden)

    Charles W Higdon

    Full Text Available In order to facilitate understanding of pigment cell biology, we developed a method to concomitantly purify melanocytes, iridophores, and retinal pigmented epithelium from zebrafish, and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co-enrichment in melanocytes and retinal pigmented epithelium, as well as in melanocytes and iridophores. We found 214 genes co-enriched in melanocytes and retinal pigmented epithelium, indicating the shared functions of melanin-producing cells. We found 62 genes significantly co-enriched in melanocytes and iridophores, illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine-based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate-limiting substrate for purine synthesis, phosphoribosyl pyrophosphate, thus constituting a guanine cycle. The purification procedure and expression analysis described here, along with the accompanying transcriptome-wide expression data, provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types, and will be a useful resource for further studies of pigment cell biology.

  9. [Undergraduate and postgraduate studies in the biological sciences in Chile (1985)].

    Science.gov (United States)

    Niemeyer, H

    1986-01-01

    teaching undergraduate students in sciences. Teachers in graduate programs should be qualified active researchers. 4. The creation is proposed of a Consejo Nacional de Universidades (National Council of Universities), to be autonomous and composed primarily of outstanding scientists. One of the main functions of this Council would be to licence universities to grant undergraduate and graduate academic degrees in science. 5. The Sociedad de Biología de Chile must maintain an interest in the evaluation of undergraduate and graduate studies in life sciences.

  10. Use of fish functional traits to associate in-stream suspended sediment transport metrics with biological impairment.

    Science.gov (United States)

    Schwartz, John S; Simon, Andrew; Klimetz, Lauren

    2011-08-01

    Loss of ecological integrity due to excessive suspended sediment in rivers and streams is a major cause of water quality impairment in the USA. Current assessment protocols for development of sediment total maximum daily loads (TMDLs) lack a means to link temporally variable sediment transport rates with specific losses of ecological functions as loads increase. In order to accomplish this linkage assessment, a functional traits-based approach was used to correlate site occurrences of 17 fish species traits in three main groups (preferred rearing habitat, trophic feeding guild, and spawning behavior) with suspended sediment transport metrics. The sediment transport metrics included concentrations, durations, and dosages for a range of exceedance frequencies; and mean annual suspended sediment yields (SSY). In addition, this study in the Northwestern Great Plains Ecoregion examined trait relationships with three environmental gradients: channel stability, drainage area, and elevation. Potential stressor responses due to elevated suspended sediment concentration (SSC) levels were correlated with occurrences of five traits: preferred pool habitat; feeding generalists, omnivores, piscivores, and nest-building spawners; and development of ecologically based TMDL targets were demonstrated for specific SSC exceedance frequencies. In addition, reduced site occurrences for preferred pool habitat and nest-building spawners traits were associated with unstable channels and higher SSY. At an ecoregion scale, a functional traits assessment approach provided a means to quantify relations between biological impairment and episodically elevated levels of suspended sediment, supporting efforts to develop ecologically based sediment TMDLs.

  11. Isolation and culture of human hematopoietic progenitors for studies of dendritic cell biology.

    Science.gov (United States)

    Svensson, Mattias

    2009-01-01

    Understanding the regulation of distinct dendritic cell (DC) function and differentiation pathways is important in many physiological and pathophysiological processes. This includes infectious and neoplastic diseases, vaccination and immunotherapy, allograft rejection, and the pathogenesis of autoimmune diseases. Isolation and culture of human hematopoietic progenitor cells provide a valuable model for studies on DC biology and may help uncover new means to manipulate DC differentiation and function in therapeutic settings. Here, a detailed protocol for the isolation of CD34+ hematopoietic progenitor cells from human cord blood is described. The isolated cell population consists of approximately 85% CD34+ CD45+ hematopoietic progenitor cells that in response to granulocyte-macrophage colony-stimulating factor (GM-CSF) plus tumor necrosis factor (TNF) expand and differentiate into CD11c+ HLA-DR+ DC-expressing CD1a.

  12. Systems Biology based studies on anti-inflammatory compounds

    NARCIS (Netherlands)

    Verhoeckx, Kitty Catharina Maria

    2005-01-01

    The introduction of the ‘omics’ techniques (transcriptomics, proteomics, and metabolomics) and systems biology, has caused fundamental changes in the drug discovery process and many other fields in the life science area. In this thesis we explored the possibilities to apply these holistic technologi

  13. Study on Biological Characters of Asparagus macowanii Baker.

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Asparagus macowanfi Baker, is a climbing herbaceous foliage species in genus Asparagus of Liliaceae, This paper summarized its multiple uses, morphologi- cal characteristics, biological habit, reproduction methods, management after cultiva- tion, prevention and control of pests and disease, as well as harvest and grading, with the objective to provide references for the exploitation and utilization of As- paragus macowanii Baker.

  14. Teacher's Study Guide on the Biology of Human Populations: Asia.

    Science.gov (United States)

    United Nations Educational, Scientific, and Cultural Organization, Paris (France).

    Factual and conceptual information dealing with the biology of human populations is offered in this guide for secondary science teachers. Instructional approaches are reviewed and suggestions are offered for use of the problem method approach, the discussion technique, and the project option. Information is organized into an introduction and five…

  15. Teacher's Study Guide on the Biology of Human Populations: Africa.

    Science.gov (United States)

    United Nations Educational, Scientific, and Cultural Organization, Paris (France).

    This teacher's guide is designed to give background information on current biological subjects not usually treated in student texts. The book is divided into five parts, each representing one of the following topics: (1) evolution of human populations; (2) environment of human populations; (3) dynamics of human populations; (4) reproduction in…

  16. Mössbauer study of some biological iron complexes

    Indian Academy of Sciences (India)

    Sikander Ali; Alimuddin; V R Reddy

    2005-12-01

    Some biological complexes containing iron are investigated experimentally at room temperature using the Mössbauer resonance. The complexes show quadrupole doublet and Kramer's degeneracy is found to exist. The electric field gradient, difference in -electron densities and quadrupole coupling constant have been calculated in each case. These parameters are used to obtain information on the surroundings of the Mössbauer atom.

  17. An "enigmatic" L-carnosine (β-alanyl-L-histidine)? Cell proliferative activity as a fundamental property of a natural dipeptide inherent to traditional antioxidant, anti-aging biological activities: balancing and a hormonally correct agent, novel patented oral therapy dosage formulation for mobility, skeletal muscle power and functional performance, hypothalamic-pituitary- brain relationship in health, aging and stress studies.

    Science.gov (United States)

    Babizhayev, Mark A; Yegorov, Yegor E

    2015-01-01

    Hypothalamic releasing and inhibiting hormones are major neuroendocrine regulators of human body metabolism being driven directly to the anterior pituitary gland via hypothalamic-hypophyseal portal veins. The alternative physiological or therapeutic interventions utilizing the pharmaco-nutritional boost of imidazole-containing dipeptides (non-hydrolized oral form of carnosine, carcinine, N-acetylcarnosine lubricant eye drops) can maintain health, enhance physical exercise performance and prevent ageing. Carnosine (β-alanyl-L-histidine) is synthesized in mammalian skeletal muscle. There is an evidence that the release of carnosine from the skeletal muscle sarcomeres moieties during physical exercise affects autonomic neurotransmission and physiological functions. Carnosine released from skeletal muscle during exercise acts as a powerful afferent physiological signaling stimulus for hypothalamus, may be transported into the hypothalamic tuberomammillary nucleus (TMN), specifically to TMN-histamine neurons and hydrolyzed herewith via activities of carnosine-degrading enzyme (carnosinase 2) localized in situ. Through the colocalized enzymatic activity of Histidine decarboxylase in the histaminergic neurons, the resulting L-histidine may subsequently be converted into histamine, which could be responsible for the effects of carnosine on neurotransmission and physiological function. Carnosine and its imidazole-containing dipeptide derivatives are renowned for their anti-aging, antioxidant, membrane protective, metal ion chelating, buffering, anti-glycation/ transglycating activities used to prevent and treat a spectrum of age-related and metabolic diseases, such as neurodegenerative disease, sight threatening eye diseases, Diabetes mellitus and its complications, cancers and other disorders due to their wide spectrum biological activities. The precursor of carnosine (and related imidazole containing compounds) synthesis in skeletal muscles beta-alanine is used as the

  18. Cry1Ab rice does not impact biological characters and functional response ofCyrtorhinus lividipennispreying onNilaparvata lugens eggs

    Institute of Scientific and Technical Information of China (English)

    CHEN Yang; LAI Feng-xiang; SUN Yan-qun; HONG Li-ying; TIAN Jun-ce; ZHANG Zhi-tao; FU Qiang

    2015-01-01

    One concern about the use of transgenic plants is their potential risk to natural enemies. In this study, using the eggs of the rice brown planthopper,Nilaparvata lugens, as a food source, we investigated the effects of Cry1Ab rice on the biological characteristics and functional response of an important predatorCyrtorhinus lividipennis. The results showed that the survival ability (adult emergence rate and egg hatching rate), development (egg duration, nymphal developmental duration), adult fresh weight, adult longevity and fecundity ofC. lividipennis on Bt rice plants were not signiifcantly different compared to those on non-Bt rice plants. Furthermore, two important parameters of functional response (instantaneous search rate and handling time) were not signiifcantly affected by Bt rice. In conclusion, the tested Cry1Ab rice does not adversely impact the biological character and functional response ofC. lividipennis.

  19. 2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function.

    Science.gov (United States)

    González-Díaz, Humberto; Agüero-Chapin, Guillermín; Varona, Javier; Molina, Reinaldo; Delogu, Giovanna; Santana, Lourdes; Uriarte, Eugenio; Podda, Gianni

    2007-04-30

    Methods for prediction of proteins, DNA, or RNA function and mapping it onto sequence often rely on bioinformatics alignment approach instead of chemical structure. Consequently, it is interesting to develop computational chemistry approaches based on molecular descriptors. In this sense, many researchers used sequence-coupling numbers and our group extended them to 2D proteins representations. However, no coupling numbers have been reported for 2D-RNA topology graphs, which are highly branched and contain useful information. Here, we use a computational chemistry scheme: (a) transforming sequences into RNA secondary structures, (b) defining and calculating new 2D-RNA-coupling numbers, (c) seek a structure-function model, and (d) map biological function onto the folded RNA. We studied as example 1-aminocyclopropane-1-carboxylic acid (ACC) oxidases known as ACO, which control fruit ripening having importance for biotechnology industry. First, we calculated tau(k)(2D-RNA) values to a set of 90-folded RNAs, including 28 transcripts of ACO and control sequences. Afterwards, we compared the classification performance of 10 different classifiers implemented in the software WEKA. In particular, the logistic equation ACO = 23.8 . tau(1)(2D-RNA) + 41.4 predicts ACOs with 98.9%, 98.0%, and 97.8% of accuracy in training, leave-one-out and 10-fold cross-validation, respectively. Afterwards, with this equation we predict ACO function to a sequence isolated in this work from Coffea arabica (GenBank accession DQ218452). The tau(1)(2D-RNA) also favorably compare with other descriptors. This equation allows us to map the codification of ACO activity on different mRNA topology features. The present computational-chemistry approach is general and could be extended to connect RNA secondary structure topology to other functions.

  20. Structure-Function Studies on the Prolactin Receptor

    DEFF Research Database (Denmark)

    Haxholm, Gitte Wolfsberg

    Class 1 Cytokine receptors are involved in important biological functions mediated through complex networks of intracellular signaling. However, the molecular details of how signaling is regulated are poorly understood. One of the primary reasons for this limited knowledge is the lack of structural...... information on the intracellular domains (ICDs) of these receptors. The overall aim of this study was to obtain an improved understanding of cytokine receptor signaling through structure-function studies on the prolactin receptor (PRLR). The primary focus of this thesis was to structurally characterize...... the PRLR-ICD and the ICD of the related growth hormone receptor (GHR). We showed that both ICDs were intrinsically disordered throughout their entire lengths and that they associated with lipids characteristic of the inner plasma membrane leaflet through conserved motifs, implicating the membrane...

  1. Biological Actions of Artemisinin: Insights from Medicinal Chemistry Studies

    Directory of Open Access Journals (Sweden)

    Jian Li

    2010-03-01

    Full Text Available Artemisinins have become essential antimalarial drugs for increasingly widespread drug-resistant malaria strains. Although tremendous efforts have been devoted to decipher how this class of molecules works, their exact antimalarial mechanism is still an enigma. Several hypotheses have been proposed to explain their actions, including alkylation of heme by carbon-centered free radicals, interference with proteins such as the sarcoplasmic/endoplasmic calcium ATPase (SERCA, as well as damaging of normal mitochondrial functions. Besides artemisinins, other endoperoxides with various backbones have also been synthesized, some of which showed comparable or even higher antimalarial effects. It is noteworthy that among these artemisinin derivatives, some enantiomers displayed similar in vitro malaria killing efficacy. In this article, the proposed mechanisms of action of artemisinins are reviewed in light of medicinal chemistry findings characterized by efficacy-structure studies, with the hope of gaining more insight into how these potent drugs work.

  2. The Biological Function of the Prion Protein: A Cell Surface Scaffold of Signaling Modules

    Science.gov (United States)

    Linden, Rafael

    2017-01-01

    The prion glycoprotein (PrPC) is mostly located at the cell surface, tethered to the plasma membrane through a glycosyl-phosphatydil inositol (GPI) anchor. Misfolding of PrPC is associated with the transmissible spongiform encephalopathies (TSEs), whereas its normal conformer serves as a receptor for oligomers of the β-amyloid peptide, which play a major role in the pathogenesis of Alzheimer’s Disease (AD). PrPC is highly expressed in both the nervous and immune systems, as well as in other organs, but its functions are controversial. Extensive experimental work disclosed multiple physiological roles of PrPC at the molecular, cellular and systemic levels, affecting the homeostasis of copper, neuroprotection, stem cell renewal and memory mechanisms, among others. Often each such process has been heralded as the bona fide function of PrPC, despite restricted attention paid to a selected phenotypic trait, associated with either modulation of gene expression or to the engagement of PrPC with a single ligand. In contrast, the GPI-anchored prion protein was shown to bind several extracellular and transmembrane ligands, which are required to endow that protein with the ability to play various roles in transmembrane signal transduction. In addition, differing sets of those ligands are available in cell type- and context-dependent scenarios. To account for such properties, we proposed that PrPC serves as a dynamic platform for the assembly of signaling modules at the cell surface, with widespread consequences for both physiology and behavior. The current review advances the hypothesis that the biological function of the prion protein is that of a cell surface scaffold protein, based on the striking similarities of its functional properties with those of scaffold proteins involved in the organization of intracellular signal transduction pathways. Those properties are: the ability to recruit spatially restricted sets of binding molecules involved in specific signaling

  3. Allergen structures and biologic functions: the cutting edge of allergy research.

    Science.gov (United States)

    Pomés, Anna

    2008-09-01

    Studies of structure and function of allergens using state-of-the-art technologies have led to a better understanding of allergenicity, including aspects related to cross-reactivity, allergen nomenclature, and the identification of antigenic determinants. This information is being applied to the design and production of allergy vaccines, some of which already have proven efficacy and safety in clinical trials.

  4. Translating inter-individual genetic variation to biological function in complex phenotypes

    DEFF Research Database (Denmark)

    Yadav, Rachita

    examines epigenetic, genetic, transcriptomic and proteomic variations within different multifactorial diseases and this pivotal information is then annotated and associated to its corresponding phenotype. Childhood asthma and obesity are the two main phenotypic themes in this thesis. In the first section......The key objectives of this thesis work are to decipher and prioritise observed variations among different phenotypes. With advancements in high throughput technology leading to a surge in biological data, it is imperative to analyse and interpret this information. Consequently, this thesis work......, 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...

  5. 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...... genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT...

  6. Object-based attentional modulation of biological motion processing: spatiotemporal dynamics using functional magnetic resonance imaging and electroencephalography.

    Science.gov (United States)

    Safford, Ashley S; Hussey, Elizabeth A; Parasuraman, Raja; Thompson, James C

    2010-07-07

    Although it is well documented that the ability to perceive biological motion is mediated by the lateral temporal cortex, whether and when neural activity in this brain region is modulated by attention is unknown. In particular, it is unclear whether the processing of biological motion requires attention or whether such stimuli are processed preattentively. Here, we used functional magnetic resonance imaging, high-density electroencephalography, and cortically constrained source estimation methods to investigate the spatiotemporal effects of attention on the processing of biological motion. Directing attention to tool motion in overlapping movies of biological motion and tool motion suppressed the blood oxygenation level-dependent (BOLD) response of the right superior temporal sulcus (STS)/middle temporal gyrus (MTG), while directing attention to biological motion suppressed the BOLD response of the left inferior temporal sulcus (ITS)/MTG. Similarly, category-based modulation of the cortical current source density estimates from the right STS/MTG and left ITS was observed beginning at approximately 450 ms following stimulus onset. Our results indicate that the cortical processing of biological motion is strongly modulated by attention. These findings argue against preattentive processing of biological motion in the presence of stimuli that compete for attention. Our findings also suggest that the attention-based segregation of motion category-specific responses only emerges relatively late (several hundred milliseconds) in processing.

  7. Unexpected functional similarities between gatekeeper tumour suppressor genes and proto-oncogenes revealed by systems biology.

    Science.gov (United States)

    Zhao, Yongzhong; Epstein, Richard J

    2011-05-01

    Familial tumor suppressor genes comprise two subgroups: caretaker genes (CTs) that repair DNA, and gatekeeper genes (GKs) that trigger cell death. Since GKs may also induce cell cycle delay and thus enhance cell survival by facilitating DNA repair, we hypothesized that the prosurvival phenotype of GKs could be selected during cancer progression, and we used a multivariable systems biology approach to test this. We performed multidimensional data analysis, non-negative matrix factorization and logistic regression to compare the features of GKs with those of their putative antagonists, the proto-oncogenes (POs), as well as with control groups of CTs and functionally unrelated congenital heart disease genes (HDs). GKs and POs closely resemble each other, but not CTs or HDs, in terms of gene structure (P<0.001), expression level and breadth (P<0.01), DNA methylation signature (P<0.001) and evolutionary rate (P<0.001). The similar selection pressures and epigenetic trajectories of GKs and POs so implied suggest a common functional attribute that is strongly negatively selected-that is, a shared phenotype that enhances cell survival. The counterintuitive finding of similar evolutionary pressures affecting GKs and POs raises an intriguing possibility: namely, that cancer microevolution is accelerated by an epistatic cascade in which upstream suppressor gene defects subvert the normal bifunctionality of wild-type GKs by constitutively shifting the phenotype away from apoptosis towards survival. If correct, this interpretation would explain the hitherto unexplained phenomenon of frequent wild-type GK (for example, p53) overexpression in tumors.

  8. Melanocyte biology and function with reference to oral melanin hyperpigmentation in HIV-seropositive subjects.

    Science.gov (United States)

    Feller, Liviu; Chandran, Rakesh; Kramer, Beverley; Khammissa, Razia A G; Altini, Mario; Lemmer, Johan

    2014-09-01

    The color of normal skin and of oral mucosa is not determined by the number of melanocytes in the epithelium but rather by their melanogenic activity. Pigmented biopolymers or melanins are synthesized in melanosomes. Tyrosinase is the critical enzyme in the biosynthesis of both brown/black eumelanin and yellow/red pheomelanin. The number of the melanosomes within the melanocytes, the type of melanin within the melanosomes, and the efficacy of the transfer of melanosomes from the melanocytes to the neighboring keratinocytes all play an important role in tissue pigmentation. Melanin production is regulated by locally produced factors including proopiomelanocortin and its derivative peptides, particularly alpha-melanocyte-stimulating hormone (α-MSH), melanocortin 1 receptor (MC1R), adrenergic and cholinergic agents, growth factors, cytokines, and nitric oxide. Both eumelanin and pheomelanin can be produced by the same melanocytes, and the proportion of the two melanin types is influenced by the degree of functional activity of the α-MSH/MC1R intracellular pathway. The cause of HIV oral melanosis is not fully understood but may be associated with HIV-induced cytokine dysregulation, with the medications commonly prescribed to HIV-seropositive persons, and with adrenocortical dysfunction, which is not uncommon in HIV-seropositive subjects with AIDS. The purpose of this article is to discuss some aspects of melanocyte biology and HIV-associated oral melanin hyperpigmentation.

  9. Functional and biological diversity of foliar spectra in tree canopies throughout the Andes to Amazon region.

    Science.gov (United States)

    Asner, Gregory P; Martin, Roberta E; Carranza-Jiménez, Loreli; Sinca, Felipe; Tupayachi, Raul; Anderson, Christopher B; Martinez, Paola

    2014-10-01

    Spectral properties of foliage express fundamental chemical interactions of canopies with solar radiation. However, the degree to which leaf spectra track chemical traits across environmental gradients in tropical forests is unknown. We analyzed leaf reflectance and transmittance spectra in 2567 tropical canopy trees comprising 1449 species in 17 forests along a 3400-m elevation and soil fertility gradient from the Amazonian lowlands to the Andean treeline. We developed quantitative links between 21 leaf traits and 400-2500-nm spectra, and developed classifications of tree taxa based on spectral traits. Our results reveal enormous inter-specific variation in spectral and chemical traits among canopy trees of the western Amazon. Chemical traits mediating primary production were tightly linked to elevational changes in foliar spectral signatures. By contrast, defense compounds and rock-derived nutrients tracked foliar spectral variation with changing soil fertility in the lowlands. Despite the effects of abiotic filtering on mean foliar spectral properties of tree communities, the spectra were dominated by phylogeny within any given community, and spectroscopy accurately classified 85-93% of Amazonian tree species. Our findings quantify how tropical tree canopies interact with sunlight, and indicate how to measure the functional and biological diversity of forests with spectroscopy.

  10. 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.

  11. 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.

  12. Biological functions of glycosyltransferase genes involved in O-fucose glycan synthesis.

    Science.gov (United States)

    Okajima, Tetsuya; Matsuura, Aiko; Matsuda, Tsukasa

    2008-07-01

    Rare types of glycosylation often occur in a domain-specific manner and are involved in specific biological processes. Well-known examples of such modification are O-linked fucose (O-fucose) and O-linked glucose (O-glucose) glycans on epidermal growth factor (EGF) domains. In particular, O-fucose glycans are reported to regulate the functions of EGF domain-containing proteins such as urinary-type plasminogen activator and Notch receptors. Two glycosyltransferases catalyze the initiation and elongation of O-fucose glycans. The initiation process is catalyzed by O-fucosyltransferase 1, which is essential for Notch signalling in both Drosophila and mice. O-fucosyltransferase 1 can affect the folding, ligand interaction and endocytosis of Notch receptors, and both the glycosyltransferase and non-catalytic activities of O-fucosyltransferase 1 have been reported. The elongation of O-fucose monosaccharide is catalyzed by Fringe-related genes, which differentially modulate the interaction between Notch and two classes of ligands, namely, Delta and Serrate/Jagged. In this article, we have reviewed the recent reports addressing the distinctive features of the glycosyltransferases and O-glycans present on the EGF domains.

  13. Mechanically robust, rapidly actuating, and biologically functionalized macroporous poly(N-isopropylacrylamide)/silk hybrid hydrogels.

    Science.gov (United States)

    Gil, Eun Seok; Park, Sang-Hyug; Tien, Lee W; Trimmer, Barry; Hudson, Samuel M; Kaplan, David L

    2010-10-05

    A route toward mechanically robust, rapidly actuating, and biologically functionalized polymeric actuators using macroporous soft materials is described. The materials were prepared by combining silk protein and a synthetic polymer (poly(N-isopropylacrylamide) (PNIAPPm)) to form interpenetrating network materials and macroporous structures by freeze-drying, with hundreds of micrometer diameter pores and exploiting the features of both polymers related to dynamic materials and structures. The chemically cross-linked PNIPAAm networks provided stimuli-responsive features, while the silk interpenetrating network formed by inducing protein β-sheet crystallinity in situ for physical cross-links provided material robustness, improved expansion force, and enzymatic degradability. The macroporous hybrid hydrogels showed enhanced thermal-responsive properties in comparison to pure PNIPAAm hydrogels, nonporous silk/PNIPAAm hybrid hydrogels, and previously reported macroporous PNIPAAm hydrogels. These new systems reach near equilibrium sizes in shrunken/swollen states in less than 1 min, with the structural features providing improved actuation rates and stable oscillatory properties due to the macroporous transport and the mechanically robust silk network. Confocal images of the hydrated hydrogels around the lower critical solution temperature (LCST) revealed macropores that could be used to track changes in the real time morphology upon thermal stimulus. The material system transformed from a macroporous to a nonporous structure upon enzymatic degradation. To extend the utility of the system, an affinity platform for a switchable or tunable system was developed by immobilizing biotin and avidin on the macropore surfaces.

  14. Molecular mechanism and biological function of miRNA-155 and its target genes on endometriosis

    Institute of Scientific and Technical Information of China (English)

    Na Ji; Li Zhao; Xin Feng; Li-Mei Luo; Ting Liang; Chen-Yu Zhuang; Li-Hua Zhang

    2015-01-01

    Objective:To explore molecular mechanism and biological function of miR-155 and its target genes on endometriosis.Methods: The expression of miR-155 in Ems patient and healthy control were assayed by RT-PCR. After miR-155 mimic and inhibitor were transfected into Ems endometrial cells for 48 h, the viability of cell was detected by MTT assay. Transwell migration and invasion assay were used to detect cell migration and invasion. The expression of cell apoptotic protein Bax and Bcl-2, matrix metalloproteinase (MMP 2) and MMP 9 were assayed by western blot.Results: The expression of miR-155 in Ems patient was more than that in the health control (P<0.01). After miR-155 mimic and inhibitor were transfected into Ems endometrial cells for 48 h, miR-155 over-expression could increase cell viability, and promoted cell migration and invasion, which was related to down-regulation of Bax along with up-regulation of Bcl-2, MMP 2 and MMP 9.Conclusion:These results suggested miR-155 lower expression inhibit endometrial cell proliferation and migration of the Ems.

  15. 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.

  16. MYC function and regulation in flies: how Drosophila has enlightened MYC cancer biology

    Directory of Open Access Journals (Sweden)

    Jue Er Amanda Lee

    2014-12-01

    Full Text Available Progress in our understanding of the complex signaling events driving human cancer would have been unimaginably slow without discoveries from Drosophila genetic studies. Significantly, many of the signaling pathways now synonymous with cancer biology were first identified as a result of elegant screens for genes fundamental to metazoan development. Indeed the name given to many core cancer-signaling cascades tells of their history as developmental patterning regulators in flies—e.g. Wingless (Wnt, Notch and Hippo. Moreover, astonishing insight has been gained into these complex signaling networks, and many other classic oncogenic signaling networks (e.g. EGFR/RAS/RAF/ERK, InR/PI3K/AKT/TOR, using sophisticated fly genetics. Of course if we are to understand how these signaling pathways drive cancer, we must determine the downstream program(s of gene expression activated to promote the cell and tissue over growth fundamental to cancer. Here we discuss one commonality between each of these pathways: they are all implicated as upstream activators of the highly conserved MYC oncogene and transcription factor. MYC can drive all aspects of cell growth and cell cycle progression during animal development. MYC is estimated to be dysregulated in over 50% of all cancers, underscoring the importance of elucidating the signals activating MYC. We also discuss the FUBP1/FIR/FUSE system, which acts as a ‘cruise control’ on the MYC promoter to control RNA Polymerase II pausing and, therefore, MYC transcription in response to the developmental signaling environment. Importantly, the striking conservation between humans and flies within these major axes of MYC regulation has made Drosophila an extremely valuable model organism for cancer research. We therefore discuss how Drosophila studies have helped determine the validity of signaling pathways regulating MYC in vivo using sophisticated genetics, and continue to provide novel insight into cancer biology.

  17. Functional proteomic analysis revealed ground-base ion radiations cannot reflect biological effects of space radiations of rice

    Science.gov (United States)

    Wang, Wei; Sun, Yeqing; Zhao, Qian; Han, Lu

    2016-07-01

    Highly ionizing radiation (HZE) in space is considered as main factor causing biological effects. Radiobiological studies during space flights are unrepeatable due to the variable space radiation environment, ground-base ion radiations are usually performed to simulate of the space biological effect. Spaceflights present a low-dose rate (0.1˜~0.3mGy/day) radiation environment inside aerocrafts while ground-base ion radiations present a much higher dose rate (100˜~500mGy/min). Whether ground-base ion radiation can reflect effects of space radiation is worth of evaluation. In this research, we compared the functional proteomic profiles of rice plants between on-ground simulated HZE particle radiation and spaceflight treatments. Three independent ground-base seed ionizing radiation experiments with different cumulative doses (dose range: 2˜~20000mGy) and different liner energy transfer (LET) values (13.3˜~500keV/μμm) and two independent seed spaceflight experiments onboard Chinese 20th satellite and SZ-6 spacecraft were carried out. Alterations in the proteome were analyzed by two-dimensional difference gel electrophoresis (2-D DIGE) with MALDI-TOF/TOF mass spectrometry identifications. 45 and 59 proteins showed significant (pmetabolic process, protein folding and phosphorylation. The results implied that ground-base radiations cannot truly reflect effects of spaceflight radiations, ground-base radiation was a kind of indirect effect to rice causing oxidation and metabolism stresses, but space radiation was a kind of direct effect leading to macromolecule (DNA and protein) damage and signal pathway disorders. This functional proteomic analysis work might provide a new evaluation method for further on-ground simulated HZE radiation experiments.

  18. Density functional theory studies of etoricoxib

    Science.gov (United States)

    Sachdeva, Ritika; Kaur, Prabhjot; Singh, V. P.; Saini, G. S. S.

    2016-05-01

    Etoricoxib is a COX-2 selective inhibitor drug with molecular formula C18H15ClN2O2S. It is primarily used for the treatment of arthritis(rheumatoid, psoriatic, osteoarthritis), ankylosing spondylitis, gout and chronic low back pain. Theoretical studies of the molecule including geometry optimization and vibrational frequency calculations were carried out with the help of density functional theory calculations using 6-311++ g (d, p) basis set and B3LYP functional.

  19. Impact of AT2-receptor stimulation on vascular biology, kidney function, and blood pressure

    DEFF Research Database (Denmark)

    Danyel, L.A.; Schmerler, P.; Paulis, L.;

    2013-01-01

    angiotensin II) and with relevance for blood pressure (BP) regulation or hypertensive end-organ damage. These data will include studies on vasodilation/vasoconstriction in isolated resistance arteries ex vivo, studies on kidney function, studies on vascular remodeling, and studies that measured the net effect...... to attenuate hypertension-induced vascular remodeling and reduce arterial stiffening, which in more chronic settings and together with the natriuretic effect may result in modest lowering of BP. We conclude from these preclinical data that AT2R agonists are not suitable for antihypertensive monotherapy...

  20. 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

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

    Directory of Open Access Journals (Sweden)

    Luan Yihui

    2009-09-01

    Full Text Available 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 Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks. Conclusion Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.

  2. A transcriptomics-based biological framework for studying mechanisms of endocrine disruption in small fish species.

    Science.gov (United States)

    Wang, Rong-Lin; Bencic, David; Villeneuve, Daniel L; Ankley, Gerald T; Lazorchak, Jim; Edwards, Stephen

    2010-07-01

    This study sought to construct a transcriptomics-based framework of signal transduction pathways, transcriptional regulatory networks, and the hypothalamic-pituitary gonadal (HPG) axis in zebrafish (Danio rerio) to facilitate formulation of specific, testable hypotheses regarding the mechanisms of endocrine disruption in fish. For the analyses involved, we used data from a total of more than 300 microarrays representing 58 conditions, which encompassed 4 tissue types from zebrafish of both genders exposed for 1 of 3 durations to 10 different test chemicals (17alpha-ethynyl estradiol, fadrozole, 17beta-trenbolone, fipronil, prochloraz, flutamide, muscimol, ketoconazole, trilostane, and vinclozolin). Differentially expressed genes were identified by one class t-tests for each condition, and those with false discovery rates of less than 40% and treatment/control ratios > or =1.3-fold were mapped to orthologous human, mouse, and rat pathways by Ingenuity Pathway Analysis to look for overrepresentation of known biological pathways. To complement the analysis of known biological pathways, the genes regulated by approximately 1800 transcription factors were inferred using the ARACNE mutual information-based algorithm. The resulting gene sets for all transcriptional factors, along with a group of compiled HPG-axis genes and approximately 130 publicly available biological pathways, were analyzed for their responses to the 58 treatment conditions by Gene Set Enrichment Analysis (GSEA) and its variant, Extended-GSEA. The biological pathways and transcription factors associated with multiple distinct treatments showed substantial interactions among the HPG-axis, TGF-beta, p53, and several of their cross-talking partners. These candidate networks/pathways have a variety of profound impacts on such cellular functions as stress response, cell cycle, and apoptosis.

  3. Hazardous wastes in aquatic environments: Biological uptake and metabolism studies

    Energy Technology Data Exchange (ETDEWEB)

    Barber, J.; Apblett, A.; Ensley, H. [and others

    1996-05-02

    The projects discussed in this article include the following: the uptake, accumulation, metabolism, toxicity and physiological effects of various environmentally-important contaminants, inorganic and organic, in several wetland species that are interrelated through food webs; and investigation of the potential for developing and linking chemical and biological methods of remediation so as to encapsulate bioaccummulated ions in stable wasteforms such as ceramics and/or zeolites. 24 refs.

  4. Brachypodium as an experimental system for the study of stem parenchyma biology in grasses.

    Science.gov (United States)

    Jensen, Jacob Krüger; Wilkerson, Curtis Gene

    2017-01-01

    Stem parenchyma is a major cell type that serves key metabolic functions for the plant especially in large grasses, such as sugarcane and sweet sorghum, where it serves to store sucrose or other products of photosynthesis. It is therefore desirable to understand the metabolism of this cell type as well as the mechanisms by which it provides its function for the rest of the plant. Ultimately, this information can be used to selectively manipulate this cell type in a controlled manner to achieve crop improvement. In this study, we show that Brachypodium distachyon is a useful model system for stem pith parenchyma biology. Brachypodium can be grown under condition where it resembles the growth patterns of important crops in that it produces large amounts of stem material with the lower leaves senescing and with significant stores of photosynthate located in the stem parenchyma cell types. We further characterize stem plastid morphology as a function of tissue types, as this organelle is central for a number of metabolic pathways, and quantify gene expression for the four main classes of starch biosynthetic genes. Notably, we find several of these genes differentially regulated between stem and leaf. These studies show, consistent with other grasses, that the stem functions as a specialized storage compartment in Brachypodium.

  5. Functional extension of high-speed AFM for wider biological applications.

    Science.gov (United States)

    Uchihashi, Takayuki; Watanabe, Hiroki; Fukuda, Shingo; Shibata, Mikihiro; Ando, Toshio

    2016-01-01

    High-speed atomic force microscopy (HS-AFM) has been established and used, which can visualize biomolecules in dynamic action at high spatiotemporal resolution without disturbing their function. Various studies conducted in the past few years have demonstrated that the dynamic structure and action of biomolecules revealed with HS-AFM can provide greater insights than ever before into how the molecules function. However, this microscopy has still limitations in some regards. Recently, efforts have been carried out to overcome some of the limitations. As a result, it has now become possible to visualize dynamic processes occurring even on live cells and perform simultaneous observations of topographic and fluorescent images at a high rate. In this review, we focus on technical developments for expanding the range of objects and phenomena observable by HS-AFM as well as for granting multiple functionalities to HS-AFM.

  6. Single Fluorescent Molecules as Nano-Illuminators for Biological Structure and Function

    Science.gov (United States)

    Moerner, W. E.

    2011-03-01

    Since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. {62}, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. For example, the shape of single filaments in a living cell can be extracted simply by allowing a single molecule to move through the filament (PNAS {103}, 10929 (2006)). The addition of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (super-resolution) and a new array of acronyms (PALM, STORM, F-PALM etc.) and advances have appeared. We have used the native blinking and switching of a common yellow-emitting variant of green fluorescent protein (EYFP) reported more than a decade ago (Nature {388}, 355 (1997)) to achieve sub-40 nm super-resolution imaging of several protein structures in the bacterium Caulobacter crescentus: the quasi-helix of the actin-like protein MreB (Nat. Meth. {5}, 947 (2008)), the cellular distribution of the DNA binding protein HU (submitted), and the recently discovered division spindle composed of ParA filaments (Nat. Cell Biol. {12}, 791 (2010)). Even with these advances, better emitters would provide more photons and improved resolution, and a new photoactivatable small-molecule emitter has recently been synthesized and targeted to specific structures in living cells to provide super-resolution images (JACS {132}, 15099 (2010)). Finally, a new optical method for extracting three-dimensional position information based on

  7. Developing integrated TOF-SIMS/MALDI IMS system in studying biological systems

    Science.gov (United States)

    Wu, Ligang

    Using imaging mass spectrometry (IMS) techniques (including TOF-SIMS and MALDI IMS) to study biological systems is a relatively new concept and quickly gained popularity in recent years. Imaging mass spectrometry is a discovery technology that utilizes a focused ion beam or laser beam to desorb ions from sample surface. By detecting the desorbed ions, the chemical distributions and biological changes of a sample surface can be analyzed. These techniques offer a new analytical imaging approach to investigate biological processes at the cellular and tissue level. In this research, a novel integrated TOF-SIMS/MALDI IMS system as well as IMS based biological-sample-preparation techniques and data-reduction methods are developed. We then demonstrate the power of these techniques in studying different biological systems, including monosaccharides isomers, human breast cancer cell lines, mouse embryo tissues and mouse kidney sections. Using TOF-SIMS and statistical analysis methods, seven monosaccharide isomers are fully differentiated by analyzing their characteristic spectral pattern. In addition, a deep understanding of the fragmentation pathway of these isomers under ion bombardment is gained. In an application of TOF-SIMS to the differentiation of three human breast cancer cell lines, MCF-7, T47D, and MDA-MB-231, we show that principal component analysis (PCA) data reduction of TOF-SIMS spectra can differentiate cellular compartments (cytosol, nuclear and particulate) within the cell types, as well as homogenates from among the three cell lines. In a tissue-specific application, we extend the analytical capabilities of TOF-SIMS and PCA by imaging and differentiating Formalin-fixed paraffin-embedded (FFPE) mouse embryo tissues. We demonstrate reproducible differentiation of six tissue types based on the remaining small molecules after paraffin-embedding and the fragments of the cellular proteins. In a unique study of fresh frozen mouse kidney tissues, both TOF

  8. Gene expression-based biological test for major depressive disorder: an advanced study

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    Watanabe S

    2017-02-01

    Full Text Available Shin-ya Watanabe,1 Shusuke Numata,1 Jun-ichi Iga,2 Makoto Kinoshita,1 Hidehiro Umehara,1 Kazuo Ishii,3 Tetsuro Ohmori1 1Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 2Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, 3Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan Purpose: Recently, we could distinguished patients with major depressive disorder (MDD from nonpsychiatric controls with high accuracy using a panel of five gene expression markers (ARHGAP24, HDAC5, PDGFC, PRNP, and SLC6A4 in leukocyte. In the present study, we examined whether this biological test is able to discriminate patients with MDD from those without MDD, including those with schizophrenia and bipolar disorder.Patients and methods: We measured messenger ribonucleic acid expression levels of the aforementioned five genes in peripheral leukocytes in 17 patients with schizophrenia and 36 patients with bipolar disorder using quantitative real-time polymerase chain reaction (PCR, and we combined these expression data with our previous expression data of 25 patients with MDD and 25 controls. Subsequently, a linear discriminant function was developed for use in discriminating between patients with MDD and without MDD.Results: This expression panel was able to segregate patients with MDD from those without MDD with a sensitivity and specificity of 64% and 67.9%, respectively.Conclusion: Further research to identify MDD-specific markers is needed to improve the performance of this biological test. Keywords: depressive disorder, biomarker, gene expression, schizophrenia, bipolar disorder

  9. 前S2区突变LHBs与C53蛋白相互作用对HepG2细胞生物学功能的影响%Study on the effects on cell biology functions of HepG2 cell line by interaction between LHBs and C53

    Institute of Scientific and Technical Information of China (English)

    刘灏; 林智琪; 黄显莹; 符方勇; 叶玲; 周忠信; 刘正军

    2013-01-01

    目的 明确肝癌细胞系HepG2中前S2区突变乙型肝炎表面抗原大蛋白(hepatitis B virus large surface protein,LHBs)与C53蛋白相互作用对细胞生物学功能的影响.方法 分别构建pCMV-5a-pre S2 LHBs和pCDNA-4-C53质粒,共同转染肝癌细胞系HepG2后,分别检测其相互作用对Chk1活性的影响;BrdU法细胞增殖检测明确其对细胞有丝分裂及增殖的影响.结果 成功构建pCMV-5a-pre S2 LHBs和pCDNA-4-C53质粒;其在细胞内的相互作用增加细胞Cdk1活性并促进细胞的增殖和有丝分裂过程.结论 肝癌细胞系HepG2内pre S2 LHBs及C53的相互作用对细胞生物学功能存在影响,提示可能与HBV后肝癌的发病机制相关.%Objective To identify the effects on cell biology functions of HepG2 cells by interaction between pre-S2 LHBs and C53.Methods The plasmids pCMV-5a-pre-S2 LHBs and pCDNA-4-C53 were reconstructed.The plasmids pCMV-5a-LHBs and pCDNA-4-C53 were cotransfected into the hepatoma cell line HepG2,the roles of the binding of pre-S2 LHBs with C53 on Cdk1,Chk1 activation and mitotic entry were studied.Results The plasmids pCMV-5a-LHBs and pCDNA-4-C53 were reconstructed successfully.The binding of pre S2 LHBs with C53 increased Cdk1 activation and mitotic entry.Conclusions By counteracting C53,pre-S2 LHBs promotes Cdk1 activation and mitotic entry in both unperturbed cell cycle progression and delayed the function of Chk1,which may be a novel potential mechanism for HBV-induced hepatocellular carcinoma (HCC).

  10. Functional near-infrared spectroscopy studies in children

    Directory of Open Access Journals (Sweden)

    Nagamitsu Shinichiro

    2012-03-01

    Full Text Available Abstract Psychosomatic and developmental behavioral medicine in pediatrics has been the subject of significant recent attention, with infants, school-age children, and adolescents frequently presenting with psychosomatic, behavioral, and psychiatric symptoms. These may be a consequence of insecurity of attachment, reduced self-confidence, and peer -relationship conflicts during their developmental stages. Developmental cognitive neuroscience has revealed significant associations between specific brain lesions and particular cognitive dysfunctions. Thus, identifying the biological deficits underlying such cognitive dysfunction may provide new insights into therapeutic prospects for the management of those symptoms in children. Recent advances in noninvasive neuroimaging techniques, and especially functional near-infrared spectroscopy (NIRS, have contributed significant findings to the field of developmental cognitive neuroscience in pediatrics. We present here a comprehensive review of functional NIRS studies of children who have developed normally and of children with psychosomatic and behavioral disorders.

  11. Biologically variable respiration as a stochastic process in ventilation - a stochastic model study.

    Science.gov (United States)

    Min, Kyongyob; Hosoi, Keita; Degami, Masayuki; Kinoshita, Yoshinori

    2010-01-01

    Based on the fractal bronchial tree, we introduced a function of "asynchronous phasic contractions of lobular bronchiole", which would generate fluctuations in tidal volumes. Stochastic control theory was able to describe a genesis of biological variability in spontaneous respirations using a Schroedinger wave function.

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

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    For Yue Tso

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

  13. Using pancreas tissue slices for in situ studies of islet of Langerhans and acinar cell biology.

    Science.gov (United States)

    Marciniak, Anja; Cohrs, Christian M; Tsata, Vasiliki; Chouinard, Julie A; Selck, Claudia; Stertmann, Julia; Reichelt, Saskia; Rose, Tobias; Ehehalt, Florian; Weitz, Jürgen; Solimena, Michele; Slak Rupnik, Marjan; Speier, Stephan

    2014-12-01

    Studies on the cellular function of the pancreas are typically performed in vitro on its isolated functional units, the endocrine islets of Langerhans and the exocrine acini. However, these approaches are hampered by preparation-induced changes of cell physiology and the lack of an intact surrounding. We present here a detailed protocol for the preparation of pancreas tissue slices. This procedure is less damaging to the tissue and faster than alternative approaches, and it enables the in situ study of pancreatic endocrine and exocrine cell physiology in a conserved environment. Pancreas tissue slices facilitate the investigation of cellular mechanisms underlying the function, pathology and interaction of the endocrine and exocrine components of the pancreas. We provide examples for several experimental applications of pancreas tissue slices to study various aspects of pancreas cell biology. Furthermore, we describe the preparation of human and porcine pancreas tissue slices for the validation and translation of research findings obtained in the mouse model. Preparation of pancreas tissue slices according to the protocol described here takes less than 45 min from tissue preparation to receipt of the first slices.

  14. A study on biological media of ultrasonic nonlinear parameter B/A

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jeong Koo; Jung, Hong Ryang; Lim, Cheong Hwan [Hanseo Univ, Seosan (Korea, Republic of)

    2001-06-01

    This study deals with the relationship between the magnitude of ultrasonic nonlinear parameter B/A, and sound speed of amount of fat present in biological media to measure B/A system using a wide band ultrasonic transducer. To represent this case, mixtures of egg whites and egg yolk were studied. Even though the differences in density and sound speed of the two egg components were in the range of 1%, B/A increase parabolically as a function of the fat density, which is not in agreement with the Yoshizumi et al.'s suggestion. In skim, milk that dose not contain fat, both the B/A and the sound speed increase with the solubility. It is considered that protein could affect these values.

  15. A Study of the Probe Effect on the Apparent Image of Biological Atomic Force Microscopy

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The probe effect on the apparent image of biological atomic force microscopy was explored in this study, and the potential of AFM in conformational study of gene related biological processes was illustrated by the specific nanostructural information of a new antitumor drug binding to DNA.

  16. 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

  17. Incubation Station for the Bacterial Growth Study in Biological Samples

    Directory of Open Access Journals (Sweden)

    Carlos Rafael Duharte Rodríguez

    2015-12-01

    Full Text Available This work shows the designing and characterization of a prototype of laboratory incubator as support of Microbiology research, in particular for the research of the bacterial growth in biological samples through optic methods (Turbidimetry and electrometric measurements of bioimpedance. It shows the results of simulation and experimentation of the design proposed for the canals of measurement of the variables: temperature and humidity, with a high linearity from the adequate selection of the corresponding sensors and the analogue components of every canal, controlled with help of a microcontroller AT89C51 (ATMEL with adequate benefi ts for this type of application.

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

    Science.gov (United States)

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

    2012-04-01

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

  19. Virtual Agonist-antagonist Mechanisms Produce Biological Muscle-like Functions: An Application for Robot Joint Control

    DEFF Research Database (Denmark)

    Xiong, Xiaofeng; Wörgötter, Florentin; Manoonpong, Poramate

    2014-01-01

    or torque sensing systems; thereby capable of implementing the model on small legged robots driven by, e.g., standard servo motors. Thus, the VAAM minimizes hardware and reduces system complexity. From this point of view, the model opens up another way of simulating muscle behaviors on artificial machines......Purpose – Biological muscles of animals have a surprising variety of functions, i.e., struts, springs, and brakes. According to this, the purpose of this paper is to apply virtual agonist-antagonist mechanisms to robot joint control allowing for muscle-like functions and variably compliant joint......, variably compliant joint motions can be produced without mechanically bulky and complex mechanisms or complex force/toque sensing at each joint. Moreover, through tuning the damping coefficient of the VAAM, the functions of the VAAM are comparable to biological muscles. Originality/value – The model (i...

  20. Expression profiling and Ingenuity biological function analyses of interleukin-6- versus nerve growth factor-stimulated PC12 cells

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    Dimitriades-Schmutz Beatrice

    2009-02-01

    Full Text Available Abstract Background The major goal of the study was to compare the genetic programs utilized by the neuropoietic cytokine Interleukin-6 (IL-6 and the neurotrophin (NT Nerve Growth Factor (NGF for neuronal differentiation. Results The designer cytokine Hyper-IL-6 in which IL-6 is covalently linked to its soluble receptor s-IL-6R as well as NGF were used to stimulate PC12 cells for 24 hours. Changes in gene expression levels were monitored using Affymetrix GeneChip technology. We found different expression for 130 genes in IL-6- and 102 genes in NGF-treated PC12 cells as compared to unstimulated controls. The gene set shared by both stimuli comprises only 16 genes. A key step is upregulation of growth factors and functionally related external molecules known to play important roles in neuronal differentiation. In particular, IL-6 enhances gene expression of regenerating islet-derived 3 alpha (REG3A; 1084-fold, regenerating islet-derived 3 beta (REG3B/PAPI; 672-fold, growth differentiation factor 15 (GDF15; 80-fold, platelet-derived growth factor alpha (PDGFA; 69-fold, growth hormone releasing hormone (GHRH; 30-fold, adenylate cyclase activating polypeptide (PACAP; 20-fold and hepatocyte growth factor (HGF; 5-fold. NGF recruits GDF15 (131-fold, transforming growth factor beta 1 (TGFB1; 101-fold and brain-derived neurotrophic factor (BDNF; 89-fold. Both stimuli activate growth-associated protein 43 (GAP-43 indicating that PC12 cells undergo substantial neuronal differentiation. Moreover, IL-6 activates the transcription factors retinoic acid receptor alpha (RARA; 20-fold and early growth response 1 (Egr1/Zif268; 3-fold known to play key roles in neuronal differentiation. Ingenuity biological function analysis revealed that completely different repertoires of molecules are recruited to exert the same biological functions in neuronal differentiation. Major sub-categories include cellular growth and differentiation, cell migration, chemotaxis, cell

  1. Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices.

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    Lorenzo Pasotti

    Full Text Available BACKGROUND: Modularity is a crucial issue in the engineering world, as it enables engineers to achieve predictable outcomes when different components are interconnected. Synthetic Biology aims to apply key concepts of engineering to design and construct new biological systems that exhibit a predictable behaviour. Even if physical and measurement standards have been recently proposed to facilitate the assembly and characterization of biological components, real modularity is still a major research issue. The success of the bottom-up approach strictly depends on the clear definition of the limits in which biological functions can be predictable. RESULTS: The modularity of transcription-based biological components has been investigated in several conditions. First, the activity of a set of promoters was quantified in Escherichia coli via different measurement systems (i.e., different plasmids, reporter genes, ribosome binding sites relative to an in vivo reference promoter. Second, promoter activity variation was measured when two independent gene expression cassettes were assembled in the same system. Third, the interchangeability of input modules (a set of constitutive promoters and two regulated promoters connected to a fixed output device (a logic inverter expressing GFP was evaluated. The three input modules provide tunable transcriptional signals that drive the output device. If modularity persists, identical transcriptional signals trigger identical GFP outputs. To verify this, all the input devices were individually characterized and then the input-output characteristic of the logic inverter was derived in the different configurations. CONCLUSIONS: Promoters activities (referred to a standard promoter can vary when they are measured via different reporter devices (up to 22%, when they are used within a two-expression-cassette system (up to 35% and when they drive another device in a functionally interconnected circuit (up to 44%. This paper

  2. A Functional Model for Teaching Osmosis-Diffusion to Biology Students

    Science.gov (United States)

    Olsen, Richard W.; Petry, Douglas E.

    1976-01-01

    Described is a maternal-fetal model, operated by the student, to teach osmosis-diffusion to biology students. Included are materials needed, assembly instructions, and student operating procedures. (SL)

  3. 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.

  4. Functional magnetic resonance imaging studies of language.

    Science.gov (United States)

    Small, Steven L; Burton, Martha W

    2002-11-01

    Functional neuroimaging of language builds on almost 150 years of study in neurology, psychology, linguistics, anatomy, and physiology. In recent years, there has been an explosion of research using functional imaging technology, especially positron emission tomography (PET) and functional magnetic resonance imaging (fMRI), to understand the relationship between brain mechanisms and language processing. These methods combine high-resolution anatomic images with measures of language-specific brain activity to reveal neural correlates of language processing. This article reviews some of what has been learned about the neuroanatomy of language from these imaging techniques. We first discuss the normal case, organizing the presentation according to the levels of language, encompassing words (lexicon), sound structure (phonemes), and sentences (syntax and semantics). Next, we delve into some unusual language processing circumstances, including second languages and sign languages. Finally, we discuss abnormal language processing, including developmental and acquired dyslexia and aphasia.

  5. Abnormal expression of calcyphosine is associated with poor prognosis and cell biology function in colorectal cancer

    Science.gov (United States)

    Shao, Weiwei; Wang, Quhui; Wang, Feiran; Jiang, Yasu; Xu, Meirong; Xu, Junfei

    2016-01-01

    The aim of this study was to investigate the calcyphosine (CAPS) expression in human colorectal cancer (CRC) and to explore its clinical and prognostic significances. CAPS expression was measured by Western blot, real-time polymerase chain reaction analysis, and immunohistochemistry. The relationships between the CAPS expression levels and the clinicopathological factors were investigated. The Kaplan–Meier method and log-rank test were used to investigate the overall survival of the patients. Moreover, the effects of CAPS on biological roles of CRC cells were also evaluated by MTT assay, colony formation assay, and transwell assay. CAPS was significantly overexpressed in cancerous tissue and CRC cell lines compared with adjacent nontumor tissue and a normal human intestinal epithelial cell line. Overexpression of CAPS was significantly associated with histological grade (P=0.004), invasive depth (P<0.001), lymph node metastasis (P=0.003), tumor node metastasis stage (P=0.017), and distant metastasis (P=0.042). Furthermore, silencing of CAPS expression in CRC cells inhibited their proliferation, colony formation, migration, and invasion. Kaplan–Meier survival analysis showed that high CAPS expression might demonstrate poor prognosis in CRC patients. Cox regression analysis revealed that CAPS expression was an independent prognostic factor of CRC. Our data suggested that the upregulation of CAPS might play a role in the carcinogenesis and progression of CRC. CAPS could be used as a potential diagnostic factor and be an independent good prognostic indicator for CRC patients. PMID:26889086

  6. 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.

  7. 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

    2016-01-21

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

  8. Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation.

    Science.gov (United States)

    Wang, Xia; Yang, Jian-Guo; Chen, Li; Wang, Ji-Long; Cheng, Qi; Dixon, Ray; Wang, Yi-Ping

    2013-01-01

    Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ~100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase-LacI expression system was used to replace the σ(54)-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ~42% of the nitrogenase activity of the σ(54)-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology.

  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.; 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

    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. Biological and functional diversity of bird communities in natural and human modified habitats in Northern Flank of Knuckles Mountain Forest Range, Sri Lanka

    Directory of Open Access Journals (Sweden)

    KALYA SUBASINGHE

    2014-10-01

    Full Text Available Subasinghe K, Sumanapala AP. 2014. Biological and functional diversity of bird communities in natural and human modified habitats in Northern Flank of Knuckles Mountain Forest Range, Sri Lanka. Biodiversitas 15: 200-205. The Knuckles Mountain Forest Range (KMFR has a complex mosaic of natural and human modified habitats and the contribution of these habitats to the biological and functional diversities has not been deeply studied. Present study investigated both of these diversities in five habitat types (two natural habitats: Sub-montane forest and Pitawala Patana grassland; three modified habitats: cardamom, pinus and abandoned tea plantations in Northern Flank of KMFR using birds as the indicator group. Bird communities were surveyed using point count method. A total of 1,150 individuals belonging to 56 species were observed. The highest species richness was reported from the cardamom plantation where as sub-montane forest had the highest feeding guild diversity in terms of Shannon Weiner index. The abandoned tea plantation and the Pitawala Patana grasslands with fairly open habitats, showed relatively lower levels of feeding guild diversities. It is clear that the structurally complex habitats contribute more to the area’s biological and functional diversities and need to be taken into consideration when developing conservation plans.

  11. Combined Mechanical and Electrical Study of Polymers of Biological Origin

    Science.gov (United States)

    Zsoldos, G.; Szoda, K.; Marossy, K.

    2017-02-01

    Thermally Simulated Depolarization Current measurement is an excellent but not widely used method for identifying relaxation processes in polymers. The DMA method is used here to analyze the mechanical changes depend on temperature in biopolymers. The two techniques take advantage of the energy changes involved in the various phase transitions of certain polymer molecules. This allows for several properties of the material to be ascertained; melting points, enthalpies of melting, crystallization temperatures, glass transition temperatures and degradation temperatures. The examined biopolymer films are made from biological materials such as proteins and polysaccharides. These materials have gained wide usage in pharmaceutical, medical and food areas. The uses of biopolymer films depend on their structure and mechanical properties. This work is based on pectin and gelatin films. The films were prepared by casting. The casting technique used aqueous solutions in each case of sample preparation. The manufacturing process of the pectin and gelatin films was a single stage solving process.

  12. Biological studies of matrix metalloproteinase sensitive drug delivery systems

    DEFF Research Database (Denmark)

    Johansen, Pia Thermann

    due to severe side effects as a result of drug distribution to healthy tissues. To enhance ecacy of treatment and improve life quality of patients, tumor specific drug delivery strategies, such as liposome encapsulated drugs, which accumulate in tumor tissue, has gained increased attention. Several...... for delivery of drugs to specific tissues or cells utilizing biological knowledge of cancer tissue is getting increased attention. In this thesis a novel matrix metalloproteinase-2 (MMP-2) sensitive poly-ethylene glycol (PEG) coated liposomal drug delivery system for treatment of cancer was developed...... the use of MMP- 2 as a trigger for liposomal activation in tumor tissue. Thus, this new strategy provides a promising system for specific delivery of encapsulated drugs and controlled release in tumor tissues, resulting in enhanced drug bioavailability and decreased systemic side effects. In addition, we...

  13. Study on Biological Control Of Rhizoctonia solani via Trichoderma

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Strain T02-25 was selected from approximately 30 rhizosphere isolates of Trichoderma species isolated from roots of crops. Its biological activity against Rhizoctonia solani was determined for the control efficacy to pepper seedling blight caused by R. solani in the field. The assay methods were treating R. solani sclerotia by Trichoderma conidial suspension (106cfu ml-1) and scattering Thichoderma rice bran over the pepper root medium. The results showed that T02-25 was active against R. solani in both ways, and its control efficacy was 82.7% and 78.0%, respectively. In addition to comparison of the efficacy of the two application methods, the relationship of different factors in the control efficacy of Trichoderma against R. solani was discussed.

  14. A Comprehensive Systems Biology Approach to Studying Zika Virus

    Science.gov (United States)

    Relich, Ryan F.

    2016-01-01

    Zika virus (ZIKV) is responsible for an ongoing and intensifying epidemic in the Western Hemisphere. We examined the complete predicted proteomes, glycomes, and selectomes of 33 ZIKV strains representing temporally diverse members of the African lineage, the Asian lineage, and the current outbreak in the Americas. Derivation of the complete selectome is an ‘omics’ approach to identify distinct evolutionary pressures acting on different features of an organism. Employment of the M8 model did not show evidence of global diversifying selection acting on the ZIKV polyprotein; however, a mixed effect model of evolution showed strong evidence (P<0.05) for episodic diversifying selection acting on specific sites. Single nucleotide polymorphisms (SNPs) were predictably frequent across strains relative to the derived consensus sequence. None of the 9 published detection procedures utilize targets that share 100% identity across the 33 strains examined, indicating that ZIKV escape from molecular detection is predictable. The predicted O-linked glycome showed marked diversity across strains; however, the N-linked glycome was highly stable. All Asian and American strains examined were predicted to include glycosylation of E protein ASN154, a modification proposed to mediate neurotropism, whereas the modification was not predicted for African strains. SNP diversity, episodic diversifying selection, and differential glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a.) The recently emergent Asian/American N-glycotype is mediating the new and emerging neuropathogenic potential of ZIKV; and b.) further divergence at specific sites is predictable as endemnicity is established in the Americas. PMID:27584813

  15. Xenobiotic transporters: ascribing function from gene knockout and mutation studies.

    Science.gov (United States)

    Klaassen, Curtis D; Lu, Hong

    2008-02-01

    Transporter-mediated absorption, secretion, and reabsorption of chemicals are increasingly recognized as important determinants in the biological activities of many xenobiotics. In recent years, the rapid progress in generating and characterizing mice with targeted deletion of transporters has greatly increased our knowledge of the functions of transporters in the pharmacokinetics/toxicokinetics of xenobiotics. In this introduction, we focus on functions of transporters learned from experiments on knockout mice as well as humans and rodents with natural mutations of these transporters. We limit our discussion to transporters that either directly transport xenobiotics or are important in biliary excretion or cellular defenses, namely multidrug resistance, multidrug resistance-associated proteins, breast cancer resistance protein, organic anion transporting polypeptides, organic anion transporters, organic cation transporters, nucleoside transporters, peptide transporters, bile acid transporters, cholesterol transporters, and phospholipid transporters, as well as metal transporters. Efflux transporters in intestine, liver, kidney, brain, testes, and placenta can efflux xenobiotics out of cells and serve as barriers against the entrance of xenobiotics into cells, whereas many xenobiotics enter the biological system via uptake transporters. The functional importance of a given transporter in each tissue depends on its substrate specificity, expression level, and the presence/absence of other transporters with overlapping substrate preferences. Nevertheless, a transporter may affect a tissue independent of its local expression by altering systemic metabolism. Further studies on the gene regulation and function of transporters, as well as the interrelationship between transporters and phase I/II xenobiotic-metabolizing enzymes, will provide a complete framework for developing novel strategies to protect us from xenobiotic insults.

  16. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  17. Molecular Biological and Biochemical Studies Reveal New Pathways Important for Cotton Fiber Development

    Institute of Scientific and Technical Information of China (English)

    Yu Xu; Hong-Bin Li; Yu-Xian Zhu

    2007-01-01

    As one of the longest single-celled seed trichomes, fibers provide an excellent model for studying fundamental biological processes such as cell differentiation, cell expansion, and cell wall biosynthesis. In this review, we summarize recent progress in cotton functional genomic studies that characterize the dynamic changes in the transcriptomes of fiber cells. Extensive expression profilings of cotton fiber transcriptomes have provided comprehensive information, as quite a number of transcription factors and enzyme-coding genes have been shown to express preferentially during the fiber elongation period. Biosynthesis of the plant hormone ethylene is found significantly upregulated during the fiber growth period as revealed by both microarray analysis and by biochemical and physiological studies. It is suggested that genetic engineering of the ethylene pathway may improve the quality and the productivity of cotton lint. Many metabolic pathways, such as biosynthesis of celiulose and matrix polysaccharides are preferentially expressed in actively growing fiber cells. Five gene families, including proline-rich proteins (PRP), arabinogalactan proteins (AGP), expansins, tubulins and lipid transfer proteins (LTP) are activated during early fiber development,indicating that they may also be needed for cell elongation. In conclusion, we identify a few areas of future research for cotton functional genomic studies.

  18. [THE FUNCTIONAL CONSTITUENT OF A BIOLOGICAL COMPONENT IN PROGRAMS FOR TRAINING SPECIALISTS IN THE AREA OF PARASITOLOGY FOR ACCREDITATION].

    Science.gov (United States)

    Dovgalev, A S; Astanina, S Yu; Andreeva, N D

    2015-01-01

    The paper considers the functional aspects of a biological component in programs for training specialists in the area of Parasitology for accreditation within the current enactments, including those on modernization of public health and additional professional education. The working program of the module "Fundamental Disciplines" has been used as an example to outline approaches to molding a medical parasitologist's capacity and readiness to solve professional tasks on the basis of knowledge of fundamental disciplines: biology, immunology, and medical geography. Education fundamentalization is shown to suggest more unsupervised work of a learner in the teaching process. The fundamental constituent of a biological component of the 'programs for training learners in the specialty of Parasitology for accreditation is shown in the interaction of all sections of this area with special and allied subjects.

  19. Genetic studies of body mass index yield new insights for obesity biology

    Science.gov (United States)

    Day, Felix R.; Powell, Corey; Vedantam, Sailaja; Buchkovich, Martin L.; Yang, Jian; Croteau-Chonka, Damien C.; Esko, Tonu; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Kutalik, Zoltán; Luan, Jian’an; Mägi, Reedik; Randall, Joshua C.; Winkler, Thomas W.; Wood, Andrew R.; Workalemahu, Tsegaselassie; Faul, Jessica D.; Smith, Jennifer A.; Zhao, Jing Hua; Zhao, Wei; Chen, Jin; Fehrmann, Rudolf; Hedman, Åsa K.; Karjalainen, Juha; Schmidt, Ellen M.; Absher, Devin; Amin, Najaf; Anderson, Denise; Beekman, Marian; Bolton, Jennifer L.; Bragg-Gresham, Jennifer L.; Buyske, Steven; Demirkan, Ayse; Deng, Guohong; Ehret, Georg B.; Feenstra, Bjarke; Feitosa, Mary F.; Fischer, Krista; Goel, Anuj; Gong, Jian; Jackson, Anne U.; Kanoni, Stavroula; Kleber, Marcus E.; Kristiansson, Kati; Lim, Unhee; Lotay, Vaneet; Mangino, Massimo; Leach, Irene Mateo; Medina-Gomez, Carolina; Medland, Sarah E.; Nalls, Michael A.; Palmer, Cameron D.; Pasko, Dorota; Pechlivanis, Sonali; Peters, Marjolein J.; Prokopenko, Inga; Shungin, Dmitry; Stančáková, Alena; Strawbridge, Rona J.; Sung, Yun Ju; Tanaka, Toshiko; Teumer, Alexander; Trompet, Stella; van der Laan, Sander W.; van Setten, Jessica; Van Vliet-Ostaptchouk, Jana V.; Wang, Zhaoming; Yengo, Loïc; Zhang, Weihua; Isaacs, Aaron; Albrecht, Eva; Ärnlöv, Johan; Arscott, Gillian M.; Attwood, Antony P.; Bandinelli, Stefania; Barrett, Amy; Bas, Isabelita N.; Bellis, Claire; Bennett, Amanda J.; Berne, Christian; Blagieva, Roza; Blüher, Matthias; Böhringer, Stefan; Bonnycastle, Lori L.; Böttcher, Yvonne; Boyd, Heather A.; Bruinenberg, Marcel; Caspersen, Ida H.; Chen, Yii-Der Ida; Clarke, Robert; Daw, E. Warwick; de Craen, Anton J. M.; Delgado, Graciela; Dimitriou, Maria; Doney, Alex S. F.; Eklund, Niina; Estrada, Karol; Eury, Elodie; Folkersen, Lasse; Fraser, Ross M.; Garcia, Melissa E.; Geller, Frank; Giedraitis, Vilmantas; Gigante, Bruna; Go, Alan S.; Golay, Alain; Goodall, Alison H.; Gordon, Scott D.; Gorski, Mathias; Grabe, Hans-Jörgen; Grallert, Harald; Grammer, Tanja B.; Gräßler, Jürgen; Grönberg, Henrik; Groves, Christopher J.; Gusto, Gaëlle; Haessler, Jeffrey; Hall, Per; Haller, Toomas; Hallmans, Goran; Hartman, Catharina A.; Hassinen, Maija; Hayward, Caroline; Heard-Costa, Nancy L.; Helmer, Quinta; Hengstenberg, Christian; Holmen, Oddgeir; Hottenga, Jouke-Jan; James, Alan L.; Jeff, Janina M.; Johansson, Åsa; Jolley, Jennifer; Juliusdottir, Thorhildur; Kinnunen, Leena; Koenig, Wolfgang; Koskenvuo, Markku; Kratzer, Wolfgang; Laitinen, Jaana; Lamina, Claudia; Leander, Karin; Lee, Nanette R.; Lichtner, Peter; Lind, Lars; Lindström, Jaana; Lo, Ken Sin; Lobbens, Stéphane; Lorbeer, Roberto; Lu, Yingchang; Mach, François; Magnusson, Patrik K. E.; Mahajan, Anubha; McArdle, Wendy L.; McLachlan, Stela; Menni, Cristina; Merger, Sigrun; Mihailov, Evelin; Milani, Lili; Moayyeri, Alireza; Monda, Keri L.; Morken, Mario A.; Mulas, Antonella; Müller, Gabriele; Müller-Nurasyid, Martina; Musk, Arthur W.; Nagaraja, Ramaiah; Nöthen, Markus M.; Nolte, Ilja M.; Pilz, Stefan; Rayner, Nigel W.; Renstrom, Frida; Rettig, Rainer; Ried, Janina S.; Ripke, Stephan; Robertson, Neil R.; Rose, Lynda M.; Sanna, Serena; Scharnagl, Hubert; Scholtens, Salome; Schumacher, Fredrick R.; Scott, William R.; Seufferlein, Thomas; Shi, Jianxin; Smith, Albert Vernon; Smolonska, Joanna; Stanton, Alice V.; Steinthorsdottir, Valgerdur; Stirrups, Kathleen; Stringham, Heather M.; Sundström, Johan; Swertz, Morris A.; Swift, Amy J.; Syvänen, Ann-Christine; Tan, Sian-Tsung; Tayo, Bamidele O.; Thorand, Barbara; Thorleifsson, Gudmar; Tyrer, Jonathan P.; Uh, Hae-Won; Vandenput, Liesbeth; Verhulst, Frank C.; Vermeulen, Sita H.; Verweij, Niek; Vonk, Judith M.; Waite, Lindsay L.; Warren, Helen R.; Waterworth, Dawn; Weedon, Michael N.; Wilkens, Lynne R.; Willenborg, Christina; Wilsgaard, Tom; Wojczynski, Mary K.; Wong, Andrew; Wright, Alan F.; Zhang, Qunyuan; Brennan, Eoin P.; Choi, Murim; Dastani, Zari; Drong, Alexander W.; Eriksson, Per; Franco-Cereceda, Anders; Gådin, Jesper R.; Gharavi, Ali G.; Goddard, Michael E.; Handsaker, Robert E.; Huang, Jinyan; Karpe, Fredrik; Kathiresan, Sekar; Keildson, Sarah; Kiryluk, Krzysztof; Kubo, Michiaki; Lee, Jong-Young; Liang, Liming; Lifton, Richard P.; Ma, Baoshan; McCarroll, Steven A.; McKnight, Amy J.; Min, Josine L.; Moffatt, Miriam F.; Montgomery, Grant W.; Murabito, Joanne M.; Nicholson, George; Nyholt, Dale R.; Okada, Yukinori; Perry, John R. B.; Dorajoo, Rajkumar; Reinmaa, Eva; Salem, Rany M.; Sandholm, Niina; Scott, Robert A.; Stolk, Lisette; Takahashi, Atsushi; Tanaka, Toshihiro; van ’t Hooft, Ferdinand M.; Vinkhuyzen, Anna A. E.; Westra, Harm-Jan; Zheng, Wei; Zondervan, Krina T.; Heath, Andrew C.; Arveiler, Dominique; Bakker, Stephan J. L.; Beilby, John; Bergman, Richard N.; Blangero, John; Bovet, Pascal; Campbell, Harry; Caulfield, Mark J.; Cesana, Giancarlo; Chakravarti, Aravinda; Chasman, Daniel I.; Chines, Peter S.; Collins, Francis S.; Crawford, Dana C.; Cupples, L. Adrienne; Cusi, Daniele; Danesh, John; de Faire, Ulf; den Ruijter, Hester M.; Dominiczak, Anna F.; Erbel, Raimund; Erdmann, Jeanette; Eriksson, Johan G.; Farrall, Martin; Felix, Stephan B.; Ferrannini, Ele; Ferrières, Jean; Ford, Ian; Forouhi, Nita G.; Forrester, Terrence; Franco, Oscar H.; Gansevoort, Ron T.; Gejman, Pablo V.; Gieger, Christian; Gottesman, Omri; Gudnason, Vilmundur; Gyllensten, Ulf; Hall, Alistair S.; Harris, Tamara B.; Hattersley, Andrew T.; Hicks, Andrew A.; Hindorff, Lucia A.; Hingorani, Aroon D.; Hofman, Albert; Homuth, Georg; Hovingh, G. Kees; Humphries, Steve E.; Hunt, Steven C.; Hyppönen, Elina; Illig, Thomas; Jacobs, Kevin B.; Jarvelin, Marjo-Riitta; Jöckel, Karl-Heinz; Johansen, Berit; Jousilahti, Pekka; Jukema, J. Wouter; Jula, Antti M.; Kaprio, Jaakko; Kastelein, John J. P.; Keinanen-Kiukaanniemi, Sirkka M.; Kiemeney, Lambertus A.; Knekt, Paul; Kooner, Jaspal S.; Kooperberg, Charles; Kovacs, Peter; Kraja, Aldi T.; Kumari, Meena; Kuusisto, Johanna; Lakka, Timo A.; Langenberg, Claudia; Marchand, Loic Le; Lehtimäki, Terho; Lyssenko, Valeriya; Männistö, Satu; Marette, André; Matise, Tara C.; McKenzie, Colin A.; McKnight, Barbara; Moll, Frans L.; Morris, Andrew D.; Morris, Andrew P.; Murray, Jeffrey C.; Nelis, Mari; Ohlsson, Claes; Oldehinkel, Albertine J.; Ong, Ken K.; Madden, Pamela A. F.; Pasterkamp, Gerard; Peden, John F.; Peters, Annette; Postma, Dirkje S.; Pramstaller, Peter P.; Price, Jackie F.; Qi, Lu; Raitakari, Olli T.; Rankinen, Tuomo; Rao, D. C.; Rice, Treva K.; Ridker, Paul M.; Rioux, John D.; Ritchie, Marylyn D.; Rudan, Igor; Salomaa, Veikko; Samani, Nilesh J.; Saramies, Jouko; Sarzynski, Mark A.; Schunkert, Heribert; Schwarz, Peter E. H.; Sever, Peter; Shuldiner, Alan R.; Sinisalo, Juha; Stolk, Ronald P.; Strauch, Konstantin; Tönjes, Anke; Trégouët, David-Alexandre; Tremblay, Angelo; Tremoli, Elena; Virtamo, Jarmo; Vohl, Marie-Claude; Völker, Uwe; Waeber, Gérard; Willemsen, Gonneke; Witteman, Jacqueline C.; Zillikens, M. Carola; Adair, Linda S.; Amouyel, Philippe; Asselbergs, Folkert W.; Assimes, Themistocles L.; Bochud, Murielle; Boehm, Bernhard O.; Boerwinkle, Eric; Bornstein, Stefan R.; Bottinger, Erwin P.; Bouchard, Claude; Cauchi, Stéphane; Chambers, John C.; Chanock, Stephen J.; Cooper, Richard S.; de Bakker, Paul I. W.; Dedoussis, George; Ferrucci, Luigi; Franks, Paul W.; Froguel, Philippe; Groop, Leif C.; Haiman, Christopher A.; Hamsten, Anders; Hui, Jennie; Hunter, David J.; Hveem, Kristian; Kaplan, Robert C.; Kivimaki, Mika; Kuh, Diana; Laakso, Markku; Liu, Yongmei; Martin, Nicholas G.; März, Winfried; Melbye, Mads; Metspalu, Andres; Moebus, Susanne; Munroe, Patricia B.; Njølstad, Inger; Oostra, Ben A.; Palmer, Colin N. A.; Pedersen, Nancy L.; Perola, Markus; Pérusse, Louis; Peters, Ulrike; Power, Chris; Quertermous, Thomas; Rauramaa, Rainer; Rivadeneira, Fernando; Saaristo, Timo E.; Saleheen, Danish; Sattar, Naveed; Schadt, Eric E.; Schlessinger, David; Slagboom, P. Eline; Snieder, Harold; Spector, Tim D.; Thorsteinsdottir, Unnur; Stumvoll, Michael; Tuomilehto, Jaakko; Uitterlinden, André G.; Uusitupa, Matti; van der Harst, Pim; Walker, Mark; Wallaschofski, Henri; Wareham, Nicholas J.; Watkins, Hugh; Weir, David R.; Wichmann, H-Erich; Wilson, James F.; Zanen, Pieter; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Heid, Iris M.; O’Connell, Jeffrey R.; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Abecasis, Gonçalo R.; Franke, Lude; Frayling, Timothy M.; McCarthy, Mark I.; Visscher, Peter M.; Scherag, André; Willer, Cristen J.; Boehnke, Michael; Mohlke, Karen L.; Lindgren, Cecilia M.; Beckmann, Jacques S.; Barroso, Inês; North, Kari E.; Ingelsson, Erik; Hirschhorn, Joel N.; Loos, Ruth J. F.; Speliotes, Elizabeth K.

    2015-01-01

    Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P account for ~2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis. PMID:25673413

  20. Pharmacognostic and Biological Studies of the Roots of Rubia Cordifolia Linn. (Rubiaceae

    Directory of Open Access Journals (Sweden)

    RAMESH S. DEODA

    2011-06-01

    Full Text Available Rubia cordifolia (Rubiaceae is also known as, Manjishtha, Indian madder known to contain substantial amounts of anthraquinones, especially in the roots which is responsible for anti-tumor, anti-inflammatory, urinary disorders, antistress antimicrobial, hepatoprotective, radio protective, and anticancer, antimicrobial, antifungal, hypotensive, analgesic, antimalarial, antioxidant, antileukemic and mutagenic functions, immunomodulatory, anti-inflammatory and antioxidant activity. The plant contains substantial amounts of anthraquinones, triterpenoids especially in the roots, which is responsible for most of its pharmacological activity. In present study the chloroform fraction from methanolic extract of roots of R. cordifolia were evaluated for its biological effect and compared with the parent extract and remaining fraction, where chloroform fraction showed potent protective action for stress induced complications in mice.

  1. A computational functional genomics based self-limiting self-concentration mechanism of cell specialization as a biological role of jumping genes.

    Science.gov (United States)

    Lötsch, Jörn; Ultsch, Alfred

    2016-01-01

    Specialization is ubiquitous in biological systems and its manifold mechanisms are active research topics. Although clearly adaptive, the way in which specialization of cells is realized remains incompletely understood as it requires the reshaping of a cell's genome to favor particular biological processes in the competition on a cell's functional capacity. Here, a self-specialization mechanism is identified as a possible biological role of jumping genes, in particular LINE-1 retrotransposition. The mechanism is self-limiting and consistent with its evolutionary preservation despite its likely gene-breaking effects. The scenario we studied was the need for a cell to process a longer exposition to an extraordinary situation, for example continuous exposure to the nociceptive input or the intake of addictive drugs. Both situations may evolve toward chronification. The mechanism involves competition within a gene set in which a subset of genes cooperating in particular biological processes. The subset carries a piece of information, consisting of the LINE-1 sequence, about the destruction of their functional competitor genes which are not involved in that process. During gene transcription, an active copy of LINE-1 is co-transcribed. At a certain low probability, a subsequently transcribed and thus actually exposed gene can be rendered nonfunctional by LINE-1 retrotransposition in a relevant gene part. As retrotransposition needs time it is unlikely that LINE-1 retrotranspose into its own carrier gene. This reshapes the cell genome toward self-specializing of those biological processes that are carried out with a high number of LINE-1 containing genes. Self-termination of the mechanism is achieved by allowing LINE-1 to also occasionally jump into the coding region of itself, thus destroying the information about competitor destruction by successively decreasing the number of LINE-1 until the mechanism ceases. Employing a computational functional genomics approach, we

  2. Expression patterns of cysteine peptidase genes across the Tribolium castaneum life cycle provide clues to biological function.

    Science.gov (United States)

    Perkin, Lindsey; Elpidina, Elena N; Oppert, Brenda

    2016-01-01

    The red flour beetle, Tribolium castaneum, is a major agricultural pest responsible for considerable loss of stored grain and cereal products worldwide. T. castaneum larvae have a highly compartmentalized gut, with cysteine peptidases mostly in the acidic anterior part of the midgut that are critical to the early stages of food digestion. In previous studies, we described 26 putative cysteine peptidase genes in T. castaneum (types B, L, O, F, and K) located mostly on chromosomes 3, 7, 8, and 10. In the present study, we hypothesized that specific cysteine peptidase genes could be associated with digestive functions for food processing based on comparison of gene expression profiles in different developmental stages, feeding and non-feeding. RNA-Seq was used to determine the relative expression of cysteine peptidase genes among four major developmental stages (egg, larvae, pupae, and adult) of T. castaneum. We also compared cysteine peptidase genes in T. castaneum to those in other model insects and coleopteran pests. By combining transcriptome expression, phylogenetic comparisons, response to dietary inhibitors, and other existing data, we identified key cysteine peptidases that T. castaneum larvae and adults use for food digestion, and thus new potential targets for biologically-based control products.

  3. New themes in the biological functions of 5-methylcytosine and 5-hydroxymethylcytosine.

    Science.gov (United States)

    Moen, Erika L; Mariani, Christopher J; Zullow, Hayley; Jeff-Eke, Meselle; Litwin, Edward; Nikitas, John N; Godley, Lucy A

    2015-01-01

    5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) play a critical role in development and normal physiology. Alterations in 5-mC and 5-hmC patterns are common events in hematopoietic neoplasms. In this review, we begin by emphasizing the importance of 5-mC, 5-hmC, and their enzymatic modifiers in hematological malignancies. Then, we discuss the functions of 5-mC and 5-hmC at distinct genic contexts, including promoter regions, gene bodies, intron-exon boundaries, alternative promoters, and intragenic microRNAs. Recent advances in technology have allowed for the study of 5-mC and 5-hmC independently and specifically permitting distinction between the bases that show them to have transcriptional effects that vary by their location relative to gene structure. We extend these observations to their functions at enhancers and transcription factor binding sites. We discuss dietary influences on 5-mC and 5-hmC levels and summarize the literature on the effects of folate and vitamin C on 5-mC and 5-hmC, respectively. Finally, we discuss how these new themes in the functions of 5-mC and 5-hmC will likely influence the broader research field of epigenetics.

  4. Biological couplings: Classification and characteristic rules

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The phenomena that biological functions originate from biological coupling are the important biological foundation of multiple bionics and the significant discoveries in the bionic fields. In this paper, the basic concepts related to biological coupling are introduced from the bionic viewpoint. Constitution, classification and characteristic rules of biological coupling are illuminated, the general modes of biological coupling studies are analyzed, and the prospects of multi-coupling bionics are predicted.

  5. Gene expression-based biological test for major depressive disorder: an advanced study

    Science.gov (United States)

    Watanabe, Shin-ya; Numata, Shusuke; Iga, Jun-ichi; Kinoshita, Makoto; Umehara, Hidehiro; Ishii, Kazuo; Ohmori, Tetsuro

    2017-01-01

    Purpose Recently, we could distinguished patients with major depressive disorder (MDD) from nonpsychiatric controls with high accuracy using a panel of five gene expression markers (ARHGAP24, HDAC5, PDGFC, PRNP, and SLC6A4) in leukocyte. In the present study, we examined whether this biological test is able to discriminate patients with MDD from those without MDD, including those with schizophrenia and bipolar disorder. Patients and methods We measured messenger ribonucleic acid expression levels of the aforementioned five genes in peripheral leukocytes in 17 patients with schizophrenia and 36 patients with bipolar disorder using quantitative real-time polymerase chain reaction (PCR), and we combined these expression data with our previous expression data of 25 patients with MDD and 25 controls. Subsequently, a linear discriminant function was developed for use in discriminating between patients with MDD and without MDD. Results This expression panel was able to segregate patients with MDD from those without MDD with a sensitivity and specificity of 64% and 67.9%, respectively. Conclusion Further research to identify MDD-specific markers is needed to improve the performance of this biological test. PMID:28260899

  6. Studying of Phenomenon of Biological Adaptation to Heavy Water

    Directory of Open Access Journals (Sweden)

    Oleg Mosin

    2014-12-01

    Full Text Available Biological influence of deuterium on cells of various taxonomic groups of prokaryotic and eucaryotic microorganisms realizing methylotrophic, chemoheterotrophic, photo-organotrophic, and photosynthetic ways of assimilation of carbon substrates (methylotrophic bacteria Brevibacterium methylicum, chemoheterotrophic bacteria Bacillus subtilis, photo-organotrophic halobacteria Halobacterium halobium, and green micro algae Chlorella vulgaris was investigated at the growth on media with heavy water (2H2O. For investigated microorganisms are submitted the data on growth and adaptation on the growth media containing as sources of deuterated substrates 2H2O, [2H]methanol and hydrolisates of deutero-biomass of methylotrophic bacteria B. methylicum, obtained after multistage adaptation to 2H2O. The qualitative and quantitative composition of intra- and endocellular amino acids, proteins, carbohydrates and fatty acids in conditions of adaptation to 2H2O is investigated. It is shown, that the effects observed at adaptation to 2H2O, possess a complex multifactorial character and connected to cytological, morphological and physiological changes – the magnitude of the lag- period, time of cellular generation, output of biomass, a parity ratio of synthesized amino acids, proteins, carbohydrates and lipids, and also with an evolutionary level of the organization of the investigated object and the pathways of assimilation of carbon substrates as well.

  7. Applied Bayesian statistical studies in biology and medicine

    CERN Document Server

    D’Amore, G; Scalfari, F

    2004-01-01

    It was written on another occasion· that "It is apparent that the scientific culture, if one means production of scientific papers, is growing exponentially, and chaotically, in almost every field of investigation". The biomedical sciences sensu lato and mathematical statistics are no exceptions. One might say then, and with good reason, that another collection of bio­ statistical papers would only add to the overflow and cause even more confusion. Nevertheless, this book may be greeted with some interest if we state that most of the papers in it are the result of a collaboration between biologists and statisticians, and partly the product of the Summer School th "Statistical Inference in Human Biology" which reaches its 10 edition in 2003 (information about the School can be obtained at the Web site http://www2. stat. unibo. itleventilSito%20scuolalindex. htm). is common experience - and not only This is rather important. Indeed, it in Italy - that encounters between statisticians and researchers are spora...

  8. Preliminary Study of Greywater Treatment through Rotating Biological Contactor

    Directory of Open Access Journals (Sweden)

    Ashfaq Ahmed Pathan

    2011-07-01

    Full Text Available The characteristics of the greywater vary from country to country and it depends upon the cultural and social behavior of the respective country. There was a considerable need to characterize and recycle the greywater. In this regard greywater was separated from the black water and analyzed for various physiochemical parameters. Among various greywater recycling treatment technologies, RBC (Rotating Biological Contactor is more effective treatment technique in reducing COD (Chemical Oxygen Demand and organic matters from the greywater. But this technology was not applied and tested in Pakistan. There was extensive need to investigate the RBC technology for greywater recycling at small scale before applying at mass scale. To treat the greywater, a single-stage RBC simulator was designed and developed at laboratory scale. An electric motor equipped with gear box to control the rotations of the disks was mounted on the tank. The simulator was run at the rate of 1.7 rpm. The disc area of the RBC was immersed about 40% in the greywater. Water samples were collected at each HRT (Hydraulic Retention Time and analyzed for the parameters such as pH, conductivity, TDS (Total Dissolved Solids, salinity, BOD5 (Biochemical Oxygen Demand, COD and suspended solids by using standard methods. The results are encouraging with percentage removal of BOD5 and COD being 53 and 60% respectively.

  9. An ESR study on biological dosimeters: Human hair

    Energy Technology Data Exchange (ETDEWEB)

    Colak, Seyda, E-mail: seyda@hacettepe.edu.t [Hacettepe University, Physics Engineering Department, 06800 Ankara (Turkey); Ozbey, Turan [Hacettepe University, Physics Engineering Department, 06800 Ankara (Turkey)

    2011-05-15

    In the present work, characteristic features of the radicals found in untreated, gamma and UV-irradiated and mechanical damaged human hair samples were investigated by ESR spectroscopy. Heights of the resonance peaks measured with respect to the spectrum base line were used to monitor microwave power, dose-response, storage time and temperature dependent kinetic features of the radical species contributing to the formation of recorded experimental ESR spectra. Peak heights and g-values (2.0037-2.0052) determined from recorded spectra of hair were color dependent with {Delta}Hpp-0.47 mT. The act of cutting hair samples gene rates sulfur centered radicals which are found in the a-keratin structure of hair. The variations of the peak heights with temperature were related with the water content found in the hair samples. In the 6-1100 Gy dose range, a linear + quadratic dose-response curve was recorded for hair and the mean radiation yield (G{sub mean}) was calculated to be 0.4. The gamma radiation induced radicals were stable for a several hours at room temperature storage conditions. Based on these findings it was concluded that human hair samples could be used as biological/personnel dosimeters and that ESR spectroscopy could be successfully used as a potential technique for monitoring its dosimetric behaviours.

  10. Abnormal expression of calcyphosine is associated with poor prognosis and cell biology function in colorectal cancer

    Directory of Open Access Journals (Sweden)

    Shao W

    2016-01-01

    Full Text Available Weiwei Shao,* Quhui Wang,* Feiran Wang, Yasu Jiang, Meirong Xu, Junfei XuDepartment of General Surgery, Affiliated Hospital of Nantong University, Nantong, People’s Republic of China*These authors contributed equally to this workAbstract: The aim of this study was to investigate the calcyphosine (CAPS expression in human colorectal cancer (CRC and to explore its clinical and prognostic significances. CAPS expression was measured by Western blot, real-time polymerase chain reaction analysis, and immunohistochemistry. The relationships between the CAPS expression levels and the clinicopathological factors were investigated. The Kaplan–Meier method and log-rank test were used to investigate the overall survival of the patients. Moreover, the effects of CAPS on biological roles of CRC cells were also evaluated by MTT assay, colony formation assay, and transwell assay. CAPS was significantly overexpressed in cancerous tissue and CRC cell lines compared with adjacent nontumor tissue and a normal human intestinal epithelial cell line. Overexpression of CAPS was significantly associated with histological grade (P=0.004, invasive depth (P<0.001, lymph node metastasis (P=0.003, tumor node metastasis stage (P=0.017, and distant metastasis (P=0.042. Furthermore, silencing of CAPS expression in CRC cells inhibited their proliferation, colony formation, migration, and invasion. Kaplan–Meier survival analysis showed that high CAPS expression might demonstrate poor prognosis in CRC patients. Cox regression analysis revealed that CAPS expression was an independent prognostic factor of CRC. Our data suggested that the upregulation of CAPS might play a role in the carcinogenesis and progression of CRC. CAPS could be used as a potential diagnostic factor and be an independent good prognostic indicator for CRC patients.Keywords: calcyphosine, colorectal cancer, prognosis

  11. 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.

  12. The Biological Function and Clinical Utilization of CD147 in Human Diseases: A Review of the Current Scientific Literature

    Directory of Open Access Journals (Sweden)

    Lijuan Xiong

    2014-09-01

    Full Text Available CD147 or EMMPRIN is a member of the immunoglobulin superfamily in humans. It is widely expressed in human tumors and plays a central role in the progression of many cancers by stimulating the secretion of matrix metalloproteinases (MMPs and cytokines. CD147 regulates cell proliferation, apoptosis, and tumor cell migration, metastasis and differentiation, especially under hypoxic conditions. CD147 is also important to many organ systems. This review will provide a detailed overview of the discovery, characterization, molecular structure, diverse biological functions and regulatory mechanisms of CD147 in human physiological and pathological processes. In particular, recent studies have demonstrated the potential application of CD147 not only as a phenotypic marker of activated regulatory T cells but also as a potential diagnostic marker for early-stage disease. Moreover, CD147 is recognized as an effective therapeutic target for hepatocellular carcinoma (HCC and other cancers, and exciting clinical progress has been made in HCC treatment using CD147-directed monoclonal antibodies.

  13. Production of sorption functional media (SFM) from clinoptilolite tailings and its performance investigation in a biological aerated filter (BAF) reactor.

    Science.gov (United States)

    Feng, Yan; Qi, Jingyao; Chi, Liying; Wang, Dong; Wang, Zhaoyang; Li, Ke; Li, Xin

    2013-02-15

    The few reuse and large stockpile of zeolite tailings led to a series of social and environmental problems. This study investigated the possibility of using the zeolite tailings as one of principal raw materials to prepare sorption functional media (SFM) by a high temperature sintering process. The SFM was used to serve as a biomedium in a biological aerated filter (BAF) reactor for domestic wastewater treatment, and its purification performance was examined. The physical, chemical and sorption properties of SFM were also determined. The microstructure of the SFM was analyzed by scanning electron microscopy (SEM). Results revealed that: (1) zeolite tailings could be used to produce the SFM under the optimal sintering parameters; (2) the sorption and desorption isotherm of ammonia nitrogen on SFM could be well described by the Langmuir formula; (3) in terms of removing organic matter, ammonia nitrogen, turbidity and colourity, the performance of the biofilter with SFM was superior to that with haydite; and (4) SFM BAF has a stronger adaptability to low temperature (6-11°C) for NH(3)-N removal compared to haydite BAF. Therefore, the SFM produced from the zeolite tailings was suitable to serve as the biomedium in the domestic wastewater treatment.

  14. Porphyrins from Messel oil shale (Eocene, Germany): Structure elucidation, geochemical and biological significance, and distribution as a function of depth

    Science.gov (United States)

    Ocampo, Rubén; Bauder, Claude; Callot, Henry J.; Albrecht, Pierre

    1992-02-01

    The extraction and isolation procedures of twenty nickel porphyrins (seven alkylporphyrins, thirteen carboxylic acids) from lacustrine Messel shale (Eocene, Germany), as well as the unequivocal structural assignments (obtained using 200 and 400 MHz nuclear magnetic resonance (NMR), nuclear Overhauser effect, mass spectrometry and total or partial synthesis of six reference compounds) are described. Ten porphyrins could be specifically correlated with biological precursors: algal chlorophyll c (4), bacteriochlorophylls d (3) and heme (3), while the remaining ones may arise from several chlorophylls. The structures of these fossil pigments mostly confirm the classical "Treibs scheme," including the origin of some porphyrins from nonchlorophyll sources. They also show that, even in a very immature sediment, deep modifications occur, including, in particular, extensive degradation of chlorophyll E ring. The composition of the porphyrin fractions of Messel oil shale was also studied as a function of depth. A porphyrin acids/alkylporphyrins ratio varying from 0.35 to 24.8 demonstrated that the apparent homogeneity of the shale is not reflected on the molecular scale. This was confirmed when the abundance of the twenty individual porphyrins of known structure was measured along the core. Significant correlations between individual porphyrins were found: fossils of bacteriochlorophylls d, homolog pairs of porphyrins (3-H/3-ethyl), etc.

  15. EFFECT OF BcL-2 ANTISENSE DRUG WITH DIFFERENT STRUCTURE ON THE BIOLOGICAL FUNCTION OF K562 CELLS

    Institute of Scientific and Technical Information of China (English)

    雷小勇; 张洹; 何冬梅

    2004-01-01

    Objective: To study the differences and similarities of the antisense drugs with different structures on the biological functions of K562 cells. Methods: Cytotoxic effects were measured by use of a cell viability assay. Flow cytometric analysis and agarose gel electrophoresis of DNA fragmentation were also performed. The expression level of protein was assayed by immunofluorescence using fluoresce isothiocyanate label. Results: PNA targeting the coding region of the Bcl-2 messenger RNA could effectively inhibit K562 cell viability, down-regulate the synthesis of the Bcl-2 protein and increase cell apoptosis. By 72 h after the Bcl-2 antisense PNA treatment, K562 cells showed more reduction in the level of Bcl-2 protein compared with cells treated with the antisense ODN. After treatment with 10μmol/L of Bcl-2 antisense PNA or antisense ODN for 72 h, apoptotic rates of K562 cells were 13.15±1.13 and 11.72±1.12, respectively. Furthermore, there was significant difference in the percentage of apoptotic cells between antisense PNA group and antisense ODN group. Conclusion: The results suggest that antisense PNA targeting the coding region of Bcl-2 mRNA has better antisense effects than the antisense oligonucleotides on inducing apoptosis of K562 cells.

  16. Studying Plant-Rhizobium Mutualism in the Biology Classroom: Connecting the Big Ideas in Biology through Inquiry

    Science.gov (United States)

    Suwa, Tomomi; Williamson, Brad

    2014-01-01

    We present a guided-inquiry biology lesson, using the plant-rhizobium symbiosis as a model system. This system provides a rich environment for developing connections between the big ideas in biology as outlined in the College Board's new AP Biology Curriculum. Students gain experience with the practice of scientific investigation, from…

  17. 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

  18. 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.

  19. Human embryonic stem cells : advancing biology and cardiogenesis towards functional applications l

    NARCIS (Netherlands)

    Braam, Stefan Robbert

    2010-01-01

    Human embryonic stem cells (hESC) hold great potential as a model for human development, disease pathology, drug discovery and safety pharmacology. All these applications will depend on comprehensive knowledge of their biology and control of their signaling mechanisms and fate choices. To begin to a

  20. Production of sorption functional media (SFM) from clinoptilolite tailings and its performance investigation in a biological aerated filter (BAF) reactor

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yan [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); School of Civil Engineering and Architecture, University of Jinan, Jinan 250022 (China); Qi, Jingyao, E-mail: qjy_hit@yahoo.cn [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Chi, Liying [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wang, Dong [School of Civil Engineering and Architecture, University of Jinan, Jinan 250022 (China); Wang, Zhaoyang; Li, Ke; Li, Xin [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China)

    2013-02-15

    Highlights: ► Sorption functional media (SFM) were prepared using zeolite tailings. ► Two upflow BAFs were applied to treat municipal wastewater. ► SFM BAF brought a relative superiority to haydite reactor. ► SFM BAF has a stronger adaptability to low temperature (6–11°C) for NH{sub 3}-N removal. ► The application provided a promising way in zeolite tailings utilization. -- Abstract: The few reuse and large stockpile of zeolite tailings led to a series of social and environmental problems. This study investigated the possibility of using the zeolite tailings as one of principal raw materials to prepare sorption functional media (SFM) by a high temperature sintering process. The SFM was used to serve as a biomedium in a biological aerated filter (BAF) reactor for domestic wastewater treatment, and its purification performance was examined. The physical, chemical and sorption properties of SFM were also determined. The microstructure of the SFM was analyzed by scanning electron microscopy (SEM). Results revealed that: (1) zeolite tailings could be used to produce the SFM under the optimal sintering parameters; (2) the sorption and desorption isotherm of ammonia nitrogen on SFM could be well described by the Langmuir formula; (3) in terms of removing organic matter, ammonia nitrogen, turbidity and colourity, the performance of the biofilter with SFM was superior to that with haydite; and (4) SFM BAF has a stronger adaptability to low temperature (6–11 °C) for NH{sub 3}-N removal compared to haydite BAF. Therefore, the SFM produced from the zeolite tailings was suitable to serve as the biomedium in the domestic wastewater treatment.

  1. Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

    Science.gov (United States)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

  2. Effects and biological limitations of +Gz acceleration on the autonomic functions-related circulation in rats.

    Science.gov (United States)

    Nishida, Yasuhiro; Maruyama, Satoshi; Shouji, Ichiro; Kemuriyama, Takehito; Tashiro, Akimasa; Ohta, Hiroyuki; Hagisawa, Kohsue; Hiruma, Megumi; Yokoe, Hidetake

    2016-11-01

    The effects of gravitational loading (G load) on humans have been studied ever since the early 20th century. After the dangers of G load in the vertical head-to-leg direction (+Gz load) became evident, many animal experiments were performed between 1920 and 1945 in an effort to identify the origins of high G-force-induced loss of consciousness (G-LOC), which led to development of the anti-G suit. The establishment of norms and training for G-LOC prevention resulted in a gradual decline in reports of animal experiments on G load, a decline that steepened with the establishment of anti-G techniques in humans, such as special breathing methods and skeletal muscle contraction, called an anti-G straining maneuver, which are voluntary physiological functions. Because the issue involves humans during flight, the effects on humans themselves are clearly of great importance, but ethical considerations largely preclude any research on the human body that probes to any depth the endogenous physiological states and functions. The decline in reports on animal experiments may therefore signify a general decline in research into the changes seen in the various involuntary, autonomic functions. The declining number of related reports on investigations of physiological autonomic systems other than the circulatory system seems to bear this out. In this review, we therefore describe our findings on the effects of G load on the autonomic nervous system, cardiac function, cerebral blood flow, tissue oxygen level, and other physiological autonomic functions as measured in animal experiments, including denervation or pharmacological blocking, in an effort to present the limits and the mechanisms of G-load response extending physiologically. We demonstrate previously unrecognized risks due to G load, and also describe fundamental research aimed at countering these effects and development of a scientific training measure devised for actively enhancing +Gz tolerance in involuntary

  3. A multiwell platform for studying stiffness-dependent cell biology.

    Directory of Open Access Journals (Sweden)

    Justin D Mih

    Full Text Available Adherent cells are typically cultured on rigid substrates that are orders of magnitude stiffer than their tissue of origin. Here, we describe a method to rapidly fabricate 96 and 384 well platforms for routine screening of cells in tissue-relevant stiffness contexts. Briefly, polyacrylamide (PA hydrogels are cast in glass-bottom plates, functionalized with collagen, and sterilized for cell culture. The Young's modulus of each substrate can be specified from 0.3 to 55 kPa, with collagen surface density held constant over the stiffness range. Using automated fluorescence microscopy, we captured the morphological variations of 7 cell types cultured across a physiological range of stiffness within a 384 well plate. We performed assays of cell number, proliferation, and apoptosis in 96 wells and resolved distinct profiles of cell growth as a function of stiffness among primary and immortalized cell lines. We found that the stiffness-dependent growth of normal human lung fibroblasts is largely invariant with collagen density, and that differences in their accumulation are amplified by increasing serum concentration. Further, we performed a screen of 18 bioactive small molecules and identified compounds with enhanced or reduced effects on soft versus rigid substrates, including blebbistatin, which abolished the suppression of lung fibroblast growth at 1 kPa. The ability to deploy PA gels in multiwell plates for high throughput analysis of cells in tissue-relevant environments opens new opportunities for the discovery of cellular responses that operate in specific stiffness regimes.

  4. Laboratory studies of biological effects of sulfur oxides

    Energy Technology Data Exchange (ETDEWEB)

    Dalbey, W. E.

    1979-01-01

    Selected results from exposures of laboratory animals to airborne sulfur oxides were briefly summarized. The main observation during acute exposures was reflex bronchoconstriction and a resultant increase in pulmonary resistance. The increase in resistance due to sulfur dioxide (SO/sub 2/) was potentiated by simultaneous exposure to aerosols under conditions which would increase the transfer of sulfur oxides into the respiratory tract and promote transformation to a higher oxidation state, especially one that is acid. Sulfate aerosols, particularly sulfuric acid aerosols, were more potent than SO/sub 2/ in causing bronchoconstriction. Chronic exposure to high concentrations (400 to 650 ppM) of SO/sub 2/ resulted in experimental bronchitis in several species. Longterm exposure to more realistic concentrations of SO/sub 2/ produced little or no changes in respiratory function or morphology. Significant alterations in both pulmonary function and morphology have been reported after chronic exposure to sulfuric acid aerosols. Recent data indicate that changes in the lung may progress after cessation of such exposures.

  5. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

    Science.gov (United States)

    Martin, O. C.; Krzywicki, A.; Zagorski, M.

    2016-07-01

    Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure.

  6. Unique biological function of cathepsin L in secretory vesicles for biosynthesis of neuropeptides.

    Science.gov (United States)

    Funkelstein, Lydiane; Beinfeld, Margery; Minokadeh, Ardalan; Zadina, James; Hook, Vivian

    2010-12-01

    Neuropeptides are essential for cell-cell communication in the nervous and neuroendocrine systems. Production of active neuropeptides requires proteolytic processing of proneuropeptide precursors in secretory vesicles that produce, store, and release neuropeptides that regulate physiological functions. This review describes recent findings indicating the prominent role of cathepsin L in secretory vesicles for production of neuropeptides from their protein precursors. The role of cathepsin L in neuropeptide production was discovered using the strategy of activity-based probes for proenkephalin-cleaving activity for identification of the enzyme protein by mass spectrometry. The novel role of cathepsin L in secretory vesicles for neuropeptide production has been demonstrated in vivo by cathepsin L gene knockout studies, cathepsin L gene expression in neuroendocrine cells, and notably, cathepsin L localization in neuropeptide-containing secretory vesicles. Cathepsin L is involved in producing opioid neuropeptides consisting of enkephalin, β-endorphin, and dynorphin, as well as in generating the POMC-derived peptide hormones ACTH and α-MSH. In addition, NPY, CCK, and catestatin neuropeptides utilize cathepsin L for their biosynthesis. The neuropeptide-synthesizing functions of cathepsin L represent its unique activity in secretory vesicles, which contrasts with its role in lysosomes. Interesting evaluations of protease gene knockout studies in mice that lack cathepsin L compared to those lacking PC1/3 and PC2 (PC, prohormone convertase) indicate the key role of cathepsin L in neuropeptide production. Therefore, dual cathepsin L and prohormone convertase protease pathways participate in neuropeptide production. Significantly, the recent new findings indicate cathepsin L as a novel 'proprotein convertase' for production of neuropeptides that mediate cell-cell communication in health and disease.

  7. Hybrid functional study of α-uranium

    Science.gov (United States)

    Kaur, Gurpreet; Chinnappan, Ravi; Panigrahi, B. K.

    2016-05-01

    We have used the hybrid density functionals to study the structural and electronic properties of alpha-U. The fraction of exact Hartree Folk exchange used is varied from 0.0 to 0.6. The equilibrium volume is found to be underestimated and bulk modulus overestimated with HSE as compared to both calculated by PBE and the experimental values. Electronic bands below the Fermi level are found to shift to lower energy with respect to PBE electronic bands which itself gives the bands shifted to lower energies as compared to UPS experiments.

  8. The Danish National Prescription Registry in studies of a biological pharmaceutical

    DEFF Research Database (Denmark)

    Haerskjold, Ann; Henriksen, Lonny; Way, Susanne

    2015-01-01

    BACKGROUND: National prescription databases are important tools in pharmacoepidemiological studies investigating potential long-term adverse events after drug use. Palivizumab is a biological pharmaceutical used as passive prophylaxis against severe infection with respiratory syncytial virus in h...

  9. Environmental Contaminants Monitoring in Selected Wetlands of Wyoming: Biologically Active Elements Study

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Sediment, water and biota were collected from selected wetlands in Wyoming for the Biologically Active Elements (BAE) Study in 1988, 1989 and 1990 to identify...

  10. Neutron scattering and diffraction instrument for structural study on biology in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Ibaraki-ken (Japan)

    1994-12-31

    Neutron scattering and diffraction instruments in Japan which can be used for structural studies in biology are briefly introduced. Main specifications and general layouts of the instruments are shown.

  11. [Biological adaptation and immune status of preschool children with visual function disorders in conditions of preschool educational institutions of compensating type].

    Science.gov (United States)

    Bannikova, L P; Koksharov, A V

    2013-01-01

    For implementation of a comprehensive approach in the elaboration of preventive and corrective measures in children with impaired visual function in conditions of preschool educational institutions of compensating type there were studied adaptation reserves of their organism, as well as indices of immune status. Biological adaptation was studied with the help ofcardiointervalography in 111 children aged 6-7years. With the use of ELISA 88 children were examined in terms of IgA, IgM, IgG, slgA in saliva.

  12. The Viable Mitral Annular Dynamics and Left Ventricular Function after Mitral Valve Repair by Biological Rings

    Directory of Open Access Journals (Sweden)

    Farideh Roshanali

    2012-12-01

    Full Text Available Objective: Considering the importance of annular dynamics in the valvular and ventricular function, we sought to evaluate the effects of treated pericardial annuloplasty rings on mitral annular dynamics and left-ventricular (LV function after mitral valve repair. The results were compared with the mitral annular dynamics and LV function in patients with rigid and flexible rings and also in those without any heart problems. Materials and Methods: One hundred and thirty-six consecutive patients with a myxomatous mitral valve and severe regurgitation were prospectively enrolled in this observational cohort study. The patients underwent comparable surgical mitral valve reconstruction; of these 100 received autologous pericardium rings (Group I, 20 were given flexible prosthetic rings (Group II, and 16 received rigid rings (Group III. Other repair modalities were also performed, depending on the involved segments. The patients were compared with 100 normal subjects in whom an evaluation of the coronary artery was not indicative of valvular or myocardial abnormalities (Group IV. At follow-up, LV systolic indices were assessed via two-dimensional echocardiography at rest and during dobutamine stress echocardiography. Mitral annular motion was examined through mitral annulus systolic excursion (MASE. Peak transmitral flow velocities (TMFV and mitral valve area (MVA were also evaluated by means of continuous-wave Doppler. Results: A postoperative echocardiographic study showed significant mitral regurgitation (>=2+ in one patient in Group I, one patient in Group II, and none in Group III. None of the patients died. There was a noteworthy increase in TMFV with stress in all the groups, the increase being more considerable in the prosthetic ring groups (Group I from 1.10 ± 0.08 to 1.36 ± 0.13 m/s, Group II from 1.30 ± 0.11 to 1.59 ± 0.19 m/s, Group III from 1.33 ± 0.09 to 1.69 ± 0.21 m/s, and Group IV from 1.08 ± 0.08 to 1.21 ± 0.12 m

  13. Studying Functions of All Yeast Genes Simultaneously

    Science.gov (United States)

    Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

    2006-01-01

    A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

  14. Impact on disease development, genomic location and biological function of copy number alterations in non-small cell lung cancer.

    Directory of Open Access Journals (Sweden)

    Yen-Tsung Huang

    Full Text Available Lung cancer, of which more than 80% is non-small cell, is the leading cause of cancer-related death in the United States. Copy number alterations (CNAs in lung cancer have been shown to be positionally clustered in certain genomic regions. However, it remains unclear whether genes with copy number changes are functionally clustered. Using a dense single nucleotide polymorphism array, we performed genome-wide copy number analyses of a large collection of non-small cell lung tumors (n = 301. We proposed a formal statistical test for CNAs between different groups (e.g., non-involved lung vs. tumors, early vs. late stage tumors. We also customized the gene set enrichment analysis (GSEA algorithm to investigate the overrepresentation of genes with CNAs in predefined biological pathways and gene sets (i.e., functional clustering. We found that CNAs events increase substantially from germline, early stage to late stage tumor. In addition to genomic position, CNAs tend to occur away from the gene locations, especially in germline, non-involved tissue and early stage tumors. Such tendency decreases from germline to early stage and then to late stage tumors, suggesting a relaxation of selection during tumor progression. Furthermore, genes with CNAs in non-small cell lung tumors were enriched in certain gene sets and biological pathways that play crucial roles in oncogenesis and cancer progression, demonstrating the functional aspect of CNAs in the context of biological pathways that were overlooked previously. We conclude that CNAs increase with disease progression and CNAs are both positionally and functionally clustered. The potential functional capabilities acquired via CNAs may be sufficient for normal cells to transform into malignant cells.

  15. Study Reveals Brain Biology behind Self-Control

    Science.gov (United States)

    Sparks, Sarah D.

    2011-01-01

    A new neuroscience twist on a classic psychology study offers some clues to what makes one student able to buckle down for hours of homework before a test while his classmates party. The study published in the September 2011 edition of "Proceedings of the National Academy of Science," suggests environmental cues may "hijack" the brain's mechanisms…

  16. Functional genomics in the study of yeast cell polarity: moving in the right direction.

    Science.gov (United States)

    Styles, Erin; Youn, Ji-Young; Mattiazzi Usaj, Mojca; Andrews, Brenda

    2013-01-01

    The budding yeast Saccharomyces cerevisiae has been used extensively for the study of cell polarity, owing to both its experimental tractability and the high conservation of cell polarity and other basic biological processes among eukaryotes. The budding yeast has also served as a pioneer model organism for virtually all genome-scale approaches, including functional genomics, which aims to define gene function and biological pathways systematically through the analysis of high-throughput experimental data. Here, we outline the contributions of functional genomics and high-throughput methodologies to the study of cell polarity in the budding yeast. We integrate data from published genetic screens that use a variety of functional genomics approaches to query different aspects of polarity. Our integrated dataset is enriched for polarity processes, as well as some processes that are not intrinsically linked to cell polarity, and may provide new areas for future study.

  17. Applying systems biology methods to the study of human physiology in extreme environments.

    Science.gov (United States)

    Edwards, Lindsay M; Thiele, Ines

    2013-03-22

    Systems biology is defined in this review as 'an iterative process of computational model building and experimental model revision with the aim of understanding or simulating complex biological systems'. We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and repeated experimental perturbation of the system of interest. The number of ethical and physiologically relevant perturbations that can be used in experiments on healthy humans is extremely limited and principally comprises exercise, nutrition, infusions (e.g. Intralipid), some drugs and altered environment. Thus, we argue that systems biology and environmental physiology are natural symbionts for those interested in a system-level understanding of human biology. However, despite excellent progress in high-altitude genetics and several proteomics studies, systems biology research into human adaptation to extreme environments is in its infancy. A brief description and overview of systems biology in its current guise is given, followed by a mini review of computational methods used for modelling biological systems. Special attention is given to high-altitude research, metabolic network reconstruction and constraint-based modelling.

  18. A Trade Study of Two Membrane-Aerated Biological Water Processors

    Science.gov (United States)

    Allada, Ram; Lange, Kevin; Vega. Leticia; Roberts, Michael S.; Jackson, Andrew; Anderson, Molly; Pickering, Karen

    2011-01-01

    Biologically based systems are under evaluation as primary water processors for next generation life support systems due to their low power requirements and their inherent regenerative nature. This paper will summarize the results of two recent studies involving membrane aerated biological water processors and present results of a trade study comparing the two systems with regards to waste stream composition, nutrient loading and system design. Results of optimal configurations will be presented.

  19. Functional analysis of variance for association studies.

    Directory of Open Access Journals (Sweden)

    Olga A Vsevolozhskaya

    Full Text Available While progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain in finding additional unknown genetic variants predisposing to complex diseases. With the advance in next-generation sequencing technologies, sequencing studies have become commonplace in genetic research. The ongoing exome-sequencing and whole-genome-sequencing studies generate a massive amount of sequencing variants and allow researchers to comprehensively investigate their role in human diseases. The discovery of new disease-associated variants can be enhanced by utilizing powerful and computationally efficient statistical methods. In this paper, we propose a functional analysis of variance (FANOVA method for testing an association of sequence variants in a genomic region with a qualitative trait. The FANOVA has a number of advantages: (1 it tests for a joint effect of gene variants, including both common and rare; (2 it fully utilizes linkage disequilibrium and genetic position information; and (3 allows for either protective or risk-increasing causal variants. Through simulations, we show that FANOVA outperform two popularly used methods - SKAT and a previously proposed method based on functional linear models (FLM, - especially if a sample size of a study is small and/or sequence variants have low to moderate effects. We conduct an empirical study by applying three methods (FANOVA, SKAT and FLM to sequencing data from Dallas Heart Study. While SKAT and FLM respectively detected ANGPTL 4 and ANGPTL 3 associated with obesity, FANOVA was able to identify both genes associated with obesity.

  20. Recombinant hamster oviductin is biologically active and exerts positive effects on sperm functions and sperm-oocyte binding.

    Directory of Open Access Journals (Sweden)

    Xiaojing Yang

    Full Text Available Studies carried out in several mammalian species suggest that oviductin, also known as oviduct-specific glycoprotein or OVGP1, plays a key role in sperm capacitation, fertilization, and development of early embryos. In the present study, we used recombinant DNA technology to produce, for the first time, recombinant hamster OVGP1 (rHamOVGP1 in human embryonic kidney 293 (HEK293 cells. rHamOVGP1 secreted in the culture medium was purified by affinity chromatography. The resulting protein migrated as a poly-dispersed band of 160-350 kDa on SDS-PAGE corresponding to the molecular mass of the native HamOVGP1. Subsequent mass spectrometric analysis of the purified rHamOVGP1 confirmed its identity as HamOVGP1. Immunocytochemistry demonstrated binding of rHamOVGP1 to the mid-piece and head of hamster sperm and to the zona pellucida (ZP of ovarian oocytes. In vitro functional experiments showed that addition of rHamOVGP1 in the capacitation medium further enhanced tyrosine phosphorylation of two sperm proteins of approximately 75 kDa and 83 kDa in a time-dependent manner. After 3 hours of incubation in the presence of rHamOVGP1, a significant increase in acrosome reaction was measured. Pretreatment of either sperm or oocyte with 20 μg/ml of rHamOVGP1 prior to sperm-egg binding assay significantly increased the number of sperm bound to the ZP. Addition of rHamOVGP1 in the medium during sperm-egg binding with either oocyte or sperm pretreated with rHamOVGP1 also saw an increase in the number of sperm bound to ZP. In all experimental conditions, the effect of rHamOVGP1 on sperm-oocyte binding was negated by the addition of monoclonal anti-HamOVGP1 antibody. The successful production and purification of a biologically active rHamOVGP1 will allow further exploration of the function of this glycoprotein in reproductive function.

  1. Recombinant hamster oviductin is biologically active and exerts positive effects on sperm functions and sperm-oocyte binding.

    Science.gov (United States)

    Yang, Xiaojing; Zhao, Yuewen; Yang, Xiaolong; Kan, Frederick W K

    2015-01-01

    Studies carried out in several mammalian species suggest that oviductin, also known as oviduct-specific glycoprotein or OVGP1, plays a key role in sperm capacitation, fertilization, and development of early embryos. In the present study, we used recombinant DNA technology to produce, for the first time, recombinant hamster OVGP1 (rHamOVGP1) in human embryonic kidney 293 (HEK293) cells. rHamOVGP1 secreted in the culture medium was purified by affinity chromatography. The resulting protein migrated as a poly-dispersed band of 160-350 kDa on SDS-PAGE corresponding to the molecular mass of the native HamOVGP1. Subsequent mass spectrometric analysis of the purified rHamOVGP1 confirmed its identity as HamOVGP1. Immunocytochemistry demonstrated binding of rHamOVGP1 to the mid-piece and head of hamster sperm and to the zona pellucida (ZP) of ovarian oocytes. In vitro functional experiments showed that addition of rHamOVGP1 in the capacitation medium further enhanced tyrosine phosphorylation of two sperm proteins of approximately 75 kDa and 83 kDa in a time-dependent manner. After 3 hours of incubation in the presence of rHamOVGP1, a significant increase in acrosome reaction was measured. Pretreatment of either sperm or oocyte with 20 μg/ml of rHamOVGP1 prior to sperm-egg binding assay significantly increased the number of sperm bound to the ZP. Addition of rHamOVGP1 in the medium during sperm-egg binding with either oocyte or sperm pretreated with rHamOVGP1 also saw an increase in the number of sperm bound to ZP. In all experimental conditions, the effect of rHamOVGP1 on sperm-oocyte binding was negated by the addition of monoclonal anti-HamOVGP1 antibody. The successful production and purification of a biologically active rHamOVGP1 will allow further exploration of the function of this glycoprotein in reproductive function.

  2. Northeast Cooperative Research Study Fleet (SF) Program Biological Sampling Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Northeast Cooperative Research Study Fleet (SF) Program partners with a subset of commercial fishermen to collect high quality, high resolution, haul by haul...

  3. Functional biology and ecological role of krill in Northern marine ecosystems

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard

    Krill is an understudied key group of zooplankton, which transfers energy through the food web by linking lower and higher trophic levels. Furthermore, krill play an important role in the biological pump by transporting carbon out of the euphotic zone to depth by diel vertical migration (DVM......) and by production of fast sinking carbon-rich faecal pellets. Hence, the large schools of krill greatly influence the pelagic food web and the flux of organic matter in the sea. However, knowledge of the distribution and feeding biology in krill from northern areas is scarce, although of importance to get a better...... in regions with colder temperatures. Results from stable isotope analyses and feeding experiments show that there is an overlap in the diet of the species and that they are able to exploit several trophic levels. Trophic positions are related to available prey. However, the size of the krill seemed...

  4. Functional Components of Carob Fruit: Linking the Chemical and Biological Space.

    Science.gov (United States)

    Goulas, Vlasios; Stylos, Evgenios; Chatziathanasiadou, Maria V; Mavromoustakos, Thomas; Tzakos, Andreas G

    2016-11-10

    The contribution of natural products to the drug-discovery pipeline has been remarkable since they have served as a rich source for drug development and discovery. Natural products have adapted, during the course of evolution, optimum chemical scaffolds against a wide variety of diseases, including cancer and diabetes. Advances in high-throughput screening assays, assisted by the continuous development on the instrumentation's capabilities and omics, have resulted in charting a large chemical and biological space of drug-like compounds, originating from natural sources. Herein, we attempt to integrate the information on the chemical composition and the associated biological impact of carob fruit in regards to human health. The beneficial and health-promoting effects of carob along with the clinical trials and the drug formulations derived from carob's natural components are presented in this review.

  5. Functional Components of Carob Fruit: Linking the Chemical and Biological Space

    Directory of Open Access Journals (Sweden)

    Vlasios Goulas

    2016-11-01

    Full Text Available The contribution of natural products to the drug-discovery pipeline has been remarkable since they have served as a rich source for drug development and discovery. Natural products have adapted, during the course of evolution, optimum chemical scaffolds against a wide variety of diseases, including cancer and diabetes. Advances in high-throughput screening assays, assisted by the continuous development on the instrumentation’s capabilities and omics, have resulted in charting a large chemical and biological space of drug-like compounds, originating from natural sources. Herein, we attempt to integrate the information on the chemical composition and the associated biological impact of carob fruit in regards to human health. The beneficial and health-promoting effects of carob along with the clinical trials and the drug formulations derived from carob’s natural components are presented in this review.

  6. A functional neuroimaging study of motivation and executive function.

    Science.gov (United States)