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. PMID:23828605

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

    OpenAIRE

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  4. Functions in Biological Kind Classification

    Science.gov (United States)

    Lombrozo, Tania; Rehder, Bob

    2012-01-01

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

  5. The relativity of biological function.

    Science.gov (United States)

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

    2015-12-01

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

  6. Functional Aspects of Biological Networks

    Science.gov (United States)

    Sneppen, Kim

    2007-03-01

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

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

    Science.gov (United States)

    Uyeda, T Q; Yumura, S

    2000-04-15

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

  9. Photosynthetic system as a biological functional element

    International Nuclear Information System (INIS)

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

  10. Studies on the biological functions of CPS1 in AFB1 induced hepatocarcinogenesis.

    Science.gov (United States)

    Yang, Chi; Fu, Rao; Zhuang, Zhenhong; Wang, Shihua

    2016-10-10

    Carbamyl phosphate synthetase 1 (CPS1) was down-regulated in hepatocellular carcinoma (HCC), as treated by aflatoxin B1 (AFB1), a potent hepatocarcinogenesis mycotoxin. In this study, we firstly confirmed that AFB1 down-regulated the expression of CPS1 in a dose-dependent manner. At the meantime, both siRNA knock down of CPS1 and AFB1 treatment inhibited cell proliferation, and induced cell apoptosis. To further analysis the function of CPS1, the interacting proteins of CPS1 were searched by Co-IP, and three interacting proteins including type II cytoskeletal 1 (KRT1), albumin (ALB), and ubiquitin C (UBC) were found. Both KRT1 and ALB were new interacting proteins for CPS1. Our further study showed that CPS1 was regulating interacted and colocalized with KRT1 and ALB, and the intensity correlation was changed by AFB1. KRT1, ALB and CPS1 were all reported to play an important role in differentiation and tissue specialization. These results may offer an increasing understand that CPS1 might have a function in differentiation. PMID:27425868

  11. 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

  12. Interferon-γ: biological function and application for study of cellular immune response

    Directory of Open Access Journals (Sweden)

    A. A. Lutckii

    2015-01-01

    Full Text Available Cellular immune response plays a central role in control of intracellular pathogens like viruses, some bacteria and parasites. Evaluation of presence, specificity and strength of cellular immune response can be done by investigation of reaction of immune cells to specific stimulus, like antigen. The major cellular reactions to antigen stimulation are production of cytokines, proliferation and cytotoxicity. This review is focused on interferon-gamma as one of the central Th1 cytokines: its biology, immunological role and application as marker of cellular immune response.

  13. 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.

  14. Reproductive function and biological dosimetry prospective study of young thyroid differentiated cancer patients treated with I-131

    International Nuclear Information System (INIS)

    Full text: The administration of I-131 in the management of differentiated thyroid cancer (DTC) is a well established practice. As the spermatogonia is highly sensitive to radiation, large doses of internal radiation could result in adverse effects on reproductive function such as oligo/azoospermia and infertility. During spermiogenesis, mammalian chromatin undergoes replacement of nuclear histones by protamines, which yields a DNA sixfold more highly condensed in spermatozoa than in mitotic chromosomes. The structure of this highly packaged chromatin shows a low binding capacity for several fluoro chromes and dyes such as chromo mycin A3 (CMA3). The aim of this study is to assess the correlation between reproductive function (endocrine and exocrine testicular function, and levels of CMA3 stainability) and biological dosimetry in a prospective study of 4 young DTC patients treated with I-131. In this context, a background level of CMA3 binding in mature human sperm was established. It revealed a variable accessibility of CMA3 to the DNA that is dependant on packaging quality and thus, indicative of protamine deficiency. The identification of altered stainability suggests DNA damage as well as epigenetic effects, which may be indicators of male infertility. Transient impairment of spermatogenesis associated with an increase in FSH, an altered spermiogram and even azoospermia was observed after the administration of cumulative activities. Overall, testosterone levels were preserved, except in one case, which presented a drastically diminished value associated with an increase in LH level. As peripheral blood lymphocytes and spermatogonia have equivalent radiosensitivity (interphase death) we hypothesize that the knowledge of DNA damage recovery in peripheral lymphocytes could correlate with spermatogonia recovery and with FSH evolution. Therefore, a prospective study on the decline of unstable chromosome aberrations is being conducted, considering the damage induced

  15. Reproductive function and biological dosimetry prospective study of young thyroid differentiated cancer patients treated with I-131

    International Nuclear Information System (INIS)

    The administration of I-131 in the management of differentiated thyroid cancer (DTC) is a well established practice. As the spermatogonia is highly sensitive to radiation, large doses of internal radiation could result in adverse effects on reproductive function such as oligo/azoospermia and infertility. During spermiogenesis, mammalian chromatin undergoes replacement of nuclear histones by protamines, which yields a DNA sixfold more highly condensed in spermatozoa than in mitotic chromosomes. The structure of this highly packaged chromatin shows a low binding capacity for several fluorochromes and dyes such as chromomycin A3 (CMA3). The aim of this study is to assess the correlation between reproductive function (endocrine and exocrine testicular function, and levels of CMA3 stainability) and biological dosimetry in a prospective study of 4 young DTC patients treated with I-131. In this context, a background level of CMA3 binding in mature human sperm was established. It revealed a variable accessibility of CMA3 to the DNA that is dependant on packaging quality and thus, indicative of protamine deficiency. The identification of altered stainability suggests DNA damage as well as epigenetic effects, which may be indicators of male infertility. Transient impairment of spermatogenesis associated with an increase in FSH, an altered spermiogram and even azoospermia was observed after the administration of cumulative activities. Overall, testosterone levels were preserved, except in one case, which presented a drastically diminished value associated with an increase in LH level. As peripheral blood lymphocytes and spermatogonia have equivalent radiosensitivity (interphase death) we hypothesize that the knowledge of DNA damage recovery in peripheral lymphocytes could correlate with spermatogonia recovery and with FSH evolution. (authors)

  16. 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.

  17. 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.

  18. Structure and function in biology

    International Nuclear Information System (INIS)

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

  19. Metacognition: computation, biology and function.

    Science.gov (United States)

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

    2012-05-19

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

  20. Marine Carotenoids: Biological Functions and Commercial Applications

    OpenAIRE

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

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesised by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for wide range of commercial applications. Indeed, recent interest in the carotenoids has be...

  1. Structure and Associated Biological Functions of Viroids.

    Science.gov (United States)

    Steger, Gerhard; Perreault, Jean-Pierre

    2016-01-01

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

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

    OpenAIRE

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

    2010-01-01

    Fibroblast growth factors (FGFs) that signal through FGF receptors (FGFRs) regulate a broad spectrum of biological functions, including cellular proliferation, survival, migration, and differentiation. The FGF signal pathways are the RAS/MAP kinase pathway, PI3 kinase/AKT pathway, and PLCγ pathway, among which the RAS/MAP kinase pathway is known to be predominant. Several studies have recently implicated the in vitro biological functions of FGFs for tissue regeneration. However, to obtain opt...

  3. 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.

  4. 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.

  5. 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…

  6. Insights into the functional biology of schistosomes

    OpenAIRE

    Walker Anthony

    2011-01-01

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

  7. 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.)

  8. Functional biology of sympatric krill species

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Nielsen, Torkel Gissel

    2016-01-01

    Here we compare the functional biology of the sympatric krill species, Meganyctiphanes norvegica and Thysanoessa inermis. For M. norvegica, we investigated functional responses on diatoms and copepods, together with prey size spectra on plankton ,400 mm and copepods in the size range 500–3220 mm....... For T. inermis, only prey size spectrum on plankton ,400 mm were investigated. The prey size ranges of both species include organisms ,400 mm, and they consequently graze on several trophic levels. However, T. inermis feed on cells ,10 mm equivalent spherical diameter (ESD), whereas M. norvegica only...... feed on cells .10 mm. Meganyctiphanes norvegica show maximum predation on 800–1600 mm sized copepods, corresponding to a predator:prey size ratio of 17.0+2.2. Functional response experiments with M. norvegica follow a Holling type III functional response, both when feeding on diatoms and copepods, but...

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

    Science.gov (United States)

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

    2015-12-15

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. PMID:26668171

  10. Biological study in schizophrenia

    International Nuclear Information System (INIS)

    Schizophrenia is associated with enormous morbidity, mortality, personal disability, and social cost. Although considerable research on schizophrenia has been performed, the etiology of this disease has not been fully elucidated. In recent years, imaging and genetic technologies have been developed dramatically. Disturbances in glutamate and gamma-aminobutyric acid (GABA)ergic neurotransmission may underlie the pathophysiology of schizophrenia. We attempted an integrative review, of studies pertaining to recent advances of schizophrenia research with a focus on neuroimaging and genetic studies. Additionally, we present the preliminary findings of the clinical research in our outpatient unit, specialized for early intervention, at the University of Tokyo Hospital. (author)

  11. Multi-element neutron activation analysis of biological tissues: contribution to the study of trace element accumulation as a function of aging

    International Nuclear Information System (INIS)

    The accumulation of trace elements in various organs as a function of age was studied in rats, in connection with tissue aging phenomena. Part one reviews the various methods available to develop a programme of simultaneous multi-element analysis in biological matrices. Part two studies the precision and accuracy offered by neutron activation analysis. Special attention is paid to the problem of sample contamination by the silica glass irradiation supports. The possible causes of this effect are mentioned and a procedure limiting its harmful influence is proposed. Part three defines the restrictions introduced by the use of a method to separate the activable matrix. The fourth and last chapter describes the development of a multielement chemical separation system, designed to work semi-automatically for the simultaneous treatment of three samples and a standard in a shielded cell of small dimensions. The principles of a multi-comparator calibration where a knowledge of certain conventional but imprecise nuclear data is unnecessary owing to an experimental expedient are outlined briefly. Finally the separation method is tried out on various biological samples, including a reference (bovine liver SRM1577-NBS), and some results are given

  12. An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus

    International Nuclear Information System (INIS)

    The long-sought three-dimensional structure of the M2 proton channel of influenza A virus was successfully determined recently by the high-resolution NMR [J.R. Schnell, J.J. Chou, Structure and mechanism of the M2 proton channel of influenza A virus, Nature 451 (2008) 591-595]. Such a milestone work has provided a solid structural basis for studying drug-resistance problems. However, the action mechanism revealed from the NMR structure is completely different from the traditional view and hence prone to be misinterpreted as 'conflicting' with some previous biological functional studies. To clarify this kind of confusion, an in-depth analysis was performed for these functional studies, particularly for the mutations D44N, D44A and N44D on position 44, and the mutations on positions 27-38. The analyzed results have provided not only compelling evidences to further validate the NMR structure but also very useful clues for dealing with the drug-resistance problems and developing new effective drugs against H5N1 avian influenza virus, an impending threat to human beings.

  13. Structure, function and management of semi-natural habitats for conservation biological control: a review of European studies.

    Science.gov (United States)

    Holland, John M; Bianchi, Felix Jja; Entling, Martin H; Moonen, Anna-Camilla; Smith, Barbara M; Jeanneret, Philippe

    2016-09-01

    Different semi-natural habitats occur on farmland, and it is the vegetation's traits and structure that subsequently determine their ability to support natural enemies and their associated contribution to conservation biocontrol. New habitats can be created and existing ones improved with agri-environment scheme funding in all EU member states. Understanding the contribution of each habitat type can aid the development of conservation control strategies. Here we review the extent to which the predominant habitat types in Europe support natural enemies, whether this results in enhanced natural enemy densities in the adjacent crop and whether this leads to reduced pest densities. Considerable variation exists in the available information for the different habitat types and trophic levels. Natural enemies within each habitat were the most studied, with less information on whether they were enhanced in adjacent fields, while their impact on pests was rarely investigated. Most information was available for woody and herbaceous linear habitats, yet not for woodland which can be the most common semi-natural habitat in many regions. While the management and design of habitats offer potential to stimulate conservation biocontrol, we also identified knowledge gaps. A better understanding of the relationship between resource availability and arthropod communities across habitat types, the spatiotemporal distribution of resources in the landscape and interactions with other factors that play a role in pest regulation could contribute to an informed management of semi-natural habitats for biocontrol. © 2016 Society of Chemical Industry. PMID:27178745

  14. Neutron scattering studies of the dynamics of biological systems as a function of hydration, temperature and pressure

    International Nuclear Information System (INIS)

    Incoherent elastic and quasi-elastic neutron scattering were used to measure membrane and protein dynamics in the nano- to picosecond time and Angstrom length scale. The hydration dependent dynamics of DMPC model membranes was studied using elastic and quasi-elastic neutron scattering. The elastic experiments showed a clear shift of the temperature of the main phase transition to higher temperatures with decreasing hydration level. The performed quasi-elastic measurements demonstrated nicely the influence, hydration has on the diffusive motions of the head lipid groups. Different models are necessary to fit the Q-dependence of the elastic incoherent structure factor and show therefore the reduced mobility as a result of reduced water content. In addition to temperature, pressure as a second thermodynamic variable was used to explore dynamics of DMPC membranes. The ordering introduced by applying pressure has similar effect to decreased hydration, therefore both approaches are complementary. Covering three orders of magnitude in observation time, the dynamics of native AChE and its complexed counterpart in presence of Huperzin A was investigated in the range from 1 ns to 100 ps. The mean square displacements obtained from the elastic data allowed the determination of activation energies and gave evidence that a hierarchy of motions contributes to the enzymatic activity. Diffusion constants and residence times were extracted from the quasi-elastic broadening. (author)

  15. Tunable ultrasensitivity: functional decoupling and biological insights.

    Science.gov (United States)

    Wang, Guanyu; Zhang, Mengshi

    2016-01-01

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

  16. 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.

  17. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

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

  18. Biological studies of radiation effects

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, J.H.

    1949-11-16

    This paper discusses procedures for research on biological effects of radiation, using mouse tissue: activation trace analysis including methods and proceedures for handling samples before during and after irradiation; methods and procedures for ion exchange study; method of separation and recovery of copper, iron, zinc, cobalt, pubidium and cesium. Also included are studies of trace elements with radioactive isotopes: the distribution of cobalt 60, zinc 65, and copper 64 in the cytoplasm and nuclei of normal mice and those with tumors. 16 figs., 2 tabs.

  19. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  1. Receptor studies in biological psychiatry

    International Nuclear Information System (INIS)

    Recent advances in the pharmacological treatment of endogenous psychosis have led to the development of biological studies in psychiatry. Studies on neurotransmitter receptors were reviewed in order to apply positron-emission tomograph (PET) for biological psychiatry. The dopamine (DA) hypothesis for schizophrenia was advanced on the basis of the observed effects of neuroleptics and methamphetamine, and DA(D2) receptor supersensitivity measured by PET and receptor binding in the schizophrenic brain. The clinical potencies of neuroleptics for schizophrenia were correlated with their abilities to inhibit the D2 receptor, and not other receptors. The σ receptor was expected to be a site of antipsychotic action. However, the potency of drugs action on it was not correlated with clinical efficacy. Haloperidol binds with high affinity to the σ receptor, which may mediate acute dystonia, an extrapyramidal side effect of neuroleptics. Behavioral and neurochemical changes induced by methamphetamine treatment were studied as an animal model of schizophrenia, and both a decrease of D2 receptor density and an increase of DA release were detected. The monoamine hypothesis for manic-depressive psychosis was advanced on the basis of the effect of reserpine, monoamine oxidase inhibitor and antidepressants. 3H-clonidine binding sites were increased in platelet membranes of depressive patients, 3H-imipramine binding sites were decreased. The GABAA receptor is the target site for the action of anxiolytics and antiepileptics such as benzodiazepines and barbiturates. Recent developments in molecular biology techniques have revealed the structure of receptor proteins, which are classified into two receptor families, the G-protein coupled type (D2) and the ion-channel type (GABAA). (J.P.N.)

  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. Labeling and functionalizing amphipols for biological applications.

    Science.gov (United States)

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

    2014-10-01

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

  4. 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.

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

    International Nuclear Information System (INIS)

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

  6. Marine Carotenoids: Biological Functions and Commercial Applications

    NARCIS (Netherlands)

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

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functi

  7. Lipids in the structure and functions of biological membranes

    Directory of Open Access Journals (Sweden)

    Kuznetsov V.I.

    2014-06-01

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

  8. 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

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

    Science.gov (United States)

    Li, Lin; Yang, Xiang-Jiao

    2015-11-01

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

  10. 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...

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

    Science.gov (United States)

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

    2013-01-01

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

  12. Printable Bioelectronics To Investigate Functional Biological Interfaces.

    Science.gov (United States)

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

    2015-10-19

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

  13. 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.

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

    OpenAIRE

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

    2013-01-01

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

  15. Genomic Functionalization: The Next Revolution In Biology

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  17. 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.

  18. Labeling and Functionalizing Amphipols for Biological Applications

    OpenAIRE

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

    2014-01-01

    Amphipols (APols) are short amphipathic polymers developed as an alternative to detergents for handling membrane proteins (MPs) in aqueous solution. MPs are, as a rule, much more stable following trapping with APols than they are in detergent solutions. The best-characterized APol to date, called A8-35, is a mixture of short-chain sodium polyacrylates randomly derivatized with octylamine and isopropylamine. Its solution properties have been studied in detail, and it has been used extensively ...

  19. Nuclear biological studies in France

    International Nuclear Information System (INIS)

    On the occasion of a colloquium on radiobiological research programmes, a number of documents dealing with French accomplishments and projects in this field were collected together. We felt that it would be useful to assemble these papers in one report; although they are brief and leave gaps to be filled in, they provide certain data, give an overall view of the situation, and can also suggest a rough plan for the general policy to adopt in the field of 'nuclear' biological research; i.e. research based on the nuclear tracer method or devoted to the action of ionising radiations. (author)

  20. Systematic Functional Annotation and Visualization of Biological Networks.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-06-22

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

  1. Biological activity of lactoferrin-functionalized biomimetic hydroxyapatite nanocrystals

    Directory of Open Access Journals (Sweden)

    Nocerino N

    2014-03-01

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

  2. 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

  3. Spectroscopic study of biologically active glasses

    Science.gov (United States)

    Szumera, M.; Wacławska, I.; Mozgawa, W.; Sitarz, M.

    2005-06-01

    It is known that the chemical activity phenomenon is characteristic for some inorganic glasses and they are able to participate in biological processes of living organisms (plants, animals and human bodies). An example here is the selective removal of silicate-phosphate glass components under the influence of biological solutions, which has been applied in designing glasses acting as ecological fertilizers of controlled release rate of the nutrients for plants. The structure of model silicate-phosphate glasses containing the different amounts of the glass network formers, i.e. Ca 2+ and Mg 2+, as a binding components were studied. These elements besides other are indispensable of the normal growth of plants. In order to establish the function and position occupied by the particular components in the glass structure, the glasses were examined by FTIR spectroscopy (with spectra decomposition) and XRD methods. It has been found that the increasing amount of MgO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes systematically from a structure of the cristobalite type to a structure corresponding to forsterite type. Whilst the increasing content of CaO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes from a structure typical for cristobalite through one similar to the structure of calcium orthophosphate, to a structure corresponding to calcium silicates. The changing character of domains structure is the reason of different chemical activity of glasses.

  4. 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

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

    Science.gov (United States)

    Li, Jun; Zhao, Patrick X

    2016-01-01

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/. PMID:27446133

  6. 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

  7. Biomarkers of Aging: From Function to Molecular Biology

    OpenAIRE

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

    2016-01-01

    Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a sing...

  8. Diverse Biological Functions of Extracellular Collagen Processing Enzymes

    OpenAIRE

    Trackman, Philip C.

    2005-01-01

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

  9. 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

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

    Science.gov (United States)

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

    2000-01-01

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

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

    Science.gov (United States)

    Cole, Daniel J; Hine, Nicholas D M

    2016-10-01

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

  12. 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.

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

    Science.gov (United States)

    Hunt, Andrew P; Lehnert, Nicolai

    2015-07-21

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

  14. 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

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

    Science.gov (United States)

    Strukov, A I; Kakturskiĭ, L V

    1977-01-01

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

  16. 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.

  17. Functionalized Conjugated Polyelectrolytes for Biological Sensing and Imaging.

    Science.gov (United States)

    Zhan, Ruoyu; Liu, Bin

    2016-06-01

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

  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

    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.

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

    OpenAIRE

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

    2007-01-01

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

  20. 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 the...

  1. Biological properties of extracellular vesicles and their physiological functions.

    Science.gov (United States)

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

    2015-01-01

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

  2. 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.

  3. 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.

  4. Studies on Semantic Systems Chemical Biology

    Science.gov (United States)

    Chen, Bin

    2012-01-01

    Current "one disease, one target and one drug" drug development paradigm is under question as relatively few drugs have reached the market in the last two decades. Increasingly research focus is being placed on the study of drug action against biological systems as a whole rather than against a single component (called "Systems…

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

    Science.gov (United States)

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

    2016-05-01

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

  6. Dynamic function studies

    International Nuclear Information System (INIS)

    Dynamic function studies can be defined as a measure of the variation of a quantity of a substance in an organ with time. Such studies are clinically useful only when the underlying physiological model is realistic. Usually the measurements are of three kinds: the uptake function, the transit function and the removal function. Sensitivity of these measurements can be enhanced in several clinical situations by intervention, such as exercise or drugs. It is possible to display a nuclear image in a variety of ways through computer manipulations which are justified only if based on a valid physiological model. The newer radiopharmaceuticals have also increased the range of functions that can be studied, especially in the case of the heart and the brain. Positron emission tomography (PET) images are fascinating but they are prohibitively expensive and routine clinical nuclear medicine will have to rely on information obtained with single photon emission computer tomography (SPECT). In the diagnosis of cancer, the instrument alone would not improve the diagnosis. It is necessary to have radiopharmaceuticals with a high degree of specificity of uptake. This can possibly be achieved with immunoscintigraphy. There also, the kinetics of uptake of the labelled antibody enable one to differentiate specific from non-specific uptake. The need for good reliable dynamic function studies is as great in the developing as in the developed countries, but a nuclear medicine specialist in a developing country would need more skills and experience because of the heavy odds against which one would be working. (author). 43 refs, 2 figs

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

    OpenAIRE

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

    2016-01-01

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

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

    Science.gov (United States)

    Rheinstadter, Maikel

    2008-03-01

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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. NMR Studies on Organic and Biological Solids

    OpenAIRE

    Yang, Chen

    2015-01-01

    Solid-state NMR (SSNMR) studies on biomolecules and organic molecular crystals are presented here. The biological part of the work is focused on improving resolution and sensitivity of SSNMR techniques for larger protein systems, while the studies on organic molecular crystals extend the application of SSNMR to determining the crystal structure of a photoreaction intermediate. First, a long-observation-window band-selective homonuclear decoupling scheme is introduced. The homonuclear decoupli...

  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. 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...... binding domain (LBD) has been associated with EDCs, a significant number of EDCs do not appear to influence the LBDs of these receptors. Therefore, we evaluated the potential biological effects of EDCs in humans with the aim to rationalize the etiology of certain disorders associated with the reproductive...

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

    Science.gov (United States)

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

    2010-06-01

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

  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. Functions of microRNAs in cardiovascular biology and disease.

    Science.gov (United States)

    Hata, Akiko

    2013-01-01

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

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

    OpenAIRE

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

    2011-01-01

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

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

    CERN Document Server

    Kolb, Brian; 10.1142/S1793984412300063

    2012-01-01

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

  1. Thyroid function study

    International Nuclear Information System (INIS)

    A short revision of thyroid physiology is done. The radioisotopes of common use in thyroid investigation and the choice of the most appropriated ones are discussed. A table showing radioisotopes frequently used in this study, with their main characteristics is presented. Among several isotopic assays in thyroid propaedeutics, those that refer to the function study, topographic studies and tests 'in vitro' are pointed out. Exploration methods 'in vivo' are treated, such as: thyroid uptake; urinary excretion; thyroid scintigraphy, with scintigraphic imagings; stimulation test by TSH; suppression test; pbi; clearance test with perchlorate; iodine deficiency test and thyroid study with technetium. 'In vitro' proofs like triiodothyronine (T3) and thyroxine (T4) assays, as well as free thyroxine index, are treated. At last, the therapeutics by Iodine 131 is commented and emphasis is given to its application on the treatment of hyperthyroidism and thyroid carcinoma

  2. Functional studies using NMR

    International Nuclear Information System (INIS)

    This volume is based on a series of lectures delivered at a one-day teaching symposium on functional and metabolic aspects of NMR measurements held at the Middlesex Hospital Medical School on 1st September 1985 as a part of the European Nuclear Medicine Society Congress. Currently the major emphasis in medical NMR in vivo is on its potential to image and display abnormalities in conventional radiological images, providing increased contrast between normal and abnormal tissue, improved definition of vasculature, and possibly an increased potential for differential diagnosis. Although these areas are undeniably of major importance, it is probable that NMR will continue to complement conventional measurement methods. The major potential benefits to be derived from in vivo NMR measurements are likely to arise from its use as an instrument for functional and metabolic studies in both clinical research and in the everyday management of patients. It is to this area that this volume is directed

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

    Directory of Open Access Journals (Sweden)

    Xiaowei eMa

    2014-02-01

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

  4. 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

  5. AFM imaging of functionalized carbon nanotubes on biological membranes

    Science.gov (United States)

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

    2009-10-01

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

  6. 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.

  7. Genome-wide survey for biologically functional pseudogenes.

    Science.gov (United States)

    Svensson, Orjan; Arvestad, Lars; Lagergren, Jens

    2006-05-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

  10. Biochemical Properties and Biological Functions of FET Proteins.

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    de Souza, Amancio José; Pauly, Markus

    2015-01-01

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

  12. 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.

  13. 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.

  14. 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.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  16. Experimental models to study cholangiocyte biology

    Institute of Scientific and Technical Information of China (English)

    Pamela S. Tietz; Xian-Ming Chen; Ai-Yu Gong; Robert C. Huebert; Anatoliy Masyuk; Tatyana Masyuk; Patrick L. Splinter; Nicholas F. LaRusso

    2002-01-01

    Cholangiocytes-the epithelial cells which line the bileducts-are increasingly recognized as importanttransporting epithelia actively involved in the absorptionand secretion of water, ions, and solutes. Thisrecognition is due in part to the recent development ofnew experimental models. New biologic concepts haveemerged including the identification and topography ofreceptors and flux proteins on the apical and/orbasolateral membrane which are involved in the molecularmechanisms of ductal bile secretion. Individually isolatedand/or perfused bile duct units from livers of rats andmice serve as new, physiologically relevant in vitromodels to study cholangiocyte transport. Biliary treedimensions and novel insights into anatomic remodeling ofproliferating bile ducts have emerged from three-dimensional reconstruction using CT scanning andsophisticated software. Moreover, new pathologicconcepts have arisen regarding the interaction ofcholangiocytes with pathogens such as Cryptosporidiumparvum. These concepts and associated methodologiesmay provide the framework to develop new therapies for the cholangiopathies, a group of important hepatobiliarydiseases in which cholangiocytes are the target cell.Tietz PS, Chen XM, Gong AY, Huebert RC, Masyuk A, MasyukT, Splinter PL, LaRusso NF. Experimental models to studycoholangiocyte biology.

  17. 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.

  18. 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.

  19. 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.

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

    OpenAIRE

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  2. 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

  3. 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

  4. 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. PMID:23047775

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

    OpenAIRE

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

    2009-01-01

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

  6. 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.

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

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

    2013-01-01

    Background Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such “bio-models” necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natu...

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

    Science.gov (United States)

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

    2015-12-01

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

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

    DEFF Research Database (Denmark)

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

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

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

    OpenAIRE

    Raes, J.; Bork, P.

    2008-01-01

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

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

    OpenAIRE

    Knüpfer, Christian; Beckstein, Clemens

    2013-01-01

    Background Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. Results In this paper we describe different functional aspects of dynamic models. This descriptio...

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

    Science.gov (United States)

    Wang, Xiu-Xia

    2014-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Isganitis Timothy

    2006-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Kathleen H Wood

    2016-05-01

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use...

  17. 15N in biological nitrogen fixation studies

    International Nuclear Information System (INIS)

    A bibliography with 298 references on the use of the stable nitrogen isotope 15N in the research on the biological fixation of dinitrogen is presented. The literature pertaining to this bibliography covers the period from 1975 to the middle of 1985. (author)

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

    International Nuclear Information System (INIS)

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

  19. Novel nuclear magnetic resonance techniques for studying biological molecules

    International Nuclear Information System (INIS)

    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.

  20. 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.

  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. 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].

  3. 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.

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

    OpenAIRE

    Sukanto Bhattacharya; Kuldeep Kumar

    2007-01-01

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

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

    OpenAIRE

    Kuldeep Kumar; Sukanto Bhattacharya

    2007-01-01

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

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

    International Nuclear Information System (INIS)

    The H2O substitution for D2O either in environment or in the culture medium of the living systems generates changes in their main functions and composition. In this paper some of the heavy water effects in biological systems such as structural and functional changes were reviewed: normal cell architecture alterations, cell division and membrane functions disturbance, muscular contractility and the perturbations of biological oscillators such as circadian rhythm, heart rate, respiratory cycle, tidal and ultradian rhythm. (authors)

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

    International Nuclear Information System (INIS)

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

  8. 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.

  9. 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.

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

    Science.gov (United States)

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

    2012-08-01

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

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

    Science.gov (United States)

    Hombach, Sonja; Kretz, Markus

    2016-01-01

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

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

    OpenAIRE

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

    2011-01-01

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

  13. Molecular biology in studies of oceanic primary production

    Energy Technology Data Exchange (ETDEWEB)

    LaRoche, J.; Falkowski, P.G. [Brookhaven National Lab., Upton, NY (United States); Geider, R. [Delaware Univ., Lewes, DE (United States). Coll. of Marine Studies

    1992-07-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  14. Molecular biology in studies of oceanic primary production

    Energy Technology Data Exchange (ETDEWEB)

    LaRoche, J.; Falkowski, P.G. (Brookhaven National Lab., Upton, NY (United States)); Geider, R. (Delaware Univ., Lewes, DE (United States). Coll. of Marine Studies)

    1992-01-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  15. Molecular biology in studies of oceanic primary production

    International Nuclear Information System (INIS)

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies

  16. PENGEMBANGAN BAHAN AJAR BIOLOGI SEL PADA PROGRAM STUDI PENDIDIKAN BIOLOGI UIN ALAUDDIN MAKASSAR

    OpenAIRE

    Muriati, St

    2015-01-01

    Learning in UIN Alauddin is still limited knowledge to students, while, one mission to improve the quality of educators Biology in terms of belief, moral and scientific attitudes have not been implemented. This is caused by a lack of learning resources that connects Biology Science and its relation to scientific Qur'an. Cell Biology as subjects that reveal about the phenomenon of the smallest unit of life, it can be studied with scientific Qur'an. Therefore, it is necessary to develop teachin...

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

    International Nuclear Information System (INIS)

    Hydroxyapatite (HA) [Ca10(PO4)6(OH)2] is the primary mineral content, representing 43% by weight, of bone. Applying a thin layer of HA, to the surface of a metal implant, can promote osseointegration and increase the mechanical stability of the implant. In this study, a biocompatible coating comprising an HA film with functionally graded crystallinity is being deposited on a heated substrate in an Ion Beam Assisted Deposition (IBAD) system. The microstructure of the film was studied using Transmission Electron Microscopy techniques. Finally, initial cell adhesion and cell differentiation on the coating was evaluated using ATCC CRL 1486 human embryonic palatal mesenchymal cell, an osteoblast precursor cell line. The results have shown superior mechanical properties and biological response to the functionally graded HA film

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-04-15

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

  19. 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...

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

    OpenAIRE

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2007-04-24

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

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

    Science.gov (United States)

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

    2016-08-01

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

  3. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

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

    OpenAIRE

    Mazereeuw, M.

    2013-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

  7. A systems biology approach for the study of smoking and myocardial infarction

    OpenAIRE

    Xu, Tao

    2015-01-01

    Metabolomics has been proven to be a powerful tool to study complex phenotypes. It can present a snapshot of the current status of metabolism and provide a functional readout of the gene products. Complementing with other ‘omics’ techniques in systems biology studies, the integration of metabolomics with other ‘omics’, e.g. trancriptomics and epigenomics, will help to illustrate complex biological processes which are related to disease and environmental exposure. This thesis presents three...

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

    Science.gov (United States)

    Baker, Sarah E.

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

  9. 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.

  10. MicroRNA function in NK cell biology

    OpenAIRE

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

    2013-01-01

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

  11. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  14. Organization principles of biological networks: An explorative study.

    Science.gov (United States)

    Kohestani, Havva; Giuliani, Alessandro

    2016-03-01

    The definition of general topological principles allowing for graph characterization is an important pre-requisite for investigating structure-function relationships in biological networks. Here we approached the problem by means of an explorative, data-driven strategy, building upon a size-balanced data set made of around 200 distinct biological networks from seven functional classes and simulated networks coming from three mathematical graph models. A clear link between topological structure and biological function did emerge in terms of class membership prediction (average 67% of correct predictions, p<0.0001) with a varying degree of 'peculiarity' across classes going from a very low (25%) recognition efficiency for neural and brain networks to the extremely high (80%) peculiarity of amino acid-amino acid interaction (AAI) networks. We recognized four main dimensions (principal components) as main organization principles of biological networks. These components allowed for an efficient description of network architectures and for the identification of 'not-physiological' (in this case cancer metabolic networks acting as test set) wiring patterns. We highlighted as well the need of developing new theoretical generative models for biological networks overcoming the limitations of present mathematical graph idealizations. PMID:26845173

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

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

    International Nuclear Information System (INIS)

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

  18. 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.

  19. The biology and function of exosomes in cancer.

    Science.gov (United States)

    Kalluri, Raghu

    2016-04-01

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

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

    Science.gov (United States)

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

    2012-06-15

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

  1. 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.

  2. 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...... transcriptomic to mention 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 sequenced Aspergilli are a known human pathogen (Aspergillus fumigatus), a model organism for cellular mechanisms (Aspergillus nidulans) and two industrial workhorses (Aspergillus niger and Aspergillus oryzae). In the presented work, new analytical and computational tools have been designed...

  3. BIOLOGICAL EFFECTS OF PULSED SHORT WAVE TREATMENT. AN EXPERIMENTAL STUDY

    OpenAIRE

    Dogaru Gabriela; Crăciun Constantin

    2015-01-01

    Pulsed short waves are short electromagnetic waves emitted as intermittent trains with a fixed duration, separated by free intervals of variable duration. The biological effects of pulsed short waves could be explained according to most of the authors by an activation of cellular enzymatic reactions, a stimulation of energy metabolism, a stimulation of liver function, of adrenal gland function and of the reticulocyte system, changes in cell permeability, by an increase of peripheral blood flo...

  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. 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

  6. 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.

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

    Science.gov (United States)

    Hijova, E

    2005-01-01

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

  8. 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.

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

    Science.gov (United States)

    Michaelian, K.

    2011-01-01

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

  10. 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...

  11. BIOLOGICAL EFFECTS OF PULSED SHORT WAVE TREATMENT. AN EXPERIMENTAL STUDY

    Directory of Open Access Journals (Sweden)

    Dogaru Gabriela

    2015-02-01

    Full Text Available Pulsed short waves are short electromagnetic waves emitted as intermittent trains with a fixed duration, separated by free intervals of variable duration. The biological effects of pulsed short waves could be explained according to most of the authors by an activation of cellular enzymatic reactions, a stimulation of energy metabolism, a stimulation of liver function, of adrenal gland function and of the reticulocyte system, changes in cell permeability, by an increase of peripheral blood flow through the enhancement of local vascularization. This research aimed to investigate the biological effects of exposure to pulsed short waves at different doses on the adrenal glands of experimental animals, by structural and ultrastructural studies. The study included 35 animals assigned to 4 groups. Group I included 10 experimental animals exposed to radiation at a dose of 1/80 impulses/sec, group II, 10 animals exposed to a dose of 4/400 impulses/sec, group III, 10 animals exposed to a dose of 6/600 impulses/sec, for 10 min/day, and the control group consisted of 5 unexposed animals. Structural and ultrastructural changes of adrenal glands induced by the dose of 4/400 impulses/sec, compared to the unexposed control group and the dose of 1/80 impulses/sec, include an intensification of protein synthesis processes, an enhancement of energy metabolism in providing the energy required for an increased production of hormones, an intensification of collagen fiber synthesis processes in the capsule, necessary for healing. It was demonstrated that this dose induced an intensification of hormone synthesis and secretion, a stimulation of adrenal function. At the dose of 6/600 cycles/sec, a slight diminution of hormone synthesis and secretion activity was found, which was not below the limits existing in the unexposed control group, but was comparable to group II. This dose is probably too strong for experimental animals, inducing them a state of stress. The

  12. Monovalent monatomic ions in biological environments : insights from computational biophysics studies

    OpenAIRE

    Zhang, Chao

    2012-01-01

    Monovalent monoatomic ions (Na+, K+, Cl-, H+) are ubiquitously present in biological systems. They are indispensable for various life functions, such as keeping the heart beating and converting the energy from food. Complementary to experiments, molecular simulations indeed provide a computational microscope to probe the structure, dynamics and energetics of these ions in biological environments. One big challenge of computational studies is to accurately model the potential energy surface of...

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

    Science.gov (United States)

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

    2016-05-25

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

  14. 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.

  15. Phenolic Phytoalexins in Rice: Biological Functions and Biosynthesis

    OpenAIRE

    Man-Ho Cho; Sang-Won Lee

    2015-01-01

    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....

  16. Antioxidant properties of violacein: possible relation on its biological function.

    Science.gov (United States)

    Konzen, Marlon; De Marco, Daniela; Cordova, Clarissa A S; Vieira, Tiago O; Antônio, Regina V; Creczynski-Pasa, Tânia B

    2006-12-15

    Violacein, a violet pigment produced by Chromobacterium violaceum, has attracted much attention in recent literature due to its pharmacological properties. In this work, the antioxidant properties of violacein were investigated. The reactivity with oxygen and nitrogen reactive species and 1,1-diphenyl-2-picryl-hydrazyl (DPPH), a stable free radical, was evaluated. EPR studies were carried out to evaluate the reactivity with the hydroxyl radical. The action of violacein against lipid peroxidation in three models of lipid membranes, including rat liver microsomes, Egg and Soy bean phosphathidylcholine liposomes were also evaluated. The compound reacted with DPPH (IC(50)=30microM), nitric oxide (IC(50)=21microM), superoxide radicals (IC(50)=125microM) and decreased the hydroxyl radical EPR signal. The compound protected the studied membranes against peroxidation induced by reactive species in the micromolar range. The reconstitution of violacein into the membranes increased its antioxidant effect. These results indicate that the compound has strong antioxidant potential. Based on these results we suggest violacein plays an important role with the microorganism membrane in defense against oxidative stress. PMID:17011197

  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. PMID:27111421

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

    Science.gov (United States)

    Cho, Man-Ho; Lee, Sang-Won

    2015-01-01

    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. PMID:26690131

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

    OpenAIRE

    Schultz, M.J.; Spronk, P.E.; Royakkers, A.A.N.M.

    2014-01-01

    The purpose of the investigations described in this thesis was to seek for answers to two relevant questions in ICUs in resource-rich settings, i.e., can new biological markers play a role in early recognition of AKI, and can new biological markers predict recovery of renal function in patients who receive CVVH? A second aim was to answer a relevant question in ICUs in resource-poor settings, i.e., can novel biological markers predict development of AKI and need for RRT in patients with sever...

  20. Nuclear magnetic resonance studies of biological systems

    International Nuclear Information System (INIS)

    The difference between intracellular and extracellular proton relaxation rates provides the basis for the determination of the mean hemoglobin concentration (MHC) in red blood cells. The observed water T1 relaxation data from red blood cell samples under various conditions were fit to the complete equation for the time-dependent decay of magnetization for a two-compartment system including chemical exchange. The MHC for each sample was calculated from the hematocrit and the intracellular water fraction as determined by NMR. The binding of the phosphorylcholine (PC) analogue, 2-(trimethylphosphonio)-ethylphosphate (phosphoryl-phosphocholine, PPC) to the PC binding myeloma proteins TEPC-15, McPC 603, and MOPC 167 was studied by 31P NMR

  1. 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

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

    OpenAIRE

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

    2013-01-01

    In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors a...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-15

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

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

    Science.gov (United States)

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

    2012-08-01

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

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

    Science.gov (United States)

    Heussler, Gary E; O'Toole, George A

    2016-05-15

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

  7. What Trends Do Turkish Biology Education Studies Indicate?

    Science.gov (United States)

    Topsakal, Unsal Umdu; Calik, Muammer; Cavus, Ragip

    2012-01-01

    The aim of this study is to determine what trends Turkish biology education studies indicate. To achieve this aim, the researchers examined online databases of the Higher Education Council and open access archives of graduate theses in web sites of Turkish universities. Finally, totally 138 graduate theses were elicited to analyze in regard to…

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

    Science.gov (United States)

    Regelmann, J P

    1982-01-01

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

  9. 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...

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-01-01

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

  12. 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...

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

    Directory of Open Access Journals (Sweden)

    MarCia T Ekworomadu

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

  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

    OpenAIRE

    M. Rajeswara Rao; Angel, Michael F.; Das, Suman K.; Margot S. Koelle; Don Obenhuber; Reno, William L.; Asit Panja; Hari H. P. Cohly

    2005-01-01

    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 i...

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

    Science.gov (United States)

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

    1991-01-01

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

  16. 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.

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

    Science.gov (United States)

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

    2015-08-01

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

  18. 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....

  19. Stable isotope methods in biological and ecological studies of arthropods

    NARCIS (Netherlands)

    Hood-Nowotny, R.C.; Knols, B.G.J.

    2007-01-01

    This is an eclectic review and analysis of contemporary and promising stable isotope methodologies to study the biology and ecology of arthropods. It is augmented with literature from other disciplines, indicative of the potential for knowledge transfer. It is demonstrated that stable isotopes can b

  20. 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.

  1. 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

  2. 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,…

  3. 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. PMID:25707959

  4. Systems Biology Approaches to Epidemiological Studies of Complex Diseases

    OpenAIRE

    Li, Hongzhe

    2013-01-01

    Systems biology approaches to epidemiological studies of complex diseases include collection of genetic, genomic, epigenomic and metagenomic data in large-scale epidemiological studies of complex phenotypes. Designs and analyses of such studies raise many statistical challenges. This paper reviews some issues related to integrative analysis of such high dimensional and inter-related data sets and outline some possible solutions. I focus my review on integrative approaches for genome-wide gene...

  5. Structural and Computational Studies of Small Organic and Biological Molecules

    OpenAIRE

    Lozano-Casal, Patricia

    2006-01-01

    Over the last three decades high-pressure X-ray diffraction techniques have been widely utilised to perform structural studies in many areas of research. For example, physicists make use of these experimental techniques to investigate metals, conductor and semi-conductor compounds among others, whereas geochemists apply them to study the conditions deep within the Earth’s interior. Furthermore, pressure studies have reached an important status in chemistry, biology and planetary science, and ...

  6. 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

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

    Science.gov (United States)

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

    2016-01-01

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

  8. The formation, function and regulation of amyloids: insights from structural biology.

    Science.gov (United States)

    Landreh, M; Sawaya, M R; Hipp, M S; Eisenberg, D S; Wüthrich, K; Hartl, F U

    2016-08-01

    Amyloid diseases are characterized by the accumulation of insoluble, β-strand-rich aggregates. The underlying structural conversions are closely associated with cellular toxicity, but can also drive the formation of functional protein assemblies. In recent years, studies in the field of structural studies have revealed astonishing insights into the origins, mechanisms and implications of amyloid formation. Notably, high-resolution crystal structures of peptides in amyloid-like fibrils and prefibrillar oligomers have become available despite their challenging chemical nature. Nuclear magnetic resonance spectroscopy has revealed that dynamic local polymorphisms in the benign form of the prion protein affect the transformation into amyloid fibrils and the transmissibility of prion diseases. Studies of the structures and interactions of chaperone proteins help us to understand how the cellular proteostasis network is able to recognize different stages of aberrant protein folding and prevent aggregation. In this review, we will focus on recent developments that connect the different aspects of amyloid biology and discuss how understanding the process of amyloid formation and the associated defence mechanisms can reveal targets for pharmacological intervention that may become the first steps towards clinically viable treatment strategies. PMID:27237473

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

  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. PMID:25910818

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

    DEFF Research Database (Denmark)

    Stranne, Maria

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

  13. Studies on Biological Development of Hybrid Bees Families

    OpenAIRE

    Monica Pârvu; Ioana Cristina Andronie; Violeta-Elena Simion; Carmen Bergheş; Adriana Amfim

    2010-01-01

    It has made a study concerning the biological development of hybrid bee’s families (Italian x Carpathian) comparative with Carpathian bee’s families. The bees were housed in multi-storey hives. The following parameters were studied: the queen bee prolificacy, the flight intensity during harvesting, the flight intensity during bad weather the irascibility, the behaviour of the bees during the survey and the predisposition to swarming. At the hybrid families, queen bee prolificacy and the rate ...

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

    DEFF Research Database (Denmark)

    Petersen, Anders; Andersen, Tobias

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

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

    Science.gov (United States)

    Zammito, John

    2006-12-01

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

  16. Quantum mechanical simulation methods for studying biological systems

    International Nuclear Information System (INIS)

    Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)

  17. A decontamination study of simulated chemical and biological agents

    International Nuclear Information System (INIS)

    A comprehensive decontamination scheme of the chemical and biological agents, including airborne agents and surface contaminating agents, is presented. When a chemical and biological attack occurs, it is critical to decontaminate facilities or equipments to an acceptable level in a very short time. The plasma flame presented here may provide a rapid and effective elimination of toxic substances in the interior air in isolated spaces. As an example, a reaction chamber, with the dimensions of a 22 cm diameter and 30 cm length, purifies air with an airflow rate of 5000 l/min contaminated with toluene, the simulated chemical agent, and soot from a diesel engine, the simulated aerosol for biological agents. Although the airborne agents in an isolated space are eliminated to an acceptable level by the plasma flame, the decontamination of the chemical and biological agents cannot be completed without cleaning surfaces of the facilities. A simulated sterilization study of micro-organisms was carried out using the electrolyzed ozone water. The electrolyzed ozone water very effectively kills endospores of Bacillus atrophaeus (ATCC 9372) within 3 min. The electrolyzed ozone water also kills the vegetative micro-organisms, fungi, and virus. The electrolyzed ozone water, after the decontamination process, disintegrates into ordinary water and oxygen without any trace of harmful materials to the environment

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

    International Nuclear Information System (INIS)

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

  20. 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

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

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

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

  2. Radiolabelled substrates for studying biological effects of trace contaminants

    International Nuclear Information System (INIS)

    A programme of coordinated isotopic tracer-aided investigations of the biological side-effects of foreign chemical residues in food and agriculture, initiated in 1973, was reviewed. The current status of representative investigations from the point of view of techniques and priorities was assessed. Such investigations involved radioactive substrates for studying DNA injury and its repair; 14C-labelled acetylcholine as substrate for measuring enzyme inhibition due to the presence of, or exposure to, anticholinesteratic contaminants; radioactive substrates as indication of side-effects in non-target organisms and of their comparative susceptibilities; radioactive substrates as indicators of persistence or biodegradability of trace contaminants of soil or water; and labelled pools for studying the biological side-effects of trace contaminants. Priorities were identified

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

    OpenAIRE

    Korytowski, Agatha Anna

    2016-01-01

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

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

    OpenAIRE

    Mancuso, James J.; Jie Cheng

    2014-01-01

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

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

    Science.gov (United States)

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

    2015-05-01

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

  6. Sleep and Multisystem Biological Risk: A Population-Based Study

    OpenAIRE

    Carroll, Judith E.; Irwin, Michael R.; Merkin, Sharon Stein; Seeman, Teresa E

    2015-01-01

    Background Short sleep and poor sleep quality are associated with risk of cardiovascular disease, diabetes, cancer, and mortality. This study examines the contribution of sleep duration and sleep quality on a multisystem biological risk index that is known to be associated with morbidity and mortality. Methods Analyses include a population-based sample from the Midlife Development in the United States survey recruited to the Biomarker substudy. A total of 1,023 participants aged 54.5 years (S...

  7. Marine Sponges and Symbionts: Chemical and Biological Studies

    OpenAIRE

    Schmidt, Eric W.

    1999-01-01

    This thesis concerns two quite different types of research that are separated into distinct sections of the thesis, but which seek to answer the same question using diametrically opposite approaches. The first part (Chapters 1-8) covers research leading to novel, bioactive compounds in marine sponges, while the second (Chapters 9-10) involves molecular biological studies of symbiosis between microbes and sponges. Although these topics seem at first glance completely separate, they are in real...

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

    OpenAIRE

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

    2015-01-01

    Steady state analysis of dynamical systems for biological networks give 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. Current methods from computational algebraic geometry and combinatorics are applied to analyze this model.

  9. Supramolecular approaches to cryorelaxors for biological NMR studies

    OpenAIRE

    Cuda, F.

    2010-01-01

    The work reported in this thesis concerns the development of Cryorelaxors having potential applications in very low temperature NMR studies of biological materials. Two approaches have been explored, namely calixarene host-guest complexes incorporating rotationally labile methyl groups, and endohedral fullerene complexes. The first chapter provides an overview of the background of the project and of potential approaches to the problem of low temperature relaxation agents, particularly thos...

  10. Physicochemical and biological treatability study of textile dye wastewater

    OpenAIRE

    Gorgone, Christine Ann

    1995-01-01

    The textile industry discharges a highly colored wastewater characterized by high organic levels. Industrial wastewater with these characteristics can be harmful to receiving streams and municipal plants, and must be treated prior to discharge. In this project, a yam dyeing facility was studied that uses biological treatment followed by chemical coagulation to treat their highly colored wastewater prior to discharging to the local river. Occasionally, color, organic, and metal ...

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

    Science.gov (United States)

    Ran, Jihua; Li, Hui; Li, Huiwu

    2016-01-01

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

  12. Best Practices for Promoting Functional Biology Education: Activity-Based, Laboratory-Oriented Instruction

    Directory of Open Access Journals (Sweden)

    Abigail Mgboyibo Osuafor

    2016-08-01

    Full Text Available A major goal of science education is fostering students’ intellectual competencies. This goal can only be achieved when students are actively involved in the teaching-learning process. This study therefore, investigated the extent to which the biology teachers employ pupil-centered activities such as laboratory/practical instructional methods in order to improve the learning outcome of their students. The descriptive survey involved 73 Biology teachers randomly selected from all the six education zones of Anambra state, Nigeria. Four research questions and two hypotheses guided the conduct of the study. A 32-item structured questionnaire which has reliability co-efficient of 0.82 was used to collect data. Data were analyzed using mean, standard deviation and t-test. Results show that Biology teachers adopt practical-oriented strategies in teaching biology, conduct practical activities to a high extent, and perceive practical exercises as essential to effective teaching and learning of the subject. Provision of adequate number of laboratory materials, employment of adequate number of biology teachers, making provision for well designed laboratory activities in the curriculum and training of teachers on how to effectively combine theory with practical are some of the strategies that will encourage biology teachers to conduct practical lessons. There was no significant difference between male and female biology teachers in their responses to the different aspects investigated. Based on these findings, some recommendations were made which include that curriculum designers should incorporate guides for practical activities that go with each topic in the curriculum so as to encourage the teachers to teach theory with practical.

  13. Interrogating the Role of Receptor-Mediated Mechanisms: Biological Fate of Peptide-Functionalized Radiolabeled Gold Nanoparticles in Tumor Mice.

    Science.gov (United States)

    Silva, Francisco; Zambre, Ajit; Campello, Maria Paula Cabral; Gano, Lurdes; Santos, Isabel; Ferraria, Ana Maria; Ferreira, Maria João; Singh, Amolak; Upendran, Anandhi; Paulo, António; Kannan, Raghuraman

    2016-04-20

    To get a better insight on the transport mechanism of peptide-conjugated nanoparticles to tumors, we performed in vivo biological studies of bombesin (BBN) peptide functionalized gold nanoparticles (AuNPs) in human prostate tumor bearing mice. Initially, we sought to compare AuNPs with thiol derivatives of acyclic and macrocyclic chelators of DTPA and DOTA types. The DTPA derivatives were unable to provide a stable coordination of (67)Ga, and therefore, the functionalization with the BBN analogues was pursued for the DOTA-containing AuNPs. The DOTA-coated AuNPs were functionalized with BBN[7-14] using a unidentate cysteine group or a bidentate thioctic group to attach the peptide. AuNPs functionalized with thioctic-BBN displayed the highest in vitro cellular internalization (≈ 25%, 15 min) in gastrin releasing peptide (GRP) receptor expressing cancer cells. However, these results fail to translate to in vivo tumor uptake. Biodistribution studies following intravenous (IV) and intraperitoneal (IP) administration of nanoconjugates in tumor bearing mice indicated that the presence of BBN influences to some degree the biological profile of the nanoconstructs. For IV administration, the receptor-mediated pathway appears to be outweighed by the EPR effect. By contrast, in IP administration, it is reasoned that the GRPr-mediated mechanism plays a role in pancreas uptake. PMID:27003101

  14. Unmanned Aircraft Systems complement biologging in spatial ecology studies.

    Science.gov (United States)

    Mulero-Pázmány, Margarita; Barasona, Jose Ángel; Acevedo, Pelayo; Vicente, Joaquín; Negro, Juan José

    2015-11-01

    The knowledge about the spatial ecology and distribution of organisms is important for both basic and applied science. Biologging is one of the most popular methods for obtaining information about spatial distribution of animals, but requires capturing the animals and is often limited by costs and data retrieval. Unmanned Aircraft Systems (UAS) have proven their efficacy for wildlife surveillance and habitat monitoring, but their potential contribution to the prediction of animal distribution patterns and abundance has not been thoroughly evaluated. In this study, we assess the usefulness of UAS overflights to (1) get data to model the distribution of free-ranging cattle for a comparison with results obtained from biologged (GPS-GSM collared) cattle and (2) predict species densities for a comparison with actual density in a protected area. UAS and biologging derived data models provided similar distribution patterns. Predictions from the UAS model overestimated cattle densities, which may be associated with higher aggregated distributions of this species. Overall, while the particular researcher interests and species characteristics will influence the method of choice for each study, we demonstrate here that UAS constitute a noninvasive methodology able to provide accurate spatial data useful for ecological research, wildlife management and rangeland planning. PMID:26640661

  15. Biological dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in hematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes cytokinetic blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y=c+ α D+β D2 where. Y is the number micronuclei per cell and D the dose. the curve is compared with those produced elsewhere

  16. The use of analysis of variance procedures in biological studies

    Science.gov (United States)

    Williams, B.K.

    1987-01-01

    The analysis of variance (ANOVA) is widely used in biological studies, yet there remains considerable confusion among researchers about the interpretation of hypotheses being tested. Ambiguities arise when statistical designs are unbalanced, and in particular when not all combinations of design factors are represented in the data. This paper clarifies the relationship among hypothesis testing, statistical modelling and computing procedures in ANOVA for unbalanced data. A simple two-factor fixed effects design is used to illustrate three common parametrizations for ANOVA models, and some associations among these parametrizations are developed. Biologically meaningful hypotheses for main effects and interactions are given in terms of each parametrization, and procedures for testing the hypotheses are described. The standard statistical computing procedures in ANOVA are given along with their corresponding hypotheses. Throughout the development unbalanced designs are assumed and attention is given to problems that arise with missing cells.

  17. Study of nanoscale structural biology using advanced particle beam microscopy

    Science.gov (United States)

    Boseman, Adam J.

    This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

  18. Biological Dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ αD+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs

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

    International Nuclear Information System (INIS)

    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. (author)

  20. 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.

  1. 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.

  2. 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. PMID:26645985

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

    Science.gov (United States)

    Himschoot, Agnes Rose

    2012-01-01

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

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

    Science.gov (United States)

    Lace, Beatrice; Prandi, Cristina

    2016-08-01

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

  5. 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.

  6. Biological studies of the US Subseabed Disposal Program

    International Nuclear Information System (INIS)

    The Subseabed Disposal Program (SDP) of the US is assessing the feasibility of emplacing high level radioactive wastes (HLW) within deep-sea sediments and is developing the means for assessing the feasibility of the disposal practices of other nations. This paper discusses the role and status of biological research in the SDP. Studies of the disposal methods and of the conceived barriers (canister, waste form and sediment) suggest that biological knowledge will be principally needed to address the impact of accidental releases of radionuclides. Current experimental work is focusing on the deep-sea ecosystem to determine: (1) the structure of benthic communities, including their microbial component; (2) the faunal composition of deep midwater nekton; (3) the biology of deep-sea amphipods; (4) benthic community metabolism; (5) the rates of bacterial processes; (6) the metabolism of deep-sea animals, and (7) the radiation sensitivity of deep-sea organisms. A multicompartment model is being developed to assess quantitatively the impact (on the environment and on man) of releases of radionuclides into the sea

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

    Directory of Open Access Journals (Sweden)

    Ward Alister C

    2007-10-01

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

  8. 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.

  9. The first characterization of gene structure and biological function for echinoderm translationally controlled tumor protein (TCTP).

    Science.gov (United States)

    Ren, Chunhua; Chen, Ting; Jiang, Xiao; Wang, Yanhong; Hu, Chaoqun

    2014-12-01

    Translationally controlled tumor protein (TCTP) is a multifunctional protein that existed ubiquitously in different eukaryote species and distributed widely in various tissues and cell types. In this study, the gene structure and biological function of TCTP were first characterized in echinoderm. An echinoderm TCTP named StmTCTP was identified from sea cucumber (Stichopus monotuberculatus) by expression sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The StmTCTP cDNA is 1219 bp in length, containing a 5'-untranslated region (UTR) of 77 bp, a 3'-UTR of 623 bp and an open reading frame (ORF) of 519 bp that encoding a protein of 172 amino acids with a deduced molecular weight of 19.80 kDa and a predicted isolectric point of 4.66. Two deduced signal signatures termed TCTP1 and TCTP2, a microtubule binding domain, a Ca(2+) binding domain and the conserved residues forming Rab GTPase binding surface were found in the StmTCTP amino acid sequence. For the gene structure, StmTCTP contains four exons separated by three introns. The anti-oxidation and heat shock protein activities of recombinant TCTP protein were also demonstrated in this study. In addition, the expression of StmTCTP was found to be significantly upregulated by polyriboinosinic polyribocytidylic acid [poly (I:C)], lipopolysaccharides (LPS) or inactivated bacteria challenge in in vitro primary culture experiments of coelomocytes, suggested that the sea cucumber TCTP might play critical roles not only in the defense against oxidative and thermal stresses, but also in the innate immune defense against bacterial and viral infections. PMID:25193395

  10. 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.

  11. 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.

  12. The dynamics of the biological membrane surrounding the buffalo milk fat globule investigated as a function of temperature.

    Science.gov (United States)

    Nguyen, Hanh T H; Madec, Marie-Noëlle; Ong, Lydia; Kentish, Sandra E; Gras, Sally L; Lopez, Christelle

    2016-08-01

    The biological membrane surrounding fat globules in milk (the MFGM) is poorly understood, despite its importance in digestion and in determining the properties of fat globules. In this study, in situ structural investigations of buffalo MFGM were performed as a function of temperature (4-60°C), using confocal microscopy. We demonstrate that temperature and rate of temperature change affected the lipid domains formed in the MFGM with the lateral segregation (i) of high Tm lipids and cholesterol in a Lo phase for both TTm and (ii) of high Tm lipids in a gel phase for Tfunction of temperature, could modulate the functions of fat globules during processing and digestion. PMID:26988511

  13. 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

  14. Beach cleaning in Belgium: a social and biological study

    OpenAIRE

    Domínguez Tejo, H.M.

    2006-01-01

    A study on beach cleaning in Belgium was conducted from a social and biological perspective, to confront the lack of information regarding the two methods used: manual and mechanical beach cleaning. Through direct participation in the pilot project on manual beach cleaning of the municipality of Koksijde, during summer 2004, around 42 kg of man-made waste/km/month were estimated during July and September, and 87 kg during August. An average 1.5h/km was needed for two persons to manually clean...

  15. Functionalised isocoumarins as antifungal compounds: Synthesis and biological studies.

    Science.gov (United States)

    Simic, Milena; Paunovic, Nikola; Boric, Ivan; Randjelovic, Jelena; Vojnovic, Sandra; Nikodinovic-Runic, Jasmina; Pekmezovic, Marina; Savic, Vladimir

    2016-01-01

    A series of novel 3-substituted isocoumarins was prepared via Pd-catalysed coupling processes and screened in vitro for antifungal activity against Candida species. The study revealed antifungal potential of isocoumarins possessing the azole substituents, which, in some cases, showed biological properties equal to those of clinically used voriconazole. Selected compounds were also screened against voriconazole resistant Candida krusei 6258 and a clinical isolate Candida parapsilosis CA-27. Although the activity against these targets needs to be improved further, the results emphasise additional potential of this new class of antifungal compounds. PMID:26586600

  16. Studies of the reproductive biology of deep-sea megabenthos

    International Nuclear Information System (INIS)

    The final report describes the general biology and ecology of the 15 holothurians, 3 asteroids, 2 zoanthids and 1 crustacea species studied in Reports I-XIII, the sampling methods used and the station data. A summary of the histological, histochemical and biochemical results for the species examined is given. The data suggest that the reproductive processes in the deep-sea species examined are highly unlikely to be part of a pathway for the transfer of radionuclides from the deep-sea back to man. (author)

  17. Bemisia tabaci: A new clip-cage for biological studies

    OpenAIRE

    Muñiz, M.; Nombela, G.

    2001-01-01

    This new clip-cage has been designed in our laboratory. It is a transparent plastic truncated cone clip-cage (3.6 cm x 2.6 cm diameter; 4 cm high). A very thin polypropylene mesh (30 holes/inch) is attached to the bottom by paraffin wax. We have used this clip-cage attached to the under surface of the leaves in our studies on the biology of both B and Q biotypes of Bemisia tabaci with excellent results.

  18. Integrative biological studies of anti-tumour agents

    OpenAIRE

    Johnson, L. A.

    2009-01-01

    3, 11-difluoro-6, 8, 13-trimethyl-8H- quino [4, 3, 2-kl] acridinium methosulfate (RHPS4) is a member of a series of pentacyclic acridines developed at the University of Nottingham, which bind to, and stabilise the structure of G-quadruplex DNA and inhibit the action of telomerase at sub-micromolar concentrations in the cell free TRAP assay and limit cancer cell growth therefore leading to the conclusion that RHPS4 has potential anti-tumour activity. Previous biological studies, however, have...

  19. 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.

  20. 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.

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    James J Mancuso

    2014-11-01

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

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

    Science.gov (United States)

    Xia, W D; Fu, K Y

    2016-03-01

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

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

    Science.gov (United States)

    Himschoot, Agnes Rose

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-15

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

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

    Science.gov (United States)

    Price, S A; Schmitz, L

    2016-04-01

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

  7. Biological functioning of PAH-polluted and thermal desorption-treated soils assessed by fauna and microbial bioindicators.

    Science.gov (United States)

    Cébron, Aurélie; Cortet, Jérôme; Criquet, Stéven; Biaz, Asmaa; Calvert, Virgile; Caupert, Cécile; Pernin, Céline; Leyval, Corinne

    2011-11-01

    A large number of soil bioindicators were used to assess biological diversity and activity in soil polluted with polycyclic aromatic hydrocarbons (PAHs) and the same soil after thermal desorption (TD) treatment. Abundance and biodiversity of bacteria, fungi, protozoa, nematodes and microarthropods, as well as functional parameters such as enzymatic activities and soil respiration, were assessed during a two year period of in situ monitoring. We investigated the influence of vegetation (spontaneous vegetation and Medicago sativa) and TD treatment on biological functioning. Multivariate analysis was performed to analyze the whole data set. A principal response curve (PRC) technique was used to evaluate the different treatments (various vegetation and contaminated vs. TD soil) contrasted with control (bare) soil over time. Our results indicated the value of using a number of complementary bioindicators, describing both diversity and functions, to assess the influence of vegetation on soil and discriminate polluted from thermal desorption (TD)-treated soil. Plants had an influence on the abundance and activity of all organisms examined in our study, favoring the whole trophic chain development. However, although TD-treated soil had a high abundance and diversity of microorganisms and fauna, enzymatic activities were weak because of the strong physical and chemical modifications of this soil. PMID:21392572

  8. Small-angle scattering studies of biological macromolecules in solution

    International Nuclear Information System (INIS)

    Small-angle scattering (SAS) of x-rays and neutrons is a fundamental tool in the study of biological macromolecules. The major advantage of the method lies in its ability to provide structural information about partially or completely disordered systems. SAS allows one to study the structure of native particles in near physiological environments and to analyse structural changes in response to variations in external conditions. In this review we concentrate on SAS studies of isotropic systems, in particular, solutions of biological macromolecules, an area where major progress has been achieved during the last decade. Solution scattering studies are especially important, given the challenge of the 'post-genomic' era with vast numbers of protein sequences becoming available. Numerous structural initiatives aim at large-scale expression and purification of proteins for subsequent structure determination using x-ray crystallography and NMR spectroscopy. Because of the requirement of good crystals for crystallography and the low molecular mass requirement of NMR, a significant fraction of proteins cannot be analysed using these two high-resolution methods. Progress in SAS instrumentation and novel analysis methods, which substantially improve the resolution and reliability of the structural models, makes the method an important complementary tool for these initiatives. The review covers the basics of x-ray and neutron SAS, instrumentation, mathematical methods used in data analysis and major modelling techniques. Examples of applications of SAS to different types of biomolecules (proteins, nucleic acids, macromolecular complexes, polyelectrolytes) are presented. A brief account of the new opportunities offered by third and fourth generation synchrotron radiation sources (time-resolved studies, coherent scattering and single molecule scattering) is also given

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

    Science.gov (United States)

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

    2010-07-01

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

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

    Science.gov (United States)

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

    2012-03-21

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

  11. Studies on Biological Development of Hybrid Bees Families

    Directory of Open Access Journals (Sweden)

    Monica Pârvu

    2010-10-01

    Full Text Available It has made a study concerning the biological development of hybrid bee’s families (Italian x Carpathian comparative with Carpathian bee’s families. The bees were housed in multi-storey hives. The following parameters were studied: the queen bee prolificacy, the flight intensity during harvesting, the flight intensity during bad weather the irascibility, the behaviour of the bees during the survey and the predisposition to swarming. At the hybrid families, queen bee prolificacy and the rate of old bee’s replacement were significantly higher (p≤0.01. In terms of the flight intensity during bad weather and the swarming instinct, were not found significant differences (p≥0.05.

  12. 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.

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

    Science.gov (United States)

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

    2014-12-16

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

  14. A Snapshot of Functional Genetic Studies in Medicago truncatula

    Science.gov (United States)

    Kang, Yun; Li, Minguye; Sinharoy, Senjuti; Verdier, Jerome

    2016-01-01

    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. PMID:27555857

  15. A Snapshot of Functional Genetic Studies in Medicago truncatula.

    Science.gov (United States)

    Kang, Yun; Li, Minguye; Sinharoy, Senjuti; Verdier, Jerome

    2016-01-01

    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. PMID:27555857

  16. Phytochemicals and biological studies of plants from the genus Balanophora

    Directory of Open Access Journals (Sweden)

    Wang Xiaohong

    2012-08-01

    Full Text Available Abstract This review focus on the phytochemical progress and biological studies of plants from the genus Balanophora (Balanophoraceae over the past few decades, in which most plants growth in tropical and subtropical regions of Asia and Oceania, and nearly 20 species ranged in southwest China. These dioeciously parasitic plants are normally growing on the roots of the evergreen broadleaf trees, especially in the family of Leguminosae, Ericaceae, Urticaceae, and Fagaceae. The plants are mainly used for clearing away heat and toxic, neutralizing the effect of alcoholic drinks, and as a tonic for the treatment of hemorrhoids, stomachache and hemoptysis. And it has been used widely throughtout local area by Chinese people. Cinnamic acid derivative tannins, possessing a phenylacrylic acid derivative (e. g. caffeoyl, coumaroyl, feruloyl or cinnamoyl, which connected to the C(1 position of a glucosyl unit by O-glycosidic bond, are the characteristic components in genus Balanophora. In addition, several galloyl, caffeoyl and hexahydroxydiphenoyl esters of dihydrochalcone glucosides are found in B. tobiracola, B. harlandii, and B. papuana. Other compounds like phenylpropanoids, flavonoids, terpenoids and sterols are also existed. And their biological activities, such as radical scavenging activities, HIV inhibiting effects, and hypoglycemic effects are highlighted in the review.

  17. Application of the protocol for marine biological valuation to selected case study areas

    OpenAIRE

    Derous, S.; Courtens, W; Deckers, P.; Deneudt, K.; Forero, C.E.; Hostens, K.; Moulaert, I.; Stienen, E.W.M.; Vanden Eede, S.; Van Lancker, V. R. M; Verfaillie, E; Vincx, M.; Degraer, S.

    2008-01-01

    Marine biological valuation integrates all biological and ecological information that is available for a study area into a relative biological value. The resulting biological valuation map (BVM) is easy to interpret and translates complex scientific data into a tool that can be used by policy makers as a baseline layer for spatial planning at sea. When such BVM is lacking, managers can only trust on the available best expert judgement to include biological aspects into their decisions, a proc...

  18. 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.

  19. Epistemological Syncretism in a Biology Classroom: A Case Study

    Science.gov (United States)

    Bennett, William D.; Park, Soonhye

    2011-02-01

    In teaching science, the beliefs of teachers may come into conflict and inhibit the implementation of reformed teaching practice. An experienced biology teacher, Mr. Hobbs, was found to have two different sets of epistemological beliefs while his classroom practice was predominantly teacher-centered. A case study was then performed in order to investigate the underlying issues that contributed to his classroom practice. Data sources included preliminary and follow-up interviews and classroom observations. Data analysis indicated that factors that prevented the epistemological conflict from reaching a resolution included Mr. Hobbs' beliefs about learning, contextual teaching factors, personal experiences as a student, and views of the nature of science. The findings from this case indicate that science teachers possess complex belief systems that are not immediately obvious to either the teacher or science teacher educators, and science teacher educators need to address teacher beliefs when they encourage teachers to implement reformed teaching practices.

  20. Biochemical studies on certain biologically active nitrogenous compounds

    International Nuclear Information System (INIS)

    Certain biologically active nitrogenous compounds such as alkaloids are widely distributed in many wild and medicinal plants such as peganum harmala L. (Phycophyllaceae). However, less literature cited on the natural compounds was extracted from the aerial parts of this plant; therefore this study was conducted on harmal leaves using several solvents. Data indicated that methanol extract was the inhibitoriest effect against some pathogenic bacteria, particularly Streptococcus pyogenus. Chromatographic separation illustrated that presence of four compounds; the most active one was the third compound (3). Elementary analysis (C, H, N) revealed that the primary chemical structure of the active antibacterial compound (C3) was: C17 H21 N3 O7 S with molecular weight 411. Spectroscopic analysis proved that coninical structure was = 1- thioformyl, 8?- D glucoperanoside- Bis- 2, 3 dihydroisopyridino pyrrol. This new compound is represented as a noval ?- carboline alkaloid compound

  1. 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.

  2. Studies on influence of biological factors on concentration of radionuclides

    International Nuclear Information System (INIS)

    Biological factors influencing the concentration of radionuclides were studied from the points of uptake through digestive tract, food as pathways, and metabolic activities. The uptake of radionuclides by marine fishes through digestive tract was determined by whole body counter. 137Cs, 65Zn, 131I, 54Mn, 60Co, 85Sr, and 144Ce were used as tracers and was given with solid feed. The feed given was excreated 24 to 48 hours later in small of middle sized fishes, and 20 to 48 hours later in large sized fishes. The uptake rate of 137Cs and 65Zn was high absorption of 20 to 80 per cent, that of 131I, 60Co and 54Mn was not remarkable, and that of 85Sr and 144Ce was low absorption. The biological concentration of 137Cs through pathways of food. In fishes taking up radionuclides through contaminated food, concentration factor increased in accordance with contamination level. In addition, radionuclides with small uptake but delayed excretion and those with high concentration rate could be the factors to decide the concentration factors of marine organisms. In order to study the relationship between metabolic activities and concentration, the uptake of one-year old fishes and adult fishes, and fishes fed and those non-fed were compared. One-year fishes took up large amount of 85Sr during short period, however, concentration by metabolism in adult fishes was slow. Comparing feeding group and non-feeding group, the former showed 85Sr concentration factor of 1.5 to 2 times that of the later, and the later showed 137Cs concentration factor of 2 to 4 times that of the former. However, both uptake and excretion were rapid suggesting that taking food activated the metabolism of substances. (Kanao, N.)

  3. 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.

  4. Diversity and dynamics of eco-units in the biological reserves of the Fontainebleau forest (France): contribution of soil biology to a functional approach

    OpenAIRE

    Arpin, Pierre; Ponge, Jean-François; Faille, André; Blandin, Patrick

    1998-01-01

    Beech integral biological reserves of the Fontainebleau forest (France) display varied site conditions due to geomorphological heterogeneity and to interactions between biological components of the ecosystem. Taking examples in shifts observed in plant communities following gap opening, the authors show that, as Oldeman viewed it, tree-fall gaps seem to be the driving force in sylvigenesis as well as a source of spatial biodiversity. Studies carried out on macromorphological features of humus...

  5. Summary of diamino pyrazoles derived and study their biological activities

    International Nuclear Information System (INIS)

    The work involves the synthesis of new heterocyclic structures diamino pyrazoles derivatives that are present in many natural products and products of pharmacological and therapeutic interests and study their biological activities. In order to develop a radiotracer interest and use in diagnostic nuclear medicine, we are interested to synthesis a pyrazole derivative with the precursor [Re(CO)5Br] and studying the antibacterial and antifungal activity of 3.5-diamino pyrazole and even thioamide complex rhenium. The objectives of our workout: 1/ Synthesis of molecules 3,5-diamino pyrazole and thioamide. 2/ Synthesis of 3,5-diamino pyrazole-rhenium complex. 3/ The in vitro study: Bacteriological Tests (Study of antibacterial and antifungal activity of 3,5-diamino pyrazole and thioamide). The first part of this work concerns the chemical synthesis of molecules such as: thioamide, Amp z1 Ampz2 and then we had synthesized the complex 3,5-diamino pyrazole-rhenium. Similarly we determined the physicochemical characteristics of the compounds synthesized by CLHP, CCM and RMN (1H, 13C). The second part is devoted to the study in vitro of biological activities of the synthesized molecules and complex 3,5 diaminopyrazole-rhenium with concentration 1 mg/mL and 2 mg/mL. The results allow us to say that the thioamide and Ampz2 have antibacterial activity against S. enterica and Ampz2 has low activity against S. aureus and P. aeruginossa. Other pyrazole derivatives have no significant antibacterial and antifungal activity. The results also show that the synthesized compounds of concentration 2 mg/mL in relation to the inhibition zones of amoxicillin and DMSO: 1/ Escherichia coli, there is antibacterial activity for thioamide, and the Amp z1-Re Ampz2 compound. 2/ Staphylococcus aureus, the complex Ampz 1-Re and the thioamide have significant antibacterial activity. 3/ Salmonella, we observe that the thioamide molecules, Ampz2 and Amp z1-Re have significant antibacterial activity while

  6. Reproductive biology and functional response of Dineulophus phtorimaeae, a natural enemy of the tomato moth, Tuta absoluta.

    Science.gov (United States)

    Savino, Vivina; Coviella, Carlos E; Luna, María G

    2012-01-01

    The tomato moth, Tuta absoluta (Lepidoptera: Gelechiidae), is a major pest in South America and is at present an important invasive species in the Mediterranean Basin. The larval stadium mines leaves, stems, and fruits, and chemical control is the most used control method in both its original range and the invaded distribution regions. Since current T. absoluta control strategies seem limited, biological control is a prominent tool to be applied abroad. The naturally occurring larval ectoparasitoid in Argentina and Chile Dineulophus phtorimaeae (Hymenoptera: Eulophidae) has been reported to have potential biocontrol efficiency. In this study, the ovigeny strategy of D. phtorimaeae was analyzed throughout the adult female lifetime, and the functional response of females offered a range of 2-15 T. absoluta larvae was measured over a 48-hour period. Mean D. phtorimaeae egg load was 4.15 eggs, and egg production resulted in extremely synovigenic behavior. Meanwhile, a decreasing number of eggs, due to resorption, was found. Proportions of attacked (host-fed and/or parasitized) and only host-fed hosts by the ectoparasitoid were density independent for the tested host range, exhibiting a type I functional response to T. absoluta, with an attack rate of 0.20 host larvae. Meanings of this reproductive strategy in evolutionary time as well as the consequences for augmentative biological control programs are discussed. PMID:23464576

  7. A case study of two exemplary biology teachers

    Science.gov (United States)

    Treagust, David F.

    Research has indicated that most science classrooms are not intellectually demanding and place little emphasis on small group discussions and laboratory activities. However, successful science programs and competent science teaching that can provide models for other science teachers do exist. This study sought to document the teaching practices of two exemplary biology teachers of grades 11 and 12 by means of an interpretive research methodology. Both teachers had a thorough and comprehensive knowledge of the content they were to teach and had a range of teaching strategies that could be used without a great deal of thought. Their expectations for student performance were high, consistent, and firm. Students were expected to complete a high level of academic work in discussions, in problem work, and in laboratory activities, and were encouraged to take responsibility for their own learning. A distinctive feature of these biology classes was the high level of managerial efficiency, where lessons were busy occasions for both teacher and students; students had little opportunity for off-task behavior. Both teachers actively monitored the behavior of both high- and low-ability students by moving around the room and speaking with individuals, while still maintaining control of the entire class. By manipulating questioning and the social environment, both teachers encouraged students to engage in work, gave effective praise to the whole class and to individuals, encouraged student input by referring to it, helped students to effectively use their time, and gave marks for completion of set work. Compared to research with less-successful teachers, these teaching behaviors contributed to exemplary practice.

  8. Study on biological monitoring of n-hexane exposure

    Energy Technology Data Exchange (ETDEWEB)

    Iwata, M.; Takeuchi, Y.; Hisanaga, N.; Ono, Y.

    1983-03-01

    n-Hexane is one of the solvents widely used in industry well known to be neurotoxic. Recently it was clearly revealed that n-hexane is metabolized in vivo and its metabolites are excreted in the urine. However, the relationship between the exposed dose of n-hexane and the metabolites in the urine has not yet been substantially determined. Therefore, this investigation was intended to clarify the above relationship in order to establish its usefulness for biological monitoring of n-hexane exposure. The exposed dose was measured by means of a personal monitoring badge worn by workers in seven factories manufacturing vinyl sandals. The timeweighted average (TWA) concentration of n-hexane was 0.2-47.4 ppm. The n-hexane metabolites in the urine of 22 workers were measured with modified Perbellini's method (12) in the early morning (6:00-7:00 hrs) and at 17:00 hrs, 2,5-Dimethylfuran, 2,5-hexanedione and ..gamma..-valerolactone were identified by gas chromatography and mass spectrometory. At 17:00 hrs the means +- SD of the metabolites were 0.21+-0.11 mg/l for 2,5-dimethylfuran, 1.13+-0.71 mg/l for 2,5-hexanedione, and 2.04+-2.31 mg/l for ..gamma..-valerolactone. The metabolites were also found in the urine in the early morning. 2-Hexanol was not detected in the urine of any worker examined. A strong correlation between TWA concentration of n-hexane and 2,5-hexanedione in the urine was found at 17:00 hrs (r=0.895, P<0.001). The results suggest that the urinary metabolites of n-hexane, especially 2,5-hexanedione, could be useful indicators for biological monitoring of n-hexane exposure. Furthermore the present study offers the advantage of a better estimate of n-hexane TWA.

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

    Directory of Open Access Journals (Sweden)

    Marc Torrent

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

  10. 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.

  11. 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.

  12. 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.

  13. Study on the radiation-induced biological responses based on the analysis of metabolites

    International Nuclear Information System (INIS)

    1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation

  14. Study on the radiation-induced biological responses based on the analysis of metabolites

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Sungkee; Jung, Uhee; Park, Haeran; Roh, Changhyun; Shin, Heejune; Ryu, Dongkyoung

    2013-01-15

    1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation.

  15. Studying of ion implantation effect on the biology in China

    International Nuclear Information System (INIS)

    Since low energy ion effect on the biology was observed, the ion implantation as a new mutagenic source has been widely used in improving crops and modifying microbes in China. The basic phenomenon of ion implantation effect on the biology and analytical results are reported, and the examples of its application and its further development are shown

  16. An Experimental Evaluation of the Effectiveness of the Biological Sciences Curriculum Study Special Materials Approach to Teaching Biology to the Slow Learner.

    Science.gov (United States)

    Welford, John Mack

    Students (comparable in intelligence and ability) in slow-learning classes using either "Biological Sciences Curriculum Study (BSCS) Special Materials" or some other slow-learner biology materials, were compared on the basis of scores on the "Nelson Biology Test", the "Biological Sciences; Patterns and Processes Final Examination", and two short…

  17. 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.

  18. 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

  19. Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

    Science.gov (United States)

    Singh, Sunil; Gupta, Rashi; Kumari, Madhu; Sharma, Shilpi

    2015-08-01

    Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments. PMID:25801369

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

    Science.gov (United States)

    Buckley, Mark Raymond

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

  1. 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...

  2. Studies of biological aerosols as ice nuclei: Existing constraints and new measurements (Invited)

    Science.gov (United States)

    Demott, P. J.; Prenni, A. J.; Georgakopoulos, D. G.; Franc, G. D.; Sullivan, R. C.; Kreidenweis, S. M.

    2009-12-01

    The sources, abundance and nature of atmospheric particles that serve as ice nuclei (IN) for cold cloud formation remain some of the most important, yet poorly-characterized, features of aerosol-cloud interactions that indirectly affect climate. Although much is known about mineral dusts as important sources of atmospheric IN, much less is known about various carbonaceous particles, which also make up a significant fraction of atmospheric IN based on past elemental composition measurements. Among carbonaceous IN and other known atmospheric IN, certain biological particles (bacteria with a known IN gene) are the most efficient ice nucleators. These bacteria are highly efficient at freezing water at just a few degrees below 0°C. This characteristic has raised the possibility that these and other biological particles may represent a population in the atmosphere that influences mixed-phase clouds, precipitation and climate in important and dynamic ways. Significant, enigmatic, questions are the activation properties, source strengths, and number concentrations (and their variability) of all biological ice nuclei in cold cloud regions of the free troposphere. In this presentation we describe constraints on the contribution of biological particles to atmospheric IN populations based on our existing IN measurements, and based on measurements of specific known biological IN in air and precipitation made by other groups. Then we describe new measurement efforts targeted toward identification of the proportion of active IN as a function of temperature below 0°C that are of biological origin, using an ice nucleation instrument to activate and measure total IN concentrations, collection of activated particles, and analyses of the IN using the same DNA analyses used for identifying biological particles and biological IN types in total air and precipitation samples. This new method permits direct quantification of the number concentrations of biological IN. Our first studies

  3. 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.

  4. A Zebrafish Model for Studies on Esophageal Epithelial Biology

    OpenAIRE

    Chen, Hao; Beasley, Andrea; Hu, Yuhui; Chen, Xiaoxin

    2015-01-01

    Mammalian esophagus exhibits a remarkable change in epithelial structure during the transition from embryo to adult. However, the molecular mechanisms of esophageal epithelial development are not well understood. Zebrafish (Danio rerio), a common model organism for vertebrate development and gene function, has not previously been characterized as a model system for esophageal epithelial development. In this study, we characterized a piece of non-keratinized stratified squamous epithelium simi...

  5. 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

  6. Engineering scalable biological systems

    OpenAIRE

    Lu, Timothy K.

    2010-01-01

    Synthetic biology is focused on engineering biological organisms to study natural systems and to provide new solutions for pressing medical, industrial, and environmental problems. At the core of engineered organisms are synthetic biological circuits that execute the tasks of sensing inputs, processing logic, and performing output functions. In the last decade, significant progress has been made in developing basic designs for a wide range of biological circuits in bacteria, yeast, and mammal...

  7. Comparing protein VEGF inhibitors: In vitro biological studies

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Lanlan; Liang, Xiao Huan [Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (United States); Ferrara, Napoleone, E-mail: nf@gene.com [Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (United States)

    2011-05-06

    Highlights: {yields} VEGF is a mediator of angiogenesis. {yields} VEGF inhibitors have clinical applications in cancer and eye disorders. {yields} Five protein VEGF inhibitors were compared for their ability to inhibit. {yields} VEGF-induced activities in cultured endothelial cells. -- Abstract: VEGF inhibitors are widely used as a therapy for tumors and intravascular neovascular disorders, but limited and conflicting data regarding their relative biological potencies are available. The purpose of the study is to compare different protein VEGF inhibitors for their ability to inhibit VEGF-stimulated activities. We tested ranibizumab, the full-length variant of ranibizumab (Mab Y0317), bevacizumab, the VEGF-TrapR1R2 and Flt(1-3)-IgG in bioassays measuring VEGF-stimulated proliferation of bovine retinal microvascular endothelial cells or chemotaxis of human umbilical vein endothelial cells (HUVEC). The inhibitors were also compared for their ability to inhibit MAP kinase activation in HUVECs following VEGF addition. Ranibizumab, VEGF-TrapR1R2 and Flt(1-3)-IgG had very similar potencies in the bioassays tested. Bevacizumab was over 10-fold less potent than these molecules. Mab Y0317 was over 30-fold more potent than bevacizumab. The findings reported in this manuscript describe important intrinsic characteristics of several VEGF inhibitors that may be useful to design and interpret preclinical or clinical studies.

  8. 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...... well as structural studies of cytokine receptors. The results presented in this thesis have the potential to inspire future studies on how specific associations and PTMs affect PRLR signaling....

  9. Synthesis of potentially bioactive compounds and tools for biological studies

    International Nuclear Information System (INIS)

    NMR spectroscopy is one of the most versatile tools for studying structural parameters of organic and bioorganic compounds. It became a highly suitable method to achieve spectra simplification of macromolecules in combination with isotope labeling techniques. This technique is used to study protein structures, folding properties and mechanisms of chemical and biochemical reactions. Proteins typically feature a high molecular mass showing a high number of spin systems, being responsible for increasingly difficult to interpret NMR spectra, which is why it is essential to introduce 13C- and 15N- isotopes to obtain reasonable signal intensities. The development of a new synthetic route towards 13C-isotope labeled Phenylalanine or precursors thereof, starting from inexpensive and easily accessible labeled starting materials, is the main purpose of this work. Label sources such as [13C]-acetic acid, [13C]-formaldehyde, [13C]-allyl alcohol and [13C]-glycine will be used. The synthetic pathway will be carried out in a way where the position-selective incorporation of labeled isotopes can be performed. This important feature of the synthesis may open access towards newly designed NMR-experiments. Key steps for the tested route are ring closing metatheses as well as indium mediated reactions. The second part of this work focuses on the field of sugar chemistry, in particular on the family of deoxy sugars, components of many natural products, found in different plants, fungi and bacteria. Deoxy sugars also participate in a wide range of biological processes. Special focus is given to 3-deoxy sugars and the research of a versatile and flexible synthetic route for their preparation starting from the easily accessible D-glyceraldehyde. These sugars are found on Gram-negative bacteria where they are a key component of the lipopolysaccharides, or where they can take place in the biosynthesis of aromatic amino acids in bacteria and plants. Being able to perform this synthesis on a

  10. Growth control of the eukaryote cell: a systems biology study in yeast

    Directory of Open Access Journals (Sweden)

    Castrillo Juan I

    2007-04-01

    Full Text Available Abstract Background Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for

  11. 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 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

  12. 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. PMID:25673413

  13. 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.

  14. 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.

  15. 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...

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

    Science.gov (United States)

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

    2017-02-01

    In the present work, optimization of hot water extraction, structural characteristics, functional properties, and biological activities of polysaccharides extracted from watermelon rinds (WMRP) were investigated. The physicochemical characteristics and the monosaccharide composition of these polysaccharides were then determined using chemical composition analysis, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and gas chromatography-flame ionization detection (GC-FID). SEM images showed that extracted polysaccharides had a rough surface with many cavities. GC-FID results proved that galactose was the dominant sugar in the extracted polysaccharides, followed by arabinose, glucose, galacturonic acid, rhamnose, mannose, xylose and traces of glucuronic acid. The findings revealed that WMRP displayed excellent antihypertensive and antioxidant activities. Those polysaccharides had also a protection effect against hydroxyl radical-induced DNA damage. Functional properties of extracted polysaccharides were also evaluated. WMRP showed good interfacial dose-dependent proprieties. Overall, the results suggested that WMRP presents a promising natural source of antioxidants and antihypertensive agents. PMID:27596431

  17. Self-assembly and stability of double rosette nanostructures with biological functionalities.

    Science.gov (United States)

    ten Cate, Mattijs G J; Omerović, Merdan; Oshovsky, Gennady V; Crego-Calama, Mercedes; Reinhoudt, David N

    2005-10-21

    The syntheses of calix[4]arene dimelamines that are functionalized with alkyl, aminoalkyl, ureido, pyridyl, carbohydrate, amino acid and peptide functionalities, and their self-assembly with barbituric acid or cyanuric acid derivatives into well-defined hydrogen-bonded nanostructures are described. The thermodynamic stability of these hydrogen-bonded assemblies was studied by CD spectroscopy in mixtures of CHCl3 and MeOH. The stability of the assemblies depends on several steric factors and the polarity of the functional groups connected to the assembly components. PMID:16211109

  18. A study on biological monitoring of n-hexane exposure

    Energy Technology Data Exchange (ETDEWEB)

    Iwata, M.; Takeuchi, Y.; Hisanaga, N.; Ono, Y.

    1983-01-01

    n-Hexane is one of the solvents widely used in industry and well known to be neurotoxic. Recently it was clearly revealed that n-hexane is metabolized in vivo and its metabolites are excreted in the urine. However, the relationship between the exposed dose of n-hexane and the metabolites in the urine has not yet been substantially determined. Therefore, in this investigation we intended to clarify the above relationship in order to establish its usefulness for biological monitoring of n-hexane exposure. The exposed dose was measured by means of a personal monitoring badge worn by workers in seven factories manufacturing vinyl sandals. The time-weighted average (TWA) concentration of n-hexane was 0.2-47.4 ppm. The n-hexane metabolites in the urine of 22 workers were measured with modified Perbellini's method (12) in the early morning (6:00-7:00 hrs) and at 17:00 hrs. 2,5-Dimethylfuran, 2,5-hexanedione and gamma-valerolactone were identified by gas chromatography and mass spectrometory. At 17:00 hrs the means +/- SD of the metabolites were 0.21 +/- 0.11 mg/l for 2,5-dimethylfuran, 1.13 +/- 0.71 mg/l for 2,5-hexanedione, and 2.04 +/- 2.31 mg/l for gamma-valerolactone. The metabolites were also found in the urine in the early morning. 2-Hexanol was not detected in the urine of any worker examined. A strong correlation between TWA concentration of n-hexane and 2,5-hexanedione in the urine was found at 17:00 hrs (r . 0.895, P less than 0.001). The results suggest that the urinary metabolites of n-hexane, especially 2,5-hexanedione, could be useful indicators for biological monitoring of n-hexane exposure. Furthermore the present study offers the advantage of a better estimate of n-hexane TWA.

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

    OpenAIRE

    Snezana Stavrova Veselinovskaa

    2011-01-01

    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 Lab...

  20. Suzhou Creek Rehabilitation Project ECOLOGICAL STUDY 1998 Biological monitoring program

    OpenAIRE

    Lien, L.; Haowen, Yin

    1998-01-01

    Suzhou Creek, flowing through the central parts of Shanghai, is heavy polluted by sewage, metals and organic micro pollutants. Due to the pollution, lower parts of the creek have virtually no life of fish or macro-invertebrates, and the other biological communities are totally disturbed. Even at upstream sections the flora and fauna suffer from pollution. During the last decade the contamination has been slightly reduced in the creek. A biological monitoring program was designed for the creek...

  1. Study of Transport of Biologically Important Compounds in\

    Czech Academy of Sciences Publication Activity Database

    Navrátil, Tomáš; Šestáková, Ivana; Vodičková, H.; Jaklová Dytrtová, Jana; Gál, M.

    Singapore: IACSIT Press, 2015, s. 43-50. (International Proceedings of Chemical, Biological & Environmental Engineering. Vol. 90). ISBN 978-981-09-7382-7. [International Conference on Environment, Chemistry and Biology (ICECB 2015) /4./. Auckland (NZ), 19.11.2015-21.11.2015] R&D Projects: GA ČR(CZ) GAP208/12/1645 Institutional support: RVO:61388955 ; RVO:61388963 Keywords : membrane * cell * protoplast Subject RIV: CG - Electrochemistry

  2. Using functional genomics to study PINK1 and metabolic physiology

    DEFF Research Database (Denmark)

    Scheele, Camilla; Larsson, Ola; Timmons, James A

    2009-01-01

    Genome sequencing projects have provided the substrate for an unimaginable number of biological experiments. Further, genomic technologies such as microarrays and quantitative and exquisitely sensitive techniques such as real-time quantitative polymerase chain reaction have made it possible to...... or experimental control. Thus, functional genomics is now being applied to study metabolic physiology with varying degrees of success. From the genome sequencing projects we also have the information needed to design chemical tools that can knock down a gene transcript, even distinguishing between...... experiences have been ignored by users of siRNA technologies. What we provide in this chapter is some considerations and observations from functional genomic studies. We are largely concerned with the phase that follows a microarray study, where a candidate gene is selected for manipulation in a system that...

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

    Science.gov (United States)

    An, Lin

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

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

    Science.gov (United States)

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

    2010-08-31

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

  5. Experimental study of the biological properties of 188Re-Hepama-1 biologic superparamagnetic nanoparticles

    International Nuclear Information System (INIS)

    Objective: To investigate a new biologic-superparamagnetic nanoparticles's characteristics of immunological activity, biological distributing in vivo, targeting and inhibiting tumor effect. Methods: The experimental group 188Re-Hepama-l-superparamagnetic nanoparticles, and control groups, including 188ReO4-, 188Re-Hepama-1, and 188Re-superparamagnetic nanoparticles, were set up. The distributions were measured after injection 4 h and 24 h by caudal vein of Kuming mice. The magnetic targeting experiments in vivo were clone with and without magnetic field in liver after injection in New Zealand rabbit. The inhibiting tumor effect on hepatic cancer cell lines SMMC-7721 of the above four 188Re labeled products were measured by mono nuclear cell direct cytotoxicity assay method. Results: After injection 4 h and 24 h by vein, the liver taking was highest in group 188Re-Hepama-l-superparamagnetic nanoparticles. The radiative activity in liver in magnetism zoo was higher than in non magnetism zoo in 188Re- Hepama-1-superparamagnetic nanoparticles after applying magnetic field in left lobe of liver, and the ratio of in magnetism zoo to non magnetism zoo was 1.87. And the half effective inhibition radioactive concentrations (IC50) in 188Re-Hepama-l-superparamagnetic nanoparticles was one forth of 188ReO4-. Conclusion: 188Re- Hepama-l-superparamagnetic nanoparticles showed its fine stability in intro, good immunological activity and significant liver target. (authors)

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

    DEFF Research Database (Denmark)

    Yadav, Rachita

    , Chapter 1 provides an introduction to various methodologies utilised in this thesis work. Subsequently, chapters 2, 3 and 4 in the second section, address finding causal variations in childhood asthma. Chapter 2 focuses on a genome wide association study (GWAS) performed on asthma exacerbation case cohort...... changing proteome and phosphor-proteome in chemotherapy resistant breast cancer cell lines with high TIMP-1 gene expression. In summary, this thesis work demonstrates applications of various omic variations at different levels of complexity and their integration using systems biology based methodologies to...... associate them to multifactorial phenotypes. These studies help in revealing pivotal mechanistic details concerning the phenotypes, which can be further utilized in drug designing and disease management....

  7. Biological function of Foot-and-mouth disease virus non-structural proteins and non-coding elements.

    Science.gov (United States)

    Gao, Yuan; Sun, Shi-Qi; Guo, Hui-Chen

    2016-01-01

    Foot-and-mouth disease virus (FMDV) represses host translation machinery, blocks protein secretion, and cleaves cellular proteins associated with signal transduction and the innate immune response to infection. Non-structural proteins (NSPs) and non-coding elements (NCEs) of FMDV play a critical role in these biological processes. The FMDV virion consists of capsid and nucleic acid. The virus genome is a positive single stranded RNA and encodes a single long open reading frame (ORF) flanked by a long structured 5'-untranslated region (5'-UTR) and a short 3'-UTR. The ORF is translated into a polypeptide chain and processed into four structural proteins (VP1, VP2, VP3, and VP4), 10 NSPs (L(pro), 2A, 2B, 2C, 3A, 3B1-3, 3C(pro), and 3D(pol)), and some cleavage intermediates. In the past decade, an increasing number of studies have begun to focus on the molecular pathogenesis of FMDV NSPs and NCEs. This review collected recent research progress on the biological functions of these NSPs and NCEs on the replication and host cellular regulation of FMDV to understand the molecular mechanism of host-FMDV interactions and provide perspectives for antiviral strategy and development of novel vaccines. PMID:27334704

  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. 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 (pquantitative differences in ground-base ion radiation and spaceflight experiments respectively. The functions of ground-base radiation and spaceflight proteins were both involved in a wide range of biological processes. Gene Ontology enrichment analysis further revealed that ground-base radiation responsive proteins were mainly involved in removal of superoxide radicals, defense response to stimulus and photosynthesis, while spaceflight responsive proteins mainly participate in nucleoside metabolic 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

  10. 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...

  11. Radionuclide renal dynamic and function study

    International Nuclear Information System (INIS)

    The radionuclide dynamic and function study, glomerular filtration rate (GFR) and effective renal plasma flow (ERPF) were reported in 14 cases of renal and ureteral calculi patients before and after extracorporeal shock wave lithotripsy (ESWL). In 12 cases with normal renal blood flow, within 3 months after ESWL, the GFR of shock and non-shock side decreased with different extent, while the individual ERPF had little change. In 5 cases followed up 1 year after ESWL, the individual GFR and ERPF were normal. In 2 cases of severe renal function insufficiency, there was no improvement in renal function in shock side, after 5 months and 1 year, the renal function was still at low level. Thereby it is considered that ESWL is not suitable for the renal calculi patients with severe renal function insufficiency

  12. 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

  13. Studies on floral biology of passion fruit (passiflora spp.)

    International Nuclear Information System (INIS)

    Floral biology of purple, yellow, giant and Passiflora foetida was studied at the ICAR Research Complex, Mizoram Centre, Kolasib, Mizoram, India during 2005-07. Purple, giant and P. foetida had major bloom during March-April, July-August and September-October. While major bloom in yellow was mainly during May-June and September-October. Purple, giant and P. foetida had the maximum duration of bloom of 42.4, 22.5 and 32.6 days, respectively during March-April with the maximum duration of effective bloom of 12.5 8.6 and 10.4 days in purple, giant and P. foetida, respectively. Yellow had the maximum duration of bloom for 28.4 days and effective bloom of 10.5 days during May-June. Most of the flowers of purple (54.5%) and giant (58.5%) opened between 6-7 hrs, while the maximum per cent of anthesis in yellow (70%) took place between 12-13 hrs. Pollen dehiscence and pollination in purple and giant mainly occurred between 7-8 hrs, while 13-14 hrs was the major period of pollen dehiscence and pollination in yellow. The earliest anthesis (5-6 hrs), anther dehiscence (6-7 hrs) and pollination (6-7 hrs) were recorded in P. foetida. The maximum stigma receptivity was recorded on the day of anthesis in all the passion fruits. Completely curved style was more common in all passion fruits that gave the maximum fruit set. The maximum number of bees observed between 7-8 hrs in purple and giant and between 13-14 hrs in yellow. The most common pollinating bee in purple, giant and yellow was Apis mellifera, while A. cerena was in P. foetida. (author)

  14. The wetland continuum: a conceptual framework for interpreting biological studies

    Science.gov (United States)

    Euliss, N.H., Jr.; LaBaugh, J.W.; Fredrickson, L.H.; Mushet, D.M.; Swanson, G.A.; Winter, T.C.; Rosenberry, D.O.; Nelson, R.D.

    2004-01-01

    We describe a conceptual model, the wetland continuum, which allows wetland managers, scientists, and ecologists to consider simultaneously the influence of climate and hydrologic setting on wetland biological communities. Although multidimensional, the wetland continuum is most easily represented as a two-dimensional gradient, with ground water and atmospheric water constituting the horizontal and vertical axis, respectively. By locating the position of a wetland on both axes of the continuum, the potential biological expression of the wetland can be predicted at any point in time. The model provides a framework useful in the organization and interpretation of biological data from wetlands by incorporating the dynamic changes these systems undergo as a result of normal climatic variation rather than placing them into static categories common to many wetland classification systems. While we developed this model from the literature available for depressional wetlands in the prairie pothole region of North America, we believe the concept has application to wetlands in many other geographic locations.

  15. Study of quality indices of functional vegetal oil mixture

    Directory of Open Access Journals (Sweden)

    Cristina POPOVICI

    2010-08-01

    Full Text Available Solution of the problem of alimentation structure improvement is related to creation of functional foodstuff with a balanced content of the major nutrient materials enriched in missing micronutrients and, at the same time, being daily products. Multicomponent structure of vegetable oils provides ample opportunities for developing of products preventing deficiency in essential fatty acids, vitamins andother physiologically functional ingredients. Grape-seed oil is of high bioavailability determined by a complex of biologically active substances, bioflavanoids, a group of vitamins, being the most important of them. Physiological effect of grape-seed oil includes anti-cholesterol property preventing cardio-vascular diseases.The thesis covers studies of vegetable oil mixtures made on the basis of sunflower and grape-seed oils. The study covers oxidative stability of vegetable oil mixture, based on determination of intensity of primary and secondary oxidation products formation.

  16. Phytochemical and biological studies of plants from the genus Meconopsis.

    Science.gov (United States)

    Li, Mao-Xing; Wang, Jin-Hui; He, Xi-Rui; Fan, Peng-Cheng; Zhang, Ru-Xue; Jia, Zheng-Ping

    2010-08-01

    In this review, the literature data on the phytochemical and biological investigations on the genus of Meconopsis are summarized from 49 references. Up to now, more than 95 compounds were isolated from 19 Meconopsis plant species. The chemical constituents are mostly alkaloids, flavonoids, phenols, steroids, and terpenes, together with minor constituents of essential oil, and others. The crude extracts and metabolites have been found to possess various bioactivities including antitumor activity, central action, cardiovascular system effects, antibiosis, antiviral activity, anti-inflammatory effects, and other biological activities. PMID:20730958

  17. 'Buildings in Use' Study. Functional Factors.

    Science.gov (United States)

    Wisconsin Univ., Milwaukee. School of Architecture and Urban Planning.

    The third report of the 'Buildings in Use' study specifically addresses those aspects of a building that directly support user activity. These are areas of 'activity support' exclusive of furniture that include studies of specialized areas and functions within the school as well as storage, classroom display, window usage, and some activity…

  18. Cabin Air Sampling Study Functionality Test.

    OpenAIRE

    Muir, Helen; Walton, Christopher; McKeown, Rebecca

    2008-01-01

    The Department for Transport (DFT), on behalf of the Government’s Aviation Health Working Group (AHWG), commissioned Cranfield University to organise, manage and deliver a functionality test of a variety of air sampling devices capable of detecting a wide range of compounds in a cabin air environment. The functionality test was to be the preliminary stage of a major monitoring study of the cabin air environment, which the Department intends to conduct. Report prepared for the Department f...

  19. 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.

  20. [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. PMID:3448995

  1. Transfer RNA: From pioneering crystallographic studies to contemporary tRNA biology.

    Science.gov (United States)

    Fernández-Millán, Pablo; Schelcher, Cédric; Chihade, Joseph; Masquida, Benoît; Giegé, Philippe; Sauter, Claude

    2016-07-15

    Transfer RNAs (tRNAs) play a key role in protein synthesis as adaptor molecules between messenger RNA and protein sequences on the ribosome. Their discovery in the early sixties provoked a worldwide infatuation with the study of their architecture and their function in the decoding of genetic information. tRNAs are also emblematic molecules in crystallography: the determination of the first tRNA crystal structures represented a milestone in structural biology and tRNAs were for a long period the sole source of information on RNA folding, architecture, and post-transcriptional modifications. Crystallographic data on tRNAs in complex with aminoacyl-tRNA synthetases (aaRSs) also provided the first insight into protein:RNA interactions. Beyond the translation process and the history of structural investigations on tRNA, this review also illustrates the renewal of tRNA biology with the discovery of a growing number of tRNA partners in the cell, the involvement of tRNAs in a variety of regulatory and metabolic pathways, and emerging applications in biotechnology and synthetic biology. PMID:26968773

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

    Science.gov (United States)

    Kim, Se H; Kim, Moon S; Lee, Bun Y; Lee, Pyung C

    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-α-tocopherol. 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 4,4'-diapotorulene on rat bone marrow mesenchymal stem cells. Our results demonstrate that a series of structurally novel carotenoids possessing biologically beneficial properties can be synthesized in E. coli. PMID:26902326

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

    Science.gov (United States)

    Ludvigsen, Eva

    2007-01-01

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

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

    Science.gov (United States)

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

    2009-02-01

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

  5. Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions

    Science.gov (United States)

    Basu, Mahashweta; Bhattacharyya, Nitai P.; Mohanty, Pradeep K.

    2013-01-01

    Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched () GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins. PMID:23741403

  6. 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.

  7. Melatonin and its potential biological functions in the fruits of sweet cherry.

    Science.gov (United States)

    Zhao, Yu; Tan, Dun-Xian; Lei, Qiong; Chen, Hao; Wang, Lin; Li, Qing-tian; Gao, Yinan; Kong, Jin

    2013-08-01

    Melatonin is a well-known molecule which possesses many beneficial effects on human health. Many agriculture products provide natural melatonin in the diet. Cherry is one such fruit as they are rich in melatonin. In order to understand the biological roles of melatonin in cherry fruit, melatonin synthesis and its changes over 24 hr period were systematically monitored both during their development and in the ripe cherries in two cultivars, 'Hongdeng' (Prunus avium L. cv. Hongdeng) and 'Rainier' (Prunus avium L. cv. Rainier). It was found that both darkness and oxidative stress induced melatonin synthesis, which led to dual melatonin synthetic peaks during a 24 hr period. The high levels of malondialdehyde induced by high temperature and high intensity light exposure were directly related to up-regulated melatonin production. A primary function of melatonin in cherry fruits is speculated to be as an antioxidant to protect the cherry from the oxidative stress. Importantly, plant tryptophan decaboxylase gene (PaTDC) was identified in cherry fruits. Our data shows that PaTDC expression is positively related to the melatonin production in the cherry. This provides additional information to suggest that tryptophan decaboxylase is a rate-limiting enzyme of melatonin synthesis in plants. PMID:23480341

  8. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  10. 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.

  11. 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.

  12. Studying of Phenomenon of Biological Adaptation to Heavy Water

    OpenAIRE

    Oleg Mosin; Ignat Ignatov; Dmitry Skladnev; Vitaly Shvets

    2014-01-01

    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 wate...

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  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

    Purpose – Biological muscles of animals have a surprising variety of functions, i.e., struts, springs, and brakes. According to this, the purpose of this paper is to apply virtual agonist-antagonist mechanisms to robot joint control allowing for muscle-like functions and variably compliant joint...... motions. Design/methodology/approach – Each joint is driven by a pair of virtual agonist-antagonist mechanism (VAAM, i.e., passive components). The muscle-like functions as well as the variable joint compliance are simply achieved by tuning the damping coefficient of the VAAM. Findings – With the VAAM......, variably compliant joint motions can be produced without mechanically bulky and complex mechanisms or complex force/toque sensing at each joint. Moreover, through tuning the damping coefficient of the VAAM, the functions of the VAAM are comparable to biological muscles. Originality/value – The model (i...

  20. Mechanical properties of lipid bilayers and regulation of mechanosensitive function: from biological to biomimetic channels.

    Science.gov (United States)

    Balleza, Daniel

    2012-01-01

    Material properties of lipid bilayers, including thickness, intrinsic curvature and compressibility regulate the function of mechanosensitive (MS) channels. This regulation is dependent on phospholipid composition, lateral packing and organization within the membrane. Therefore, a more complete framework to understand the functioning of MS channels requires insights into bilayer structure, thermodynamics and phospholipid structure, as well as lipid-protein interactions. Phospholipids and MS channels interact with each other mainly through electrostatic forces and hydrophobic matching, which are also crucial for antimicrobial peptides. They are excellent models for studying the formation and stabilization of membrane pores. Importantly, they perform equivalent responses as MS channels: (1) tilting in response to tension and (2) dissipation of osmotic gradients. Lessons learned from pore forming peptides could enrich our knowledge of mechanisms of action and evolution of these channels. Here, the current state of the art is presented and general principles of membrane regulation of mechanosensitive function are discussed. PMID:22790280

  1. Predicting Function of Biological Macromolecules: A Summary of LDRD Activities: Project 10746

    Energy Technology Data Exchange (ETDEWEB)

    FRINK, LAURA J. D.; REMPE, SUSAN L.; MEANS, SHAWN A.; STEVENS, MARK J.; CROZIER, PAUL S.; MARTIN, MARCUS G.; SEARS, MARK P.; HJALMARSON, HAROLD P.

    2002-11-01

    This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.

  2. Intravital microscopy: a novel tool to study cell biology in living animals

    OpenAIRE

    Weigert, Roberto; Sramkova, Monika; Parente, Laura; Masedunskas, Andrius

    2010-01-01

    Intravital microscopy encompasses various optical microscopy techniques aimed at visualizing biological processes in live animals. In the last decade, the development of non-linear optical microscopy resulted in an enormous increase of in vivo studies, which have addressed key biological questions in fields such as neurobiology, immunology and tumor biology. Recently, few studies have shown that subcellular processes can be imaged dynamically in the live animal at a resolution comparable to t...

  3. Isolation and study of the functional properties of pea proteins.

    Science.gov (United States)

    Tömösközi, S; Lásztity, R; Haraszi, R; Baticz, O

    2001-10-01

    Proteins of pea seeds were isolated after defatting with hexane using alkaline (0.1 M sodium hydroxide) extraction and acid (HCl) precipitation. Concentrates were also prepared by hexane extraction and ethanolic extraction (pH = 5). Gross chemical composition amino acid content and functional properties (solubility profile, emulsifying--and foaming properties, water--and oil absorption) were studied. The results were compared with the same parameters of soy and lupin protein products. Although the majority of functional characteristics of isolates were lower in comparison to soy isolates, pea protein concentrate and isolate could be successfully used in bakery products for enrichment in protein and improvement of biological value. Their utilization as meat protein substitute in some Frankfurter type sausages is also possibly. PMID:11712241

  4. 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.

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

    OpenAIRE

    Carlos Rafael Duharte Rodríguez; Ibrain Ceballo Acosta; Carmen B. Busoch Morlán; Ángel Regueiro Gómez

    2015-01-01

    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...

  6. Distinct Regions of Right Temporal Cortex Are Associated with Biological and Human-Agent Motion: Functional Magnetic Resonance Imaging and Neuropsychological Evidence

    OpenAIRE

    Han, Zaizhu; Bi, Yanchao; Chen, Jing; Chen, Quanjing; He, Yong; Caramazza, Alfonso

    2013-01-01

    In human lateral temporal cortex, some regions show specific sensitivity to human motion. Here we examine whether such effects reflect a general biological-nonbiological organizational principle or a process specific to human-agent processing by comparing processing of human, animal, and tool motion in a functional magnetic resonance imaging (fMRI) experiment with healthy participants and a voxel-based lesion-symptom mapping (VLSM) study of patients with brain damage (77 stroke patients). The...

  7. A Review of Cell Adhesion Studies for Biomedical and Biological Applications

    Science.gov (United States)

    Ahmad Khalili, Amelia; Ahmad, Mohd Ridzuan

    2015-01-01

    Cell adhesion is essential in cell communication and regulation, and is of fundamental importance in the development and maintenance of tissues. The mechanical interactions between a cell and its extracellular matrix (ECM) can influence and control cell behavior and function. The essential function of cell adhesion has created tremendous interests in developing methods for measuring and studying cell adhesion properties. The study of cell adhesion could be categorized into cell adhesion attachment and detachment events. The study of cell adhesion has been widely explored via both events for many important purposes in cellular biology, biomedical, and engineering fields. Cell adhesion attachment and detachment events could be further grouped into the cell population and single cell approach. Various techniques to measure cell adhesion have been applied to many fields of study in order to gain understanding of cell signaling pathways, biomaterial studies for implantable sensors, artificial bone and tooth replacement, the development of tissue-on-a-chip and organ-on-a-chip in tissue engineering, the effects of biochemical treatments and environmental stimuli to the cell adhesion, the potential of drug treatments, cancer metastasis study, and the determination of the adhesion properties of normal and cancerous cells. This review discussed the overview of the available methods to study cell adhesion through attachment and detachment events. PMID:26251901

  8. 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

  9. Structural methods for studying IRES function.

    Science.gov (United States)

    Kieft, Jeffrey S; Costantino, David A; Filbin, Megan E; Hammond, John; Pfingsten, Jennifer S

    2007-01-01

    Internal ribosome entry sites (IRESs) substitute RNA sequences for some or all of the canonical translation initiation protein factors. Therefore, an important component of understanding IRES function is a description of the three-dimensional structure of the IRES RNA underlying this mechanism. This includes determining the degree to which the RNA folds, the global RNA architecture, and higher resolution information when warranted. Knowledge of the RNA structural features guides ongoing mechanistic and functional studies. In this chapter, we present a roadmap to structurally characterize a folded RNA, beginning from initial studies to define the overall architecture and leading to high-resolution structural studies. The experimental strategy presented here is not unique to IRES RNAs but is adaptable to virtually any RNA of interest, although characterization of RNA-protein interactions requires additional methods. Because IRES RNAs have a specific function, we present specific ways in which the data are interpreted to gain insight into that function. We provide protocols for key experiments that are particularly useful for studying IRES RNA structure and that provide a framework onto which additional approaches are integrated. The protocols we present are solution hydroxyl radical probing, RNase T1 probing, native gel electrophoresis, sedimentation velocity analytical ultracentrifugation, and strategies to engineer RNA for crystallization and to obtain initial crystals. PMID:17913644

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

    OpenAIRE

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

    2012-01-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe3O4) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zer...

  11. Biochemical Properties and Biological Function of a Monofunctional Microbial Biotin Protein Ligase

    OpenAIRE

    Daniels, Kyle G.; Beckett, Dorothy

    2010-01-01

    Biotin protein ligases constitute a family of enzymes that catalyze biotin linkage to biotin-dependent carboxylases. In bacteria these enzymes are functionally divided into two classes; the monofunctional enzymes that only catalyze biotin addition and the bifunctional enzymes that also bind to DNA to regulate transcription initiation. Biochemical and biophysical studies of the bifunctional Escherichia coli ligase suggest that several properties of the enzyme have evolved to support its additi...

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

    OpenAIRE

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    For Yue Tso

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

  14. Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach.

    Directory of Open Access Journals (Sweden)

    Chia-Wei Hu

    Full Text Available BACKGROUND: Rhodopseudomonas palustris (R. palustris is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin-Benson-Bassham (CBB cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach. METHODOLOGY/PRINCIPAL FINDINGS: By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth

  15. 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

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

    Science.gov (United States)

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

    2015-09-01

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

  17. Molecular imaging with radionuclides, a powerful technique for studying biological processes in vivo

    Science.gov (United States)

    Cisbani, E.; Cusanno, F.; Garibaldi, F.; Magliozzi, M. L.; Majewski, S.; Torrioli, S.; Tsui, B. M. W.

    2007-02-01

    Our team is carrying on a systematic study devoted to the design of a SPECT detector with submillimeter resolution and adequate sensitivity (1 cps/kBq). Such system will be used for functional imaging of biological processes at molecular level in small animal. The system requirements have been defined by two relevant applications: study of atherosclerotic plaques characterization and stem cells diffusion and homing. In order to minimize costs and implementation time, the gamma detector will be based—as much as possible—on conventional components: scintillator crystal and position sensitive PhotoMultipliers read by individual channel electronics. A coded aperture collimator should be adapted to maximize the efficiency. The optimal selection of the detector components is investigated by systematic use of Monte-Carlo simulations (and laboratory validation tests); and finally preliminary results are presented and discussed here.

  18. Temperature Dependent Studies of Conformational Vibrational Modes of Biological Molecules

    Science.gov (United States)

    Markelz, A. G.; Pawar, A.

    2001-03-01

    Low frequency vibrational modes of proteins are correlated to conformation and conformational change critical to biochemical activity, however direct measurements of these modes has been impeded by limitations in spectroscopic techniques. We are presently exploring the use of the high sensitivity FIR spectroscopic technique of pulsed terahertz spectroscopy to measure these modes as a function of conformational state. Initial measurements have been preformed using bovine heart cytochrome c and the chromophore of photoactive yellow protein, p-coumaric acid (PCA). We have measured the temperature dependence (77 K - 300 K) of the far infrared absorption (2-100 cm-1) using both solid state and solution samples. Sample preparation techniques to eliminate etalon in the spectra will be discussed. For cytochrome c, a distinct absorption at 10 cm-1 is seen at room temperature that narrows and slightly red shifts as the temperature decreases. For PCA, the FIR absorption remains broad at lower temperatures, with an overall increase in FIR absorption at lower temperatures. We will discuss the implications of these measurements for future studies of conformational dynamics in these proteins.

  19. Use of aerosols in lung function studies

    International Nuclear Information System (INIS)

    Since aerosol inhalation lung scintigraphy was introduced in 1965 following perfusion lung imaging, both imaging modalities have offered powerful tools not only for the study of respiratory lung function but also for the exploration of non-respiratory lung function studies. Visualization of the distribution of ventilation and perfusion in the lungs has made it possible to determine whether ventilation and perfusion are well matched or not, thus leading to the diagnosis of vascular diseases if perfusion is absent in the well ventilated lung regions, whereas airway diseases show matched ventilation and perfusion abnormalities. The reasons for the above principles have been physiologically clarified by perfusion and inhalation techniques using radioactive particulates, aerosols and radioactive gases. Regional ventilation always regulates regional perfusion; regional hypoventilation causes regional hypoxia which in turn causes hypoxic vasoconstriction and a consequent decrease in perfusion. Regional perfusion does not regulate regional ventilation except in the very early phase of perfusion changes when hypoperfusion can cause a transient bronchoconstriction and hypoventilation. This reaction disappears within 6 hours in dogs. Deposition patterns of inhaled aerosol in the lungs help differentiate the nature of the obstructive airways disease. Aerosol inhalation imaging can offer a unique technique for the study of mucociliary clearance function in the lungs. 'Radioaerosol inhalation lung cinescintigraphy' has made it possible to visualize the actual mucociliary clearance status in the lungs in vivo. Indexes to quantify the mucociliary clearance function have been proposed. Effects of pharmaceutical agents on mucociliary clearance function in the lungs can now be objectively evaluated by aerosol inhalation lung imaging and its quantification. The study of pulmonary epithelial permeability by inhalation of 99Tcm DTPA aerosol has also been mentioned. 26 refs, 8 figs, 3

  20. What should be computed to understand and model brain function? from robotics, soft computing, biology and neuroscience to cognitive philosophy

    CERN Document Server

    Kitamura, Tadashi

    2001-01-01

    This volume is a guide to two types of transcendence of academic borders which seem necessary for understanding and modelling brain function. The first type is technical transcendence needed to make intelligent machines such as a humanoid robot, an animal-like behavior architecture, an interpreter of fiction, and an evolving learning machine. This technical erosion is conducted into areas such as biology, ethology, neuroscience and psychology, as well as robotics and soft computing. The second type of transcendence of cross-disciplinary boundaries cuts across scientific areas such as biology a

  1. Structure-Property-Function Relationship in Humic Substances to Explain the Biological Activity in Plants

    Science.gov (United States)

    García, Andrés Calderín; de Souza, Luiz Gilberto Ambrosio; Pereira, Marcos Gervasio; Castro, Rosane Nora; García-Mina, José María; Zonta, Everaldo; Lisboa, Francy Junior Gonçalves; Berbara, Ricardo Luis Louro

    2016-02-01

    Knowledge of the structure-property-function relationship of humic substances (HSs) is key for understanding their role in soil. Despite progress, studies on this topic are still under discussion. We analyzed 37 humic fractions with respect to their isotopic composition, structural characteristics, and properties responsible for stimulating plant root parameters. We showed that regardless of the source of origin of the carbon (C3 or C4), soil-extracted HSs and humic acids (HAs) are structurally similar to each other. The more labile and functionalized HS fraction is responsible for root emission, whereas the more recalcitrant and less functionalized HA fraction is related to root growth. Labile structures promote root stimulation at lower concentrations, while recalcitrant structures require higher concentrations to promote a similar stimulus. These findings show that lability and recalcitrance, which are derived properties of humic fractions, are related to the type and intensity of their bioactivity. In summary, the comparison of humic fractions allowed a better understanding of the relationship between the source of origin of plant carbon and the structure, properties, and type and intensity of the bioactivity of HSs in plants. In this study, scientific concepts are unified and the basis for the agronomic use of HSs is established.

  2. 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.

  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. Functionalization of Self-Organized Nanoparticles for Biological Targeting and Active Drug Release

    DEFF Research Database (Denmark)

    Jølck, Rasmus Irming

    and drug delivery. The objective of this PhD thesis was to expand the field of liposomal drug delivery by developing novel methods to efficienctly functionalize and subsequently sensitize liposomes towards internal stimuli, such as matrix metalloproteinases. Initially, we investigated a novel method...... to the importance of the relative position of the reactive functionalities. Surface conjugation reactions of octreotate by Michael addition, Click chemistry, Cu-free Click chemistry or oxime bond formation were investigated. From these studies it was evident that chemical reactions performed directly on the surface...... was significantly higher than for the controlliposomes, which indicated that active targeting can improve tumor-to-muscle contrast, thus, improving bioimaging for diagnostic applications. Finally, a novel drug delivery system based on charge-triggering of matrix metalloproteinase 2/9 sensitive PEGylated...

  5. 2K09 and Thereafter : The Coming Era of Integrative Bioinformatics, Systems Biology and Intelligent Computing for Functional Genomics and Personalized Medicine Research

    OpenAIRE

    2010-01-01

    Abstract Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Co...

  6. 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

    2016-01-01

    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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    . With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has...... system (the cell), also at the quantitative level, and this is the goal of systems biology. Clearly this will have a significant impact on microbial physiology as well as on metabolic engineering....

  10. Atomic Force Microscopy Application in Biological Research: A Review Study

    Directory of Open Access Journals (Sweden)

    Surena Vahabi

    2013-06-01

    Full Text Available Atomic force microscopy (AFM is a three-dimensional topographic technique with a high atomic resolution to measure surface roughness. AFM is a kind of scanning probe microscope, and its near-field technique is based on the interaction between a sharp tip and the atoms of the sample surface. There are several methods and many ways to modify the tip of the AFM to investigate surface properties, including measuring friction, adhesion forces and viscoelastic properties as well as determining the Young modulus and imaging magnetic or electrostatic properties. The AFM technique can analyze any kind of samples such as polymers, adsorbed molecules, films or fibers, and powders in the air whether in a controlled atmosphere or in a liquid medium. In the past decade, the AFM has emerged as a powerful tool to obtain the nanostructural details and biomechanical properties of biological samples, including biomolecules and cells. The AFM applications, techniques, and -in particular- its ability to measure forces, are not still familiar to most clinicians. This paper reviews the literature on the main principles of the AFM modality and highlights the advantages of this technique in biology, medicine, and- especially- dentistry. This literature review was performed through E-resources, including Science Direct, PubMed, Blackwell Synergy, Embase, Elsevier, and Scholar Google for the references published between 1985 and 2010.

  11. 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.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-02-17

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

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

    Directory of Open Access Journals (Sweden)

    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

  15. Using Genomics to Study Human Biology and Disease

    Energy Technology Data Exchange (ETDEWEB)

    Myers, Ricard M. (Stanford University School of Medicine)

    2005-04-06

    The Human Genome Project culminated in April 2003 with the finished DNA sequence of all of the human chromosomes. This book of information, particularly in conjunction with the genome sequences of many other organisms, has already begun to revolutionize the way that biomedical scientists study our species. The identification of essentially all of our genes has provided a template upon which researchers can discover basic processes that govern cells, organs, and the whole organism, and to understand the fundamental causes of the diseases that occur when something goes wrong with a gene or a set of genes. The Genome Project has already made it possible to identify the genes that are defective in more than 1,000 rare inherited diseases, and these discoveries have helped to understand the mechanisms of the more common forms of these disorders. This understanding of primary defects in diseases - which is translated as mutations in genes that encode proteins that serve specific functions - is transforming the way that biotechnology and pharmaceutical companies identify drug targets, and a few notable cases have already had a striking impact on specific diseases. In addition, it has become clear that the differential response to drugs in human populations is heavily influenced by genes, and a whole field called pharmacogenetics has begun to identify these genetic factors. Such knowledge will allow physicians to prescribe drugs targeted to each individual, with the potential to increase efficacy and decrease side-effects. Determining the DNA sequence of the human genome and identifying the genes has been an exciting endeavor, but we are only just beginning to understand the treasures present in all of our DNA. My presentation will briefly describe the road we took to get the sequence, as well as the tools that we are developing to unlock its secrets.

  16. Studies on the biological behaviors of taxol derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Awh, Ok Doo; Yoo, Dae Wung [College of Medicine, Yonsei Univ., Wonju (Korea, Republic of); Im, Sang Moo [College of Medicine, Korea Cancer Center, Seoul (Korea, Republic of)

    1997-07-01

    This study was designed to prospect the {sup 111}In-labelled paclitaxel as tumor imaging agent. In order to provide a taxol molecule with a functional -group which is able to chelate In-111, taxol-DTPA conjugate and 2'-hemisuccinyltaxol were synthesized by esterification of taxol at C-2' on C-13 carbon with DTPA anhydride and succinic anhydride, respectively. Synthesis yield of the taxol derivatives was 34% for taxol-DTPA and 80% for 2'-hemisuccinyltaxol. Cytotoxicity of the taxol derivatives were measured by MTT method toward cell lines HT29, B16, P388, and CT26. The cytotoxic activities of the taxol derivatives were maintained, although less active than taxol. Radiolabelling of the taxol derivatives were proceeded directly with {sup 111}InCl{sub 3} or indirectly with {sup 111}In-citrate(ligand-exchange method). The ligand-exchange method was not suitable because some precipitates appeared during the reaction. On the contrary, by direct radiolabelling method, we were able to obtain taxol-DTPA-{sup 111}In in 100% radiochemical yield. However, 2'-hemisuccinyltaxol was not labelled by both methods. Yield and radiochemical purity of the radiolabelled compound were determined by HPLC, paper chromatography and instant thin layer chromatography. Taxol-DTPA -{sup 111}In was characterized to be hydrophilic by lipophilicity test, and nearly non-adhesive to HT29, B16, P388, and CT26 by cell binding affinity test. Binding affinity of the taxol-DTPA-{sup 111}In complex to serum proteins was also examined by protein precipitation with 30% trichloroacetic acid. The results showed that 30% of the taxol-DTPA-{sup 111}In complex binds with serum proteins.

  17. Structural and Functional Studies of Peptide-Carbohydrate Mimicry

    Science.gov (United States)

    Johnson, Margaret A.; Pinto, B. Mario

    Certain peptides act as molecular mimics of carbohydrates in that they are specifically recognized by carbohydrate-binding proteins. Peptides that bind to anti-carbohydrate antibodies, carbohydrate-processing enzymes, and lectins have been identified. These peptides are potentially useful as vaccines and therapeutics; for example, immunologically functional peptide molecular mimics (mimotopes) can strengthen or modify immune responses induced by carbohydrate antigens. However, peptides that bind specifically to carbohydrate-binding proteins may not necessarily show the corresponding biological activity, and further selection based on biochemical studies is always required. The degree of structural mimicry required to generate the desired biological activity is therefore an interesting question. This review will discuss recent structural studies of peptide-carbohydrate mimicry employing NMR spectroscopy, X-ray crystallography, and molecular modeling, as well as relevant biochemical data. These studies provide insights into the basis of mimicry at the molecular level. Comparisons with other carbohydrate-mimetic compounds, namely proteins and glycopeptides, will be drawn. Finally, implications for the design of new therapeutic compounds will also be presented.

  18. 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.

  19. 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.

  20. Biological studies of matrix metalloproteinase sensitive drug delivery systems

    DEFF Research Database (Denmark)

    Johansen, Pia Thermann

    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......Cancer, which is a group of diseases characterized by cells with elevated replication rate and compromised DNA damage response, is often treated with cytotoxic drugs, chemotherapeutics, inducing DNA damage that results in cell death. The use of chemotherapeutics in the clinic, however, is limited...... 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...

  1. Phytochemical and biological study of radal Lomatia hirsuta (Proteaceae).

    Science.gov (United States)

    Erazo, S; García, R; Backhouse, N; Lemus I 1st; Delporte, C; Andrade, C

    1997-07-01

    The anti-inflammatory property of Lomatia hirsuta (Lam.) Diels ex Macbr. (Proteaceae), leaves (radal), a plant used in Chilean traditional medicine for bronchial troubles and asthma, was evaluated. The biological assays showed infusion of L. hirsuta leaves inhibits the inflammation induced by lambda-carrageenan corresponding to a 29.2% anti-inflammatory effect, and to 53.5% of the maximum effect observed with sodium naproxen (4 mg/kg) in the same experimental conditions. The coumarins, umbelliferone and scopoletin, were the major compounds isolated, along with quercetine, rhamnetin and iso-rhamnetin, with minor quantities or quercitrine and no presence of toxic naphthoquinone derivates. These results supported the folk use of L. hirsuta. PMID:9254109

  2. Studies of the reproductive biology of deep sea megabenthos

    International Nuclear Information System (INIS)

    Specimens of six species of aspidochirota from depths between 1245 and 2315m in the N.E. Atlantic have been examined and their reproductive biology determined. Two species Paelopatides grisea and Benthothuria funebris produce the large eggs typical of direct development. Mesothuria lactea and M. verrilli have an intermediate egg size of c. 400μm whilst Bathyplotes natans has an egg size of c. 280μm, which may be indicative of indirect development. The last species Paroriza pallens is an hermaphrodite producing an egg of c. 250μm. With the exception of Bathyplotes natans, which appears to show periodic reproduction if not seasonal, the species show no evidence of reproductive seasonality. (author)

  3. Prospects for the study of biological systems with high power sources of terahertz radiation

    International Nuclear Information System (INIS)

    The emergence of intense sources of terahertz radiation based on lasers and electron accelerators has considerable potential for research on biological systems. This perspective gives a brief survey of theoretical work and the results of experiments on biological molecules and more complex biological systems. Evidence is accumulating that terahertz radiation influences biological systems and this needs to be clarified in order to establish safe levels of human exposure to this radiation. The use of strong sources of terahertz radiation may contribute to the resolution of controversies over the mechanism of biological organization. However the potential of these sources will only be realized if they are accompanied by the development of sophisticated pump–probe and multidimensional experimental techniques and by the study of biological systems in the controlled environments necessary for their maintenance and viability. (perspective)

  4. Sample validity in biological trace element and organic nutrient research studies

    International Nuclear Information System (INIS)

    The state of the art of the biological trace element investigations is overviewed. Questions of biological validity, such as the influence of the 'status of sampling' of human subjects on the concentrations of selected elements are studied. Analytical validity problems, e.g. stability of Cd, Hg and Pb concentration in selected specimens, stability of selected organic nutrients in NBS SRMs, etc. are also discussed. Finally, it is concluded that the development of new biological reference materials should take into account the multidisciplinary demands of biological trace element investigations. (author) 20 refs.; 6 tables

  5. A Comprehensive Systems Biology Approach to Studying Zika Virus.

    Science.gov (United States)

    May, Meghan; 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

  6. Phenomenological study of the nucleon structure functions

    International Nuclear Information System (INIS)

    This thesis is devoted to the study of the deep inelastic scattering. Its purpose is the development of phenomenological models describing experimental results on unpolarized (F2) and polarized (g1) nucleon structure functions in the wide range of the kinematical domain. Special attention is paid to the small-x behaviour of F2 and to the link between deep inelastic scattering and photoproduction process. The investigation of the Pomeron in deep inelastic scattering shows that one single Pomeron compatible with the Froissard-Martin limit can account for all the present HERA data. A phenomenological model of the proton structure function is developed, based on a two-component structure including various features expected from both perturbative quantum chromodynamics and non perturbative Regge theory. A link with the photoproduction process is provided. A detailed analysis of the perturbative components, based on the Gribov-Lipatov-Altarelli-Parisi evolution equations is presented. Taking into account the different parton distribution, this approach allows to describe data on proton and neutron structure functions, on deep inelastic neutrino scattering, and to reproduce the gluons distribution extracted by the ZEUS collaboration. The model is applied to the polarized deep inelastic scattering and the axial anomaly effect appearing both in the description of results on the spin dependent structure functions gp,n,d and in the interpretation of the nucleon spin structure is discussed. (J.S.). 260 refs., 34 figs., 8 tabs., 6 appends

  7. Intercepting Functions for Memoization: A Case Study Using Transcendental Functions

    OpenAIRE

    Suresh, Arjun; Narasimha Swamy, Bharath; Rohou, Erven; Seznec, André

    2015-01-01

    Memoization is the technique of saving result of executions so that future executions can be omitted when the input set repeats. Memoization has been proposed in previous literature at the instruction level, basic block level and function level using hardware as well as pure software level approaches including changes to programming language.In this paper, we focus on software memoization for procedural languages like C and Fortran, at the granularity of a function. We propose a simple linker...

  8. Functional MR imaging study of the shoulder

    International Nuclear Information System (INIS)

    This paper presents a functional MR study of the shoulder performed with the positioning in which patients were about to complain of shoulder pain. A 0.064-T permanent MR system was used. The effectiveness of this study was evaluated in the diagnosis of rotator cuff impingement syndrome. Thirteen patients (11 males and two female) were examined prospectively. Three-dimensional Fourier transformation coronal images were obtained with patients' arms at the maximal abduction. They were compared with images obtained while patients' arms were at their sides, chiefly from the viewpoint of severity of impingement and intensity change of the supraspinatus muscle

  9. Uranium speciation studies in biological medium by capillary electrophoresis and time-resolved laser-induced fluorescence

    International Nuclear Information System (INIS)

    Uranium speciation studies in biological medium by capillary electrophoresis and time-resolved laser-induced fluorescence. The knowledge of the chemical state of uranium in biological medium requires more detailed investigations to understand the behaviour of uranium in the organism. The characterization of the different complexes of uranium can be improved by combining two techniques: time-resolved laser-induced fluorescence (TRLIF) and capillary electrophoresis (CE). CE, indeed, using the isoelectric focusing mode (CIEF), allows for the separation of the different complexes as a function of their isoelectric points (pI) and TRLIF as a speciation method leads to the identification at very low level of different uranyl complexes by temporal resolution and spectral unfolding. Results obtained on various inorganic chemical systems (phosphate, bicarbonate) together with biological systems (citrate, transferrin) will be presented and discussed. The complexation between uranium and human transferrin has been pointed out through CIEF. (authors)

  10. 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.

  11. Analytical and biological studies of kanji and extracts of its ingredient, daucus carota L

    International Nuclear Information System (INIS)

    A fermented beverage, Kanji, prepared from roots of Daucus carota L. subsp. sativus (Hoffm.) Arcang. var. vavilovii Mazk. (Apiaceae), despite long usage history has not been investigated for analytical studies and biological activities. Therefore, the present study aimed to investigate different types of Kanji samples and various types of extracts/fractions of root of the plant for a number of analytical studies and in vitro antioxidant activities. The Kanji sample, Lab-made Kanji, having better analytical and biological profile was further investigated for preliminary clinical studies. The analytical studies indicated that Lab-made Kanji was having comparatively higher contents of phytochemicals than that of the commercial Kanji samples, different types of extracts and fractions (P < 0.05). All the Kanji samples and aqueous and ethanol extracts of fresh roots exhibited comparable antioxidant activities in DPPH assay (52.20 - 54.19%) that were higher than that of methanol extract (48.78%) of dried roots. The antiradical powers (1/ EC50) of Lab-made Kanji and aqueous extract were found to be higher than that of the ethanol and methanol extracts. In beta-carotene linoleate assay, the Kanji samples showed higher activity than that of the methanol extract, but comparable to that of the vitamin-E and butylated hydroxyl anisole (BHA) (P < 0.05). A preliminary clinical evaluation indicated that Kanji has no harmful effect on blood components, liver function and serum lipid profile. The results of the present study indicate that Kanji is an effective antioxidant beverage. (author)

  12. 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.

  13. Setup for studying kinetics of fluorescence anisotropy decay in biological objects

    Energy Technology Data Exchange (ETDEWEB)

    Akimov, A.V.; Dem`yanov, G.V.; Kurek, N.K. [Lebedev Physics Institute, Moscow (Russian Federation)] [and others

    1995-02-01

    A setup for studying the decay of the fluorescence intensity and anisotropy in biological objects, brought into use at an S-60 FIAN synchrotron radiation source, is described. The setup allows one to extend investigations of a spatial structure of biological membranes and lipoproteins. 5 refs., 2 figs.

  14. Studies of cell toxicity of complexes of magnetic fluids and biological macromolecules

    International Nuclear Information System (INIS)

    In this study, we performed a comparative investigation of the binding properties of two surface-coated (carboxymethyldextran/glucuronic acid), magnetite-based biocompatible magnetic fluids with different biological macromolecules (BSA, HSA, and LDL). We also investigated the in vitro toxicity of the complex formed between the magnetic fluid and the biological macromolecule in the neoplastic cell line J774-A

  15. Studies of cell toxicity of complexes of magnetic fluids and biological macromolecules

    Science.gov (United States)

    Macaroff, Patrícia P.; Oliveira, Daniela M.; Ribeiro, Karina F.; Lacava, Zulmira G. M.; Lima, Emília C. D.; Morais, Paulo C.; Tedesco, Antonio C.

    2005-05-01

    In this study, we performed a comparative investigation of the binding properties of two surface-coated (carboxymethyldextran/glucuronic acid), magnetite-based biocompatible magnetic fluids with different biological macromolecules (BSA, HSA, and LDL). We also investigated the in vitro toxicity of the complex formed between the magnetic fluid and the biological macromolecule in the neoplastic cell line J774-A.

  16. Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region

    Science.gov (United States)

    Bowker, M.A.; Miller, M.E.; Belnap, J.; Sisk, T.D.; Johnson, N.C.

    2008-01-01

    Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r = 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands. ?? 2008 Society for Conservation Biology.

  17. Renal function studies with radioisotopes: an appraisal

    International Nuclear Information System (INIS)

    The use of radioisotopes in renal disorders has grown out of the development of scintillation detectors and gamma cameras and the availability of appropriate radioactive pharmaceuticals. It is now time to approach these studies from a different point of view. What further information would the practising nephrologist or urologist, physician or surgeon like to know about patients' kidney function that is not easily obtainable by non-radioactive methods. He would like a simple and reliable measurement of individual renal function; a test to demonstrate the presence or absence of obstruction in a patient with oliguria or uraemia; some help as to whether nephrectomy or a more difficult restorative operation is better for the patient with hydronephrosis, calculus or renal artery stenosis; a measure of the degree to which an obstructive uropathy is causing an obstructive nephropathy; clarification of which kidney to operate upon first when bilateral obstructive nephropathy presents with uraemia; a quantitative index of the progress following an operation to relieve an outflow system disorder; a screening procedure for renal disorders in the hypertensive and other populations; a prognostic guide to the likely evolution of glomerulonephritis and pyelonephritis, a prediction of the onset of rejection in the renal transplant, particularly in the presence of acute tubular necrosis. This review attempts to define the extent to which renal function studies with radioisotopes meet or fail to meet these needs and to indicate areas for potential development. (author)

  18. 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

  19. Mechanistic approaches to the study of evolution: the functional synthesis

    OpenAIRE

    Dean, Antony M; Joseph W Thornton

    2007-01-01

    An emerging synthesis of evolutionary biology and experimental molecular biology is providing much stronger and deeper inferences about the dynamics and mechanisms of evolution than were possible in the past. The new approach combines statistical analyses of gene sequences with manipulative molecular experiments to reveal how ancient mutations altered biochemical processes and produced novel phenotypes. This functional synthesis has set the stage for major advances in our understanding of fun...

  20. BIOLOGICAL FUNCTION OF TOMBUSVIRUS-ENCODED SUPPRESSOR OF RNA SILENCING IN PLANTS

    Directory of Open Access Journals (Sweden)

    Omarov R.T.

    2012-08-01

    Full Text Available RNA interference (RNAi plays multiple biological roles in eukaryotic organisms to regulate gene expression. RNAi also operates as a conserved adaptive molecular immune mechanism against invading viruses. The antiviral RNAi pathway is initiated with the generation of virus-derived short-interfering RNAs (siRNAs that are used for subsequent sequence-specific recognition and degradation of the cognate viral RNA molecules. As an efficient counter-defensive strategy, most plant viruses evolved the ability to encode specific proteins capable of interfering with RNAi, and this process is commonly known as RNA silencing suppression. Virus-encoded suppressors of RNAi (VSRs operate at different steps in the RNAi pathway and display distinct biochemical properties that enable these proteins to efficiently interfere with the host-defense system. Tombusvirus-encoded P19 is an important pathogenicity factor, required for symptom development and elicitation of a hypersensitive response in a host-dependent manner. Protein plays a crucial role of TBSV P19 in protecting viral RNA during systemic infection on Nicotiana benthamiana. The X-ray crystallographic studies conducted by two independent groups revealed the existence of a P19-siRNA complex; a conformation whereby caliper tryptophan residues on two subunits of P19 dimers measure and bind 21-nt siRNA duplexes. These structural studies provided the first details on the possible molecular mechanism of any viral suppressor to block RNAi. The association between P19 and siRNAs was also shown to occur in infected plants These and related studies revealed that in general the ability of P19 to efficiently sequester siRNAs influences symptom severity, however this is not a strict correlation in all hosts.The current working model is that during TBSV infection of plants, P19 appropriates abundantly circulating Tombusvirus-derived siRNAs thereby rendering these unavailable to program RISC, to prevent degradation of

  1. Targeted metabolomics to study lipid peroxidation in biological systems

    NARCIS (Netherlands)

    Labuschagne, C.F.

    2013-01-01

    During normal cellular metabolism reactive oxygen species (ROS) are inevitably formed as by-products of respiration. ROS are extremely reactive molecules and can react with and damage surrounding DNA, protein and lipid molecules and subsequently alter their normal function in the cell. This oxidativ

  2. UV effects on the primary productivity of picophytoplankton: biological weighting functions and exposure response curves of Synechococcus

    OpenAIRE

    Neale, P.J.; A. L. Pritchard; R. Ihnacik

    2014-01-01

    A model that predicts UV effects on marine primary productivity using a biological weighting function (BWF) coupled to the photosynthesis–irradiance response (BWF/P-E model) has been implemented for two strains of the picoplanktonic cyanobacteria Synechococcus, WH7803 and WH8102, which were grown at two irradiances (77 and 174 μmol m−2 s−1 photosynthetically available radiation (PAR)) and two temperatures (20 and 26 °C). The model was fit using photosynthesis measured in a ...

  3. Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology

    OpenAIRE

    Donner, Erica; Punshon, Tracy; Guerinot, Mary Lou; Lombi, Enzo

    2011-01-01

    Functional characterisation of the genes regulating metal(loid) homeostasis in plants is a major focus of crop biofortification, phytoremediation, and food security research. This paper focuses on the potential for advancing plant metal(loid) research by combining molecular biology and synchrotron-based techniques. Recent advances in x-ray focussing optics and fluorescence detection have greatly improved the potential of synchrotron techniques for plant science research, allowing metal(loids)...

  4. The biology of myeloid-derived suppressor cells: The blessing and the curse of morphological and functional heterogeneity

    OpenAIRE

    Youn, Je-in; Gabrilovich, Dmitry I.

    2010-01-01

    Myeloid-derived suppressor cells (MDSC) play an important role in the cellular network regulating immune responses in cancer, chronic infectious diseases, autoimmunity, and in other pathologic conditions. Morphological, phenotypic and functional heterogeneity is a hallmark of MDSC. This heterogeneity demonstrates the plasticity of this immune suppressive myeloid compartment, and shows how various tumors and infectious agents can have similar biological effects on myeloid cells despite the dif...

  5. The Biological Role of the Medial Olivocochlear Efferents in Hearing: Separating Evolved Function from Exaptations

    Directory of Open Access Journals (Sweden)

    David W. Smith

    2015-02-01

    Full Text Available Cochlear outer hair cells (OHCs are remarkable, mechanically-active receptors that determine the exquisite sensitivity and frequency selectivity characteristic of the mammalian auditory system. While there are three to four times as many OHCs compared with inner hair cells, OHCs lack a significant afferent innervation and, instead, receive a rich efferent innervation from medial olivocochlear (MOC efferent neurons. Activation of the MOC has been shown to exert a considerable suppressive effect over OHC activity. The precise function of these efferent tracts in auditory behavior, however, is the matter of considerable debate. The most frequent functions assigned to the MOC tracts are to protect the cochlea from traumatic damage associated with intense sound and to aid the detection of signals in noise. While considerable evidence shows that interruption of MOC activity exacerbates damage due to high-level sound exposure, the well characterized MOC physiology and evolutionary studies do not support such a role. Instead, a MOC protective effect is well explained as being a byproduct of the suppressive nature of MOC action on OHC mechanical behavior. A role in the enhancement of signals in noise backgrounds, on the other hand, is well supported by (1 an extensive physiological literature (2 examination of naturally 0ccuring environmental acoustic conditions (3 recent data from multiple laboratories showing that the MOC plays a significant role in auditory selective attention by suppressing the response to unattended or ignored stimuli. This presentation will argue that, based on the extant literature combining the suppression of background noise through MOC-mediated rapid adaptation with the suppression of non-attended signals, in concert with the corticofugal pathways descending from the auditory cortex, the MOC system has one evolved function – to increase the signal-to-noise ratio, aiding in the detection of target signals. By contrast, the MOC

  6. The biological role of the medial olivocochlear efferents in hearing: separating evolved function from exaptation.

    Science.gov (United States)

    Smith, David W; Keil, Andreas

    2015-01-01

    Cochlear outer hair cells (OHCs) are remarkable, mechanically-active receptors that determine the exquisite sensitivity and frequency selectivity characteristic of the mammalian auditory system. While there are three to four times as many OHCs compared with inner hair cells, OHCs lack a significant afferent innervation and, instead, receive a rich efferent innervation from medial olivocochlear (MOC) efferent neurons. Activation of the MOC has been shown to exert a considerable suppressive effect over OHC activity. The precise function of these efferent tracts in auditory behavior, however, is the matter of considerable debate. The most frequent functions assigned to the MOC tracts are to protect the cochlea from traumatic damage associated with intense sound and to aid the detection of signals in noise. While considerable evidence shows that interruption of MOC activity exacerbates damage due to high-level sound exposure, the well characterized MOC physiology and evolutionary studies do not support such a role. Instead, a MOC protective effect is well explained as being a byproduct of the suppressive nature of MOC action on OHC mechanical behavior. A role in the enhancement of signals in noise backgrounds, on the other hand, is well supported by (1) an extensive physiological literature (2) examination of naturally occurring environmental acoustic conditions (3) recent data from multiple laboratories showing that the MOC plays a significant role in auditory selective attention by suppressing the response to unattended or ignored stimuli. This presentation will argue that, based on the extant literature combining the suppression of background noise through MOC-mediated rapid adaptation (RA) with the suppression of non-attended signals, in concert with the corticofugal pathways descending from the auditory cortex, the MOC system has one evolved function-to increase the signal-to-noise ratio, aiding in the detection of target signals. By contrast, the MOC system role

  7. Growth of novel ceramic layers on metals via chemical and heat treatments for inducing various biological functions

    Directory of Open Access Journals (Sweden)

    Tadashi eKokubo

    2015-10-01

    Full Text Available The present authors’ systematic studies on growth of novel ceramic layers on Ti metal and its alloys by chemical and heat treatments for inducing bone-bonding bioactivity and some other biological functions are reviewed. Ti metal formed an apatite on its surface in a simulated body fluid (SBF, when heat-treated after exposure to strong acid solutions to form rutile surface layer, or to strong alkali solutions to form sodium titanate surface layer. Both types of Ti metal tightly bonded to the living bone.The alkali and heat treatment was applied to the surface Ti metal of an artificial hip joint and successfully used in the clinic since 2007. The acid and heat treatments was applied to porous Ti metal to induce osteoconductivity as well as osteoinductivity. The resulting product was successfully used in clinical trials for spinal fusion devices. For the Ti-based alloys, the alkali and heat treatment was a little modified to form calcium titanate surface layer. Bone-growth promoting Mg, Sr, and Zn ions as well as the antibacterial Ag ion were successfully incorporated into the calcium titanate layer.

  8. Growth of Novel Ceramic Layers on Metals via Chemical and Heat Treatments for Inducing Various Biological Functions.

    Science.gov (United States)

    Kokubo, Tadashi; Yamaguchi, Seiji

    2015-01-01

    The present authors' systematic studies on growth of novel ceramic layers on Ti metal and its alloys by chemical and heat treatments for inducing bone-bonding bioactivity and some other biological functions are reviewed. Ti metal formed an apatite on its surface in a simulated body fluid, when heat-treated after exposure to strong acid solutions to form rutile surface layer, or to strong alkali solutions to form sodium titanate surface layer. Both types of Ti metal tightly bonded to the living bone. The alkali and heat treatment was applied to the surface Ti metal of an artificial hip joint and successfully used in the clinic since 2007. The acid and heat treatments was applied to porous Ti metal to induce osteoconductivity as well as osteoinductivity. The resulting product was successfully used in clinical trials for spinal fusion devices. For the Ti-based alloys, the alkali and heat treatment was little modified to form calcium titanate surface layer. Bone-growth promoting Mg, Sr, and Zn ions as well as the antibacterial Ag ion were successfully incorporated into the calcium titanate layer. PMID:26579517

  9. 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.

  10. An ESR study on biological dosimeters: Human hair

    International Nuclear Information System (INIS)

    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 ΔHpp-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 (Gmean) 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.

  11. 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...

  12. 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.

  13. 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.

  14. 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.

  15. Technical and conceptual considerations for performing and interpreting functional MRI studies in awake rats

    OpenAIRE

    MarceloFebo

    2011-01-01

    Functional neuroimaging studies in rodents have the potential to provide insight into neurodevelopmental and psychiatric conditions. The strength of the technique lies in its non-invasive nature that can permit longitudinal functional studies in the same animal over its adult life. The relatively good spatial and temporal resolution and the ever-growing database on the biological and biophysical basis of the blood oxygen level dependent (BOLD) signal make it a unique technique in preclinical ...

  16. Technical and Conceptual Considerations for Performing and Interpreting Functional MRI Studies in Awake Rats

    OpenAIRE

    Febo, Marcelo

    2011-01-01

    Functional neuroimaging studies in rodents have the potential to provide insight into neurodevelopmental and psychiatric conditions. The strength of the technique lies in its non-invasive nature that can permit longitudinal functional studies in the same animal over its adult life. The relatively good spatial and temporal resolution and the ever-growing database on the biological and biophysical basis of the blood oxygen level dependent (BOLD) signal make it a unique technique in preclinical ...

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

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

    This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project...

  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. 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

  20. Two Studies on the Interplay between Social Preferences and Individual Biological Features

    OpenAIRE

    Sanchez-Pages, Santiago; Turiegano, E.

    2013-01-01

    Biological features and social preferences have been studied separately as factors influencing human strategic behavior. We run two studies in order to explore the interplay between these two sets of factors. In the first study, we investigate to what extent social preferences may have some biological underpinnings. We use simple one-shot distribution experiments to attribute subjects one out of four types of social preferences: Self-interested (SI), Competitive (C), Inequality averse (IA), a...

  1. Production of sorption functional media (SFM) from clinoptilolite tailings and its performance investigation in a biological aerated filter (BAF) reactor

    International Nuclear Information System (INIS)

    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 NH3-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 NH3-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

  2. 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.

  3. Density Functional Study of Calcium Nitride

    OpenAIRE

    Römer, Rebecca; Schnick, Wolfgang; Kroll, Peter

    2009-01-01

    The high-pressure behavior of Ca3N2 is studied up 100 GPa using density functional theory. Evaluation of many hypothetical polymorphs of composition A3X2 leads us to propose four high-pressure polymorphs for both α- and β-Ca3N2: (1) an anti-Rh2O3−II structure at 5 GPa, (2) an anti-B-sesquioxide structure at 10 GPa, (3) an anti-A-sesquioxide structure at 27 GPa, and (4) a hitherto unknown hexagonal structure (P63/mmc), derived from the post-perovskite structure of CaIrO3, at 38 GPa. The develo...

  4. 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.

  5. Study and design of a function generator

    International Nuclear Information System (INIS)

    The aim of this study is to design the function generators that will make it possible to obtain the n and n' analog voltages for controlling the auxiliary power supplies of the quadripoles of Saturne II (pulsed magnetic field synchrotron). These analog voltages are of shape: u=f1 (B) + f2 (t). These generators will be integrated in the data processing facility associated with the power supplies of the quadripoles The generators will therefore be piloted by the central computer of Saturne I. As this computer will be monitoring all the equipments of Saturne, it must not be immobilised by the generators in any event

  6. Ackermann Functions --A Survey and Empirical Study

    Institute of Scientific and Technical Information of China (English)

    Li Yunpeng; Lai Rong; Song Fangmin

    2002-01-01

    Ackermann functions are examples of nonprimitive recursive function which grow so fast with respect to their arguments. In this paper, we present Ackermann functions in detail and introduce its influence on theoretical computer science.

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

    Science.gov (United States)

    Upadhyayula, Venkata K K

    2012-02-17

    There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad range of threat agents, including radioactive substances, explosive compounds, chemical warfare agents, biotoxins, and biothreat pathogens through any of the four sensory means mentioned previously. PMID:22244163

  8. 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.

  9. Chemistry and biology of Tc-99m renal function agents. Final report

    International Nuclear Information System (INIS)

    A major aim of the project was to develop a Tc-99m renal tubular function radiopharmaceutical. Progress was made in synthesizing and evaluating Tc-99m 2,3-dimercaptoaceta-midoprepanoate (CO2DADS). In animals and clinical studies the A epimer (early component on reversed phase HPLC) demonstrated high efficiency and specificity for renal tubular secretion. We were unable to obtain only the desired stereoisomer. Synthesis of about twenty diamide dimercaptide N2S2 ligand analogs suggested two others that were of comparable efficiency in humans, but with less difference between stereoisomers; Tc-99m 1,3-dimercaptoacetamide-2-hydroxypropane (HoDADS) and 1,8-dithiol- 2,7-dioxo-3,6-diazanonanoate (α -S-CO2DADS). 15 refs

  10. 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…

  11. Study on optimization of parameters in a biological model

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    According to the data observed in a China- Japan Joint Investigation, the parameters of an ecosystem dynamics model (Qiao et al., 2000) were optimized. The values of eighteen parameters for the model were obtained, with nutrient haft saturation constant, Kn = 1.4 μmol/dm3, Kp = 0.129 μmol/dm3 and Ks= 1.16μmol/dm3 for the diatom and Kn=0.345μmol/dm3, Kp=0.113 μmol/dm3 for the flagellate. Three proposals to set up a function for this multiple objective problem were discussed in detail.

  12. Biological Soil Crusts Influence Hydrologic Function Differently in Various Deserts And Future Climate and Land Use will Affect These Relationships

    Science.gov (United States)

    Belnap, J.; Wilcox, B.; Barger, N.; Herrick, J.; van Soyoc, M.

    2012-04-01

    Biological soil crusts (biocrusts) can completely cover plant interspaces in dryland regions, and can constitute 70% or more of the living ground cover. In these areas, where precipitation is low and soils have low fertility, native plants often rely on intact biological soil crusts to provide water and nutrient flow to the broadly scattered vegetation. In cool desert systems, well-developed biocrusts (dominated by lichens and mosses) roughen the soil surface, increasing residence time of surface water flow. This results in increased and relatively homogenous infiltration of water into the soils. Filaments associated with cyanobacteria, fungi, mosses and lichens increase aggregate formation and stabilize soils, thus reducing sediment production, with well-developed biocrusts conferring much more stability on soils than less developed cyanobacterial dominated biocrusts. In hot and hyper-arid desert systems, biocrusts are generally less developed and dominated by cyanobacteria. These biocrusts generally increase runoff from plant interspaces to downslope vegetation. While reduced infiltration may seem to be negative, it can actually be advantageous to the downslope plants, as they may require small watersheds above them to provide the needed amount of water and nutrients required for their growth. Thus, infiltration and nutrient additions are more heterogenous than in cool desert systems. Soil surface disturbance and climate change have the potential to dramatically alter the species composition and thereby function of biological soil crusts in different deserts. Compressional disturbances results in reduced cover and a loss of lichen and moss species. Changes in climate regimes, such as an increase in temperature or a shift in the amount, timing, or intensity of rainfall, will influence the composition and physiological functioning of biological soil crusts, as various crust components have different photosynthetic and respiration responses to temperature and

  13. 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.

  14. 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.

  15. A Structure of Biological System and Functionality using Artificial Neural Networks

    Directory of Open Access Journals (Sweden)

    Khaled Mohammed Beer Gamal

    2014-07-01

    Full Text Available Artificial neural networks have, as initial motivation, the structure of biological systems, and constitute an alternative computability paradigm. For that reason we will review some aspects of the way in which biological systems perform information processing. The fascination which still pervades this research field has much to do with the points of contact with the surprisingly elegant methods used by neurons in order to process information at the cellular level. Several million years of evolution have led to very sophisticated solutions to the problem of dealing with an uncertain environment. In this chapter we will discuss some elements of these strategies in order to determine what features we want to adopt in our abstract models of neural networks.

  16. 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...

  17. STUDIES OF RELATIONSHIPS BETWEEN MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY BY PATTERN RECOGNITION METHODS

    Science.gov (United States)

    The attempt to rationalize the connections between the molecular structures of organic compounds and their biological activities comprises the field of structure-activity relations (SAR) studies. Correlations between structure and activity are important for the understanding and ...

  18. 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.

  19. Quantitative assessments of morphological and functional properties of biological trees based on their fractal nature.

    Science.gov (United States)

    Kamiya, Akira; Takahashi, Tatsuhisa

    2007-06-01

    The branching systems in our body (vascular and bronchial trees) and those in the environment (plant trees and river systems) are characterized by a fractal nature: the self-similarity in the bifurcation pattern. They increase their branch density toward terminals according to a power function with the exponent called fractal dimension (D). From a stochastic model based-on this feature, we formulated the fractal-based integrals to calculate such morphological parameters as aggregated branch length, surface area, and content volume for any given range of radius (r). It was followed by the derivation of branch number and cross-sectional area, by virtue of the logarithmic sectioning of the r axis and of the branch radius-length relation also given by a power function of r with an exponent (alpha). These derivatives allowed us to quantify various hydrodynamic parameters of vascular and bronchial trees as fluid conduit systems, including the individual branch flow rate, mean flow velocity, wall shear rate and stress, internal pressure, and circumferential tension. The validity of these expressions was verified by comparing the outcomes with actual data measured in vivo in the vascular beds. From additional analyses of the terminal branch number, we found a simple equation relating the exponent (m) of the empirical power law (Murray's so-called cube law) to the other exponents as (m=D+alpha). Finally, allometric studies of mammalian vascular trees revealed uniform and scale-independent distributions of terminal arterioles in organs, which afforded an infarct index, reflecting the severity of tissue damage following arterial infarction. PMID:17347385

  20. Compound Activity Mapping: Integrating Chemical and Biological Profiling for the Functional Annotation of Natural Product Libraries

    OpenAIRE

    Kurita, Kenji Long

    2015-01-01

    Natural products research has had a significant impact on human-health and our understanding of the natural world as a pillar of pharmacognosy, organic chemistry, ecology, and chemical biology. But while this science has yielded countless discoveries such as penicillin, taxol, and artimesinin and will continue to improve quality of life around the world, the idea that natural products is a panacea of chemical diversity has been challenged by problems including the endless rediscovery of known...

  1. Biological rhythms, higher brain function, and behavior: gaps, opportunities and challenges”

    OpenAIRE

    Benca, Ruth; Duncan, Marilyn J.; Frank, Ellen; McClung, Colleen; Nelson, Randy J.; Vicentic, Aleksandra

    2009-01-01

    Increasing evidence suggests that disrupted temporal organization impairs behavior, cognition, and affect; further, disruption of circadian clock genes impairs sleep/wake cycle and social rhythms which may be implicated in mental disorders. Despite this strong evidence, a gap in understanding the neural mechanisms of this interaction obscures whether biological rhythms disturbances are the underlying causes or merely symptoms of these diseases. Here, we review current understanding, emerging ...

  2. Beyond the hydrophobic effect: Critical function of water at biological phase boundaries--A hypothesis.

    Science.gov (United States)

    Damodaran, Srinivasan

    2015-07-01

    Many life-sustaining processes in living cells occur at the membrane-water interface. The pertinent questions that need to be asked are what is the evolutionary reason for biology to choose the membrane-water interface as the site for performing and/or controlling crucial biological reactions and what is the key physical principle that is singular to the membrane-water interface that biology exploits for regulating metabolic processes in cells? In this review, a hypothesis is developed, which espouses that cells control activities of membrane-bound enzymes and receptor activated processes via manipulating the thermodynamic activity of water at the membrane-water interfacial region. In support of this hypothesis, first we establish that the surface pressure of a lipid monolayer is a direct measure of a reduction in the thermodynamic activity of interfacial water. Second, we show that the surface pressure-dependent activation/inactivation of interfacial enzymes is fundamentally related to their dependence on interfacial water activity. We extend this argument to infer that cells might manipulate activities of membrane-associated biological processes via manipulating the activity of interfacial water via localized compression or expansion of the interface. In this paper, we critically analyze literature data on mechano-activation of large pore ion channels in Escherichia coli spheroplasts and G-proteins in reconstituted lipid vesicles, and show that these pressure-induced activation processes are fundamentally and quantitatively related to changes in the thermodynamic state of interfacial water, caused by mechanical stretching of the bilayer. PMID:25888225

  3. Adipocyte-derived basement membrane extract with biological activity: applications in hepatocyte functional augmentation in vitro

    OpenAIRE

    Sharma, Nripen S.; Nagrath, Deepak; Martin L Yarmush

    2010-01-01

    Natural and synthetic biomaterials utilized in tissue engineering applications require a dynamic interplay of complex macromolecular compositions of hydrated extracellular matrices (ECMs) and soluble growth factors. The challenges in utilizing synthetic ECMs is the effective control of temporal and spatial complexity of multiple signal presentation, as compared to natural ECMs that possess the inherent properties of biological recognition, including presentation of receptor-binding ligands, s...

  4. 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...

  5. 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…

  6. Applications of continuum mechanics : computational studies in biological and discrete systems

    OpenAIRE

    Tang, Yik-sau; 鄧亦修

    2015-01-01

    This thesis is divided into two parts: part A and part B. Part A mainly focused on the biological systems while part B emphasized on discrete systems. Both studies can be applied readily in the scientific world. Part A: Computational Fluid Dynamics Study of Biological Systems Cerebrovascular and cardiovascular diseases are life threatening diseases, and are leading causes of death and disability in the civilized world. Thoracic aortic dissection (TAD), a form of cardiovascular disease...

  7. Physicochemical and biological study of a renal scintigraphy agent: the DMSA - 99mTc complex

    International Nuclear Information System (INIS)

    This research thesis deals with the study of the dimercaptosuccinic acid (DMSA) marked with 99mTc, a recently developed scintigraphy agent used for the kidney isotopic exploration. The author notably studied the relationships between the physicochemical properties of solutions of dimercaptosuccinic acid marked with 99mTc and the biological distribution of 99mTc in order to reach a better understanding of the biological mechanism which results in technetium fixation to the kidney

  8. Affective variables as predictors of biology achievement: A study on 11th grade students

    OpenAIRE

    Alpmen Ayten

    2016-01-01

    The purpose of this study was to examine the contribution of the gender, self-efficacy beliefs, task value, and learning strategies to the 11th grade students’ biology achievement. A total of 1035 students from different high schools in Yenimahalle and Çankaya districts of Ankara participated in the study. The Motivated Strategies for Learning Questionnaire [21], (MSLQ) and Biology Achievement Test (BAT) were used to collect data. Results of the the simultaneous multiple regression analysis i...

  9. 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.

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

    International Nuclear Information System (INIS)

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

  11. Identification of biological corridors in highly fragmented landscapes through GIS tools Case study Microcuenca La Bolsa, Marinilla Town

    International Nuclear Information System (INIS)

    The study object is to identify biological corridors as recovery time strategy in highly fragmented landscapes through tools of Geographic Information Systems, taking as a case study of microcuenca La Balsa, Marinilla Town. GIS tools such as V- Late, allowed assessing landscape structure through statistical analysis of forest fragments of local biodiversity importance, that from a cost raster that allowed the tracing of the biological corridor using Cost weight, shortest path and a buffer width of 100 meters as optimal for the use of certain animal species such as small and medium-sized mammals and birds. This allowed us to propose the biological corridor that will allow functional linkage of strategic ecosystems of the watershed and the recovery time, preservation and protection of biodiversity in the areas. Importantly, the use of birds as indicators of biodiversity and ecosystem disruption with which you intend to measure susceptibility to fragmentation, risk status due to loss of habitat and migratory frugivorous species which are sensitive to these changes and allow monitoring by evaluating the success of the biological corridor, because although the present study took a hypothetical data, the use of these indicators are intended to establish the need to identify key species of flora and fauna that allow for monitoring and verifying the success or otherwise of posed recovery strategy.

  12. A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology

    NARCIS (Netherlands)

    Seidl, M.F.; Schneider, A.; Govers, F.; Snel, B.

    2013-01-01

    Background - Associations between proteins are essential to understand cell biology. While this complex interplay between proteins has been studied in model organisms, it has not yet been described for the oomycete late blight pathogen Phytophthora infestans. Results - We present an integrative prob

  13. Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging.

    Science.gov (United States)

    Nicodemus, Kristin K; Callicott, Joseph H; Higier, Rachel G; Luna, Augustin; Nixon, Devon C; Lipska, Barbara K; Vakkalanka, Radhakrishna; Giegling, Ina; Rujescu, Dan; St Clair, David; Muglia, Pierandrea; Shugart, Yin Yao; Weinberger, Daniel R

    2010-04-01

    The etiology of schizophrenia likely involves genetic interactions. DISC1, a promising candidate susceptibility gene, encodes a protein which interacts with many other proteins, including CIT, NDEL1, NDE1, FEZ1 and PAFAH1B1, some of which also have been associated with psychosis. We tested for epistasis between these genes in a schizophrenia case-control study using machine learning algorithms (MLAs: random forest, generalized boosted regression andMonteCarlo logic regression). Convergence of MLAs revealed a subset of seven SNPs that were subjected to 2-SNP interaction modeling using likelihood ratio tests for nested unconditional logistic regression models. Of the 7C2 = 21 interactions, four were significant at the α = 0.05 level: DISC1 rs1411771-CIT rs10744743 OR = 3.07 (1.37, 6.98) p = 0.007; CIT rs3847960-CIT rs203332 OR = 2.90 (1.45, 5.79) p = 0.003; CIT rs3847960-CIT rs440299 OR = 2.16 (1.04, 4.46) p = 0.038; one survived Bonferroni correction (NDEL1 rs4791707-CIT rs10744743 OR = 4.44 (2.22, 8.88) p = 0.00013). Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls; risk associated alleles at both SNPs predicted prefrontal cortical inefficiency during the N-back task, a schizophrenia-linked intermediate biological phenotype: rs3847960-rs440299; rs1411771-rs10744743, rs4791707-rs10744743 (SPM5 p < 0.05, corrected), although we were unable to statistically replicate the interactions in other clinical samples. Interestingly, the CIT SNPs are proximal to exons that encode theDISC1 interaction domain. In addition, the 3' UTR DISC1 rs1411771 is predicted to be an exonic splicing enhancer and the NDEL1 SNP is ~3,000 bp from the exon encoding the region of NDEL1 that interacts with the DISC1 protein, giving a plausible biological basis for epistasis signals validated by fMRI. PMID:20084519

  14. Cyanoacetamide based Barbiturates, Thiobarbiturates and their Biological Studies

    International Nuclear Information System (INIS)

    Various cyanoacetamide based Knoevenagel adducts were coupled with barbituric acid / thiobarbituric acid and triethylorthoformate via a one pot three component reaction in 2-butanol availing the desired compound in excellent yields. All the synthesized compounds (2-15) were extensively characterized by 1H-NMR, 13C-NMR, Mass spectrometry and elemental analysis and were screened for antibacterial, antiurease, antioxidant, cytotoxicity and chymotrypsin inhibition studies. In case of antibacterial studies 2 was found appreciably active against the six selected strains whereas the rest of the compounds were moderately active. The urease inhibition studies revealed compound 5 and 12 as potent whereas the rest were found inactive where thiourea was used as control. Antioxidant activity results exhibited with 2 as the most active and rest of compounds showed good activity. In case of chymotrypsin inhibition studies all the synthesized compounds were found inactive with the exception of 6 which was moderately active. (author)

  15. 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...

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

    OpenAIRE

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

    2010-01-01

    GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis t...

  17. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.;

    2016-01-01

    The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies....... applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems....

  18. Functional study of elafin cleaved by Pseudomonas aeruginosa metalloproteinases.

    LENUS (Irish Health Repository)

    Guyot, Nicolas

    2010-06-01

    Elafin is a 6-kDa innate immune protein present at several epithelial surfaces including the pulmonary epithelium. It is a canonical protease inhibitor of two neutrophil serine proteases [neutrophil elastase (NE) and proteinase 3] with the capacity to covalently bind extracellular matrix proteins by transglutamination. In addition to these properties, elafin also possesses antimicrobial and immunomodulatory activities. The aim of the present study was to investigate the effect of Pseudomonas aeruginosa proteases on elafin function. We found that P. aeruginosa PAO1-conditioned medium and two purified Pseudomonas metalloproteases, pseudolysin (elastase) and aeruginolysin (alkaline protease), are able to cleave recombinant elafin. Pseudolysin was shown to inactivate the anti-NE activity of elafin by cleaving its protease-binding loop. Interestingly, antibacterial properties of elafin against PAO1 were found to be unaffected after pseudolysin treatment. In contrast to pseudolysin, aeruginolysin failed to inactivate the inhibitory properties of elafin against NE. Aeruginolysin cleaves elafin at the amino-terminal Lys6-Gly7 peptide bond, resulting in a decreased ability to covalently bind purified fibronectin following transglutaminase activity. In conclusion, this study provides evidence that elafin is susceptible to proteolytic cleavage at alternative sites by P. aeruginosa metalloproteinases, which can affect different biological functions of elafin.

  19. Functional, radiological and biological markers of alveolitis and infections of the lower respiratory tract in patients with systemic sclerosis

    Directory of Open Access Journals (Sweden)

    Danza Francesco

    2005-08-01

    Full Text Available Abstract Background A progressive lung disease and a worse survival have been observed in patients with systemic sclerosis and alveolitis. The objective of this study was to define the functional, radiological and biological markers of alveolitis in SSc patients. Methods 100 SSc patients (76 with limited and 24 with diffuse disease underwent a multistep assessment of cardiopulmonary system: pulmonary function tests (PFTs every 6–12 months, echocardiography, high resolution computed tomography (HRCT and bronchoalveolar lavage (BAL, if clinically advisable. Alveolar and interstitial scores on HRCT and IL-6 plasma levels were also assessed as lung disease activity indices. Results 90 SSc patients with abnormal PFTs and 3 with signs and/or symptoms of lung involvement and normal PFTs underwent HRCT and echocardiography. HRCT revealed evidence of fibrosis in 87 (93.5% patients, with 55 (59.1% showing both ground glass attenuation and fibrosis. In 42 patients who had exhibited ground glass on HRCT and consented to undergo BAL, 16 (38.1% revealed alveolitis. 12 (75% of these patients had restrictive lung disease (p 14 (OR(95%CIs:7.03(1.40–34.33. The alveolar score showed a significant correlation with IL-6 plasma levels (r = 0.36, p = 0.001 and with the skin score (r = 0.33, p = 0.001. Cultures of BAL fluid resulted positive in 10 (23.8% of the 42 patients that underwent BAL and after one year a deterioration in PFTs occurred in 8 (80% of these patients (p = 0.01. Pulmonary artery systolic pressure ≥ 40 mmHg was found in 6 (37.5% patients with alveolitis. Conclusion We found alveolitis only in 38.1% of the patients who had exhibited ground glass on HRCT and then underwent BAL, probably because the concomitant fibrosis influenced results. A diffuse skin involvement and a restrictive pattern on PFTs together with ground glass on HRCT were judged possible markers of alveolitis, a BAL examination being indicated as the next step. Nevertheless BAL

  20. Investigation of interactions in a biological membrane using structure factor/pair correlation function approach: a first communication on nerve myelin

    International Nuclear Information System (INIS)

    Interactions in biological and artificial membranes have been studied by applying mostly the methods of biochemical analysis and determination of thermodynamic parameters related to phase transition phenomena. Structure factor, obtained by measuring scattered intensity from small-angle X-ray or neutron scattering experiments, has been used mainly for determining electron density distribution. Drawing upon the experience of the theory of liquids, where Johnson and March (1963) and Johnson, Hutchinson and March (1964) first established the possibility of deriving interparticle potential from experimental measurement of structure factor, it is suggested that structure factor/distance correlation function approach, can be a useful method for studying interactions between various membrane components. Preliminary experimental data presented for nerve myelin are to demonstrate the possibility of studying interactions from the distance correlation function of a membrane pair. (author)