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Sample records for adapter protein tsad

  1. Protein Adaptations in Archaeal Extremophiles

    Directory of Open Access Journals (Sweden)

    Christopher J. Reed

    2013-01-01

    Full Text Available Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.

  2. Protein cold adaptation : Role of physico-chemical parameters in adaptation of proteins to low temperatures

    NARCIS (Netherlands)

    Shokrollahzade, Soheila; Sharifi, Fatemeh; Vaseghi, Akbar; Faridounnia, Maryam; Jahandideh, Samad

    2015-01-01

    During years 2007 and 2008, we published three papers (Jahandideh, 2007a, JTB, 246, 159-166; Jahandideh, 2007b, JTB, 248, 721-726; Jahandideh, 2008, JTB, 255, 113-118) investigating sequence and structural parameters in adaptation of proteins to low temperatures. Our studies revealed important featu

  3. Adaptive resolution simulation of an atomistic protein in MARTINI water

    NARCIS (Netherlands)

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-01-01

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coa

  4. Adaptation in protein fitness landscapes is facilitated by indirect paths.

    OpenAIRE

    Wu, N.; Dai, L.; Olson, CA; Lloyd-Smith, JO; Sun, R

    2016-01-01

    The structure of fitness landscapes is critical for understanding adaptive protein evolution. Previous empirical studies on fitness landscapes were confined to either the neighborhood around the wild type sequence, involving mostly single and double mutants, or a combinatorially complete subgraph involving only two amino acids at each site. In reality, the dimensionality of protein sequence space is higher (20(L)) and there may be higher-order interactions among more than two sites. Here we e...

  5. Adaptation in protein fitness landscapes is facilitated by indirect paths

    Science.gov (United States)

    Wu, Nicholas C; Dai, Lei; Olson, C Anders; Lloyd-Smith, James O; Sun, Ren

    2016-01-01

    The structure of fitness landscapes is critical for understanding adaptive protein evolution. Previous empirical studies on fitness landscapes were confined to either the neighborhood around the wild type sequence, involving mostly single and double mutants, or a combinatorially complete subgraph involving only two amino acids at each site. In reality, the dimensionality of protein sequence space is higher (20L) and there may be higher-order interactions among more than two sites. Here we experimentally characterized the fitness landscape of four sites in protein GB1, containing 204 = 160,000 variants. We found that while reciprocal sign epistasis blocked many direct paths of adaptation, such evolutionary traps could be circumvented by indirect paths through genotype space involving gain and subsequent loss of mutations. These indirect paths alleviate the constraint on adaptive protein evolution, suggesting that the heretofore neglected dimensions of sequence space may change our views on how proteins evolve. DOI: http://dx.doi.org/10.7554/eLife.16965.001 PMID:27391790

  6. Protein and ligand adaptation in a retinoic acid binding protein.

    OpenAIRE

    Pattanayek, R.; Newcomer, M E

    1999-01-01

    A retinoic acid binding protein isolated from the lumen of the rat epididymis (ERABP) is a member of the lipocalin superfamily. ERABP binds both the all-trans and 9-cis isomers of retinoic acid, as well as the synthetic retinoid (E)-4-[2-(5,6,7,8)-tetrahydro-5,5,8,8-tetramethyl-2 napthalenyl-1 propenyl]-benzoic acid (TTNPB), a structural analog of all-trans retinoic acid. The structure of ERABP with a mixture of all-trans and 9-cis retinoic acid has previously been reported. To elucidate any ...

  7. Adaption of Saccharomyces cerevisiae expressing a heterologous protein

    DEFF Research Database (Denmark)

    Krogh, Astrid Mørkeberg; Beck, Vibe; Højlund Christensen, Lars;

    2008-01-01

    Production of the heterologous protein, bovine aprotinin, in Saccharomyces cerevisiae was shown to affect the metabolism of the host cell to various extent depending on the strain genotype. Strains with different genotypes, industrial and laboroatory, respectively, were investigated. The maximal ...... result of the adaptation. Determination of the level of mRNA encoding aprotinin and the plasmid copy number pointed to different mechanisms responsible for the decline in aprotinin yield in the different strains. (C) 2008 Elsevier B.V. All rights reserved....

  8. Adaptive evolution of centromere proteins in plants and animals

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    Henikoff Steven

    2004-08-01

    Full Text Available Abstract Background Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3, which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C, that is characterized by a single 24 amino-acid motif (CENPC motif. Results Whereas we find no evidence that mammalian CenH3 (CENP-A has been evolving adaptively, mammalian CENP-C proteins contain adaptively evolving regions that overlap with regions of DNA-binding activity. In plants we find that CENP-C proteins have complex duplicated regions, with conserved amino and carboxyl termini that are dissimilar in sequence to their counterparts in animals and fungi. Comparisons of Cenpc genes from Arabidopsis species and from grasses revealed multiple regions that are under positive selection, including duplicated exons in some grasses. In contrast to plants and animals, yeast CENP-C (Mif2p is under negative selection. Conclusions CENP-Cs in all plant and animal lineages examined have regions that are rapidly and adaptively evolving. To explain these remarkable evolutionary features for a single-copy gene that is needed at every mitosis, we propose that CENP-Cs, like some CenH3s, suppress meiotic drive of centromeres during female meiosis. This process can account for the rapid evolution and the complexity of centromeric DNA in plants and animals as compared to fungi.

  9. Adaptive Simulated Annealing Based Protein Loop Modeling of Neurotoxins

    Institute of Scientific and Technical Information of China (English)

    陈杰; 黄丽娜; 彭志红

    2003-01-01

    A loop modeling method, adaptive simulated annealing, for ab initio prediction of protein loop structures, as an optimization problem of searching the global minimum of a given energy function, is proposed. An interface-friendly toolbox-LoopModeller in Windows and Linux systems, VC++ and OpenGL environments is developed for analysis and visualization. Simulation results of three short-chain neurotoxins modeled by LoopModeller show that the method proposed is fast and efficient.

  10. Metabolic adaptation in transplastomic plants massively accumulating recombinant proteins.

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    Julia Bally

    Full Text Available BACKGROUND: Recombinant chloroplasts are endowed with an astonishing capacity to accumulate foreign proteins. However, knowledge about the impact on resident proteins of such high levels of recombinant protein accumulation is lacking. METHODOLOGY/PRINCIPAL FINDINGS: Here we used proteomics to characterize tobacco (Nicotiana tabacum plastid transformants massively accumulating a p-hydroxyphenyl pyruvate dioxygenase (HPPD or a green fluorescent protein (GFP. While under the conditions used no obvious modifications in plant phenotype could be observed, these proteins accumulated to even higher levels than ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco, the most abundant protein on the planet. This accumulation occurred at the expense of a limited number of leaf proteins including Rubisco. In particular, enzymes involved in CO(2 metabolism such as nuclear-encoded plastidial Calvin cycle enzymes and mitochondrial glycine decarboxylase were found to adjust their accumulation level to these novel physiological conditions. CONCLUSIONS/SIGNIFICANCE: The results document how protein synthetic capacity is limited in plant cells. They may provide new avenues to evaluate possible bottlenecks in recombinant protein technology and to maintain plant fitness in future studies aiming at producing recombinant proteins of interest through chloroplast transformation.

  11. Adaptation to cell culture induces functional differences in measles virus proteins

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    Rota Paul A

    2008-10-01

    Full Text Available Abstract Background Live, attenuated measles virus (MeV vaccine strains were generated by adaptation to cell culture. The genetic basis for the attenuation of the vaccine strains is unknown. We previously reported that adaptation of a pathogenic, wild-type MeV to Vero cells or primary chicken embryo fibroblasts (CEFs resulted in a loss of pathogenicity in rhesus macaques. The CEF-adapted virus (D-CEF contained single amino acid changes in the C and matrix (M proteins and two substitutions in the shared amino terminal domain of the phosphoprotein (P and V protein. The Vero-adapted virus (D-VI had a mutation in the cytoplasmic tail of the hemagglutinin (H protein. Results In vitro assays were used to test the functions of the wild-type and mutant proteins. The substitution in the C protein of D-CEF decreased its ability to inhibit mini-genome replication, while the wild-type and mutant M proteins inhibited replication to the same extent. The substitution in the cytoplasmic tail of the D-VI H protein resulted in reduced fusion in a quantitative fusion assay. Co-expression of M proteins with wild-type fusion and H proteins decreased fusion activity, but the mutation in the M protein of D-CEF did not affect this function. Both mutations in the P and V proteins of D-CEF reduced the ability of these proteins to inhibit type I and II interferon signaling. Conclusion Adaptation of a wild-type MeV to cell culture selected for genetic changes that caused measurable functional differences in viral proteins.

  12. Heat shock proteins and hypometabolism: adaptive strategy for proteome preservation

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    Storey KB

    2011-03-01

    Full Text Available Kenneth B Storey, Janet M StoreyDepartments of Biology and Chemistry, Carleton University, Ottawa, ON, CanadaAbstract: To survive under harsh environmental conditions many organisms retreat into hypometabolic states where metabolic rate may be reduced by 80% or more and energy use is reprioritized to emphasize key functions that sustain viability and provide cytoprotection. ATP-expensive activities, such as gene expression, protein turnover (synthesis and degradation, and the cell cycle, are largely shut down. As a consequence, mechanisms that stabilize the existing cellular proteome can become critical for long-term survival. Heat shock proteins (HSPs are well-known for their actions as chaperones that act to fold new proteins or refold proteins that are damaged. Indeed, they are part of the “minimal stress proteome” that appears to be a ubiquitous response by all cells as they attempt, successfully or unsuccessfully, to deal with stress. The present review summarizes evidence that HSPs are also a conserved feature of natural animal hypometabolism including the phenomena of estivation, hibernation, diapause, cold-hardiness, anaerobiosis, and anhydrobiosis. That is, organisms that retreat into dormant or torpid states in anticipation that environmental conditions may become too difficult for normal life also integrate the use of HSPs to protect their proteome while hypometabolic. Multiple studies show a common upregulation of expression of hsp genes and/or HSP proteins prior to or during hypometabolism in organisms as diverse as ground squirrels, turtles, land snails, insects, and brine shrimp and in situations of both preprogrammed dormancies (eg, seasonal or life stage specific and opportunistic hypometabolism (eg, triggered by desiccation or lack of oxygen. Hence, HSPs are not just a “shock” response that attempts to rescue cells from damaging stress but are a key protective strategy that is an integral component of natural states of

  13. High-Resolution Mapping of Protein Concentration Reveals Principles of Proteome Architecture and Adaptation

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    Emmanuel D. Levy

    2014-05-01

    Full Text Available A single yeast cell contains a hundred million protein molecules. How these proteins are organized to orchestrate living processes is a central question in biology. To probe this organization in vivo, we measured the local concentration of proteins based on the strength of their nonspecific interactions with a neutral reporter protein. We first used a cytosolic reporter and measured local concentrations for ∼2,000 proteins in S. cerevisiae, with accuracy comparable to that of mass spectrometry. Localizing the reporter to membranes specifically increased the local concentration measured for membrane proteins. Comparing the concentrations measured by both reporters revealed that encounter frequencies between proteins are primarily dictated by their abundances. However, to change these encounter frequencies and restructure the proteome, as in adaptation, we find that changes in localization have more impact than changes in abundance. These results highlight how protein abundance and localization contribute to proteome organization and reorganization.

  14. Characterization of Adapter Protein NRBP as a Negative Regulator of T Cell Activation

    Institute of Scientific and Technical Information of China (English)

    WANG Hui; LIN Zhi-xin; WU Jun

    2008-01-01

    Adapter proteins can regulate the gene transcriptions in disparate signaling pathway by interacting with multiple signaling molecules, including T cell activation signaling. Nuclear receptor binding protein (NRBP), a novel adapter protein, represents a small family of evolutionarily conserved proteins with homologs in Caenorhabditis elegans (C. elegans), Drosophila melanogaster (D.melanogaster), mouse and human. Here, we demonstrated that overexpression of NRBP in Jurkat TAg cells specifically impairs T cell receptor (TCR) or phorbol myristate acetate (PMA)/ionomycin-mediated signaling leading to nuclear factor of activated T cells (NFAT) promoter activation. Furthermore, the N-terminal of NRBP is necessary for its regulation of NFAT activation. Finally, we showed that NRBP has minimal effect on both TCR- and PMA-induced CD69 up-regulation in Jurkat TAg cells, which suggests that NRBP may function downstream of protein kinase C (PKC)/Ras pathway.

  15. Influence of Histidine-Containing Tags on the Biodistribution of ADAPT Scaffold Proteins.

    Science.gov (United States)

    Lindbo, Sarah; Garousi, Javad; Åstrand, Mikael; Honarvar, Hadis; Orlova, Anna; Hober, Sophia; Tolmachev, Vladimir

    2016-03-16

    Engineered scaffold proteins (ESP) are high-affinity binders that can be used as probes for radionuclide imaging. Histidine-containing tags enable both efficient purification of ESP and radiolabeling with (99m)Tc(CO)3. Earlier studies demonstrated that the use of a histidine-glutamate-histidine-glutamate-histidine-glutamate (HE)3-tag instead of the commonly used hexahistidine (H6)-tag reduces hepatic uptake of radiolabeled ESP and short peptides. Here, we investigated the influence of histidine-containing tags on the biodistribution of a novel type of ESP, ADAPTs. A series of anti-HER2 ADAPT probes having H6- or (HE)3-tags in the N-termini were prepared. The constructs, (HE)3-ADAPT6 and H6-ADAPT6, were labeled with two different nuclides, (99m)Tc or (111)In. The labeling with (99m)Tc(CO)3 utilized the histidine-containing tags, while (111)In was attached through a maleimido derivative of DOTA conjugated to the N-terminus. For (111)In-labeled ADAPTs, the use of (HE)3 provided a significantly (p < 0.05) lower hepatic uptake at 1 h after injection, but there was no significant difference in hepatic uptake of (111)In-(HE)3-ADAPT6 and H6-ADAPT6 at later time points. Interestingly, in the case of (99m)Tc, (99m)Tc(CO)3-H6-ADAPT6 provided significantly (p < 0.05) lower uptake in a number of normal tissues and was more suitable as an imaging probe. Thus, the influence of histidine-containing tags on the biodistribution of the novel ADAPT scaffold proteins was different compared to its influence on other ESPs studied so far. Apparently, the effect of a histidine-containing tag on the biodistribution is highly dependent on the scaffold composition of the ESP. PMID:26781756

  16. In the light of directed evolution: Pathways of adaptive protein evolution

    OpenAIRE

    Bloom, Jesse D; Arnold, Frances H.

    2009-01-01

    Directed evolution is a widely-used engineering strategy for improving the stabilities or biochemical functions of proteins by repeated rounds of mutation and selection. These experiments offer empirical lessons about how proteins evolve in the face of clearly-defined laboratory selection pressures. Directed evolution has revealed that single amino acid mutations can enhance properties such as catalytic activity or stability and that adaptation can often occur through pathways consisting of s...

  17. [Small heat shock proteins and adaptation to hypertermia in various Drosophila species].

    Science.gov (United States)

    Shilova, V Iu; Garbuz, D G; Evgen'ev, M B; Zatsepina, O G

    2006-01-01

    Expression level and kinetics of accumulation of small heat shock proteins (21-27 kDa group) have been investigated in three Drosophila species differing significantly by temperature niche and thermosensitivity. It was shown that low-latitude thermotolerant species D. virilis exceeds the high-latitude thermosensitive closely-related species D. lummei as well as distant thermosensitive species D. melanogaster in terms of small heat shock proteins expression and accumulation after temperature elevation. The data obtained enable to postulate an important role of small heat shock proteins in organism basal thermotolerance and general adaptation to adverse conditions of environment. PMID:16637267

  18. Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wenjuan; ZHANG Yuan; ZHONG Yang

    2006-01-01

    Nonsynonymous-synonymous substitution rate ratio (dN/dS) is an important measure for evaluating selective pressure based on the protein-coding sequences. Maximum likelihood (ML) method with codon-substitution models is a powerful statistic tool for detecting amino acid sites under positive selection and adaptive evolution. We analyzed the hepatitis C virus (HCV) envelope protein-coding sequences from 18 general geno/ subtypes worldwide, and found 4 amino acid sites under positive selection. Since these sites are located in different immune epitopes, it is reasonable to anticipate that our study would have potential values in biomedicine. It also suggests that the ML method is an effective way to detect adaptive evolution in virus proteins with relatively high genetic diversity.

  19. Differential protein expression during colonic adaptation in ultra-short bowel rats

    Institute of Scientific and Technical Information of China (English)

    Hai-Ping Jiang; Tao Chen; Guang-Rong Yan; Dan Chen

    2011-01-01

    AIM: To investigate the proteins involved in colonic adaptation and molecular mechanisms of colonic adaptation in rats with ultra-short bowel syndrome (USBS). METHODS: Sprague Dawley rats were randomly assigned to three groups: USBS group (10 rats) undergoing an approximately 90%-95% small bowel resection; sham-operation group (10 rats) undergoing small bowel transaction and anastomosis; and control group (ten normal rats). Colon morphology and differential protein expression was analyzed after rats were given postsurgical enteral nutrition for 21 d. Protein expression in the colonic mucosa was analyzed by two-dimensional electrophoresis (2-DE) in all groups. Differential protein spots were detected by ImageMaster 2D Platinum software and were further analyzed with matrix-assisted laser desorption/ionization-time-of-flight/time-of-flightmass spectrometric (MALDI-TOF/TOF-MS) analysis. RESULTS: The colonic mucosal thickness significantly increased in the USBS group compared with the control group (302.1 ± 16.9 μm vs 273.7 ± 16.0 μm, P 0.05). The height of colon plica markedly improved in USBS group compared with the control group (998.4 ± 81.2 μm vs 883.4 ± 39.0 μm, P 0.05). A total of 141 differential protein spots were found in the USBS group. Forty-nine of these spots were down-regulated while 92 protein spots were up-regulated by over 2-folds. There were 133 differential protein spots in USBS group. Thirty of these spots were down-regulated and 103 were upregulated. There were 47 common differential protein spots among the three groups, including 17 downregulated protein spots and 30 up-regulated spots. Among 47 differential spots, eight up-regulated proteins were identified by MALDI-TOF/TOF-MS. These proteins were previously reported to be involved in sugar and fat metabolism, protein synthesis and oxidation reduction, which are associated with colonic adaption. CONCLUSION: Eight proteins found in this study play important roles in colonic compensation

  20. Adapt

    Science.gov (United States)

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

  1. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins.

    Science.gov (United States)

    Clifton, Ben E; Jackson, Colin J

    2016-02-18

    The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.

  2. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers

    Science.gov (United States)

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C.; Markley, John L.

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.

  3. Life at the border: Adaptation of proteins to anisotropic membrane environment

    Science.gov (United States)

    Pogozheva, Irina D; Mosberg, Henry I; Lomize, Andrei L

    2014-01-01

    This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region—between double bonds and carbonyl groups of lipids. These “midpolar” regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein–lipid binding. PMID:24947665

  4. Massively parallel sampling of lattice proteins reveals foundations of thermal adaptation

    Science.gov (United States)

    Venev, Sergey V.; Zeldovich, Konstantin B.

    2015-08-01

    Evolution of proteins in bacteria and archaea living in different conditions leads to significant correlations between amino acid usage and environmental temperature. The origins of these correlations are poorly understood, and an important question of protein theory, physics-based prediction of types of amino acids overrepresented in highly thermostable proteins, remains largely unsolved. Here, we extend the random energy model of protein folding by weighting the interaction energies of amino acids by their frequencies in protein sequences and predict the energy gap of proteins designed to fold well at elevated temperatures. To test the model, we present a novel scalable algorithm for simultaneous energy calculation for many sequences in many structures, targeting massively parallel computing architectures such as graphics processing unit. The energy calculation is performed by multiplying two matrices, one representing the complete set of sequences, and the other describing the contact maps of all structural templates. An implementation of the algorithm for the CUDA platform is available at http://www.github.com/kzeldovich/galeprot and calculates protein folding energies over 250 times faster than a single central processing unit. Analysis of amino acid usage in 64-mer cubic lattice proteins designed to fold well at different temperatures demonstrates an excellent agreement between theoretical and simulated values of energy gap. The theoretical predictions of temperature trends of amino acid frequencies are significantly correlated with bioinformatics data on 191 bacteria and archaea, and highlight protein folding constraints as a fundamental selection pressure during thermal adaptation in biological evolution.

  5. A General, Adaptive, Roadmap-Based Algorithm for Protein Motion Computation.

    Science.gov (United States)

    Molloy, Kevin; Shehu, Amarda

    2016-03-01

    Precious information on protein function can be extracted from a detailed characterization of protein equilibrium dynamics. This remains elusive in wet and dry laboratories, as function-modulating transitions of a protein between functionally-relevant, thermodynamically-stable and meta-stable structural states often span disparate time scales. In this paper we propose a novel, robotics-inspired algorithm that circumvents time-scale challenges by drawing analogies between protein motion and robot motion. The algorithm adapts the popular roadmap-based framework in robot motion computation to handle the more complex protein conformation space and its underlying rugged energy surface. Given known structures representing stable and meta-stable states of a protein, the algorithm yields a time- and energy-prioritized list of transition paths between the structures, with each path represented as a series of conformations. The algorithm balances computational resources between a global search aimed at obtaining a global view of the network of protein conformations and their connectivity and a detailed local search focused on realizing such connections with physically-realistic models. Promising results are presented on a variety of proteins that demonstrate the general utility of the algorithm and its capability to improve the state of the art without employing system-specific insight.

  6. Shared and Unique Proteins in Human, Mouse and Rat Saliva Proteomes: Footprints of Functional Adaptation

    Directory of Open Access Journals (Sweden)

    Robert C. Karn

    2013-12-01

    Full Text Available The overall goal of our study was to compare the proteins found in the saliva proteomes of three mammals: human, mouse and rat. Our first objective was to compare two human proteomes with very different analysis depths. The 89 shared proteins in this comparison apparently represent a core of highly-expressed human salivary proteins. Of the proteins unique to each proteome, one-half to 2/3 lack signal peptides and probably are contaminants instead of less highly-represented salivary proteins. We recently published the first rodent saliva proteomes with saliva collected from the genome mouse (C57BL/6 and the genome rat (BN/SsNHsd/Mcwi. Our second objective was to compare the proteins in the human proteome with those we identified in the genome mouse and rat to determine those common to all three mammals, as well as the specialized rodent subset. We also identified proteins unique to each of the three mammals, because differences in the secreted protein constitutions can provide clues to differences in the evolutionary adaptation of the secretions in the three different mammals.

  7. An adaptive bin framework search method for a beta-sheet protein homopolymer model

    Directory of Open Access Journals (Sweden)

    Hoos Holger H

    2007-04-01

    Full Text Available Abstract Background The problem of protein structure prediction consists of predicting the functional or native structure of a protein given its linear sequence of amino acids. This problem has played a prominent role in the fields of biomolecular physics and algorithm design for over 50 years. Additionally, its importance increases continually as a result of an exponential growth over time in the number of known protein sequences in contrast to a linear increase in the number of determined structures. Our work focuses on the problem of searching an exponentially large space of possible conformations as efficiently as possible, with the goal of finding a global optimum with respect to a given energy function. This problem plays an important role in the analysis of systems with complex search landscapes, and particularly in the context of ab initio protein structure prediction. Results In this work, we introduce a novel approach for solving this conformation search problem based on the use of a bin framework for adaptively storing and retrieving promising locally optimal solutions. Our approach provides a rich and general framework within which a broad range of adaptive or reactive search strategies can be realized. Here, we introduce adaptive mechanisms for choosing which conformations should be stored, based on the set of conformations already stored in memory, and for biasing choices when retrieving conformations from memory in order to overcome search stagnation. Conclusion We show that our bin framework combined with a widely used optimization method, Monte Carlo search, achieves significantly better performance than state-of-the-art generalized ensemble methods for a well-known protein-like homopolymer model on the face-centered cubic lattice.

  8. Protein supplementation augments the adaptive response of skeletal muscle to resistance-type exercise training: a meta-analysis

    NARCIS (Netherlands)

    Cermak, N.M.; Res, P.T.; Groot, de C.P.G.M.; Saris, W.H.M.; Loon, van L.J.C.

    2012-01-01

    Background: Protein ingestion after a single bout of resistance-type exercise stimulates net muscle protein accretion during acute postexercise recovery. Consequently, it is generally accepted that protein supplementation is required to maximize the adaptive response of the skeletal muscle to prolon

  9. Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

    KAUST Repository

    Cannistraci, Carlo Vittorio

    2015-01-26

    Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet\\'s performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.

  10. High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes.

    Science.gov (United States)

    Martinez, N; Michoud, G; Cario, A; Ollivier, J; Franzetti, B; Jebbar, M; Oger, P; Peters, J

    2016-01-01

    Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure. PMID:27595789

  11. The orphan adapter protein SLY1 as a novel anti-apoptotic protein required for thymocyte development

    Directory of Open Access Journals (Sweden)

    Beer-Hammer Sandra

    2009-07-01

    Full Text Available Abstract Background SH3 containing Lymphocyte Protein (SLY1 is a putative adapter protein exclusively expressed in lymphocytes which is involved in antigen receptor induced activation. We previously have generated SLY1Δ/Δ mice harbouring a partial deletion in the N-terminal region of SLY1 which revealed profound immunological defects in T and B cell functions. Results In this study, T cell development in SLY1-/- and SLY1Δ/Δ mice was analysed ex vivo and upon cultivation with the bone marrow stromal cell line OP9. SLY1-deficient thymocytes were compromised in inducing nutrient receptor expression and ribosomal protein S6 phosphorylation, indicating a defect in mTOR complex activation. Furthermore, SLY1 was identified as a novel anti-apoptotic protein required for developmental progression of T cell precursors to the CD4+CD8+ double-positive stage by protecting from premature programmed cell death initiation in developing CD4-CD8- double-negative thymocytes. In addition, SLY1 phosphorylation was differentially regulated upon Notch ligand-mediated stimulation and expression of the preTCR. Conclusion Thus, our results suggest a non-redundant role for SLY1 in integrating signals from both receptors in early T cell progenitors in the thymus.

  12. The limits of adaptation of functional protein synthesis to sever undernutrition

    International Nuclear Information System (INIS)

    Our goal is to determine how the stress of infections alters the adaptation to reduced food intake in children. We think that an important element is the need for hepatic synthesis of rapidly turning over acute-phase proteins, a critical factor in overall maintenance of host defenses. When the child's prior intake has been adequate, even though growth may temporarily cease, the presence of adequate amino acid stores in tissues allows the hepatic response to stress to be maintained at the same time as an adequate rate of synthesis of nutrient transport proteins. However, when the immune system is activated in a children whose nutrition is already suboptimal the ability of the liver to synthesize nutrient transport proteins is compromised thereby further impeding nutrient utilization. We will use stable isotope tracer methodology to determine the effects of severe protein energy malnutrition, with and without infection, on the rates of synthesis of nutrient transport proteins and acute-phase proteins in undernourished children at three time points during treatment; in the early resuscitative period, after appetite has returned, and at the end of the catch-up growth phase when normal growth has resumed. (author). 12 refs, 1 fig., 1 tab

  13. Unfolding Thermodynamics of Cysteine-Rich Proteins and Molecular Thermal-Adaptation of Marine Ciliates

    Directory of Open Access Journals (Sweden)

    Giorgia Cazzolli

    2013-11-01

    Full Text Available Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the thermal unfolding of disulfide-rich protein pheromones produced by these ciliates. Recent circular dichroism (CD measurements have shown that the two psychrophilic (E. nobilii and mesophilic (E. raikovi protein families are characterized by very different melting temperatures, despite their close structural homology. The enhanced thermal stability of the E. raikovi pheromones is realized notwithstanding the fact that these proteins form, as a rule, a smaller number of disulfide bonds. We perform Monte Carlo (MC simulations in a structure-based coarse-grained (CG model to show that the higher stability of the E. raikovi pheromones is due to the lower locality of the disulfide bonds, which yields a lower entropy increase in the unfolding process. Our study suggests that the higher stability of the mesophilic E. raikovi phermones is not mainly due to the presence of a strongly hydrophobic core, as it was proposed in the literature. In addition, we argue that the molecular adaptation of these ciliates may have occurred from cold to warm, and not from warm to cold. To provide a testable prediction, we identify a point-mutation of an E. nobilii pheromone that should lead to an unfolding temperature typical of that of E. raikovi pheromones.

  14. Contractile activity-induced adaptations in the mitochondrial protein import system.

    Science.gov (United States)

    Takahashi, M; Chesley, A; Freyssenet, D; Hood, D A

    1998-05-01

    We previously demonstrated that subsarcolemmal (SS) and intermyofibrillar (IMF) mitochondrial subfractions import proteins at different rates. This study was undertaken to investigate 1) whether protein import is altered by chronic contractile activity, which induces mitochondrial biogenesis, and 2) whether these two subfractions adapt similarly. Using electrical stimulation (10 Hz, 3 h/day for 7 and 14 days) to induce contractile activity, we observed that malate dehydrogenase import into the matrix of the SS and IMF mitochondia isolated from stimulated muscle was significantly increased by 1.4-to 1.7-fold, although the pattern of increase differed for each subfraction. This acceleration of import may be mitochondrial compartment specific, since the import of Bcl-2 into the outer membrane was not affected. Contractile activity also modified the mitochondrial content of proteins comprising the import machinery, as evident from increases in the levels of the intramitochondrial chaperone mtHSP70 as well as the outer membrane import receptor Tom20 in SS and IMF mitochondria. Addition of cytosol isolated from stimulated or control muscles to the import reaction resulted in similar twofold increases in the ability of mitochondria to import malate dehydrogenase, despite elevations in the concentration of mitochondrial import-stimulating factor within the cytosol of chronically stimulated muscle. These results suggest that chronic contractile activity modifies the extra- and intramitochondrial environments in a fashion that favors the acceleration of precursor protein import into the matrix of the organelle. This increase in protein import is likely an important adaptation in the overall process of mitochondrial biogenesis. PMID:9612226

  15. Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores

    Science.gov (United States)

    Wendell, David; Jing, Peng; Geng, Jia; Subramaniam, Varuni; Lee, Tae Jin; Montemagno, Carlo; Guo, Peixuan

    2009-11-01

    Biological pores have been used to study the transport of DNA and other molecules, but most pores have channels that allow only the movement of small molecules and single-stranded DNA and RNA. The bacteriophage phi29 DNA-packaging motor, which allows double-stranded DNA to enter the virus during maturation and exit during an infection, contains a connector protein with a channel that is between 3.6 and 6 nm wide. Here we show that a modified version of this connector protein, when reconstituted into liposomes and inserted into planar lipid bilayers, allows the translocation of double-stranded DNA. The measured conductance of a single connector channel was 4.8 nS in 1 M KCl. This engineered and membrane-adapted phage connector is expected to have applications in microelectromechanical sensing, microreactors, gene delivery, drug loading and DNA sequencing.

  16. FK506 binding protein 51 integrates pathways of adaptation: FKBP51 shapes the reactivity to environmental change.

    Science.gov (United States)

    Rein, Theo

    2016-09-01

    This review portraits FK506 binding protein (FKBP) 51 as "reactivity protein" and collates recent publications to develop the concept of FKBP51 as contributor to different levels of adaptation. Adaptation is a fundamental process that enables unicellular and multicellular organisms to adjust their molecular circuits and structural conditions in reaction to environmental changes threatening their homeostasis. FKBP51 is known as chaperone and co-chaperone of heat shock protein (HSP) 90, thus involved in processes ensuring correct protein folding in response to proteotoxic stress. In mammals, FKBP51 both shapes the stress response and is calibrated by the stress levels through an ultrashort molecular feedback loop. More recently, it has been linked to several intracellular pathways related to the reactivity to drug exposure and stress. Through its role in autophagy and DNA methylation in particular it influences adaptive pathways, possibly also in a transgenerational fashion. Also see the video abstract here. PMID:27374865

  17. Human Skeletal Muscle Stem Cells in Adaptations to Exercise; Effects of Resistance Exercise Contraction Mode and Protein Supplementation

    DEFF Research Database (Denmark)

    Farup, Jean

    2014-01-01

    protein constitute key factors in regulation of human skeletal muscle mass; however, the influence of divergent resistance exercise contraction modes and protein supplementation on SC content, is not well described. The overall aim of the present thesis was to investigate whether eccentric versus...... concentric resistance training and ingestion of protein influence myocellular adaptations, with special emphasis on muscle stem cell adaptations, during both acute and prolonged resistance exercise in human skeletal muscle. Paper I. Whey protein supplementation accelerates satellite cell proliferation during....... In conclusion, protein supplementation may accelerate SC proliferation as part of regeneration or remodeling processes after maximal eccentric exercise. Paper II. Whey protein hydrolysate augments tendon and muscle hypertrophy independent of exercise contraction mode. The aim of paper II was to investigate...

  18. Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

    Directory of Open Access Journals (Sweden)

    Yoojin Hong

    Full Text Available A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc.. Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs are an informative M-dimension that is scored by quantitatively measuring the embedded or unmodified sequence alignments. Moreover, the information obtained from these alignments is informative, and remains so even in the "twilight zone" of sequence similarity (<25% identity. Although our previous embedding strategy was powerful, it suffered from contaminating alignments (embedded AND unmodified and high computational costs. Herein, we describe the logic and algorithmic process for a heuristic embedding strategy named "Adaptive GDDA-BLAST." Adaptive GDDA-BLAST is, on average, up to 19 times faster than, but has similar sensitivity to our previous method. Further, data are provided to demonstrate the benefits of embedded-alignment measurements in terms of detecting structural homology in highly divergent protein sequences and isolating secondary structural elements of transmembrane and ankyrin-repeat domains. Together, these advances allow further exploration of the embedded alignment data space within sufficiently large data sets to eventually induce relevant statistical inferences. We show that sequence embedding could serve as one of the vehicles for measurement of low

  19. Structural Adaptation of a Thermostable Biotin-binding Protein in a Psychrophilic Environment

    Science.gov (United States)

    Meir, Amit; Bayer, Edward A.; Livnah, Oded

    2012-01-01

    Shwanavidin is an avidin-like protein from the marine proteobactrium Shewanella denitrificans, which exhibits an innate dimeric structure while maintaining high affinity toward biotin. A unique residue (Phe-43) from the L3,4 loop and a distinctive disulfide bridge were shown to account for the high affinity toward biotin. Phe-43 emulates the function and position of the critical intermonomeric Trp that characterizes the tetrameric avidins but is lacking in shwanavidin. The 18 copies of the apo-monomer revealed distinctive snapshots of L3,4 and Phe-43, providing rare insight into loop flexibility, binding site accessibility, and psychrophilic adaptation. Nevertheless, as in all avidins, shwanavidin also displays high thermostability properties. The unique features of shwanavidin may provide a platform for the design of a long sought after monovalent form of avidin, which would be ideal for novel types of biotechnological application. PMID:22493427

  20. Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML.

    Directory of Open Access Journals (Sweden)

    Shamil R Sunyaev

    2009-02-01

    Full Text Available PML is a progressive and mostly fatal demyelinating disease caused by JC virus infection and destruction of infected oligodendrocytes in multiple brain foci of susceptible individuals. While JC virus is highly prevalent in the human population, PML is a rare disease that exclusively afflicts only a small percentage of immunocompromised individuals including those affected by HIV (AIDS or immunosuppressive drugs. Viral- and/or host-specific factors, and not simply immune status, must be at play to account for the very large discrepancy between viral prevalence and low disease incidence. Here, we show that several amino acids on the surface of the JC virus capsid protein VP1 display accelerated evolution in viral sequences isolated from PML patients but not in sequences isolated from healthy subjects. We provide strong evidence that at least some of these mutations are involved in binding of sialic acid, a known receptor for the JC virus. Using statistical methods of molecular evolution, we performed a comprehensive analysis of JC virus VP1 sequences isolated from 55 PML patients and 253 sequences isolated from the urine of healthy individuals and found that a subset of amino acids found exclusively among PML VP1 sequences is acquired via adaptive evolution. By modeling of the 3-D structure of the JC virus capsid, we showed that these residues are located within the sialic acid binding site, a JC virus receptor for cell infection. Finally, we go on to demonstrate the involvement of some of these sites in receptor binding by demonstrating a profound reduction in hemagglutination properties of viral-like particles made of the VP1 protein carrying these mutations. Collectively, these results suggest that a more virulent PML causing phenotype of JC virus is acquired via adaptive evolution that changes viral specificity for its cellular receptor(s.

  1. Adaptive evolution of tight junction protein claudin-14 in echolocating whales.

    Science.gov (United States)

    Xu, Huihui; Liu, Yang; He, Guimei; Rossiter, Stephen J; Zhang, Shuyi

    2013-11-10

    Toothed whales and bats have independently evolved specialized ultrasonic hearing for echolocation. Recent findings have suggested that several genes including Prestin, Tmc1, Pjvk and KCNQ4 appear to have undergone molecular adaptations associated with the evolution of this ultrasonic hearing in mammals. Here we studied the hearing gene Cldn14, which encodes the claudin-14 protein and is a member of tight junction proteins that functions in the organ of Corti in the inner ear to maintain a cationic gradient between endolymph and perilymph. Particular mutations in human claudin-14 give rise to non-syndromic deafness, suggesting an essential role in hearing. Our results uncovered two bursts of positive selection, one in the ancestral branch of all toothed whales and a second in the branch leading to the delphinid, phocoenid and ziphiid whales. These two branches are the same as those previously reported to show positive selection in the Prestin gene. Furthermore, as with Prestin, the estimated hearing frequencies of whales significantly correlate with numbers of branch-wise non-synonymous substitutions in Cldn14, but not with synonymous changes. However, in contrast to Prestin, we found no evidence of positive selection in bats. Our findings from Cldn14, and comparisons with Prestin, strongly implicate multiple loci in the acquisition of echolocation in cetaceans, but also highlight possible differences in the evolutionary route to echolocation taken by whales and bats. PMID:23965379

  2. Object-adapted trapping and shape-tracking to probe a bacterial protein chain motor

    Science.gov (United States)

    Roth, Julian; Koch, Matthias; Rohrbach, Alexander

    2015-03-01

    The helical bacterium Spiroplasma is a motile plant and anthropod pathogen which swims by propagating pairs of kinks along its cell body. As a well suited model system for bacterial locomotion, understanding the cell's molecular motor is of vital interest also regarding the combat of bacterial diseases. The extensive deformations related to these kinks are caused by a contractile cytoskeletal protein ribbon representing a linear motor in contrast to common rotary motors as, e.g., flagella. We present new insights into the working of this motor through experiments with object-adapted optical traps and shape-tracking techniques. We use the given laser irradiation from the optical trap to hinder bacterial energy (ATP) production through the production of O2 radicals. The results are compared with experiments performed under the influence of an O2-Scavenger and ATP inhibitors, respectively. Our results show clear dependences of the kinking properties on the ATP concentration inside the bacterium. The experiments are supported by a theoretical model which we developed to describe the switching of the ribbon's protein subunits.

  3. Adaptive evolution of the venom-targeted vWF protein in opossums that eat pitvipers.

    Directory of Open Access Journals (Sweden)

    Sharon A Jansa

    Full Text Available The rapid evolution of venom toxin genes is often explained as the result of a biochemical arms race between venomous animals and their prey. However, it is not clear that an arms race analogy is appropriate in this context because there is no published evidence for rapid evolution in genes that might confer toxin resistance among routinely envenomed species. Here we report such evidence from an unusual predator-prey relationship between opossums (Marsupialia: Didelphidae and pitvipers (Serpentes: Crotalinae. In particular, we found high ratios of replacement to silent substitutions in the gene encoding von Willebrand Factor (vWF, a venom-targeted hemostatic blood protein, in a clade of opossums known to eat pitvipers and to be resistant to their hemorrhagic venom. Observed amino-acid substitutions in venom-resistant opossums include changes in net charge and hydrophobicity that are hypothesized to weaken the bond between vWF and one of its toxic snake-venom ligands, the C-type lectin-like protein botrocetin. Our results provide the first example of rapid adaptive evolution in any venom-targeted molecule, and they support the notion that an evolutionary arms race might be driving the rapid evolution of snake venoms. However, in the arms race implied by our results, venomous snakes are prey, and their venom has a correspondingly defensive function in addition to its usual trophic role.

  4. Adaptive evolution of tight junction protein claudin-14 in echolocating whales.

    Science.gov (United States)

    Xu, Huihui; Liu, Yang; He, Guimei; Rossiter, Stephen J; Zhang, Shuyi

    2013-11-10

    Toothed whales and bats have independently evolved specialized ultrasonic hearing for echolocation. Recent findings have suggested that several genes including Prestin, Tmc1, Pjvk and KCNQ4 appear to have undergone molecular adaptations associated with the evolution of this ultrasonic hearing in mammals. Here we studied the hearing gene Cldn14, which encodes the claudin-14 protein and is a member of tight junction proteins that functions in the organ of Corti in the inner ear to maintain a cationic gradient between endolymph and perilymph. Particular mutations in human claudin-14 give rise to non-syndromic deafness, suggesting an essential role in hearing. Our results uncovered two bursts of positive selection, one in the ancestral branch of all toothed whales and a second in the branch leading to the delphinid, phocoenid and ziphiid whales. These two branches are the same as those previously reported to show positive selection in the Prestin gene. Furthermore, as with Prestin, the estimated hearing frequencies of whales significantly correlate with numbers of branch-wise non-synonymous substitutions in Cldn14, but not with synonymous changes. However, in contrast to Prestin, we found no evidence of positive selection in bats. Our findings from Cldn14, and comparisons with Prestin, strongly implicate multiple loci in the acquisition of echolocation in cetaceans, but also highlight possible differences in the evolutionary route to echolocation taken by whales and bats.

  5. Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse.

    Directory of Open Access Journals (Sweden)

    Jihui Ping

    Full Text Available Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA receptor and non-structural protein 1 (NS1 interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA variants obtained after 12 or 20-21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30 suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for

  6. Development of a Cold-Adapted Pseudoalteromonas Expression System for the Pseudoalteromonas Proteins Intractable for the Escherichia coli System

    OpenAIRE

    Zi-Chao Yu; Bai-Lu Tang; Dian-Li Zhao; Xiuhua Pang; Qi-Long Qin; Bai-Cheng Zhou; Xi-Ying Zhang; Xiu-Lan Chen; Yu-Zhong Zhang

    2015-01-01

    Although the Escherichia coli expression system is the most commonly used expression system, some proteins are still difficult to be expressed by this system, such as proteins with high thermolability and enzymes that cannot mature by autoprocessing. Therefore, it is necessary to develop alternative expression systems. In this study, a cold-adapted Pseudoalteromonas expression system was developed. A shuttle vector was constructed, and a conjugational transfer system between E. coli and psych...

  7. Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes

    Directory of Open Access Journals (Sweden)

    Bachtrog Doris

    2008-12-01

    Full Text Available Abstract Background Adaptive protein evolution is common in several Drosophila species investigated. Some studies point to very weak selection operating on amino-acid mutations, with average selection intensities on the order of Nes ~ 5 in D. melanogaster and D. simulans. Species with lower effective population sizes should undergo less adaptation since they generate fewer mutations and selection is ineffective on a greater proportion of beneficial mutations. Results Here I study patterns of polymorphism and divergence at 91 X-linked loci in D. miranda, a species with a roughly 5-fold smaller effective population size than D. melanogaster. Surprisingly, I find a similar fraction of amino-acid mutations being driven to fixation by positive selection in D. miranda and D. melanogaster. Genes with higher rates of amino-acid evolution show lower levels of neutral diversity, a pattern predicted by recurrent adaptive protein evolution. I fit a hitchhiking model to patterns of polymorphism in D. miranda and D. melanogaster and estimate an order of magnitude higher selection coefficients for beneficial mutations in D. miranda. Conclusion This analysis suggests that effective population size may not be a major determinant in rates of protein adaptation. Instead, adaptation may not be mutation-limited, or the distribution of fitness effects for beneficial mutations might differ vastly between different species or populations. Alternative explanation such as biases in estimating the fraction of beneficial mutations or slightly deleterious mutation models are also discussed.

  8. Evolutionary adaptation of an AraC-like regulatory protein in Citrobacter rodentium and Escherichia species.

    Science.gov (United States)

    Tan, Aimee; Petty, Nicola K; Hocking, Dianna; Bennett-Wood, Vicki; Wakefield, Matthew; Praszkier, Judyta; Tauschek, Marija; Yang, Ji; Robins-Browne, Roy

    2015-04-01

    The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogen Citrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and the grlRA operon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genus Escherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated that regA has been horizontally transferred to Escherichia spp. and C. rodentium. Comparative studies of two RegA homologues, namely, those from C. rodentium and E. coli SMS-3-5, a multiresistant environmental strain of E. coli, showed that the two regulators acted similarly in vitro but differed in terms of their abilities to activate the virulence of C. rodentium in vivo, which evidently was due to their differential activation of grlRA. Our data indicate that RegA from C. rodentium has strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence by C. rodentium and on the evolution of virulence-regulatory genes of bacterial pathogens in general.

  9. Multi-omic profiling of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael;

    2015-01-01

    Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied...... the existence of production bottlenecks in energy metabolism (i.e., glycolytic metabolites, NAD(P)H/NAD(P)+ and ANPs) in batch culture or in the secretory protein production pathway (i.e., gene dosage, transcription and post-translational processing of EPO) in chemostat culture at specific productivities up...... to 5 pg/cell/day. Time-course analysis of high- and low-producing clones in chemostat culture revealed rapid adaptation of transcription levels of amino acid catabolic genes in favor of EPO production within nine generations. Interestingly, the adaptation was followed by an increase in specific EPO...

  10. Gal3 Binds Gal80 Tighter than Gal1 Indicating Adaptive Protein Changes Following Duplication.

    Science.gov (United States)

    Lavy, Tali; Yanagida, Hayato; Tawfik, Dan S

    2016-02-01

    Derived from the yeast whole-genome duplication, Saccharomyces cerevisiae GAL1 and GAL3 encode the catabolic enzyme galactokinase (Gal1) and its transcriptional coinducer (Gal3), whereas the ancestral, preduplicated GAL1 gene performed both functions. Previous studies indicated that divergence was primarily driven by changes in upstream promoter elements, and changes in GAL3's coding region are assumed to be the result of drift. We show that replacement of GAL3's open-reading-frame with GAL1's results in an extended lag phase upon switching to growth on galactose with up to 2.5-fold differences in the initial cell masses. Accordingly, the binding affinity of Gal3 to Gal80 was found to be greater than 10-folds higher than that of Gal1, with both a higher association rate (ka) and lower dissociation (kd) rate. Thus, while changes in the noncoding, regulatory regions were the initial driving force for GAL3's subfunctionalization as a coinducer, adaptive changes in the protein sequence seem to have followed.

  11. DOC2 Proteins in rat brain: Complementary distriburion and proposed function as vesicular adapter proteins in early stages of secretion

    NARCIS (Netherlands)

    Gispen, W.H.; Verhage, M.; Vries, K.J. de; Röshol, H.; Burbach, J.P.H.; Südhof, T.C.

    1997-01-01

    DOC2 proteins constitute a novel protein family that may function in secretion and contain a double C2 domain. We have cloned and characterized two DOC2 isoforms in rat brain and studied their interactions with other proteins implicated in secretion. DOC2A was virtually brain specific, DOC2B ubiquit

  12. Development of a Cold-Adapted Pseudoalteromonas Expression System for the Pseudoalteromonas Proteins Intractable for the Escherichia coli System.

    Directory of Open Access Journals (Sweden)

    Zi-Chao Yu

    Full Text Available Although the Escherichia coli expression system is the most commonly used expression system, some proteins are still difficult to be expressed by this system, such as proteins with high thermolability and enzymes that cannot mature by autoprocessing. Therefore, it is necessary to develop alternative expression systems. In this study, a cold-adapted Pseudoalteromonas expression system was developed. A shuttle vector was constructed, and a conjugational transfer system between E. coli and psychrophilic strain Pseudoalteromonas sp. SM20429 was established. Based on the shuttle vector, three reporter vectors were constructed to compare the strength of the cloned promoters at low temperature. The promoter of xylanase gene from Pseudoalteromonas sp. BSi20429 was chosen due to its high activity at 10-15°C. An expression vector pEV containing the chosen promoter, multiple cloning sites and a His tag was constructed for protein expression and purification. With pEV as expression vector and SM20429 as the host, a cold-adapted protease, pseudoalterin, which cannot be maturely expressed in E. coli, was successfully expressed as an active extracellular enzyme when induced by 2% oat spelt xylan at 15°C for 48 h. Recombinant pseudoalterin purified from the culture by Ni affinity chromatography had identical N-terminal sequence, similar molecular mass and substrate specificity as the native pseudoalterin. In addition, another two cold-adapted enzymes were also successfully expressed by this system. Our results indicate that this cold-adapted Pseudoalteromonas expression system will provide an alternative choice for protein expression, especially for the Pseudoalteromonas proteins intractable for the E. coli system.

  13. Development of a Cold-Adapted Pseudoalteromonas Expression System for the Pseudoalteromonas Proteins Intractable for the Escherichia coli System.

    Science.gov (United States)

    Yu, Zi-Chao; Tang, Bai-Lu; Zhao, Dian-Li; Pang, Xiuhua; Qin, Qi-Long; Zhou, Bai-Cheng; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhang, Yu-Zhong

    2015-01-01

    Although the Escherichia coli expression system is the most commonly used expression system, some proteins are still difficult to be expressed by this system, such as proteins with high thermolability and enzymes that cannot mature by autoprocessing. Therefore, it is necessary to develop alternative expression systems. In this study, a cold-adapted Pseudoalteromonas expression system was developed. A shuttle vector was constructed, and a conjugational transfer system between E. coli and psychrophilic strain Pseudoalteromonas sp. SM20429 was established. Based on the shuttle vector, three reporter vectors were constructed to compare the strength of the cloned promoters at low temperature. The promoter of xylanase gene from Pseudoalteromonas sp. BSi20429 was chosen due to its high activity at 10-15°C. An expression vector pEV containing the chosen promoter, multiple cloning sites and a His tag was constructed for protein expression and purification. With pEV as expression vector and SM20429 as the host, a cold-adapted protease, pseudoalterin, which cannot be maturely expressed in E. coli, was successfully expressed as an active extracellular enzyme when induced by 2% oat spelt xylan at 15°C for 48 h. Recombinant pseudoalterin purified from the culture by Ni affinity chromatography had identical N-terminal sequence, similar molecular mass and substrate specificity as the native pseudoalterin. In addition, another two cold-adapted enzymes were also successfully expressed by this system. Our results indicate that this cold-adapted Pseudoalteromonas expression system will provide an alternative choice for protein expression, especially for the Pseudoalteromonas proteins intractable for the E. coli system. PMID:26333173

  14. The negatively charged regions of lactoferrin binding protein B, an adaptation against anti-microbial peptides.

    Directory of Open Access Journals (Sweden)

    Ari Morgenthau

    Full Text Available Lactoferrin binding protein B (LbpB is a bi-lobed membrane bound lipoprotein that is part of the lactoferrin receptor complex in a variety of Gram-negative pathogens. Despite high sequence diversity among LbpBs from various strains and species, a cluster of negatively charged amino acids is invariably present in the protein's C-terminal lobe in all species except Moraxella bovis. The function of LbpB in iron acquisition has yet to be experimentally demonstrated, whereas in vitro studies have shown that LbpB confers protection against lactoferricin, a short cationic antimicrobial peptide released from the N- terminus of lactoferrin. In this study we demonstrate that the negatively charged regions can be removed from the Neisseria meningitidis LbpB without compromising stability, and this results in the inability of LbpB to protect against the bactericidal effects of lactoferricin. The release of LbpB from the cell surface by the autotransporter NalP reduces the protection against lactoferricin in the in vitro killing assay, attributed to removal of LbpB during washing steps, but is unlikely to have a similar impact in vivo. The protective effect of the negatively charged polysaccharide capsule in the killing assay was less than the protection conferred by LbpB, suggesting that LbpB plays a major role in protection against cationic antimicrobial peptides in vivo. The selective release of LbpB by NalP has been proposed to be a mechanism for evading the adaptive immune response, by reducing the antibody binding to the cell surface, but may also provide insights into the primary function of LbpB in vivo. Although TbpB and LbpB have been shown to be major targets of the human immune response, the selective release of LbpB suggests that unlike TbpB, LbpB may not be essential for iron acquisition, but important for protection against cationic antimicrobial peptides.

  15. The negatively charged regions of lactoferrin binding protein B, an adaptation against anti-microbial peptides.

    Science.gov (United States)

    Morgenthau, Ari; Beddek, Amanda; Schryvers, Anthony B

    2014-01-01

    Lactoferrin binding protein B (LbpB) is a bi-lobed membrane bound lipoprotein that is part of the lactoferrin receptor complex in a variety of Gram-negative pathogens. Despite high sequence diversity among LbpBs from various strains and species, a cluster of negatively charged amino acids is invariably present in the protein's C-terminal lobe in all species except Moraxella bovis. The function of LbpB in iron acquisition has yet to be experimentally demonstrated, whereas in vitro studies have shown that LbpB confers protection against lactoferricin, a short cationic antimicrobial peptide released from the N- terminus of lactoferrin. In this study we demonstrate that the negatively charged regions can be removed from the Neisseria meningitidis LbpB without compromising stability, and this results in the inability of LbpB to protect against the bactericidal effects of lactoferricin. The release of LbpB from the cell surface by the autotransporter NalP reduces the protection against lactoferricin in the in vitro killing assay, attributed to removal of LbpB during washing steps, but is unlikely to have a similar impact in vivo. The protective effect of the negatively charged polysaccharide capsule in the killing assay was less than the protection conferred by LbpB, suggesting that LbpB plays a major role in protection against cationic antimicrobial peptides in vivo. The selective release of LbpB by NalP has been proposed to be a mechanism for evading the adaptive immune response, by reducing the antibody binding to the cell surface, but may also provide insights into the primary function of LbpB in vivo. Although TbpB and LbpB have been shown to be major targets of the human immune response, the selective release of LbpB suggests that unlike TbpB, LbpB may not be essential for iron acquisition, but important for protection against cationic antimicrobial peptides. PMID:24465982

  16. Plant natriuretic peptides induce proteins diagnostic for an adaptive response to stress

    KAUST Repository

    Turek, Ilona

    2014-11-26

    In plants, structural and physiological evidence has suggested the presence of biologically active natriuretic peptides (PNPs). PNPs are secreted into the apoplast, are systemically mobile and elicit a range of responses signaling via cGMP. The PNP-dependent responses include tissue specific modifications of cation transport and changes in stomatal conductance and the photosynthetic rate. PNP also has a critical role in host defense responses. Surprisingly, PNP-homologs are produced by several plant pathogens during host colonization suppressing host defense responses. Here we show that a synthetic peptide representing the biologically active fragment of the Arabidopsis thaliana PNP (AtPNP-A) induces the production of reactive oxygen species in suspension-cultured A. thaliana (Col-0) cells. To identify proteins whose expression changes in an AtPNP-A dependent manner, we undertook a quantitative proteomic approach, employing tandem mass tag (TMT) labeling, to reveal temporal responses of suspension-cultured cells to 1 nM and 10 pM PNP at two different time-points post-treatment. Both concentrations yield a distinct differential proteome signature. Since only the higher (1 nM) concentration induces a ROS response, we conclude that the proteome response at the lower concentration reflects a ROS independent response. Furthermore, treatment with 1 nM PNP results in an over-representation of the gene ontology (GO) terms “oxidation-reduction process,” “translation” and “response to salt stress” and this is consistent with a role of AtPNP-A in the adaptation to environmental stress conditions.

  17. Circadian clock proteins control adaptation to novel environment and memory formation

    Science.gov (United States)

    A.Kondratova, Anna; V.Dubrovsky, Yuliya; Antoch, Marina P.; Kondratov, Roman V.

    2010-01-01

    Deficiency of the transcription factor BMAL1, a core component of the circadian clock, results in an accelerated aging phenotype in mice. The circadian clock regulates many physiological processes and was recently implicated in control of brain-based activities, such as memory formation and the regulation of emotions. Aging is accompanied by the decline in brain physiology, particularly decline in the response and adaptation to novelty. We investigated the role of the circadian clock in exploratory behavior and habituation to novelty using the open field paradigm. We found that mice with a deficiency of the circadian transcription factor BMAL1 display hyperactivity in novel environments and impaired intra- and intersession habituation, indicative of defects in short- and long-term memory formation. In contrast, mice double-deficient for the circadian proteins CRY1 and CRY2 (repressors of the BMAL1-mediated transcription) demonstrate reduced activity and accelerated habituation when compared to wild type mice. Mice with mutation in theClock gene (encoding the BMAL1 transcription partner) show normal locomotion, but increased rearing activity and impaired intersession habituation. BMAL1 is highly expressed in the neurons of the hippocampus - a brain region associated with spatial memory formation; BMAL1 deficiency disrupts circadian oscillation in gene expression and reactive oxygen species homeostasis in the brain, which may be among the possible mechanisms involved. Thus, we suggest that the BMAL1:CLOCK activity is critical for the proper exploratory and habituation behavior, and that the circadian clock prepares organism for a new round of everyday activities through optimization of behavioral learning. PMID:20519775

  18. Plant Natriuretic Peptides induce proteins diagnostic for an adaptive response to stress

    Directory of Open Access Journals (Sweden)

    Ilona eTurek

    2014-11-01

    Full Text Available In plants, structural and physiological evidence has suggested the presence of biologically active natriuretic peptides (PNPs. PNPs are secreted into the apoplast, are systemically mobile and elicit a range of responses signaling via cGMP. The PNP-dependent responses include tissue specific modifications of cation transport and changes in stomatal conductance and the photosynthetic rate. PNP also has a critical role in host defense responses. Surprisingly, PNP-homologues are produced by several plant pathogens during host colonization suppressing host defense responses. Here we show that a synthetic peptide representing the biologically active fragment of the Arabidopsis thaliana PNP (AtPNP-A induces the production of reactive oxygen species in suspension-cultured A. thaliana (Col-0 cells. To identify proteins whose expression changes in an AtPNP-A dependent manner, we undertook a quantitative proteomic approach, employing tandem mass tag (TMT labeling, to reveal temporal responses of suspension-cultured cells to 1 nM and 10 pM PNP at two different time-points post-treatment. Both concentrations yield a distinct differential proteome signature. Since only the higher (1 nM concentration induces a ROS response, we conclude that the proteome response at the lower concentration reflects a ROS independent response. Furthermore, treatment with 1 nM PNP results in an over-representation of the gene ontology (GO terms oxidation-reduction process, translation and response to salt stress and this is consistent with a role of AtPNP-A in the adaptation to environmental stress conditions.

  19. Cardiac hypertrophy and failure--a disease of adaptation. Modifications in membrane proteins provide a molecular basis for arrhythmogenicity.

    Science.gov (United States)

    Moalic, J M; Charlemagne, D; Mansier, P; Chevalier, B; Swynghedauw, B

    1993-05-01

    Cardiac hypertrophy is the physiological adaptation of the heart to chronic mechanical overload. Cardiac failure indicates the limits of the process. Cardiac hypertrophy is only one example of biological adaptation and results from the induction of several changes in gene expression, mostly of the fetal type, including those coding for the myosin heavy chain or the alpha-subunit of the Na+,K(+)-ATPase. From a thermodynamic point of view, the decrease in Vmax allows the heart to produce a normal tension at a lower cost. This process results from changes both in the sarcomere and in the expression of certain membrane proteins. The decrease in calcium transient is determined by several changes in membrane proteins that result in a rather fragile equilibrium in terms of calcium homeostasis. Any abnormal input in calcium will have exaggerated detrimental consequences on a hypertrophied myocyte and may cause automaticity and arrhythmias or an exaggerated response to anoxia in terms of compliance. PMID:8485830

  20. Model-based adaptive control of acetate concentration during the production of recombinant proteins with E. coli

    OpenAIRE

    Rocha, I; Ferreira, E. C.

    2003-01-01

    A model-based adaptive linearizing control law was derived for the regulation of the acetate concentration during the fed-batch fermentation of recombinant proteins with high cell density culture of Escherichia coli growing on glucose. An unstructured model for the growth was applied to the major metabolic pathways: oxidative growth on glucose, fermentative growth on glucose, oxidative growth on acetate, and maintenance. A model order reduction method was used to allow the d...

  1. Gab1 Acts as an Adapter Molecule Linking the Cytokine Receptor gp130 to ERK Mitogen-Activated Protein Kinase

    OpenAIRE

    Takahashi-Tezuka, Mariko; Yoshida, Yuichi; Fukada, Toshiyuki; Ohtani, Takuya; Yamanaka, Yojiro; Nishida, Keigo; NAKAJIMA, Koichi; Hibi, Masahiko; Hirano, Toshio

    1998-01-01

    Gab1 has structural similarities with Drosophila DOS (daughter of sevenless), which is a substrate of the protein tyrosine phosphatase Corkscrew. Both Gab1 and DOS have a pleckstrin homology domain and tyrosine residues, potential binding sites for various SH2 domain-containing adapter molecules when they are phosphorylated. We found that Gab1 was tyrosine phosphorylated in response to various cytokines, such as interleukin-6 (IL-6), IL-3, alpha interferon (IFN-α), and IFN-γ. Upon the stimula...

  2. Application of heat shock protein expression for detecting natural adaptation and exposure to stress in natural populations

    Directory of Open Access Journals (Sweden)

    Jesper Givskov SØRENSEN

    2010-12-01

    Full Text Available Heat-shock proteins (HSPs play an undisputed role for maintaining cellular functioning under environmental challenges and protein denaturing conditions. Compelling evidence points to an evolutionary important role of HSPs and a strict evolutionary control of these proteins as a balance between benefits and costs. While there is a great potential for using HSP expression for detecting natural adaptation and exposure to stress in natural populations, some obstacles and key issues await investigation. From an ecological perspective these key issues needs to be resolved in order to fully appreciate the complex responses and adaptations to stress and to increase our understanding of HSPs and other molecular chaperones for stress adaptation and potential use as biomarkers. Here, the current knowledge and understanding of HSPs is reviewed and a number of key issues including the interpretation of elevated HSP levels, the complications of extrapolating between laboratory and field conditions, the effects of choice of traits and methodology and the larger intra-and extracellular networks of interactions that HSPs participate in are discussed [Current Zoology 56 (6: 703–713, 2010].

  3. PSB27: A thylakoid protein enabling Arabidopsis to adapt to changing light intensity

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Xin [Univ. of California, Berkeley, CA (United States). Dept of Plant and Microbial Biology; Garcia, Veder J. [Univ. of California, Berkeley, CA (United States). Dept of Plant and Microbial Biology; Buchanan, Bob B. [Univ. of California, Berkeley, CA (United States). Dept of Plant and Microbial Biology; Luan, Sheng [Univ. of California, Berkeley, CA (United States). Dept of Plant and Microbial Biology

    2016-08-22

    complex that might be PSII supercomplex. Under objective 2, we have found that FKBP16-2 interacted with PSB27 that was further pursuited and published a research article in PNAS (attached). Under Objective 3, we have identified several mutants of other FKBPs in the thyalkoid lumen that should be further studied if future funding is available. Under Objective 4, we have started to build a network of lumenal proteins that play a number of roles in photosynthesis. For example, the CYP37 and CYP28 are linked to chloroplast signaling to nucleus, critical for controlling plant response to high light and adaptation to climate change. Unfortunately these studies have been terminated due to funding shortage.

  4. Lysine63-linked ubiquitylation of PIN2 auxin carrier protein governs hormonally controlled adaptation of Arabidopsis root growth.

    Science.gov (United States)

    Leitner, Johannes; Petrášek, Jan; Tomanov, Konstantin; Retzer, Katarzyna; Pařezová, Markéta; Korbei, Barbara; Bachmair, Andreas; Zažímalová, Eva; Luschnig, Christian

    2012-05-22

    Cross-talk between plant cells and their surroundings requires tight regulation of information exchange at the plasma membrane (PM), which involves dynamic adjustments of PM protein localization and turnover to modulate signal perception and solute transport at the interface between cells and their surroundings. In animals and fungi, turnover of PM proteins is controlled by reversible ubiquitylation, which signals endocytosis and delivery to the cell's lytic compartment, and there is emerging evidence for related mechanisms in plants. Here, we describe the fate of Arabidopsis PIN2 protein, required for directional cellular efflux of the phytohormone auxin, and identify cis- and trans-acting mediators of PIN2 ubiquitylation. We demonstrate that ubiquitin acts as a principal signal for PM protein endocytosis in plants and reveal dynamic adjustments in PIN2 ubiquitylation coinciding with variations in vacuolar targeting and proteolytic turnover. We show that control of PIN2 proteolytic turnover via its ubiquitylation status is of significant importance for auxin distribution in root meristems and for environmentally controlled adaptations of root growth. Moreover, we provide experimental evidence indicating that PIN2 vacuolar sorting depends on modification specifically by lysine(63)-linked ubiquitin chains. Collectively, our results establish lysine(63)-linked PM cargo ubiquitylation as a regulator of polar auxin transport and adaptive growth responses in higher plants.

  5. Exercise, skeletal muscle and inflammation: ARE-binding proteins as key regulators in inflammatory and adaptive networks.

    Science.gov (United States)

    Beiter, Thomas; Hoene, Miriam; Prenzler, Frauke; Mooren, Frank C; Steinacker, Jürgen M; Weigert, Cora; Nieß, Andreas M; Munz, Barbara

    2015-01-01

    The role of inflammation in skeletal muscle adaptation to exercise is complex and has hardly been elucidated so far. While the acute inflammatory response to exercise seems to promote skeletal muscle training adaptation and regeneration, persistent, low-grade inflammation, as seen in a multitude of chronic diseases, is obviously detrimental. The regulation of cytokine production in skeletal muscle cells has been relatively well studied, yet little is known about the compensatory and anti-inflammatory mechanisms that resolve inflammation and restore tissue homeostasis. One important strategy to ensure sequential, timely and controlled resolution of inflammation relies on the regulated stability of mRNAs encoding pro-inflammatory mediators. Many key transcripts in early immune responses are characterized by the presence of AU-rich elements (AREs) in the 3'-untranslated regions of their mRNAs, allowing efficient fine-tuning of gene expression patterns at the post-transcriptional level. AREs exert their function by recruiting particular RNA-binding proteins, resulting, in most cases, in de-stabilization of the target transcripts. The best-characterized ARE-binding proteins are HuR, CUGBP1, KSRP, AUF1, and the three ZFP36 proteins, especially TTP/ZFP36. Here, we give a general introduction into the role of inflammation in the adaptation of skeletal muscle to exercise. Subsequently, we focus on potential roles of ARE-binding proteins in skeletal muscle tissue in general and specifically exercise-induced skeletal muscle remodeling. Finally, we present novel data suggesting a specific function of TTP/ZFP36 in exercise-induced skeletal muscle plasticity.

  6. Characterization of promoter region and genomic structure of the murine and human genes encoding Src like adapter protein.

    Science.gov (United States)

    Kratchmarova, I; Sosinowski, T; Weiss, A; Witter, K; Vincenz, C; Pandey, A

    2001-01-10

    Src-like adapter protein (SLAP) was identified as a signaling molecule in a yeast two-hybrid system using the cytoplasmic domain of EphA2, a receptor protein tyrosine kinase (Pandey et al., 1995. Characterization of a novel Src-like adapter protein that associates with the Eck receptor tyrosine kinase. J. Biol. Chem. 270, 19201-19204). It is very similar to members of the Src family of cytoplasmic tyrosine kinases in that it contains very homologous SH3 and SH2 domains (Abram and Courtneidge, 2000. Src family tyrosine kinases and growth factor signaling. Exp. Cell. Res. 254, 1-13.). However, instead of a kinase domain at the C-terminus, it contains a unique C-terminal region. In order to exclude the possibility that an alternative form exists, we have isolated genomic clones containing the murine Slap gene as well as the human SLA gene. The coding regions of murine Slap and human SLA genes contain seven exons and six introns. Absence of any kinase domain in the genomic region confirm its designation as an adapter protein. Additionally, we have cloned and sequenced approximately 2.6 kb of the region 5' to the initiator methionine of the murine Slap gene. When subcloned upstream of a luciferase gene, this fragment increased the transcriptional activity about 6-fold in a human Jurkat T cell line and approximately 52-fold in a murine T cell line indicating that this region contains promoter elements that dictate SLAP expression. We have also cloned the promoter region of the human SLA gene. Since SLAP is transcriptionally regulated by retinoic acid and by activation of B cells, the cloning of its promoter region will permit a detailed analysis of the elements required for its transcriptional regulation.

  7. Degradation of Human PDZ-Proteins by Human Alphapapillomaviruses Represents an Evolutionary Adaptation to a Novel Cellular Niche

    Science.gov (United States)

    Van Doorslaer, Koenraad; DeSalle, Rob; Einstein, Mark H.; Burk, Robert D.

    2015-01-01

    In order to complete their life cycle, papillomaviruses have evolved to manipulate a plethora of cellular pathways. The products of the human Alphapapillomavirus E6 proteins specifically interact with and target PDZ containing proteins for degradation. This viral phenotype has been suggested to play a role in viral oncogenesis. To analyze the association of HPV E6 mediated PDZ-protein degradation with cervical oncogenesis, a high-throughput cell culture assay was developed. Degradation of an epitope tagged human MAGI1 isoform was visualized by immunoblot. The correlation between HPV E6-induced degradation of hMAGI1 and epidemiologically determined HPV oncogenicity was evaluated using a Bayesian approach within a phylogenetic context. All tested oncogenic types degraded the PDZ-containing protein hMAGI1d; however, E6 proteins isolated from several related albeit non-oncogenic viral types were equally efficient at degrading hMAGI1. The relationship between both traits (oncogenicity and PDZ degradation potential) is best explained by a model in which the potential to degrade PDZ proteins was acquired prior to the oncogenic phenotype. This analysis provides evidence that the ancestor of both oncogenic and non-oncogenic HPVs acquired the potential to degrade human PDZ-containing proteins. This suggests that HPV E6 directed degradation of PDZ-proteins represents an ancient ecological niche adaptation. Phylogenetic modeling indicates that this phenotype is not specifically correlated with oncogenic risk, but may act as an enabling phenotype. The role of PDZ protein degradation in HPV fitness and oncogenesis needs to be interpreted in the context of Alphapapillomavirus evolution. PMID:26086730

  8. Degradation of Human PDZ-Proteins by Human Alphapapillomaviruses Represents an Evolutionary Adaptation to a Novel Cellular Niche.

    Directory of Open Access Journals (Sweden)

    Koenraad Van Doorslaer

    2015-06-01

    Full Text Available In order to complete their life cycle, papillomaviruses have evolved to manipulate a plethora of cellular pathways. The products of the human Alphapapillomavirus E6 proteins specifically interact with and target PDZ containing proteins for degradation. This viral phenotype has been suggested to play a role in viral oncogenesis. To analyze the association of HPV E6 mediated PDZ-protein degradation with cervical oncogenesis, a high-throughput cell culture assay was developed. Degradation of an epitope tagged human MAGI1 isoform was visualized by immunoblot. The correlation between HPV E6-induced degradation of hMAGI1 and epidemiologically determined HPV oncogenicity was evaluated using a Bayesian approach within a phylogenetic context. All tested oncogenic types degraded the PDZ-containing protein hMAGI1d; however, E6 proteins isolated from several related albeit non-oncogenic viral types were equally efficient at degrading hMAGI1. The relationship between both traits (oncogenicity and PDZ degradation potential is best explained by a model in which the potential to degrade PDZ proteins was acquired prior to the oncogenic phenotype. This analysis provides evidence that the ancestor of both oncogenic and non-oncogenic HPVs acquired the potential to degrade human PDZ-containing proteins. This suggests that HPV E6 directed degradation of PDZ-proteins represents an ancient ecological niche adaptation. Phylogenetic modeling indicates that this phenotype is not specifically correlated with oncogenic risk, but may act as an enabling phenotype. The role of PDZ protein degradation in HPV fitness and oncogenesis needs to be interpreted in the context of Alphapapillomavirus evolution.

  9. A Reevaluation of the Role of the Unfolded Protein Response in Islet Dysfunction: Maladaptation or a Failure to Adapt?

    Science.gov (United States)

    Herbert, Terence P; Laybutt, D Ross

    2016-06-01

    Endoplasmic reticulum (ER) stress caused by perturbations in ER homeostasis activates an adaptive response termed the unfolded protein response (UPR) whose function is to resolve ER stress. If unsuccessful, the UPR initiates a proapoptotic program to eliminate the malfunctioning cells from the organism. It is the activation of this proapoptotic UPR in pancreatic β-cells that has been implicated in the onset of type 2 diabetes and thus, in this context, is considered a maladaptive response. However, there is growing evidence that β-cell death in type 2 diabetes may not be caused by a maladaptive UPR but by the inhibition of the adaptive UPR. In this review, we discuss the evidence for a role of the UPR in β-cell dysfunction and death in the development of type 2 diabetes and ask the following question: Is β-cell dysfunction the result of a maladaptive UPR or a failure of the UPR to adequately adapt? The answer to this question is critically important in defining potential therapeutic strategies for the treatment and prevention of type 2 diabetes. In addition, we discuss the potential role of the adaptive UPR in staving off type 2 diabetes by enhancing β-cell mass and function in response to insulin resistance. PMID:27222391

  10. Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test

    OpenAIRE

    Berlin Sofia; Smith Nick GC

    2005-01-01

    Abstract Background Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive ...

  11. Disruption of the acyl-coa binding protein gene delays hepatic adaptation to metabolic changes at weaning

    DEFF Research Database (Denmark)

    Neess, Ditte; Bloksgaard, Maria; Sørensen, Signe Bek;

    2011-01-01

    , little is known about the in vivo function in mammalian cells. We have generated mice with targeted disruption of ACBP (ACBP-/-). These mice are viable and fertile and develop normally. However, around weaning the ACBP-/- mice go through a crisis with overall weakness, and a slightly decreased growth...... rate. Using microarray analysis we show that the liver of ACBP-/- mice display a significantly delayed adaptation to weaning with late induction of target genes of the sterol regulatory element binding protein (SREBP) family. As a result, hepatic de novo cholesterogenesis is decreased at weaning....... The delayed induction of SREBP target genes around weaning is caused by a compromised processing and decreased expression of SREBP precursors leading to reduced binding of SREBP to target sites in chromatin. In conclusion, lack of ACBP interferes with the normal metabolic adaptation to weaning and leads...

  12. The adaptive immune response to cow's milk proteins in allergy and tolerance

    NARCIS (Netherlands)

    Ruiter, B.

    2007-01-01

    Cow's milk (CM) and related products are an important source of protein in the diet. Unfortunately, cow's milk proteins (CMPs) can also be allergenic. IgE-mediated cow's milk allergy (CMA) occurs in 1.5% of infants, as well as in 0.3% of older children and adults. Insight into the immune response to

  13. The mechanistic basis of hemoglobin adaptation in the high-flying barheaded goose: insights from ancestral protein resurrection

    DEFF Research Database (Denmark)

    Natarajan, Chandrasekhar; Kumar, Amit; Moriyama, Hideaki;

    2016-01-01

    ’ comparisons – swapping residues between proteins of contemporary species – is that the focal mutations are introduced into a sequence context that may not be evolutionarily relevant. If mutations have context-dependent effects, then introducing BHG-specific substitutions into human Hb may not recapitulate...... questions about molecular adaptation: (1) Do each of the substitutions contribute to the increased Hb-O2 affinity? If so, what are their relative effects? (2) Does the sequential order in which they occur make a difference? In other words, do the functional effects of mutations depend on which other...

  14. The adaptive response of human lymphocytes to very low doses of ionizing radiation: a case of induced chromosomal repair with the induction of specific proteins

    International Nuclear Information System (INIS)

    It appears that the adaptive response of human lymphocytes to low doses of X-rays can be mimicked by exposure to low levels of a truly radiomimetic compound, bleomycin, that induces double-strand breaks in DNA. Similarly, the adaptive response can be induced by exposure to low levels of H2O2, which produces reactive species similar to those induced by ionizing radiation. This adaptive response, which is attributed to the induction of a repair mechanism, i.e. repair enzymes, can be prevented if protein synthesis, and thus enzyme synthesis, is inhibited by cycloheximide at the crucial time (4-6 h) after exposure to the adaptive dose. Two-dimensional gel electrophoresis has shown that 1 cGy of X-rays can reproducibly induce several proteins not found in unirradiated lymphocytes. These proteins are considered to be excellent candidates for the actual repair enzyme(s). (author)

  15. Symmetry Breaking and Adaptation The Genetic Code of Retroviral Env Proteins

    CERN Document Server

    Vera, S

    1996-01-01

    Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of the synonym symmetry by mutation and recombination. We conjecture that this enhances the probability to produce mutants that are well-adapted to the current environment. Evidence is found in the codon frequencies of the HIV resistant to the current immunological attack, are found with a greater frequency than their less mutable synonyms.

  16. Role of hypothalamic melanocortin system in adaptation of food intake to food protein increase in mice.

    OpenAIRE

    Pillot, Bruno; Duraffourd, Céline; Bégeot, Martine; Joly, Aurélie; Luquet, Serge; Houberdon, Isabelle; Naville, Danielle; Vigier, Michèle; Gautier-Stein, Amandine; Magnan, Christophe; Mithieux, Gilles

    2011-01-01

    The hypothalamic melanocortin system--the melanocortin receptor of type 4 (MC4R) and its ligands: α-melanin-stimulating hormone (α-MSH, agonist, inducing hypophagia), and agouti-related protein (AgRP, antagonist, inducing hyperphagia)--is considered to play a central role in the control of food intake. We tested its implication in the mediation of the hunger-curbing effects of protein-enriched diets (PED) in mice. Whereas there was a 20% decrease in food intake in mice fed on the PED, compare...

  17. The Role of the NHERF-1 and NHERF-2 Adapter Proteins in Intestinal Ion Transport Regulation

    NARCIS (Netherlands)

    N. Broere (Nellie)

    2008-01-01

    textabstractThe chloride channel CFTR (cystic fibrosis transmembrane conductance regulator) and the sodium/proton exchanger NHE3 are key proteins involved in transepithelial ion and water transport in several epithelial tissues, including the intestine. In this thesis we mainly focus on the role of

  18. Genome adaptations of a tripartite motif protein for retroviral defense in cattle and sheep

    Science.gov (United States)

    Tripartite motif (TRIM) genes encode proteins composed of RING, B-box, and coiled coil motif domains. Primate TRIM5' has been shown to be a primary determinant of retroviral host cell range restriction in primates. TRIM5 restriction was originally thought to be a primate-specific defense mechanism...

  19. Proteins modulation in human skeletal muscle in the early phase of adaptation to hypobaric hypoxia

    DEFF Research Database (Denmark)

    Vigano, A.; Ripamonti, M.; Palma, S. De;

    2008-01-01

    investigated, pre- and post-exposure, in ten young subjects, by 2-D DIGE and MS. Ten milligram biopsies were obtained from the mid part of the vastus lateralis muscle at sea level (control) and at altitude, after 7-9 days hypoxia. Differential analysis indicates that proteins involved in iron transport...

  20. Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap

    OpenAIRE

    Gaupels, Frank; Buhtz, Anja; Knauer, Torsten; Deshmukh, Sachin; Waller, Frank; van Bel, Aart J. E.; Kogel, Karl-Heinz; Kehr, Julia

    2008-01-01

    Sieve tubes are transport conduits not only for photoassimilates but also for macromolecules and other compounds that are involved in sieve tube maintenance and systemic signalling. In order to gain sufficient amounts of pure phloem exudates from barley plants for analyses of the protein and mRNA composition, a previously described stylectomy set-up was optimized. Aphids were placed in sealed cages, which, immediately after microcauterization of the stylets, were flooded with water-saturated ...

  1. Adaptive hydrophobic and hydrophilic interactions of mussel foot proteins with organic thin films

    OpenAIRE

    Yu, J; Kan, Y.; M. Rapp; Danner, E; Wei, W.; Das, S.; Miller, DR; Chen, Y.; Waite, JH; Israelachvili, JN

    2013-01-01

    The adhesion of mussel foot proteins (Mfps) to a variety of specially engineered mineral and metal oxide surfaces has previously been investigated extensively, but the relevance of these studies to adhesion in biological environments remains unknown. Most solid surfaces exposed to seawater or physiological fluids become fouled by organic conditioning films and biofilms within minutes. Understanding the binding mechanisms of Mfps to organic films with known chemical and physical properties the...

  2. COMPARISON OF STRESS PROTEINS PARTICIPATION IN ADAPTATION MECHANISMS OF BAIKALIAN AND PALEARCTIC AMPHIPOD (AMPHIPODA; CRUSTACEA) SPECIES

    OpenAIRE

    Timofeyev M.A; Shatilina Zh.M.; Bedulina D.S.; Protopopova M.V.; Grabelnych O.I.; Pobezhimova T.P.; Kolesnichenko A.V.

    2006-01-01

    The aim of the present study was a study of the influence different stressful factor on syntheses and activity of the stress proteins (HSP70, sHSP and peroxidase) of freshwater organism. Six freshwater amphipod species were investigated: Eulimnogammarus cyaneus (Dyb.), E verrucosus (Gerstf.), E vittatus (Dyb.) - endemic species from Lake Baikal which were compared with Palearctic species - Gammarus lacustris Sars., G tigrinus (Sexton), Chaetogammarus ischnus (Stebbins). It was shown expressio...

  3. Morphological adaptation and protein modulation of myotendinous junction following moderate aerobic training.

    Science.gov (United States)

    Curzi, Davide; Baldassarri, Valentina; De Matteis, Rita; Salamanna, Francesca; Bolotta, Alessandra; Frizziero, Antonio; Fini, Milena; Marini, Marina; Falcieri, Elisabetta

    2015-04-01

    Myotendinous junction is the muscle-tendon interface through which the contractile force can be transferred from myofibrils to the tendon extracellular matrix. At the ultrastructural level, aerobic training can modify the distal myotendinous junction of rat gastrocnemius, increasing the contact area between tissues. The aim of this work is to investigate the correlation between morphological changes and protein modulation of the myotendinous junction following moderate training. For this reason, talin, vinculin and type IV collagen amount and spatial distribution were investigated by immunohistochemistry and confocal microscopy. The images were then digitally analyzed by evaluating fluorescence intensity. Morphometric analysis revealed a significant increased thickening of muscle basal lamina in the trained group (53.1 ± 0.4 nm) with respect to the control group (43.9 ± 0.3 nm), and morphological observation showed the presence of an electron-dense area in the exercised muscles, close to the myotendinous junction. Protein concentrations appeared significantly increased in the trained group (talin +22.2%; vinculin +22.8% and type IV collagen +11.8%) with respect to the control group. Therefore, our findings suggest that moderate aerobic training induces/causes morphological changes at the myotendinous junction, correlated to the synthesis of structural proteins of the muscular basal lamina and of the cytoskeleton.

  4. Characterization of an adapter subunit to a phosphatidylinositol (3)P 3-phosphatase: Identification of a myotubularin-related protein lacking catalytic activity

    OpenAIRE

    Nandurkar, H. H.; Caldwell, K K; Whisstock, J C; Layton, M. J.; Gaudet, E. A.; Norris, F. A.; Majerus, P W; Mitchell, C. A.

    2001-01-01

    The D3-phosphoinositides act as second messengers by recruiting, and thereby activating, diverse signaling proteins. We have previously described the purification of a rat phosphatidylinositol 3-phosphate [PtdIns(3)P] 3-phosphatase, comprising a heterodimer of a 78-kDa adapter subunit in complex with a 65-kDa catalytic subunit. Here, we have cloned and characterized the cDNA encoding the human 3-phosphatase adapter subunit (3-PAP). Sequence alignment showed that 3-PAP ...

  5. Human resting extracellular heat shock protein 72 concentration decreases during the initial adaptation to exercise in a hot, humid environment

    Science.gov (United States)

    Marshall, Helen C.; Ferguson, Richard A.; Nimmo, Myra A.

    2006-01-01

    Heat shock protein (Hsp) 72 is a cytosolic protein that also is present in the circulation. Extracellular Hsp72 (eHsp72) is inducible by exercise and is suggested to act as a danger signal to the immune system. The adaptive response of eHsp72 to repeated exercise-heat exposures in humans remains to be determined. An intracellular animal study found a reduced Hsp72 response, with no change in resting levels, during heat stress after a single day of passive heat acclimation. The current study therefore tested whether adaptations in human eHsp72 levels would similarly occur 24 hours after a single exercise-heat exposure. Seven males completed cycle exercise (42.5% V̇O2peak for 2 hours) in a hot, humid environment (38°C, 60% relative humidity) on each of 2 consecutive days. Blood samples were obtained from an antecubital vein before exercise and 0 hours and 22 hours postexercise for the analysis of eHsp72. Exercise-heat stress resulted in enhanced eHsp72, with a similar absolute increase found on both days (day 1: 1.26 ng/mL [0.80 ng/mL]; day 2: 1.29 ng/mL [1.60 ng/mL]). Resting eHsp72 decreased from rest on day 1 to day 2's 22-hour postexercise sample (P < 0.05). It is suggested that the reduction in resting eHsp72 after 2 consecutive exercise-heat exposures is possibly due to an enhanced removal from the circulation, for either immunoregulatory functions, or for improved cellular stress tolerance in this initial, most stressful period of acclimation. PMID:16817318

  6. Adaptation of Clostridium difficile toxin A for use as a protein translocation system

    International Nuclear Information System (INIS)

    Research highlights: → Catalytic domain of TcdA was replaced by a luciferase reporter. → Each functional domain retains activity in the context of the fusion protein. → We provide evidence that reporter proteins are delivered into vero cells. → System releases cargo into the cytosol, providing a powerful new biotechnology tool. -- Abstract: A cellular delivery system is a useful biotechnology tool, with many possible applications. Two derivatives of Clostridium difficile toxin A (TcdA) have been constructed (GFP-TcdA and Luc-TcdA), by fusing reporter genes to functional domains of TcdA, and evaluated for their ability to translocate their cargo into mammalian cells. The cysteine protease and receptor binding domains of TcdA have been examined and found to be functional when expressed in the chimeric construct. Whereas GFP failed to internalize in the context of the TcdA fusion, significant cellular luciferase activity was detected in vero cell lysates after treatment with Luc-TcdA. Treatment with bafilomycin A1, which inhibits endosomal acidification, traps the luciferase activity within endosomes. To further understand these results, clarified lysates were subjected to molecular weight sieving, demonstrating that active luciferase was released from Luc-TcdA after translocation and internal processing.

  7. Adaptation of Clostridium difficile toxin A for use as a protein translocation system

    Energy Technology Data Exchange (ETDEWEB)

    Kern, Stephanie M. [Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (United States); Feig, Andrew L., E-mail: afeig@chem.wayne.edu [Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI 48202 (United States)

    2011-02-25

    Research highlights: {yields} Catalytic domain of TcdA was replaced by a luciferase reporter. {yields} Each functional domain retains activity in the context of the fusion protein. {yields} We provide evidence that reporter proteins are delivered into vero cells. {yields} System releases cargo into the cytosol, providing a powerful new biotechnology tool. -- Abstract: A cellular delivery system is a useful biotechnology tool, with many possible applications. Two derivatives of Clostridium difficile toxin A (TcdA) have been constructed (GFP-TcdA and Luc-TcdA), by fusing reporter genes to functional domains of TcdA, and evaluated for their ability to translocate their cargo into mammalian cells. The cysteine protease and receptor binding domains of TcdA have been examined and found to be functional when expressed in the chimeric construct. Whereas GFP failed to internalize in the context of the TcdA fusion, significant cellular luciferase activity was detected in vero cell lysates after treatment with Luc-TcdA. Treatment with bafilomycin A1, which inhibits endosomal acidification, traps the luciferase activity within endosomes. To further understand these results, clarified lysates were subjected to molecular weight sieving, demonstrating that active luciferase was released from Luc-TcdA after translocation and internal processing.

  8. Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein.

    Directory of Open Access Journals (Sweden)

    Lia Rosso

    2008-06-01

    Full Text Available Gene duplication was prevalent during hominoid evolution, yet little is known about the functional fate of new ape gene copies. We characterized the CDC14B cell cycle gene and the functional evolution of its hominoid-specific daughter gene, CDC14Bretro. We found that CDC14B encodes four different splice isoforms that show different subcellular localizations (nucleus or microtubule-associated and functional properties. A microtubular CDC14B variant spawned CDC14Bretro through retroposition in the hominoid ancestor 18-25 million years ago (Mya. CDC14Bretro evolved brain-/testis-specific expression after the duplication event and experienced a short period of intense positive selection in the African ape ancestor 7-12 Mya. Using resurrected ancestral protein variants, we demonstrate that by virtue of amino acid substitutions in distinct protein regions during this time, the subcellular localization of CDC14Bretro progressively shifted from the association with microtubules (stabilizing them to an association with the endoplasmic reticulum. CDC14Bretro evolution represents a paradigm example of rapid, selectively driven subcellular relocalization, thus revealing a novel mode for the emergence of new gene function.

  9. Role of hypothalamic melanocortin system in adaptation of food intake to food protein increase in mice.

    Directory of Open Access Journals (Sweden)

    Bruno Pillot

    Full Text Available The hypothalamic melanocortin system--the melanocortin receptor of type 4 (MC4R and its ligands: α-melanin-stimulating hormone (α-MSH, agonist, inducing hypophagia, and agouti-related protein (AgRP, antagonist, inducing hyperphagia--is considered to play a central role in the control of food intake. We tested its implication in the mediation of the hunger-curbing effects of protein-enriched diets (PED in mice. Whereas there was a 20% decrease in food intake in mice fed on the PED, compared to mice fed on an isocaloric starch-enriched diet, there was a paradoxical decrease in expression of the hypothalamic proopiomelanocortin gene, precursor of α-MSH, and increase in expression of the gene encoding AgRP. The hypophagia effect of PED took place in mice with invalidation of either MC4R or POMC, and was even strengthened in mice with ablation of the AgRP-expressing neurons. These data strongly suggest that the hypothalamic melanocortin system does not mediate the hunger-curbing effects induced by changes in the macronutrient composition of food. Rather, the role of this system might be to defend the body against the variations in food intake generated by the nutritional environment.

  10. Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools.

    Science.gov (United States)

    Koo, Hyunmin; Hakim, Joseph A; Fisher, Phillip R E; Grueneberg, Alexander; Andersen, Dale T; Bej, Asim K

    2016-01-01

    In this study, we report the distribution and abundance of cold-adaptation proteins in microbial mat communities in the perennially ice-covered Lake Joyce, located in the McMurdo Dry Valleys, Antarctica. We have used MG-RAST and R code bioinformatics tools on Illumina HiSeq2000 shotgun metagenomic data and compared the filtering efficacy of these two methods on cold-adaptation proteins. Overall, the abundance of cold-shock DEAD-box protein A (CSDA), antifreeze proteins (AFPs), fatty acid desaturase (FAD), trehalose synthase (TS), and cold-shock family of proteins (CSPs) were present in all mat samples at high, moderate, or low levels, whereas the ice nucleation protein (INP) was present only in the ice and bulbous mat samples at insignificant levels. Considering the near homogeneous temperature profile of Lake Joyce (0.08-0.29 °C), the distribution and abundance of these proteins across various mat samples predictively correlated with known functional attributes necessary for microbial communities to thrive in this ecosystem. The comparison of the MG-RAST and the R code methods showed dissimilar occurrences of the cold-adaptation protein sequences, though with insignificant ANOSIM (R = 0.357; p-value = 0.012), ADONIS (R(2) = 0.274; p-value = 0.03) and STAMP (p-values = 0.521-0.984) statistical analyses. Furthermore, filtering targeted sequences using the R code accounted for taxonomic groups by avoiding sequence redundancies, whereas the MG-RAST provided total counts resulting in a higher sequence output. The results from this study revealed for the first time the distribution of cold-adaptation proteins in six different types of microbial mats in Lake Joyce, while suggesting a simpler and more manageable user-defined method of R code, as compared to a web-based MG-RAST pipeline. PMID:26578243

  11. COMPARISON OF STRESS PROTEINS PARTICIPATION IN ADAPTATION MECHANISMS OF BAIKALIAN AND PALEARCTIC AMPHIPOD (AMPHIPODA; CRUSTACEA SPECIES

    Directory of Open Access Journals (Sweden)

    Timofeyev M.A

    2006-03-01

    Full Text Available The aim of the present study was a study of the influence different stressful factor on syntheses and activity of the stress proteins (HSP70, sHSP and peroxidase of freshwater organism. Six freshwater amphipod species were investigated: Eulimnogammarus cyaneus (Dyb., E verrucosus (Gerstf., E vittatus (Dyb. - endemic species from Lake Baikal which were compared with Palearctic species - Gammarus lacustris Sars., G tigrinus (Sexton, Chaetogammarus ischnus (Stebbins. It was shown expression of sHSP by heat and toxic stresses for all amphipods species. Oxidative stress induced HSP70 for Palearctic species G tigrinus and C ischnus but not for baikalian species. Heat stress did not caused the increase of HSP70 level for Baikalian species of amphipods. The activity of the peroxidase was decrease by heat and toxic stresses. Oxidative stress caused the increase of peroxidase activity for Palearctic species, and the decrease for Baikalian once.

  12. Adaptive hydrophobic and hydrophilic interactions of mussel foot proteins with organic thin films.

    Science.gov (United States)

    Yu, Jing; Kan, Yajing; Rapp, Michael; Danner, Eric; Wei, Wei; Das, Saurabh; Miller, Dusty R; Chen, Yunfei; Waite, J Herbert; Israelachvili, Jacob N

    2013-09-24

    The adhesion of mussel foot proteins (Mfps) to a variety of specially engineered mineral and metal oxide surfaces has previously been investigated extensively, but the relevance of these studies to adhesion in biological environments remains unknown. Most solid surfaces exposed to seawater or physiological fluids become fouled by organic conditioning films and biofilms within minutes. Understanding the binding mechanisms of Mfps to organic films with known chemical and physical properties therefore is of considerable theoretical and practical interest. Using self-assembled monolayers (SAMs) on atomically smooth gold substrates and the surface forces apparatus, we explored the force-distance profiles and adhesion energies of three different Mfps, Mfp-1, Mfp-3, and Mfp-5, on (i) hydrophobic methyl (CH3)- and (ii) hydrophilic alcohol (OH)-terminated SAM surfaces between pH 3 and pH 7.5. At acidic pH, all three Mfps adhered strongly to the CH3-terminated SAM surfaces via hydrophobic interactions (range of adhesive interaction energy = -4 to -9 mJ/m(2)) but only weakly to the OH-terminated SAM surfaces through H- bonding (adhesive interaction energy ≤ -0.5 mJ/m(2)). 3, 4-Dihydroxyphenylalanine (Dopa) residues in Mfps mediate binding to both SAM surface types but do so through different interactions: typical bidentate H-bonding by Dopa is frustrated by the longer spacing of OH-SAMs; in contrast, on CH3-SAMs, Dopa in synergy with other nonpolar residues partitions to the hydrophobic surface. Asymmetry in the distribution of hydrophobic residues in intrinsically unstructured proteins, the distortion of bond geometry between H-bonding surfaces, and the manipulation of physisorbed binding lifetimes represent important concepts for the design of adhesive and nonfouling surfaces.

  13. Adaptive and maladaptive expression of the mRNA regulatory protein HuR

    Institute of Scientific and Technical Information of China (English)

    Suman; Govindaraju; Beth; S; Lee

    2013-01-01

    The RNA-binding proteins involved in regulation of mRNA post-transcriptional processing and translation control the fates of thousands of mRNA transcripts and basic cellular processes. The best studied of these, HuR, is well characterized as a mediator of mRNA stability and translation, and more recently, as a factor in nuclear functions such as pre-mRNA splicing. Due to HuR’s role in regulating thousands of mRNA transcripts, including those for other RNA-binding proteins, HuR can act as a master regulator of cell survival and proliferation. HuR itself is subject to multiple post-translationa modifications including regulation of its nucleocytoplasmic distribution. However, the mechanisms that govern HuR levels in the cell have only recently begun to be defined. These mechanisms are critical to cell health, as it has become clear in recent years that aberrant expression of HuR can lead alternately to decreased cell viability or to promotion of pathological proliferation and invasiveness. HuR is expressed as alternate mRNAs that vary in their untranslated regions, leading to differences in transcript stability and translatability. Multiple transcription factors and modulators of mRNA stability that regulate HuR mRNA expression have been identified. In addition, translation of HuR is regulated by numerous microRNAs, several of which have been demonstrated to have anti-tumor properties due to their suppression of HuR expression. This review summarizes the current state of knowledge of the factors that regulate HuR expression, along with the circumstances under which these factors contribute to cancer and inflammation.

  14. The adaptive metabolic response involves specific protein glutathionylation during the filamentation process in the pathogen Candida albicans.

    Science.gov (United States)

    Gergondey, R; Garcia, C; Serre, V; Camadro, J M; Auchère, F

    2016-07-01

    Candida albicans is an opportunist pathogen responsible for a large spectrum of infections, from superficial mycosis to the systemic disease candidiasis. Its ability to adopt various morphological forms, such as unicellular yeasts, filamentous pseudohyphae and hyphae, contributes to its ability to survive within the host. It has been suggested that the antioxidant glutathione is involved in the filamentation process. We investigated S-glutathionylation, the reversible binding of glutathione to proteins, and the functional consequences on C. albicans metabolic remodeling during the yeast-to-hyphae transition. Our work provided evidence for the specific glutathionylation of mitochondrial proteins involved in bioenergetics pathways in filamentous forms and a regulation of the main enzyme of the glyoxylate cycle, isocitrate lyase, by glutathionylation. Isocitrate lyase inactivation in the hyphal forms was reversed by glutaredoxin treatment, in agreement with a glutathionylation process, which was confirmed by proteomic data showing the binding of one glutathione molecule to the enzyme (data are available via ProteomeXchange with identifier PXD003685). We also assessed the effect of alternative carbon sources on glutathione levels and isocitrate lyase activity. Changes in nutrient availability led to morphological flexibility and were related to perturbations in glutathione levels and isocitrate lyase activity, confirming the key role of the maintenance of intracellular redox status in the adaptive metabolic strategy of the pathogen. PMID:27083931

  15. Sterol Regulatory Element Binding Protein (Srb1) Is Required for Hypoxic Adaptation and Virulence in the Dimorphic Fungus Histoplasma capsulatum

    Science.gov (United States)

    DuBois, Juwen C.; Smulian, A. George

    2016-01-01

    The Histoplasma capsulatum sterol regulatory element binding protein (SREBP), Srb1 is a member of the basic helix-loop-helix (bHLH), leucine zipper DNA binding protein family of transcription factors that possess a unique tyrosine (Y) residue instead of an arginine (R) residue in the bHLH region. We have determined that Srb1 message levels increase in a time dependent manner during growth under oxygen deprivation (hypoxia). To further understand the role of Srb1 during infection and hypoxia, we silenced the gene encoding Srb1 using RNA interference (RNAi); characterized the resulting phenotype, determined its response to hypoxia, and its ability to cause disease within an infected host. Silencing of Srb1 resulted in a strain of H. capsulatum that is incapable of surviving in vitro hypoxia. We found that without complete Srb1 expression, H. capsulatum is killed by murine macrophages and avirulent in mice given a lethal dose of yeasts. Additionally, silencing Srb1 inhibited the hypoxic upregulation of other known H. capsulatum hypoxia-responsive genes (HRG), and genes that encode ergosterol biosynthetic enzymes. Consistent with these regulatory functions, Srb1 silenced H. capsulatum cells were hypersensitive to the antifungal azole drug itraconazole. These data support the theory that the H. capsulatum SREBP is critical for hypoxic adaptation and is required for H. capsulatum virulence. PMID:27711233

  16. Peptide-polymer ligands for a tandem WW-domain, an adaptive multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands.

    Science.gov (United States)

    Koschek, Katharina; Durmaz, Vedat; Krylova, Oxana; Wieczorek, Marek; Gupta, Shilpi; Richter, Martin; Bujotzek, Alexander; Fischer, Christina; Haag, Rainer; Freund, Christian; Weber, Marcus; Rademann, Jörg

    2015-01-01

    Three polymers, poly(N-(2-hydroxypropyl)methacrylamide) (pHPMA), hyperbranched polyglycerol (hPG), and dextran were investigated as carriers for multivalent ligands targeting the adaptive tandem WW-domain of formin-binding protein (FBP21). Polymer carriers were conjugated with 3-9 copies of the proline-rich decapeptide GPPPRGPPPR-NH2 (P1). Binding of the obtained peptide-polymer conjugates to the tandem WW-domain was investigated employing isothermal titration calorimetry (ITC) to determine the binding affinity, the enthalpic and entropic contributions to free binding energy, and the stoichiometry of binding for all peptide-polymer conjugates. Binding affinities of all multivalent ligands were in the µM range, strongly amplified compared to the monovalent ligand P1 with a K D > 1 mM. In addition, concise differences were observed, pHPMA and hPG carriers showed moderate affinity and bound 2.3-2.8 peptides per protein binding site resulting in the formation of aggregates. Dextran-based conjugates displayed affinities down to 1.2 µM, forming complexes with low stoichiometry, and no precipitation. Experimental results were compared with parameters obtained from molecular dynamics simulations in order to understand the observed differences between the three carrier materials. In summary, the more rigid and condensed peptide-polymer conjugates based on the dextran scaffold seem to be superior to induce multivalent binding and to increase affinity, while the more flexible and dendritic polymers, pHPMA and hPG are suitable to induce crosslinking upon binding. PMID:26124884

  17. Gene 33/Mig-6, a Transcriptionally Inducible Adapter Protein That Binds GTP-Cdc42 and Activates SAPK/JNK*

    Science.gov (United States)

    Makkinje, Anthony; Quinn, Deborah A.; Chen, Ang; Cadilla, Carmen L.; Force, Thomas; Bonventre, Joseph V.; Kyriakis, John M.

    2013-01-01

    Chronic stresses, including the mechanical strain caused by hypertension or excess pulmonary ventilation pressure, lead to important clinical consequences, including hypertrophy and acute respiratory distress syndrome. Pathologic hypertrophy contributes to decreased organ function and, ultimately, organ failure; and cardiac and diabetic renal hypertrophy are major causes of morbidity and morality in the developed world. Likewise, acute respiratory distress syndrome is a serious potential side effect of mechanical pulmonary ventilation. Whereas the deleterious effects of chronic stress are well established, the molecular mechanisms by which these stresses affect cell function are still poorly characterized. gene 33 (also called mitogen-inducible gene-6, mig-6) is an immediate early gene that is transcriptionally induced by a divergent array of extra-cellular stimuli. The physiologic function of Gene 33 is unknown. Here we show that gene 33 mRNA levels increase sharply in response to a set of commonly occurring chronic stress stimuli: mechanical strain, vasoactive peptides, and diabetic nephropathy. Induction of gene 33 requires the stress-activated protein kinases (SAPKs)/c-Jun NH2-terminal kinases. This expression pattern suggests that gene 33 is a potential marker for diabetic nephropathy and other pathologic responses to persistent sublethal stress. The structure of Gene 33 indicates an adapter protein capable of binding monomeric GTPases of the Rho subfamily. Consistent with this, Gene 33 interacts in vivo and, in a GTP-dependent manner, in vitro with Cdc42Hs; and transient expression of Gene 33 results in the selective activation of the SAPKs. These results imply a reciprocal, positive feedback relationship between Gene 33 expression and SAPK activation. Expression of Gene 33 at sufficient levels may enable a compensatory reprogramming of cellular function in response to chronic stress, which may have pathophysiological consequences. PMID:10749885

  18. Adhesion and degranulation promoting adapter protein (ADAP is a central hub for phosphotyrosine-mediated interactions in T cells.

    Directory of Open Access Journals (Sweden)

    Marc Sylvester

    Full Text Available TCR stimulation leads to an increase in cellular adhesion among other outcomes. The adhesion and degranulation promoting adapter protein (ADAP is known to be rapidly phosphorylated after T cell stimulation and relays the TCR signal to adhesion molecules of the integrin family. While three tyrosine phosphorylation sites have been characterized biochemically, the binding capabilities and associated functions of several other potential phosphotyrosine motifs remain unclear. Here, we utilize in vitro phosphorylation and mass spectrometry to map novel phosphotyrosine sites in the C-terminal part of human ADAP (486-783. Individual tyrosines were then mutated to phenylalanine and their relevance for cellular adhesion and migration was tested experimentally. Functionally important tyrosine residues include two sites within the folded hSH3 domains of ADAP and two at the C-terminus. Furthermore, using a peptide pulldown approach in combination with stable isotope labeling in cell culture (SILAC we identified SLP-76, PLCgamma, PIK3R1, Nck, CRK, Gads, and RasGAP as phospho-dependent binding partners of a central YDDV motif of ADAP. The phosphorylation-dependent interaction between ADAP and Nck was confirmed by yeast two-hybrid analysis, immunoprecipitation and binary pulldown experiments, indicating that ADAP directly links integrins to modulators of the cytoskeleton independent of SLP-76.

  19. Time course analysis reveals gene-specific transcript and protein kinetics of adaptation to short-term aerobic exercise training in human skeletal muscle

    OpenAIRE

    Brendan Egan; Paul L O'Connor; Juleen R. Zierath; Donal J O'Gorman

    2013-01-01

    Repeated bouts of episodic myofibrillar contraction associated with exercise training are potent stimuli for physiological adaptation. However, the time course of adaptation and the continuity between alterations in mRNA expression and protein content are not well described in human skeletal muscle. Eight healthy, sedentary males cycled for 60 min at 80% of peak oxygen consumption (VO2peak) each day for fourteen consecutive days, resulting in an increase in VO2peak of 17.5±3.8%. Skeletal musc...

  20. The role of mammalian antimicrobial peptides and proteins in awakening of innate host defenses and adaptive immunity.

    Science.gov (United States)

    Yang, D; Chertov, O; Oppenheim, J J

    2001-06-01

    Since we live in a dirty environment, we have developed many host defenses to contend with microorganisms. The epithelial lining of our skin, gastrointestinal tract and bronchial tree produces a number of antibacterial peptides, and our phagocytic neutrophils rapidly ingest and enzymatically degrade invading organisms, as well as produce peptides and enzymes with antimicrobial activities. Some of these antimicrobial moieties also appear to alert host cells involved in both innate host defense and adaptive immune responses. The epithelial cells are a source of constitutively produced beta defensin (HBD1) and proinflammatory cytokine-inducible beta defensins (HBD2 and -3) and cathelicidin (LL37). The neutrophils-derived antimicrobial peptides are released on demand from their cytoplasmic granules. They include the enzymes cathepsin G and chymase, azurocidin, a defensins and cathelicidin. In contrast, C5a and C3b are produced by activation of the serum complement cascade. The antimicrobial moieties direct the migration and activate target cells by interacting with selected G-protein-coupled seven-transmembrane receptors (GPCRs) on cell surfaces. The beta defensins interact with the CCR6 chemokine GPCRs, whereas cathelicidins interact with the low-affinity FPRL-1 receptors. The neutrophil-derived cathepsin G acts on the high-affinity FMLP receptor (GPCR) known as FPR, while the receptors for chymase and azurocidin have not been identified as yet. The serum-derived C5a uses a GPCR known as C5aR to mediate its chemotactic and cell-activating effects. Consequently, all these ligand-receptor interactions in addition to mediating chemotaxis also activate receptor-expressing cells to produce other mediators of inflammation.

  1. Time course analysis reveals gene-specific transcript and protein kinetics of adaptation to short-term aerobic exercise training in human skeletal muscle.

    Directory of Open Access Journals (Sweden)

    Brendan Egan

    Full Text Available Repeated bouts of episodic myofibrillar contraction associated with exercise training are potent stimuli for physiological adaptation. However, the time course of adaptation and the continuity between alterations in mRNA expression and protein content are not well described in human skeletal muscle. Eight healthy, sedentary males cycled for 60 min at 80% of peak oxygen consumption (VO2peak each day for fourteen consecutive days, resulting in an increase in VO2peak of 17.5±3.8%. Skeletal muscle biopsies were taken at baseline, and on the morning following (+16 h after exercise the first, third, seventh, tenth and fourteenth training sessions. Markers of mitochondrial adaptation (Cyt c and COXIV expression, and citrate synthase activity were increased within the first week of training, but the mtDNA/nDNA ratio was unchanged by two weeks of training. Accumulation of PGC-1α and ERRα protein during training suggests a regulatory role for these factors in adaptations of mitochondrial and metabolic gene expression. A subset of genes were transiently increased after one training session, but returned to baseline levels thereafter, which is supportive of the concept of transcriptional capacity being particularly sensitive to the onset of a new level of contractile activity. Thus, gene-specific temporal patterns of induction of mRNA expression and protein content are described. Our results illustrate the phenomenology of skeletal muscle plasticity and support the notion that transcript level adjustments, coupled to accumulation of encoded protein, underlie the modulation of skeletal muscle metabolism and phenotype by regular exercise.

  2. Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species.

    LENUS (Irish Health Repository)

    Khaldi, Nora

    2011-07-29

    Abstract Background Milk proteins are required to proceed through a variety of conditions of radically varying pH, which are not identical across mammalian digestive systems. We wished to investigate if the shifts in these requirements have resulted in marked changes in the isoelectric point and charge of milk proteins during evolution. Results We investigated nine major milk proteins in 13 mammals. In comparison with a group of orthologous non-milk proteins, we found that 3 proteins κ-casein, lactadherin, and muc1 have undergone the highest change in isoelectric point during evolution. The pattern of non-synonymous substitutions indicate that selection has played a role in the isoelectric point shift, since residues that show significant evidence of positive selection are much more likely to be charged (p = 0.03 for κ-casein; p < 10-8 for muc1). However, this selection does not appear to be solely due to adaptation to the diversity of mammalian digestive systems, since striking changes are seen among species that resemble each other in terms of their digestion. Conclusion The changes in charge are most likely due to changes of other protein functions, rather than an adaptation to the different mammalian digestive systems. These functions may include differences in bioactive peptide releases in the gut between different mammals, which are known to be a major contributing factor in the functional and nutritional value of mammalian milk. This raises the question of whether bovine milk is optimal in terms of particular protein functions, for human nutrition and possibly disease resistance. This article was reviewed by Fyodor Kondrashov, David Liberles (nominated by David Ardell), and Christophe Lefevre (nominated by Mark Ragan).

  3. Role of Cell Cycle Regulation and MLH1, A Key DNA Mismatch Repair Protein, In Adaptive Survival Responses. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    David A. Boothman

    1999-08-11

    Due to several interesting findings on both adaptive survival responses (ASRs) and DNA mismatch repair (MMR), this grant was separated into two discrete Specific Aim sets (each with their own discrete hypotheses). The described experiments were simultaneously performed.

  4. Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yuan; ZHENG Nan; HAO Pei; ZHONG Yang

    2004-01-01

    @@ The genome organization and expression strategy of severe acute respiratory syndrome coronavirus (SARSCoV) have been described extensivelyl1- 10]. As a structural glycoprotein on the virion surface, the spike protein is responsible for binding to host cellular receptors and for the fusion between the viral envelope and the cellular membrane. It also induces neutralizing antibodies in the host and mediates cellular immunity[11]. Previous studies suggested that amino acid replacements in the spike protein could dramatically alter the pathogenesis and virulence of some coronaviruses[11]. It is therefore reasonable to test the hypothesis that radical amino acid replacements in the spike protein, favored by environmental selective pressure during the process of SARS-CoV interspecific transmission[10], might make this pathogen adapt to a new host. In this study, we investigated a total of 108complete sequences of the SARS-CoV S gene from GenBank (until March 23, 2004). After omission of those records containing frame-shift mutations or low quality sequences, e.g. ZJ01, and selection of one sequence for identical records, an alignment of 42 sequences was obtained using the program Clustal-X[13]. Then, we reconstructed the most recent common ancestor (MRCA) sequences of the SARS-CoV S gene and detected the adaptive evolution in the spike protein.

  5. Natural selection of adaptive mutations in non-structural genes increases trans-encapsidation of hepatitis C virus replicons lacking envelope protein genes.

    Science.gov (United States)

    Fournier, Carole; Helle, François; Descamps, Véronique; Morel, Virginie; François, Catherine; Dedeurwaerder, Sarah; Wychowski, Czeslaw; Duverlie, Gilles; Castelain, Sandrine

    2013-05-01

    A trans-packaging system for hepatitis C virus (HCV) replicons lacking envelope glycoproteins was developed. The replicons were efficiently encapsidated into infectious particles after expression in trans of homologous HCV envelope proteins under the control of an adenoviral vector. Interestingly, expression in trans of core or core, p7 and NS2 with envelope proteins did not enhance trans-encapsidation. Expression of heterologous envelope proteins, in the presence or absence of heterologous core, p7 and NS2, did not rescue single-round infectious particle production. To increase the titre of homologous, single-round infectious particles in our system, successive cycles of trans-encapsidation and infection were performed. Four cycles resulted in a 100-fold increase in the yield of particles. Sequence analysis revealed a total of 16 potential adaptive mutations in two independent experiments. Except for a core mutation in one experiment, all the mutations were located in non-structural regions mainly in NS5A (four in domain III and two near the junction with the NS5B gene). Reverse genetics studies suggested that D2437A and S2443T adaptive mutations, which are located at the NS5A-B cleavage site did not affect viral replication, but enhanced the single-round infectious particles assembly only in trans-encapsidation model. In conclusion, our trans-encapsidation system enables the production of HCV single-round infectious particles. This system is adaptable and can positively select variants. The adapted variants promote trans-encapsidation and should constitute a valuable tool in the development of replicon-based HCV vaccines. PMID:23288424

  6. High-intensity interval training-induced metabolic adaptation coupled with an increase in Hif-1α and glycolytic protein expression.

    Science.gov (United States)

    Abe, Takaaki; Kitaoka, Yu; Kikuchi, Dale Manjiro; Takeda, Kohei; Numata, Osamu; Takemasa, Tohru

    2015-12-01

    It is known that repeated bouts of high-intensity interval training (HIIT) lead to enhanced levels of glycolysis, glycogenesis, and lactate transport proteins in skeletal muscle; however, little is known about the molecular mechanisms underlying these adaptations. To decipher the mechanism leading to improvement of skeletal muscle glycolytic capacity associated with HIIT, we examined the role of hypoxia-inducible factor-1α (Hif-1α), the major transcription factor regulating the expression of genes related to anaerobic metabolism, in the adaptation to HIIT. First, we induced Hif-1α accumulation using ethyl 3,4-dihydroxybenzoate (EDHB) to assess the potential role of Hif-1α in skeletal muscle. Treatment with EDHB significantly increased the protein levels of Hif-1α in gastrocnemius muscles, accompanied by elevated expression of genes related to glycolysis, glycogenesis, and lactate transport. Daily administration of EDHB for 1 wk resulted in elevated glycolytic enzyme activity in gastrocnemius muscles. Second, we examined whether a single bout of HIIT could induce Hif-1α protein accumulation and subsequent increase in the expression of genes related to anaerobic metabolism in skeletal muscle. We observed that the protein levels of Hif-1α and expression of the target genes were elevated 3 h after an acute bout of HIIT in gastrocnemius muscles. Last, we examined the effects of long-term HIIT. We found that long-term HIIT increased the basal levels of Hif-1α as well as the glycolytic capacity in gastrocnemius muscles. Our results suggest that Hif-1α is a key regulator in the metabolic adaptation to high-intensity training.

  7. Verification at the protein level of the PIF4-mediated external coincidence model for the temperature-adaptive photoperiodic control of plant growth in Arabidopsis thaliana.

    Science.gov (United States)

    Yamashino, Takafumi; Nomoto, Yuji; Lorrain, Séverine; Miyachi, Miki; Ito, Shogo; Nakamichi, Norihito; Fankhauser, Christian; Mizuno, Takeshi

    2013-03-01

    Plant circadian clock controls a wide variety of physiological and developmental events, which include the short-days (SDs)-specific promotion of the elongation of hypocotyls during de-etiolation and also the elongation of petioles during vegetative growth. In A. thaliana, the PIF4 gene encoding a phytochrome-interacting basic helix-loop-helix (bHLH) transcription factor plays crucial roles in this photoperiodic control of plant growth. According to the proposed external coincidence model, the PIF4 gene is transcribed precociously at the end of night specifically in SDs, under which conditions the protein product is stably accumulated, while PIF4 is expressed exclusively during the daytime in long days (LDs), under which conditions the protein product is degraded by the light-activated phyB and also the residual proteins are inactivated by the DELLA family of proteins. A number of previous reports provided solid evidence to support this coincidence model mainly at the transcriptional level of the PIF 4 and PIF4-traget genes. Nevertheless, the diurnal oscillation profiles of PIF4 proteins, which were postulated to be dependent on photoperiod and ambient temperature, have not yet been demonstrated. Here we present such crucial evidence on PIF4 protein level to further support the external coincidence model underlying the temperature-adaptive photoperiodic control of plant growth in A. thaliana.

  8. Adaptation of HepG2 cells to a steady-state reduction in the content of protein phosphatase 6 (PP6) catalytic subunit

    Energy Technology Data Exchange (ETDEWEB)

    Boylan, Joan M. [Department of Pediatrics, Brown University and Rhode Island Hospital, Providence, RI (United States); Salomon, Arthur R. [Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI (United States); Department of Chemistry, Brown University, Providence, RI (United States); Tantravahi, Umadevi [Division of Genetics, Department of Pathology, Brown University and Women and Infants Hospital, Providence, RI (United States); Gruppuso, Philip A., E-mail: philip_gruppuso@brown.edu [Department of Pediatrics, Brown University and Rhode Island Hospital, Providence, RI (United States); Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI (United States)

    2015-07-15

    Protein phosphatase 6 (PP6) is a ubiquitous Ser/Thr phosphatase involved in an array of cellular processes. To assess the potential of PP6 as a therapeutic target in liver disorders, we attenuated expression of the PP6 catalytic subunit in HepG2 cells using lentiviral-transduced shRNA. Two PP6 knock-down (PP6KD) cell lines (90% reduction of PP6-C protein content) were studied in depth. Both proliferated at a rate similar to control cells. However, flow cytometry indicated G2/M cell cycle arrest that was accounted for by a shift of the cells from a diploid to tetraploid state. PP6KD cells did not show an increase in apoptosis, nor did they exhibit reduced viability in the presence of bleomycin or taxol. Gene expression analysis by microarray showed attenuated anti-inflammatory signaling. Genes associated with DNA replication were downregulated. Mass spectrometry-based phosphoproteomic analysis yielded 80 phosphopeptides representing 56 proteins that were significantly affected by a stable reduction in PP6-C. Proteins involved in DNA replication, DNA damage repair and pre-mRNA splicing were overrepresented among these. PP6KD cells showed intact mTOR signaling. Our studies demonstrated involvement of PP6 in a diverse set of biological pathways and an adaptive response that may limit the effectiveness of targeting PP6 in liver disorders. - Highlights: • Lentiviral-transduced shRNA was used to generate a stable knockdown of PP6 in HepG2 cells. • Cells adapted to reduced PP6; cell proliferation was unaffected, and cell survival was normal. • However, PP6 knockdown was associated with a transition to a tetraploid state. • Genomic profiling showed downregulated anti-inflammatory signaling and DNA replication. • Phosphoproteomic profiling showed changes in proteins associated with DNA replication and repair.

  9. The Role of Cold-Shock Proteins in Low-Temperature Adaptation of Food-Related Bacteria

    NARCIS (Netherlands)

    Wouters, Jeroen A.; Rombouts, Frank M.; Kuipers, Oscar P.; Vos, Willem M. de; Abee, T.

    2000-01-01

    There is a considerable interest in the cold adaptation of food-related bacteria, including starter cultures for industrial food fermentations, food spoilage bacteria and food-borne pathogens. Mechanisms that permit low-temperature growth involve cellular modifications for maintaining membrane fluid

  10. Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

    OpenAIRE

    Katharina Koschek; Vedat Durmaz; Oxana Krylova; Marek Wieczorek; Shilpi Gupta; Martin Richter; Alexander Bujotzek; Christina Fischer; Rainer Haag; Christian Freund; Marcus Weber; Jörg Rademann

    2015-01-01

    Three polymers, poly(N-(2-hydroxypropyl)methacrylamide) (pHPMA), hyperbranched polyglycerol (hPG), and dextran were investigated as carriers for multivalent ligands targeting the adaptive tandem WW-domain of formin-binding protein (FBP21). Polymer carriers were conjugated with 3–9 copies of the proline-rich decapeptide GPPPRGPPPR-NH2 (P1). Binding of the obtained peptide–polymer conjugates to the tandem WW-domain was investigated employing isothermal titration calorimetry (ITC) to determine t...

  11. Adaptation of low-resolution methods for the study of yeast microsomal polytopic membrane proteins: a methodological review.

    Science.gov (United States)

    Bochud, Arlette; Ramachandra, Nagaraju; Conzelmann, Andreas

    2013-02-01

    Most integral membrane proteins of yeast with two or more membrane-spanning sequences have not yet been crystallized and for many of them the side on which the active sites or ligand-binding domains reside is unknown. Also, bioinformatic topology predictions are not yet fully reliable. However, so-called low-resolution biochemical methods can be used to locate hydrophilic loops or individual residues of polytopic membrane proteins at one or the other side of the membrane. The advantages and limitations of several such methods for topological studies with yeast ER integral membrane proteins are discussed. We also describe new tools that allow us to better control and validate results obtained with SCAM (substituted cysteine accessibility method), an approach that determines the position of individual residues with respect to the membrane plane, whereby only minimal changes in the primary sequence have to be introduced into the protein of interest. PMID:23356255

  12. Inhibition of Translation Initiation by Protein 169: A Vaccinia Virus Strategy to Suppress Innate and Adaptive Immunity and Alter Virus Virulence.

    Directory of Open Access Journals (Sweden)

    Pavla Strnadova

    2015-09-01

    Full Text Available Vaccinia virus (VACV is the prototypic orthopoxvirus and the vaccine used to eradicate smallpox. Here we show that VACV strain Western Reserve protein 169 is a cytoplasmic polypeptide expressed early during infection that is excluded from virus factories and inhibits the initiation of cap-dependent and cap-independent translation. Ectopic expression of protein 169 causes the accumulation of 80S ribosomes, a reduction of polysomes, and inhibition of protein expression deriving from activation of multiple innate immune signaling pathways. A virus lacking 169 (vΔ169 replicates and spreads normally in cell culture but is more virulent than parental and revertant control viruses in intranasal and intradermal murine models of infection. Intranasal infection by vΔ169 caused increased pro-inflammatory cytokines and chemokines, infiltration of pulmonary leukocytes, and lung weight. These alterations in innate immunity resulted in a stronger CD8+ T-cell memory response and better protection against virus challenge. This work illustrates how inhibition of host protein synthesis can be a strategy for virus suppression of innate and adaptive immunity.

  13. Signature of protein adaptation to warm deep sea environments: the case of Initiation Factor 6 studied by molecular simulation and neutron scattering

    International Nuclear Information System (INIS)

    The protein Initiation Factor 6 (IF6) takes part in the protein synthesis regulation of several organisms. It was also found in archeaebacteria such as Methanococcus jannaschii which lives in deep-seas near hydrothermal vents where temperature reaches 80 C and pressure is between 250 bar and 500 bar. The aim of this work was to study for the first time dynamical and structural properties of IF6 produced by M. jannaschii and comparing them with those of the IF6 homologue present in Saccharomyces cerevisiae which lives at 'normal' environmental conditions (27 C and 1 bar). Molecular simulation gave here new insights into the adaptation of these two proteins to their respective physiological conditions and showed that the latter induced similar dynamical and structural properties: in their respective 'natural' conditions, IF6s show very similar structural fluctuations and the characteristic relaxation times which define their dynamical properties shows similar changes when comparing unfavorable conditions to physiological ones. The creation of these corresponding states between the two homologues has been interpreted by the fractional Brownian dynamics model and by a novel method for the characterization of protein secondary structures. The latter is presented here in detail together with some examples of other applications. Experimental data obtained from quasi-elastic neutron scattering seemed to support the results obtained by molecular simulations. (author)

  14. Secretome profile analysis of hypervirulent Mycobacterium tuberculosis CPT31 reveals increased production of EsxB and proteins involved in adaptation to intracellular lifestyle.

    Science.gov (United States)

    Vargas-Romero, Fernado; Guitierrez-Najera, Nora; Mendoza-Hernández, Guillermo; Ortega-Bernal, Daniel; Hernández-Pando, Rogelio; Castañón-Arreola, Mauricio

    2016-03-01

    Epidemiological information and animal models have shown various Mycobacterium tuberculosis phenotypes ranging from hyper- to hypovirulent forms. Recent genomic and proteomic studies suggest that the outcome of infection depends on the M. tuberculosis fitness, which is a direct consequence of its phenotype. However, little is known about the molecular and cellular mechanisms used by mycobacteria to survive, replicate and persist during infection. The aim of this study was to perform a comprehensive proteomic analysis of culture filtrate from hypo- (CPT23) and hypervirulent (CPT31) M. tuberculosis isolates. Using two-dimensional electrophoresis we observed that 70 proteins were unique, or more abundant in culture filtrate of CPT31, and 15 of these were identified by mass spectrometry. Our analysis of protein expression showed that most of the proteins identified are involved in lipid metabolism (FadA3, FbpB and EchA3), detoxification and adaptation (GroEL2, SodB and HspX) and cell wall processes (LprA, Tig and EsxB). These results suggest that overrepresented proteins in M. tuberculosis CPT31 secretome could facilitate mycobacterial infection and persistence.

  15. Rice G-protein subunits qPE9-1 and RGB1 play distinct roles in abscisic acid responses and drought adaptation.

    Science.gov (United States)

    Zhang, Dong-Ping; Zhou, Yong; Yin, Jian-Feng; Yan, Xue-Jiao; Lin, Sheng; Xu, Wei-Feng; Baluška, František; Wang, Yi-Ping; Xia, Yi-Ji; Liang, Guo-hua; Liang, Jian-Sheng

    2015-10-01

    Heterotrimeric GTP-binding protein (G-protein)-mediated abscisic acid (ABA) and drought-stress responses have been documented in numerous plant species. However, our understanding of the function of rice G-protein subunits in ABA signalling and drought tolerance is limited. In this study, the function of G-protein subunits in ABA response and drought resistance in rice plants was explored. It was found that the transcription level of qPE9-1 (rice Gγ subunit) gradually decreased with increasing ABA concentration and the lack of qPE9-1 showed an enhanced drought tolerance in rice plants. In contrast, mRNA levels of RGB1 (rice Gβ subunit) were significantly upregulated by ABA treatment and the lack of RGB1 led to reduced drought tolerance. Furthermore, the results suggested that qPE9-1 negatively regulates the ABA response by suppressing the expression of key transcription factors involved in ABA and stress responses, while RGB1 positively regulates ABA biosynthesis by upregulating NCED gene expression under both normal and drought stress conditions. Taken together, it is proposed that RGB1 is a positive regulator of the ABA response and drought adaption in rice plants, whereas qPE9-1 is modulated by RGB1 and functions as a negative regulator in the ABA-dependent drought-stress responses. PMID:26175353

  16. Identification and modulation of a growth hormone-binding protein in rainbow trout (Oncorhynchus mykiss) plasma during seawater adaptation.

    OpenAIRE

    Sohm, F.; Manfroid, Isabelle; Pezet, A.; Rentier-Delrue, Françoise; Rand-Weaver, M; Kelly, P A; Boeuf, G.; Postel-Vinay, M C; de Luze, A; Edery, M.

    1998-01-01

    A soluble protein that specifically bound 125I-human growth hormone (hGH) was identified in rainbow trout plasma, using HPLC-gel filtration. The binding affinity of the protein for hGH was 1.2 x 10(9)M-1. 125I-rainbow trout GH (tGH) was also able to bind to the protein albeit with a lower affinity (6.6 x 10(7)M-1) than hGH. Crosslinking experiments using 125I-hGH revealed two specific bands of 150 and 130 kDa. The complex 125I-hGH-BP could be precipitated by a monoclonal anti-GH receptor anti...

  17. The G-protein gamma subunit gpc-1 of the nematode C.elegans is involved in taste adaptation.

    NARCIS (Netherlands)

    G. Jansen (Gert); D. Weinkove (David); R.A. Plasterk (Ronald)

    2002-01-01

    textabstractCaenorhabditis elegans has two heterotrimeric G-protein gamma subunits, gpc-1 and gpc-2. Although GPC-1 is specifically expressed in sensory neurons, it is not essential for the detection of odorants or salts. To test whether GPC-1 is involved in sensory plasticity, we

  18. Contrast in adaptive mass gains : Eurasian golden plovers store fat before midwinter and protein before prebreeding flight

    NARCIS (Netherlands)

    Piersma, T; Jukema, J

    2002-01-01

    Before predictable periods of high nutritional demand and little or no intake, vertebrates store fuel mainly composed of energy-dense lipids or energy-poor but protein-rich muscle tissue. Documenting contrasts in fuel composition and storage patterns within species, or even within individuals, would

  19. Comparative proteomic analysis of the membrane proteins of two Haemophilus parasuis strains to identify proteins that may help in habitat adaptation and pathogenesis

    OpenAIRE

    Zhang, Luhua; Wen, Yiping; Ying LI; Wei, Xingliang; Yan, Xuefeng; wen, Xintian; Wu, Rui; Huang, Xiaobo; Huang, Yong; Yan, Qigui; Liu, Mafeng; Cao, Sanjie

    2014-01-01

    Background Haemophilus parasuis is the causative agent of Glässer’s disease characterized by polyserositis, arthritis, and meningitis in pig, leading to serious economic loss. Despite many years of study, virulence factors and the mechanisms of the entire infection process remain largely unclear. So two-dimensional gel electrophoresis and mass spectrometry were used to search for distinctions at the membrane protein expression level between two H. parasuis isolates aimed at uncovering some pr...

  20. Effects of dihydrocapsiate on adaptive and diet-induced thermogenesis with a high protein very low calorie diet: a randomized control trial

    Directory of Open Access Journals (Sweden)

    Zerlin Alona

    2010-10-01

    Full Text Available Abstract Background Dihydrocapsiate (DCT is a natural safe food ingredient which is structurally related to capsaicin from chili pepper and is found in the non-pungent pepper strain, CH-19 Sweet. It has been shown to elicit the thermogenic effects of capsaicin but without its gastrointestinal side effects. Methods The present study was designed to examine the effects of DCT on both adaptive thermogenesis as the result of caloric restriction with a high protein very low calorie diet (VLCD and to determine whether DCT would increase post-prandial energy expenditure (PPEE in response to a 400 kcal/60 g protein liquid test meal. Thirty-three subjects completed an outpatient very low calorie diet (800 kcal/day providing 120 g/day protein over 4 weeks and were randomly assigned to receive either DCT capsules three times per day (3 mg or 9 mg or placebo. At baseline and 4 weeks, fasting basal metabolic rate and PPEE were measured in a metabolic hood and fat free mass (FFM determined using displacement plethysmography (BOD POD. Results PPEE normalized to FFM was increased significantly in subjects receiving 9 mg/day DCT by comparison to placebo (p Conclusions These data provide evidence for postprandial increases in thermogenesis and fat oxidation secondary to administration of dihydrocapsiate. Trial registration clinicaltrial.govNCT01142687

  1. Disruption of the Acyl-CoA binding protein gene delays hepatic adaptation to metabolic changes at weaning

    DEFF Research Database (Denmark)

    Neess, Ditte; Marcher, Ann-Britt; Bloksgaard, Maria;

    -CoA esters between different enzymatic systems. However, little is known about the in vivo function in mammalian cells. We have generated mice with targeted disruption of ACBP (ACBP-/-). These mice are viable and fertile and develop normally. However, around weaning the ACBP-/- mice show decreased growth......) family, around the weaning period. As a result, the hepatic de novo cholesterogenesis is significantly decreased at weaning. The delayed induction of SREBP target genes around weaning is caused by a compromised processing and decreased expression of SREBP precursors leading to reduced binding of SREBP...... to target sites in chromatin. In conclusion, lack of ACBP causes elevated levels of plasma and hepatic lipids during weaning, which interferes with the normal metabolic adaptation to weaning by delaying induction of the lipogenic gene programs in the liver....

  2. Protein C Activity in Dogs: Adaptation of a Commercial Human Colorimetric Assay and Evaluation of Effects of Storage Time and Temperature

    Directory of Open Access Journals (Sweden)

    Michael M. Fry

    2011-01-01

    Full Text Available Objectives of this study were to adapt a commercial human protein C (PC colorimetric assay for use in dogs and to investigate effects of various storage conditions. The human assay was modified by using pooled canine plasma for calibration and by increasing the activation time. PC activity was measured in fresh canine plasma and in plasma stored under various conditions. PC activity of some stored samples was significantly different from that of fresh plasma; however, differences were small. No difference was detected in samples stored under similar conditions but analyzed in different laboratories using similar methodology. Results of this study indicate that the human colorimetric assay is suitable for canine samples if pooled canine plasma is used for calibration, that Clinical and Laboratory Standards Institute sample storage guidelines developed for testing in humans are appropriate for dogs, and that comparisons of results from laboratories using similar methodology are legitimate.

  3. Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding

    Science.gov (United States)

    Lee, Michael S.; Olson, Mark A.

    2011-06-01

    Temperature-based replica exchange (T-ReX) enhances sampling of molecular dynamics simulations by autonomously heating and cooling simulation clients via a Metropolis exchange criterion. A pathological case for T-ReX can occur when a change in state (e.g., folding to unfolding of a protein) has a large energetic difference over a short temperature interval leading to insufficient exchanges amongst replica clients near the transition temperature. One solution is to allow the temperature set to dynamically adapt in the temperature space, thereby enriching the population of clients near the transition temperature. In this work, we evaluated two approaches for adapting the temperature set: a method that equalizes exchange rates over all neighbor temperature pairs and a method that attempts to induce clients to visit all temperatures (dubbed "current maximization") by positioning many clients at or near the transition temperature. As a test case, we simulated the 57-residue SH3 domain of alpha-spectrin. Exchange rate equalization yielded the same unfolding-folding transition temperature as fixed-temperature ReX with much smoother convergence of this value. Surprisingly, the current maximization method yielded a significantly lower transition temperature, in close agreement with experimental observation, likely due to more extensive sampling of the transition state.

  4. Coordinated Regulation of the Neutral Amino Acid Transporter SNAT2 and the Protein Phosphatase Subunit GADD34 Promotes Adaptation to Increased Extracellular Osmolarity*

    Science.gov (United States)

    Krokowski, Dawid; Jobava, Raul; Guan, Bo-Jhih; Farabaugh, Kenneth; Wu, Jing; Majumder, Mithu; Bianchi, Massimiliano G.; Snider, Martin D.; Bussolati, Ovidio; Hatzoglou, Maria

    2015-01-01

    Cells respond to shrinkage induced by increased extracellular osmolarity via programmed changes in gene transcription and mRNA translation. The immediate response to this stress includes the induction of expression of the neutral amino acid transporter SNAT2. Increased SNAT2-mediated uptake of neutral amino acids is an essential adaptive mechanism for restoring cell volume. In contrast, stress-induced phosphorylation of the α subunit of the translation initiation factor eIF2 (eIF2α) can promote apoptosis. Here we show that the response to mild hyperosmotic stress involves regulation of the phosphorylation of eIF2α by increased levels of GADD34, a regulatory subunit of protein phosphatase 1 (PP1). The induction of GADD34 was dependent on transcriptional control by the c-Jun-binding cAMP response element in the GADD34 gene promoter and posttranscriptional stabilization of its mRNA. This mechanism differs from the regulation of GADD34 expression by other stresses that involve activating transcription factor 4 (ATF4). ATF4 was not translated during hyperosmotic stress despite an increase in eIF2α phosphorylation. The SNAT2-mediated increase in amino acid uptake was enhanced by increased GADD34 levels in a manner involving decreased eIF2α phosphorylation. It is proposed that the induction of the SNAT2/GADD34 axis enhances cell survival by promoting the immediate adaptive response to stress. PMID:26041779

  5. Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein

    Science.gov (United States)

    Krois, Alexander S.; Ferreon, Josephine C.; Martinez-Yamout, Maria A.; Wright, Peter E.

    2016-01-01

    An important component of the activity of p53 as a tumor suppressor is its interaction with the transcriptional coactivators cyclic-AMP response element-binding protein (CREB)-binding protein (CBP) and p300, which activate transcription of p53-regulated stress response genes and stabilize p53 against ubiquitin-mediated degradation. The highest affinity interactions are between the intrinsically disordered N-terminal transactivation domain (TAD) of p53 and the TAZ1 and TAZ2 domains of CBP/p300. The NMR spectra of simple binary complexes of the TAZ1 and TAZ2 domains with the p53TAD suffer from exchange broadening, but innovations in construct design and isotopic labeling have enabled us to obtain high-resolution structures using fusion proteins, uniformly labeled in the case of the TAZ2–p53TAD fusion and segmentally labeled through transintein splicing for the TAZ1–p53TAD fusion. The p53TAD is bipartite, with two interaction motifs, termed AD1 and AD2, which fold to form short amphipathic helices upon binding to TAZ1 and TAZ2 whereas intervening regions of the p53TAD remain flexible. Both the AD1 and AD2 motifs bind to hydrophobic surfaces of the TAZ domains, with AD2 making more extensive hydrophobic contacts consistent with its greater contribution to the binding affinity. Binding of AD1 and AD2 is synergistic, and structural studies performed with isolated motifs can be misleading. The present structures of the full-length p53TAD complexes demonstrate the versatility of the interactions available to an intrinsically disordered domain containing bipartite interaction motifs and provide valuable insights into the structural basis of the affinity changes that occur upon stress-related posttranslational modification. PMID:26976603

  6. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins.

    Directory of Open Access Journals (Sweden)

    Alex Boyko

    Full Text Available Epigenetic states and certain environmental responses in mammals and seed plants can persist in the next sexual generation. These transgenerational effects have potential adaptative significance as well as medical and agronomic ramifications. Recent evidence suggests that some abiotic and biotic stress responses of plants are transgenerational. For example, viral infection of tobacco plants and exposure of Arabidopsis thaliana plants to UVC and flagellin can induce transgenerational increases in homologous recombination frequency (HRF. Here we show that exposure of Arabidopsis plants to stresses, including salt, UVC, cold, heat and flood, resulted in a higher HRF, increased global genome methylation, and higher tolerance to stress in the untreated progeny. This transgenerational effect did not, however, persist in successive generations. Treatment of the progeny of stressed plants with 5-azacytidine was shown to decrease global genomic methylation and enhance stress tolerance. Dicer-like (DCL 2 and DCL3 encode Dicer activities important for small RNA-dependent gene silencing. Stress-induced HRF and DNA methylation were impaired in dcl2 and dcl3 deficiency mutants, while in dcl2 mutants, only stress-induced stress tolerance was impaired. Our results are consistent with the hypothesis that stress-induced transgenerational responses in Arabidopsis depend on altered DNA methylation and smRNA silencing pathways.

  7. Cyclic di-GMP contributes to adaption and virulence of Bacillus thuringiensis through a riboswitch-regulated collagen adhesion protein.

    Science.gov (United States)

    Tang, Qing; Yin, Kang; Qian, Hongliang; Zhao, Youwen; Wang, Wen; Chou, Shan-Ho; Fu, Yang; He, Jin

    2016-01-01

    Cyclic di-GMP is a ubiquitous second messenger that regulates diverse cellular processes in bacteria by binding to various protein or riboswitch effectors. In Bacillus thuringiensis BMB171, a c-di-GMP riboswitch termed Bc2 RNA resides in the 5'-untranslated region (5'-UTR) of an mRNA that encodes a collagen adhesion protein (Cap). The expression of cap was strongly repressed in parent strain BMB171 because of the presence of Bc2 RNA but was significantly promoted in the Bc2 RNA markerless deletion mutant. Bc2 RNA acts as a genetic "on" switch, which forms an anti-terminator structure to promote cap read-through transcription upon c-di-GMP binding. As a result, cap transcription was de-repressed under high c-di-GMP levels. Therefore, Bc2 RNA regulates cap expression using a repression/de-repression model. Bc2 RNA-regulated Cap was also found to be tightly associated with motility, aggregation, exopolysaccharide secretion, biofilm formation, and virulence of B. thuringiensis BMB171 against its host insect Helicoverpa armigera. PMID:27381437

  8. Adapting protein solubility by glycosylation. N-glycosylation mutants of Coprinus cinereus peroxidase in salt and organic solutions.

    Science.gov (United States)

    Tams, J W; Vind, J; Welinder, K G

    1999-07-13

    Protein solubility is a fundamental parameter in biology and biotechnology. In the present study we have constructed and analyzed five mutants of Coprinus cinereus peroxidase (CIP) with 0, 1, 2, 4 and 6 N-glycosylation sites. All mutants contain Man(x)(GlcNAc)(2) glycans. The peroxidase activity was the same for wild-type CIP and all the glycosylation mutants when measured with the large substrate 2,2'-azino-bis(-3-ethylbenzthiazoline-6-sulfonic acid). The solubility of the five CIP mutants showed a linear dependence on the number of carbohydrate residues attached to the protein in buffered solution of both ammonium sulfate (AMS) and acetone, increasing in AMS and decreasing in acetone. Moreover, the change in free energy of solvation appears to be a constant, though with opposite signs in these solvents, giving DeltaDeltaG degrees (sol)=-0.32+/-0.05 kJ/mol per carbohydrate residue in 2.0 M AMS, a value previously obtained comparing ordinary and deglycosylated horseradish peroxidase, and 0. 37+/-0.10 kJ/mol in 60 v/v% acetone.

  9. Cyclic di-GMP contributes to adaption and virulence of Bacillus thuringiensis through a riboswitch-regulated collagen adhesion protein.

    Science.gov (United States)

    Tang, Qing; Yin, Kang; Qian, Hongliang; Zhao, Youwen; Wang, Wen; Chou, Shan-Ho; Fu, Yang; He, Jin

    2016-07-06

    Cyclic di-GMP is a ubiquitous second messenger that regulates diverse cellular processes in bacteria by binding to various protein or riboswitch effectors. In Bacillus thuringiensis BMB171, a c-di-GMP riboswitch termed Bc2 RNA resides in the 5'-untranslated region (5'-UTR) of an mRNA that encodes a collagen adhesion protein (Cap). The expression of cap was strongly repressed in parent strain BMB171 because of the presence of Bc2 RNA but was significantly promoted in the Bc2 RNA markerless deletion mutant. Bc2 RNA acts as a genetic "on" switch, which forms an anti-terminator structure to promote cap read-through transcription upon c-di-GMP binding. As a result, cap transcription was de-repressed under high c-di-GMP levels. Therefore, Bc2 RNA regulates cap expression using a repression/de-repression model. Bc2 RNA-regulated Cap was also found to be tightly associated with motility, aggregation, exopolysaccharide secretion, biofilm formation, and virulence of B. thuringiensis BMB171 against its host insect Helicoverpa armigera.

  10. Repair of DNA Alkylation Damage by the Escherichia coli Adaptive Response Protein AlkB as Studied by ESI-TOF Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Deyu Li

    2010-01-01

    Full Text Available DNA alkylation can cause mutations, epigenetic changes, and even cell death. All living organisms have evolved enzymatic and non-enzymatic strategies for repairing such alkylation damage. AlkB, one of the Escherichia coli adaptive response proteins, uses an α-ketoglutarate/Fe(II-dependent mechanism that, by chemical oxidation, removes a variety of alkyl lesions from DNA, thus affording protection of the genome against alkylation. In an effort to understand the range of acceptable substrates for AlkB, the enzyme was incubated with chemically synthesized oligonucleotides containing alkyl lesions, and the reaction products were analyzed by electrospray ionization time-of-flight (ESI-TOF mass spectrometry. Consistent with the literature, but studied comparatively here for the first time, it was found that 1-methyladenine, 1,N 6-ethenoadenine, 3-methylcytosine, and 3-ethylcytosine were completely transformed by AlkB, while 1-methylguanine and 3-methylthymine were partially repaired. The repair intermediates (epoxide and possibly glycol of 3,N 4-ethenocytosine are reported for the first time. It is also demonstrated that O 6-methylguanine and 5-methylcytosine are refractory to AlkB, lending support to the hypothesis that AlkB repairs only alkyl lesions attached to the nitrogen atoms of the nucleobase. ESI-TOF mass spectrometry is shown to be a sensitive and efficient tool for probing the comparative substrate specificities of DNA repair proteins in vitro.

  11. Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

    OpenAIRE

    Peng Liu; Lei Yang; Daming Shi; Xianglong Tang

    2015-01-01

    A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction net...

  12. Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus

    Indian Academy of Sciences (India)

    Moncef Boulila; Sawssen Ben Tiba; Saoussen Jilani

    2013-04-01

    The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used first and led to the detection of potential recombination events in the coat protein-encoding gene of that virus. The Recco algorithm confirmed these results by identifying, additionally, the potential recombinants. For neutrality testing and evaluation of nucleotide polymorphism in PNRSV CP gene, Tajima’s , and Fu and Li’s and statistical tests were used. About selection inference, eight algorithms (SLAC, FEL, IFEL, REL, FUBAR, MEME, PARRIS, and GA branch) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of PNRSV capsid. Inferred phylogenies pointed out, in addition to the three classical groups (PE-5, PV-32, and PV-96), the delineation of a fourth cluster having the new proposed designation SW6, and a fifth clade comprising four Tunisian PNRSV isolates which underwent recombination and selective pressure and to which the name Tunisian outgroup was allocated.

  13. Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

    Directory of Open Access Journals (Sweden)

    Katharina Koschek

    2015-05-01

    Full Text Available Three polymers, poly(N-(2-hydroxypropylmethacrylamide (pHPMA, hyperbranched polyglycerol (hPG, and dextran were investigated as carriers for multivalent ligands targeting the adaptive tandem WW-domain of formin-binding protein (FBP21. Polymer carriers were conjugated with 3–9 copies of the proline-rich decapeptide GPPPRGPPPR-NH2 (P1. Binding of the obtained peptide–polymer conjugates to the tandem WW-domain was investigated employing isothermal titration calorimetry (ITC to determine the binding affinity, the enthalpic and entropic contributions to free binding energy, and the stoichiometry of binding for all peptide–polymer conjugates. Binding affinities of all multivalent ligands were in the µM range, strongly amplified compared to the monovalent ligand P1 with a KD > 1 mM. In addition, concise differences were observed, pHPMA and hPG carriers showed moderate affinity and bound 2.3–2.8 peptides per protein binding site resulting in the formation of aggregates. Dextran-based conjugates displayed affinities down to 1.2 µM, forming complexes with low stoichiometry, and no precipitation. Experimental results were compared with parameters obtained from molecular dynamics simulations in order to understand the observed differences between the three carrier materials. In summary, the more rigid and condensed peptide–polymer conjugates based on the dextran scaffold seem to be superior to induce multivalent binding and to increase affinity, while the more flexible and dendritic polymers, pHPMA and hPG are suitable to induce crosslinking upon binding.

  14. Increases in mature brain-derived neurotrophic factor protein in the frontal cortex and basal forebrain during chronic sleep restriction in rats: possible role in initiating allostatic adaptation.

    Science.gov (United States)

    Wallingford, J K; Deurveilher, S; Currie, R W; Fawcett, J P; Semba, K

    2014-09-26

    Chronic sleep restriction (CSR) has various negative consequences on cognitive performance and health. Using a rat model of CSR that uses alternating cycles of 3h of sleep deprivation (using slowly rotating activity wheels) and 1h of sleep opportunity continuously for 4 days ('3/1' protocol), we previously observed not only homeostatic but also allostatic (adaptive) sleep responses to CSR. In particular, non-rapid eye movement sleep (NREMS) electroencephalogram (EEG) delta power, an index of sleep intensity, increased initially and then declined gradually during CSR, with no rebound during a 2-day recovery period. To study underlying mechanisms of these allostatic responses, we examined the levels of brain-derived neurotrophic factor (BDNF), which is known to regulate NREMS EEG delta activity, during the same CSR protocol. Mature BDNF protein levels were measured in the frontal cortex and basal forebrain, two brain regions involved in sleep and EEG regulation, and the hippocampus, using Western blot analysis. Adult male Wistar rats were housed in motorized activity wheels, and underwent the 3/1 CSR protocol for 27 h, for 99 h, or for 99 h followed by 24h of recovery. Additional rats were housed in either locked wheels (locked wheel controls [LWCs]) or unlocked wheels that rats could rotate freely (wheel-running controls [WRCs]). BDNF levels did not differ between WRC and LWC groups. BDNF levels were increased, compared to the control levels, in all three brain regions after 27 h, and were increased less strongly after 99 h, of CSR. After 24h of recovery, BDNF levels were at the control levels. This time course of BDNF levels parallels the previously reported changes in NREMS delta power during the same CSR protocol. Changes in BDNF protein levels in the cortex and basal forebrain may be part of the molecular mechanisms underlying allostatic sleep responses to CSR. PMID:25010399

  15. Adaptive Lighting

    OpenAIRE

    Petersen, Kjell Yngve; Søndergaard, Karin; Kongshaug, Jesper

    2015-01-01

    Adaptive LightingAdaptive lighting is based on a partial automation of the possibilities to adjust the colour tone and brightness levels of light in order to adapt to people’s needs and desires. IT support is key to the technical developments that afford adaptive control systems. The possibilities offered by adaptive lighting control are created by the ways that the system components, the network and data flow can be coordinated through software so that the dynamic variations are controlled i...

  16. Adhesion- and Degranulation-Promoting Adapter Protein Promotes CD8 T Cell Differentiation and Resident Memory Formation and Function during an Acute Infection.

    Science.gov (United States)

    Fiege, Jessica K; Beura, Lalit K; Burbach, Brandon J; Shimizu, Yoji

    2016-09-15

    During acute infections, naive Ag-specific CD8 T cells are activated and differentiate into effector T cells, most of which undergo contraction after pathogen clearance. A small population of CD8 T cells persists as memory to protect against future infections. We investigated the role of adhesion- and degranulation-promoting adapter protein (ADAP) in promoting CD8 T cell responses to a systemic infection. Naive Ag-specific CD8 T cells lacking ADAP exhibited a modest expansion defect early after Listeria monocytogenes or vesicular stomatitis virus infection but comparable cytolytic function at the peak of response. However, reduced numbers of ADAP-deficient CD8 T cells were present in the spleen after the peak of the response. ADAP deficiency resulted in a greater frequency of CD127(+) CD8 memory precursors in secondary lymphoid organs during the contraction phase. Reduced numbers of ADAP-deficient killer cell lectin-like receptor G1(-) CD8 resident memory T (TRM) cell precursors were present in a variety of nonlymphoid tissues at the peak of the immune response, and consequently the total numbers of ADAP-deficient TRM cells were reduced at memory time points. TRM cells that did form in the absence of ADAP were defective in effector molecule expression. ADAP-deficient TRM cells exhibited impaired effector function after Ag rechallenge, correlating with defects in their ability to form T cell-APC conjugates. However, ADAP-deficient TRM cells responded to TGF-β signals and recruited circulating memory CD8 T cells. Thus, ADAP regulates CD8 T cell differentiation events following acute pathogen challenge that are critical for the formation and selected functions of TRM cells in nonlymphoid tissues. PMID:27521337

  17. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    . The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can......Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers...

  18. Adaptive Lighting

    DEFF Research Database (Denmark)

    Petersen, Kjell Yngve; Søndergaard, Karin; Kongshaug, Jesper

    2015-01-01

    Adaptive Lighting Adaptive lighting is based on a partial automation of the possibilities to adjust the colour tone and brightness levels of light in order to adapt to people’s needs and desires. IT support is key to the technical developments that afford adaptive control systems. The possibilities...... offered by adaptive lighting control are created by the ways that the system components, the network and data flow can be coordinated through software so that the dynamic variations are controlled in ways that meaningfully adapt according to people’s situations and design intentions. This book discusses...... distributed differently into an architectural body. We also examine what might occur when light is dynamic and able to change colour, intensity and direction, and when it is adaptive and can be brought into interaction with its surroundings. In short, what happens to an architectural space when artificial...

  19. Adaptive translation as a mechanism of stress response and adaptation

    OpenAIRE

    Pan, Tao

    2013-01-01

    The composition of the cellular proteome is commonly thought to strictly adhere to the genetic code. However, accumulating evidence indicates that cells also regulate the synthesis of mutant protein molecules that deviate from the genetic code. Production of mutant proteins varies in amounts and specificity and generally occurs when cells are stressed or undergo environmental adaptation. The deliberate synthesis of protein mutants suggests that some of these proteins can be useful in cellular...

  20. Adaptive Lighting

    DEFF Research Database (Denmark)

    Petersen, Kjell Yngve; Søndergaard, Karin; Kongshaug, Jesper

    2015-01-01

    Adaptive Lighting Adaptive lighting is based on a partial automation of the possibilities to adjust the colour tone and brightness levels of light in order to adapt to people’s needs and desires. IT support is key to the technical developments that afford adaptive control systems. The possibilities...... offered by adaptive lighting control are created by the ways that the system components, the network and data flow can be coordinated through software so that the dynamic variations are controlled in ways that meaningfully adapt according to people’s situations and design intentions. This book discusses...... the investigations of lighting scenarios carried out in two test installations: White Cube and White Box. The test installations are discussed as large-scale experiential instruments. In these test installations we examine what could potentially occur when light using LED technology is integrated and...

  1. Cleavage of group 1 coronavirus spike proteins: how furin cleavage is traded off against heparan sulfate binding upon cell culture adaptation

    NARCIS (Netherlands)

    Haan, de C.A.M.; Haijema, B.J.; Schellen, P.; Wichgers Schreur, P.J.; Lintelo, te E.; Vennema, H.; Rottier, P.J.M.

    2008-01-01

    A longstanding enigmatic feature of the group 1 coronaviruses is the uncleaved phenotype of their spike protein, an exceptional property among class I fusion proteins. Here, however, we show that some group 1 coronavirus spike proteins carry a furin enzyme recognition motif and can actually be cleav

  2. Adaptive Computing.

    Science.gov (United States)

    Harrell, William

    1999-01-01

    Provides information on various adaptive technology resources available to people with disabilities. (Contains 19 references, an annotated list of 129 websites, and 12 additional print resources.) (JOW)

  3. ADAPT Dataset

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Diagnostics and Prognostics Testbed (ADAPT) Project Lead: Scott Poll Subject Fault diagnosis in electrical power systems Description The Advanced...

  4. Expression of protein encoded by apoptosis-associated gene p53, bcl-2, and bax in adaptive response of thymocyte apoptosis in mice induced by low dose radiation with X-rays

    International Nuclear Information System (INIS)

    Objective: To explore the regulative mechanism of apoptosis-associated gene proteins on the adaptive response of thymocyte apoptosis in mice induced by low dose radiation with X-rays. Methods: Kunming male mice were irradiated with the inductive doses (D1: 25, 50, 75, 100 and 200 mGy; dose rate: 12.5 mGy ·min-1) and the challenging dose (D2: 1.5 Gy; dose rate: 287 mGy·min-1). The time interval between D1 and D2 was 6 h. The expressive levels of thymocyte apoptosis-associated gene proteins were measured with flow cytometry. Results: As compared with the sham-irradiation, the positive percentage of thymocyte Bcl-2 protein expression decreased significantly in D2 group (P<0.05), Bax increased significantly (P<0.05), and Bcl-2/Bax decreased significantly (P<0.001); p 53 increased significantly (P<0.001). As compared with D2 group, the positive percentage of thymocyte Bcl-2 protein expression increased in varying degree in D1+ D2 group of 25-75 mGy D1, Bax decreased in varying degree, and Bcl-2/Bax increased significantly (P<0.01); p53 decreased significantly (P<0.001 or P<0.05). Conclusion: The apoptotic thymocytes in the adaptive response of thymocyte apoptosis in mice induced by irradiation with 25-75 mGy decrease significantly due to the increase of apoptosis-associated gene Bcl-2 protein expression and Bcl-2/Bax, the decrease of Bax and p53 protein expressions. (authors)

  5. Expression of cold-adapted β-1,3-xylanase as a fusion protein with a ProS2 tag and purification using immobilized metal affinity chromatography with a high concentration of ArgHCl.

    Science.gov (United States)

    Kudou, Motonori; Okazaki, Fumiyoshi; Asai-Nakashima, Nanami; Ogino, Chiaki; Kondo, Akihiko

    2015-01-01

    Cold-adapted β-1,3-xylanase (P.t.Xyn26A) from the psychrotrophic bacterium, Psychroflexus torquis, was expressed as a fusion protein with tandem repeats of the N-terminal domain of Protein S from Myxocuccus xanthus (ProS2) in Escherichia coli. After cell lysis in phosphate buffer, most of the ProS2-P.t.Xyn26A was located in the insoluble fraction and aggregated during purification. Arginine hydrochloride (ArgHCl) efficiently solubilized the ProS2-P.t.Xyn26A. The solubilized ProS2-P.t.Xyn26A was purified using immobilized metal affinity chromatography (IMAC) with 500 mM ArgHCl. After cleavage of ProS2-P.t.Xyn26A by human rhinovirus 3C protease, we confirmed that recombinant P.t.Xyn26A maintained its native fold. This is the first report of the expression of a cold-adapted enzyme fused with a ProS2 tag under IMAC purification using a high concentration of ArgHCl. These insights into the expression and purification should be useful during the handling of cold-adapted enzymes. PMID:25214227

  6. Is adaptation. Truly an adaptation? Is adaptation. Truly an adaptation?

    Directory of Open Access Journals (Sweden)

    Thais Flores Nogueira Diniz

    2008-04-01

    Full Text Available The article begins by historicizing film adaptation from the arrival of cinema, pointing out the many theoretical approaches under which the process has been seen: from the concept of “the same story told in a different medium” to a comprehensible definition such as “the process through which works can be transformed, forming an intersection of textual surfaces, quotations, conflations and inversions of other texts”. To illustrate this new concept, the article discusses Spike Jonze’s film Adaptation. according to James Naremore’s proposal which considers the study of adaptation as part of a general theory of repetition, joined with the study of recycling, remaking, and every form of retelling. The film deals with the attempt by the scriptwriter Charles Kaufman, cast by Nicholas Cage, to adapt/translate a non-fictional book to the cinema, but ends up with a kind of film which is by no means what it intended to be: a film of action in the model of Hollywood productions. During the process of creation, Charles and his twin brother, Donald, undergo a series of adventures involving some real persons from the world of film, the author and the protagonist of the book, all of them turning into fictional characters in the film. In the film, adaptation then signifies something different from itstraditional meaning. The article begins by historicizing film adaptation from the arrival of cinema, pointing out the many theoretical approaches under which the process has been seen: from the concept of “the same story told in a different medium” to a comprehensible definition such as “the process through which works can be transformed, forming an intersection of textual surfaces, quotations, conflations and inversions of other texts”. To illustrate this new concept, the article discusses Spike Jonze’s film Adaptation. according to James Naremore’s proposal which considers the study of adaptation as part of a general theory of repetition

  7. Radio-adaptive response

    International Nuclear Information System (INIS)

    An adaptive response to radiation stress was found as a suppressed induction of chromosomal damage including micronuclei and sister chromatid exchanges in cultured Chinese hamster V79 cells pre-exposed to very low doses of ionizing radiations. The mechanism underlying this novel chromosomal response, called 'radio-adaptive response (RAR)' has been studied progressively. The following results were obtained in recent experiments. 1. Low doses of β-rays from tritiated water (HTO) as well as tritium-thymidine can cause RAR. 2. Thermal neutrons, a high LET radiation, can not act as tritium β-rays or γ-rays. 3. The RAR expression is suppressed not only by the treatment with an inhibitor of protein synthesis but also by RNA synthesis inhibition. 4. Several proteins are newly synthesized concurrently with the RAR expression after the adapting doses, viewed by two-dimensional electrophoresis of cellular proteins. These results suggests that the RAR might be a cellular stress response to a signal produced preferentially by very low doses of low LET radiation under restricted conditions, accompany the inducible specific gene expression. (author)

  8. Adaptive test

    DEFF Research Database (Denmark)

    Kjeldsen, Lars Peter; Eriksen, Mette Rose

    2010-01-01

    Artikelen er en evaluering af de adaptive tests, som blev indført i folkeskolen. Artiklen sætter særligt fokus på evaluering i folkeskolen, herunder bidrager den med vejledning til evaluering, evalueringsværktøjer og fagspecifkt evalueringsmateriale.......Artikelen er en evaluering af de adaptive tests, som blev indført i folkeskolen. Artiklen sætter særligt fokus på evaluering i folkeskolen, herunder bidrager den med vejledning til evaluering, evalueringsværktøjer og fagspecifkt evalueringsmateriale....

  9. Strategic Adaptation

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    2015-01-01

    This article provides an overview of theoretical contributions that have influenced the discourse around strategic adaptation including contingency perspectives, strategic fit reasoning, decision structure, information processing, corporate entrepreneurship, and strategy process. The related...... concepts of strategic renewal, dynamic managerial capabilities, dynamic capabilities, and strategic response capabilities are discussed and contextualized against strategic responsiveness. The insights derived from this article are used to outline the contours of a dynamic process of strategic adaptation....... This model incorporates elements of central strategizing, autonomous entrepreneurial behavior, interactive information processing, and open communication systems that enhance the organization's ability to observe exogenous changes and respond effectively to them....

  10. Adaptive management

    Science.gov (United States)

    Allen, Craig R.; Garmestani, Ahjond S.

    2015-01-01

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive management has explicit structure, including a careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. The process is iterative, and serves to reduce uncertainty, build knowledge and improve management over time in a goal-oriented and structured process.

  11. Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide Periplasmic Binding Protein Fold

    Energy Technology Data Exchange (ETDEWEB)

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W.; (Duke)

    2010-05-25

    Periplasmic binding proteins (PBPs) constitute a protein superfamily that binds a wide variety of ligands. In prokaryotes, PBPs function as receptors for ATP-binding cassette or tripartite ATP-independent transporters and chemotaxis systems. In many instances, PBPs bind their cognate ligands with exquisite specificity, distinguishing, for example, between sugar epimers or structurally similar anions. By contrast, oligopeptide-binding proteins bind their ligands through interactions with the peptide backbone but do not distinguish between different side chains. The extremophile Thermotoga maritima possesses a remarkable array of carbohydrate-processing metabolic systems, including the hydrolysis of cellulosic polymers. Here, we present the crystal structure of a T. maritima cellobiose-binding protein (tm0031) that is homologous to oligopeptide-binding proteins. T. maritima cellobiose-binding protein binds a variety of lengths of {beta}(1 {yields} 4)-linked glucose oligomers, ranging from two rings (cellobiose) to five (cellopentaose). The structure reveals that binding is semi-specific. The disaccharide at the nonreducing end binds specifically; the other rings are located in a large solvent-filled groove, where the reducing end makes several contacts with the protein, thereby imposing an upper limit of the oligosaccharides that are recognized. Semi-specific recognition, in which a molecular class rather than individual species is selected, provides an efficient solution for the uptake of complex mixtures.

  12. Molecular evolution and thermal adaptation

    Science.gov (United States)

    Chen, Peiqiu

    2011-12-01

    In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

  13. Estimation of immune complexes by a microplate-adapted C1q-Protein A enzyme-linked-immunosorbent-assay (C1q-PA-ELISA)

    DEFF Research Database (Denmark)

    Bjerrum, L; Glikmann, G; Jensenius, J C;

    1983-01-01

    . Bound IC was measured by use of alkaline phosphatase-labelled Protein A followed by the substrate para-nitro-phenyl-phosphate. A dose response was found for both delta IgG and BSA anti-BSA complexes, while variations in the concentration of monomer IgG did not affect the optical density. Elevated levels...

  14. The Adaptive Evolution Database (TAED)

    OpenAIRE

    Liberles, David A; Schreiber, David R.; Govindarajan, Sridhar; Chamberlin, Stephen G.; Steven A Benner

    2001-01-01

    Background The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotid...

  15. [Cellular adaptation and cancerogenesis].

    Science.gov (United States)

    La Torre, F; Silpigni, A; Tomasello, R; Picone, G S; La Torre, I; Aragona, M

    1998-06-01

    The paper describes the main adaptive mechanisms involved in the carcinogenic process. As a result of the action of carcinogenic agents (physical, chemical, biological), and in relation to the functional status of the affected cells, a number of systems are triggered off: detoxification and conjugation systems, the metabolisation of the said agents, DNA repairing enzymes, increased shock proteins (HSP), the induction of clonal proliferation. All these systems are valuable to the survival of the body and the species and culminate in the apoptosis of damaged cells as the last attempt at adaptation of a social kind for the good of the body. When these compensation mechanisms prove ineffective, imprecise or are exceeded by cell adaptive capacity, the resulting structural and functional alterations trigger off (induction) a very long process which often lasts between one and two thirds of the body's life, in various stages, multistep and multifactorial: this neoplastic transformation leads to a purposeless, egoistic, anarchic proliferation of cells which wish to survive at all costs, even to the detriment of the body of which they form part. Following the exhaustion of cell adaptive defences, there is an accumulation of additional genetic alterations (promotion and progression), the cells become manifestly neoplastic and continue their egoistic adaptation, according to the laws of natural selection: the cells which survive are those which adapt best to the hostile environment of the host's body, which are unaffected by proliferation control mechanisms (contact inhibition, differentiation factors, apoptosis, etc.), which make the best of the growth factors present in their microenvironment, which accomplish the so-called decathlon of the metastatization process, namely acquiring new capacities which can overcome the basal membrane, invade tissues to which they are attracted and continue to proliferate. Manifestly neoplastic cells become not self at a later stage

  16. Proteomics-based Identification of Proapoptotic Caspase Adapter Protein 
as A Novel Serum Marker of Non-small Cell Lung Cancer

    OpenAIRE

    Zhang, Heng; Chen, Shengxi; Huang, Lingjin

    2012-01-01

    Background and objective Early diagnosis and treatment of lung cancer contribute to a patient’s prolonged survival. Proteomics and tissue culture were used to screen potential serum markers of lung cancer. Methods The differential proteomic technique and matrix-assisted laser desorption/ionization-time of flight mass spectrometry were used to identify overexpressed proteins from cultured tumor tissues in a conditioned medium. Paired lung tissues in a conditioned medium were used as the contro...

  17. Adaptation Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Huq, Saleemul

    2011-11-15

    Efforts to help the world's poor will face crises in coming decades as climate change radically alters conditions. Action Research for Community Adapation in Bangladesh (ARCAB) is an action-research programme on responding to climate change impacts through community-based adaptation. Set in Bangladesh at 20 sites that are vulnerable to floods, droughts, cyclones and sea level rise, ARCAB will follow impacts and adaptation as they evolve over half a century or more. National and international 'research partners', collaborating with ten NGO 'action partners' with global reach, seek knowledge and solutions applicable worldwide. After a year setting up ARCAB, we share lessons on the programme's design and move into our first research cycle.

  18. Adaptive ethnography

    DEFF Research Database (Denmark)

    Berth, Mette

    2005-01-01

    This paper focuses on the use of an adaptive ethnography when studying such phenomena as young people's use of mobile media in a learning perspective. Mobile media such as PDAs and mobile phones have a number of affordances which make them potential tools for learning. However, before we begin...... formal and informal learning contexts. The paper also proposes several adaptive methodological techniques for studying young people's interaction with mobiles....... to design and develop educational materials for mobile media platforms we must first understand everyday use and behaviour with a medium such as a mobile phone. The paper outlines the research design for a PhD project on mobile learning which focuses on mobile phones as a way to bridge the gap between...

  19. Hedonic "adaptation"

    Directory of Open Access Journals (Sweden)

    Paul Rozin

    2008-02-01

    Full Text Available People live in a world in which they are surrounded by potential disgust elicitors such as ``used'' chairs, air, silverware, and money as well as excretory activities. People function in this world by ignoring most of these, by active avoidance, reframing, or adaptation. The issue is particularly striking for professions, such as morticians, surgeons, or sanitation workers, in which there is frequent contact with major disgust elicitors. In this study, we study the ``adaptation'' process to dead bodies as disgust elicitors, by measuring specific types of disgust sensitivity in medical students before and after they have spent a few months dissecting a cadaver. Using the Disgust Scale, we find a significant reduction in disgust responses to death and body envelope violation elicitors, but no significant change in any other specific type of disgust. There is a clear reduction in discomfort at touching a cold dead body, but not in touching a human body which is still warm after death.

  20. Adaptive noise

    OpenAIRE

    Viney, Mark; Reece, Sarah E.

    2013-01-01

    In biology, noise implies error and disorder and is therefore something which organisms may seek to minimize and mitigate against. We argue that such noise can be adaptive. Recent studies have shown that gene expression can be noisy, noise can be genetically controlled, genes and gene networks vary in how noisy they are and noise generates phenotypic differences among genetically identical cells. Such phenotypic differences can have fitness benefits, suggesting that evolution can shape noise ...

  1. Adaptable positioner

    International Nuclear Information System (INIS)

    This paper describes the circuits and programs in assembly language, developed to control the two DC motors that give mobility to a mechanical arm with two degrees of freedom. As a whole, the system is based in a adaptable regulator designed around a 8 bit microprocessor that, starting from a mode of regulation based in the successive approximation method, evolve to another mode through which, only one approximation is sufficient to get the right position of each motor. (Author) 22 fig. 6 ref

  2. Nutrition and training adaptations in aquatic sports.

    Science.gov (United States)

    Mujika, Iñigo; Stellingwerff, Trent; Tipton, Kevin

    2014-08-01

    The adaptive response to training is determined by the combination of the intensity, volume, and frequency of the training. Various periodized approaches to training are used by aquatic sports athletes to achieve performance peaks. Nutritional support to optimize training adaptations should take periodization into consideration; that is, nutrition should also be periodized to optimally support training and facilitate adaptations. Moreover, other aspects of training (e.g., overload training, tapering and detraining) should be considered when making nutrition recommendations for aquatic athletes. There is evidence, albeit not in aquatic sports, that restricting carbohydrate availability may enhance some training adaptations. More research needs to be performed, particularly in aquatic sports, to determine the optimal strategy for periodizing carbohydrate intake to optimize adaptations. Protein nutrition is an important consideration for optimal training adaptations. Factors other than the total amount of daily protein intake should be considered. For instance, the type of protein, timing and pattern of protein intake and the amount of protein ingested at any one time influence the metabolic response to protein ingestion. Body mass and composition are important for aquatic sport athletes in relation to power-to-mass and for aesthetic reasons. Protein may be particularly important for athletes desiring to maintain muscle while losing body mass. Nutritional supplements, such as b-alanine and sodium bicarbonate, may have particular usefulness for aquatic athletes' training adaptation.

  3. Harmonin-b, an actin-binding scaffold protein, is involved in the adaptation of mechanoelectrical transduction by sensory hair cells

    OpenAIRE

    Michalski, Nicolas; Michel, Vincent; Caberlotto, Elisa; Lefèvre, Gaelle M.; Van Aken, Alexander F J; Tinevez, Jean-Yves; Bizard, Emilie; Houbron, Christophe; Weil, Dominique; Hardelin, Jean-Pierre; Richardson, Guy P.; Kros, Corné J.; Martin, Pascal; Petit, Christine

    2009-01-01

    We assessed the involvement of harmonin-b, a submembranous protein containing PDZ domains, in the mechanoelectrical transduction machinery of inner ear hair cells. Harmonin-b is located in the region of the upper insertion point of the tip link that joins adjacent stereocilia from different rows and that is believed to gate transducer channel(s) located in the region of the tip link's lower insertion point. In Ush1c dfcr-2J/dfcr-2J mutant mice defective for harmonin-b, step deflections of the...

  4. Capsid proteins from field strains of foot-and-mouth disease virus confer a pathogenic phenotype in cattle on an attenuated, cell-culture-adapted virus

    DEFF Research Database (Denmark)

    Bøtner, Anette; Kakker, Naresh K.; Barbezange, Cyril;

    2011-01-01

    cells than the rescued parental O1K B64 virus. The two chimeric viruses displayed the expected antigenicity in serotype-specific antigen ELISAs. Following inoculation of each virus into cattle, the rescued O1K B64 strain proved to be attenuated whereas, with each chimeric virus, typical clinical signs......Chimeric foot-and-mouth disease viruses (FMDVs) have been generated from plasmids containing full-length FMDV cDNAs and characterized. The parental virus cDNA was derived from the cell-culture-adapted O1Kaufbeuren B64 (O1K B64) strain. Chimeric viruses, containing capsid coding sequences derived...... from the O/UKG/34/2001 or A/Turkey 2/2006 field viruses, were constructed using the backbone from the O1K B64 cDNA, and viable viruses (O1K/O-UKG and O1K/A-Tur, respectively) were successfully rescued in each case. These viruses grew well in primary bovine thyroid cells but grew less efficiently in BHK...

  5. Adaptive changes of pancreatic protease secretion to a short-term vegan diet: influence of reduced intake and modification of protein.

    Science.gov (United States)

    Walkowiak, Jaroslaw; Mądry, Edyta; Lisowska, Aleksandra; Szaflarska-Popławska, Anna; Grzymisławski, Marian; Stankowiak-Kulpa, Hanna; Przysławski, Juliusz

    2012-01-01

    In our previous study, we demonstrated that abstaining from meat, for 1 month, by healthy omnivores (lacto-ovovegetarian model) resulted in a statistical decrease in pancreatic secretion as measured by faecal elastase-1 output. However, no correlation between relative and non-relative changes of energy and nutrient consumption and pancreatic secretion was documented. Therefore, in the present study, we aimed to assess the changes of exocrine pancreatic secretion with a more restrictive dietetic modification, by applying a vegan diet. A total of twenty-one healthy omnivores (sixteen females and five males) participated in the prospective study lasting for 6 weeks. The nutrient intake and faecal output of pancreatic enzymes (elastase-1, chymotrypsin and lipase) were assessed twice during the study. Each assessment period lasted for 7 d: the first before the transition to the vegan diet (omnivore diet) and the second during the last week of the study (vegan diet). The dietary modification resulted in a significant decrease in faecal elastase-1 (P vegan diet resulted in an adaptation of pancreatic protease secretion in healthy volunteers.

  6. Genome-Wide Analysis of Genes Encoding Methionine-Rich Proteins in Arabidopsis and Soybean Suggesting Their Roles in the Adaptation of Plants to Abiotic Stress.

    Science.gov (United States)

    Chu, Ha Duc; Le, Quynh Ngoc; Nguyen, Huy Quang; Le, Dung Tien

    2016-01-01

    Oxidation and reduction of methionine (Met) play important roles in scavenging reactive oxygen species (ROS) and signaling in living organisms. To understand the impacts of Met oxidation and reduction in plants during stress, we surveyed the genomes of Arabidopsis and soybean (Glycine max L.) for genes encoding Met-rich proteins (MRPs). We found 121 and 213 genes encoding MRPs in Arabidopsis and soybean, respectively. Gene annotation indicated that those with known function are involved in vital cellular processes such as transcriptional control, calcium signaling, protein modification, and metal transport. Next, we analyzed the transcript levels of MRP-coding genes under normal and stress conditions. We found that 57 AtMRPs were responsive either to drought or to high salinity stress in Arabidopsis; 35 GmMRPs were responsive to drought in the leaf of late vegetative or early reproductive stages of soybean. Among the MRP genes with a known function, the majority of the abiotic stress-responsive genes are involved in transcription control and calcium signaling. Finally, Arabidopsis plant which overexpressed an MRP-coding gene, whose transcripts were downregulated by abiotic stress, was more sensitive to paraquat than the control. Taken together, our report indicates that MRPs participate in various vital processes of plants under normal and stress conditions. PMID:27635394

  7. Efficacy of an adapted granzyme B-based anti-CD30 cytolytic fusion protein against PI-9-positive classical Hodgkin lymphoma cells in a murine model

    International Nuclear Information System (INIS)

    Tumors develop when infiltrating immune cells contribute growth stimuli, and cancer cells are selected to survive within such a cytotoxic microenvironment. One possible immune-escape mechanism is the upregulation of PI-9 (Serpin B9) within cancer cells. This serine proteinase inhibitor selectively inactivates apoptosis-inducing granzyme B (GrB) from cytotoxic granules of innate immune cells. We demonstrate that most classical Hodgkin lymphoma (cHL)-derived cell lines express PI-9, which protects them against the GrB attack and thereby renders them resistant against GrB-based immunotherapeutics. To circumvent this disadvantage, we developed PI-9-insensitive human GrB mutants as fusion proteins to target the Hodgkin-selective receptor CD30. In contrast to the wild-type GrB, a R201K point-mutated GrB construct most efficiently killed PI-9-positive and -negative cHL cells. This was tested in vitro and also in vivo whereby a novel optical imaging-based tumor model with HL cell line L428 was applied. Therefore, this variant, as part of the next generation immunotherapeutics, also named cytolytic fusion proteins showing reduced immunogenicity, is a promising molecule for (targeted) therapy of patients with relapsing malignancies, such as cHL, and possibly other PI-9-positive malignancies, such as breast or lung carcinoma

  8. Genome-Wide Analysis of Genes Encoding Methionine-Rich Proteins in Arabidopsis and Soybean Suggesting Their Roles in the Adaptation of Plants to Abiotic Stress

    Science.gov (United States)

    Chu, Ha Duc; Le, Quynh Ngoc; Nguyen, Huy Quang

    2016-01-01

    Oxidation and reduction of methionine (Met) play important roles in scavenging reactive oxygen species (ROS) and signaling in living organisms. To understand the impacts of Met oxidation and reduction in plants during stress, we surveyed the genomes of Arabidopsis and soybean (Glycine max L.) for genes encoding Met-rich proteins (MRPs). We found 121 and 213 genes encoding MRPs in Arabidopsis and soybean, respectively. Gene annotation indicated that those with known function are involved in vital cellular processes such as transcriptional control, calcium signaling, protein modification, and metal transport. Next, we analyzed the transcript levels of MRP-coding genes under normal and stress conditions. We found that 57 AtMRPs were responsive either to drought or to high salinity stress in Arabidopsis; 35 GmMRPs were responsive to drought in the leaf of late vegetative or early reproductive stages of soybean. Among the MRP genes with a known function, the majority of the abiotic stress-responsive genes are involved in transcription control and calcium signaling. Finally, Arabidopsis plant which overexpressed an MRP-coding gene, whose transcripts were downregulated by abiotic stress, was more sensitive to paraquat than the control. Taken together, our report indicates that MRPs participate in various vital processes of plants under normal and stress conditions.

  9. Variations in the Regulatory Region of Alpha S1-Casein Milk Protein Gene among Tropically Adapted Indian Native (Bos Indicus) Cattle

    Science.gov (United States)

    Kishore, Amit; Mukesh, Manishi; Sobti, Ranbir C.; Mishra, Bishnu P.; Sodhi, Monika

    2013-01-01

    Regulatory region of milk protein alpha S1-casein (αS1-CN) gene was sequenced, characterized, and analyzed to detect variations among 13 Indian cattle (Bos indicus) breeds. Comparative analysis of 1,587 bp region comprising promoter (1,418 bp), exon-I (53 bp), and partial intron-I (116 bp) revealed 35 nucleotide substitutions (32 within promoter region, 1 in exon-I, and 2 in partial intron-I region) and 4 Indels. Within promoter, 15 variations at positions −1399 (A > G), −1288 (G > A), −1259 (T > C), −1158 (T > C), −1016 (A > T), −941 (T > G), −778 (C > T), −610 (G > A), −536 (A > G), −521 (A > G), −330 (A > C), −214 (A > G), −205 (A > T), −206 (C > A), and −175 (A > G) were located within the potential transcription factor binding sites (TFBSs), namely, NF-κE1/c-Myc, GATA-1, GATA-1/NF-E, Oct-1/POU3F2, MEF-2/YY1, GATA-1, AP-1, POU1F1a/GR, TMF, GAL4, YY1/Oct-1, HNF-1, GRalpha/AR, GRalpha/AR, and AP-1, respectively. Seventy-four percent (26/35) of the observed SNPs were novel to Indian cattle and 11 of these novel SNPs were located within one or more TFBSs. Collectively, these might influence the binding affinity towards their respective nuclear TFs thus modulating the level of transcripts in milk and affecting overall protein composition. The study provides information on several distinct variations across indicine and taurine αS1-CN regulatory domains. PMID:25937984

  10. Adaptive management

    DEFF Research Database (Denmark)

    Rist, Lucy; Campbell, Bruce Morgan; Frost, Peter

    2013-01-01

    in scientific articles, policy documents and management plans, but both understanding and application of the concept is mixed. This paper reviews recent literature from conservation and natural resource management journals to assess diversity in how the term is used, highlight ambiguities and consider how...... a management framework, as well as of identified challenges and pathologies, are needed. Further discussion and systematic assessment of the approach is required, together with greater attention to its definition and description, enabling the assessment of new approaches to managing uncertainty, and AM itself.......Adaptive management (AM) emerged in the literature in the mid-1970s in response both to a realization of the extent of uncertainty involved in management, and a frustration with attempts to use modelling to integrate knowledge and make predictions. The term has since become increasingly widely used...

  11. Gene 33/Mig-6, a transcriptionally inducible adapter protein that binds GTP-Cdc42 and activates SAPK/JNK. A potential marker transcript for chronic pathologic conditions, such as diabetic nephropathy. Possible role in the response to persistent stress.

    Science.gov (United States)

    Makkinje, A; Quinn, D A; Chen, A; Cadilla, C L; Force, T; Bonventre, J V; Kyriakis, J M

    2000-06-01

    Chronic stresses, including the mechanical strain caused by hypertension or excess pulmonary ventilation pressure, lead to important clinical consequences, including hypertrophy and acute respiratory distress syndrome. Pathologic hypertrophy contributes to decreased organ function and, ultimately, organ failure; and cardiac and diabetic renal hypertrophy are major causes of morbidity and morality in the developed world. Likewise, acute respiratory distress syndrome is a serious potential side effect of mechanical pulmonary ventilation. Whereas the deleterious effects of chronic stress are well established, the molecular mechanisms by which these stresses affect cell function are still poorly characterized. gene 33 (also called mitogen-inducible gene-6, mig-6) is an immediate early gene that is transcriptionally induced by a divergent array of extracellular stimuli. The physiologic function of Gene 33 is unknown. Here we show that gene 33 mRNA levels increase sharply in response to a set of commonly occurring chronic stress stimuli: mechanical strain, vasoactive peptides, and diabetic nephropathy. Induction of gene 33 requires the stress-activated protein kinases (SAPKs)/c-Jun NH(2)-terminal kinases. This expression pattern suggests that gene 33 is a potential marker for diabetic nephropathy and other pathologic responses to persistent sublethal stress. The structure of Gene 33 indicates an adapter protein capable of binding monomeric GTPases of the Rho subfamily. Consistent with this, Gene 33 interacts in vivo and, in a GTP-dependent manner, in vitro with Cdc42Hs; and transient expression of Gene 33 results in the selective activation of the SAPKs. These results imply a reciprocal, positive feedback relationship between Gene 33 expression and SAPK activation. Expression of Gene 33 at sufficient levels may enable a compensatory reprogramming of cellular function in response to chronic stress, which may have pathophysiological consequences. PMID:10749885

  12. Adaptation in CRISPR-Cas Systems.

    Science.gov (United States)

    Sternberg, Samuel H; Richter, Hagen; Charpentier, Emmanuelle; Qimron, Udi

    2016-03-17

    Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in prokaryotes. The system preserves memories of prior infections by integrating short segments of foreign DNA, termed spacers, into the CRISPR array in a process termed adaptation. During the past 3 years, significant progress has been made on the genetic requirements and molecular mechanisms of adaptation. Here we review these recent advances, with a focus on the experimental approaches that have been developed, the insights they generated, and a proposed mechanism for self- versus non-self-discrimination during the process of spacer selection. We further describe the regulation of adaptation and the protein players involved in this fascinating process that allows bacteria and archaea to harbor adaptive immunity.

  13. Biochemical adaptation to ocean acidification.

    Science.gov (United States)

    Stillman, Jonathon H; Paganini, Adam W

    2015-06-01

    The change in oceanic carbonate chemistry due to increased atmospheric PCO2  has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2 . From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid-base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the

  14. Adaptively robust filtering with classified adaptive factors

    Institute of Scientific and Technical Information of China (English)

    CUI Xianqiang; YANG Yuanxi

    2006-01-01

    The key problems in applying the adaptively robust filtering to navigation are to establish an equivalent weight matrix for the measurements and a suitable adaptive factor for balancing the contributions of the measurements and the predicted state information to the state parameter estimates. In this paper, an adaptively robust filtering with classified adaptive factors was proposed, based on the principles of the adaptively robust filtering and bi-factor robust estimation for correlated observations. According to the constant velocity model of Kalman filtering, the state parameter vector was divided into two groups, namely position and velocity. The estimator of the adaptively robust filtering with classified adaptive factors was derived, and the calculation expressions of the classified adaptive factors were presented. Test results show that the adaptively robust filtering with classified adaptive factors is not only robust in controlling the measurement outliers and the kinematic state disturbing but also reasonable in balancing the contributions of the predicted position and velocity, respectively, and its filtering accuracy is superior to the adaptively robust filter with single adaptive factor based on the discrepancy of the predicted position or the predicted velocity.

  15. Biodiversity and cold adaptive mechanisms of psychrophiles

    Directory of Open Access Journals (Sweden)

    Yuhua Xin

    2013-07-01

    Full Text Available Cold-adapted bacteria and archaea are widely distributed in cold environments on Earth, such as permafrost, cold soils and deserts, glaciers, lakes, sea ice in the Arctic, Antarctic and high mountains, as well as the deep sea, ice caves and the atmospheric stratosphere etc. Cold-adapted organisms inhabiting these environments exhibit rich diversity. Studies on the biogeography of psychrophiles will enable us to understand their biodiversity, distribution and origins. Due to long-term living in cold regions, cold-adapted bacteria and archeae have developed specific physiological mechanisms of adaptation to cold environments. These mechanisms include: regulating the fluidity of the cytoplasmic membrane through adjusting the composition of membrane lipids; achieving low-temperature protection through compatibility solute, antifreeze proteins, ice-binding proteins, ice-nucleation proteins and anti-nucleating proteins; production of heat-shock and coldshock proteins, cold acclimation protein and DEAD-box RNA helicase at low temperatures; production of cold-active enzymes; increasing energy generation and conservation. With the rapid development of sequencing technology, various omics-based approaches have been used to reveal cold-adaptive mechanisms of psychrophiles at the genomic level.

  16. Adaptive Image Denoising by Mixture Adaptation.

    Science.gov (United States)

    Luo, Enming; Chan, Stanley H; Nguyen, Truong Q

    2016-10-01

    We propose an adaptive learning procedure to learn patch-based image priors for image denoising. The new algorithm, called the expectation-maximization (EM) adaptation, takes a generic prior learned from a generic external database and adapts it to the noisy image to generate a specific prior. Different from existing methods that combine internal and external statistics in ad hoc ways, the proposed algorithm is rigorously derived from a Bayesian hyper-prior perspective. There are two contributions of this paper. First, we provide full derivation of the EM adaptation algorithm and demonstrate methods to improve the computational complexity. Second, in the absence of the latent clean image, we show how EM adaptation can be modified based on pre-filtering. The experimental results show that the proposed adaptation algorithm yields consistently better denoising results than the one without adaptation and is superior to several state-of-the-art algorithms. PMID:27416593

  17. Adaptive Modular Playware

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop; Þorsteinsson, Arnar Tumi

    2011-01-01

    In this paper, we describe the concept of adaptive modular playware, where the playware adapts to the interaction of the individual user. We hypothesize that there are individual differences in user interaction capabilities and styles, and that adaptive playware may adapt to the individual user’s...

  18. Expressing Adaptation Strategies Using Adaptation Patterns

    Science.gov (United States)

    Zemirline, N.; Bourda, Y.; Reynaud, C.

    2012-01-01

    Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition…

  19. The many shades of prion strain adaptation.

    Science.gov (United States)

    Baskakov, Ilia V

    2014-01-01

    In several recent studies transmissible prion disease was induced in animals by inoculation with recombinant prion protein amyloid fibrils produced in vitro. Serial transmission of amyloid fibrils gave rise to a new class of prion strains of synthetic origin. Gradual transformation of disease phenotypes and PrP(Sc) properties was observed during serial transmission of synthetic prions, a process that resembled the phenomenon of prion strain adaptation. The current article discusses the remarkable parallels between phenomena of prion strain adaptation that accompanies cross-species transmission and the evolution of synthetic prions occurring within the same host. Two alternative mechanisms underlying prion strain adaptation and synthetic strain evolution are discussed. The current article highlights the complexity of the prion transmission barrier and strain adaptation and proposes that the phenomenon of prion adaptation is more common than previously thought.

  20. Adaptive Rationality, Adaptive Behavior and Institutions

    Directory of Open Access Journals (Sweden)

    Volchik Vyacheslav, V.

    2015-12-01

    Full Text Available The economic literature focused on understanding decision-making and choice processes reveals a vast collection of approaches to human rationality. Theorists’ attention has moved from absolutely rational, utility-maximizing individuals to boundedly rational and adaptive ones. A number of economists have criticized the concepts of adaptive rationality and adaptive behavior. One of the recent trends in the economic literature is to consider humans irrational. This paper offers an approach which examines adaptive behavior in the context of existing institutions and constantly changing institutional environment. It is assumed that adaptive behavior is a process of evolutionary adjustment to fundamental uncertainty. We emphasize the importance of actors’ engagement in trial and error learning, since if they are involved in this process, they obtain experience and are able to adapt to existing and new institutions. The paper aims at identifying relevant institutions, adaptive mechanisms, informal working rules and practices that influence actors’ behavior in the field of Higher Education in Russia (Rostov Region education services market has been taken as an example. The paper emphasizes the application of qualitative interpretative methods (interviews and discourse analysis in examining actors’ behavior.

  1. Principles of adaptive optics

    CERN Document Server

    Tyson, Robert

    2010-01-01

    History and BackgroundIntroductionHistoryPhysical OpticsTerms in Adaptive OpticsSources of AberrationsAtmospheric TurbulenceThermal BloomingNonatmospheric SourcesAdaptive Optics CompensationPhase ConjugationLimitations of Phase ConjugationArtificial Guide StarsLasers for Guide StarsCombining the LimitationsLinear AnalysisPartial Phase ConjugationAdaptive Optics SystemsAdaptive Optics Imaging SystemsBeam Propagation Syst

  2. Adaptation to climate change

    NARCIS (Netherlands)

    J. Carmin; K. Tierney; E. Chu; L.M. Hunter; J.T. Roberts; L. Shi

    2015-01-01

    Climate change adaptation involves major global and societal challenges such as finding adequate and equitable adaptation funding and integrating adaptation and development programs. Current funding is insufficient. Debates between the Global North and South center on how best to allocate the financ

  3. Adaptation to High Grain Diets Proceeds Through Minimal Immune System Stimulation and Differences in Extracellular Matrix Protein Expression in A Model of Subacute Ruminal Acidosis in Non-lactating Dairy Cows

    Directory of Open Access Journals (Sweden)

    L. Dionissopoulos

    2012-01-01

    Full Text Available Problem statement: Subacute Ruminal Acidosis (SARA is a metabolic disorder affecting approximately 20% of all dairy cattle in North America. Although the presence of SARA has been described for some time, the etiology of the disorder remains uncertain. For example, many animals diagnosed with SARA seem to remodel and adapt their epithelium to accommodate the stresses imposed by SARA, but not before exacting a significant health and economic toll. Specifically, a search is on in which a desire to identify the system and associated pathways that are causative agents in the progression and development of SARA is evident. We hypothesize that adaptation to SARA is facilitated by the immune system. Approach: In order to answer of this question, 4 mature, non-lactating dairy cattle were transitioned from a High Fiber (HF; 0% grain diet to High Grain (HG; 65% grain diet. Having fed the HG diet for three weeks, the cattle were then transitioned back to the HF diet for an additional three weeks to facilitate adaptation. SARA was diagnosed by pH data only during the first week and not during the remaining weeks, indicating that adaptation to the HG diet took place within one week. Results: In this study, significant (pConclusion: These results indicate that the immune system is involved in the adaptation of the rumen epithelium to a HG diet, but to a lesser extent than was previously thought. This is the first time an attempt has been made to link the immune system and wound healing in the adaptation of the bovine rumen to a HG diet."""

  4. Venom Evolution: Gene Loss Shapes Phenotypic Adaptation.

    Science.gov (United States)

    Casewell, Nicholas R

    2016-09-26

    Snake venoms are variable protein mixtures with a multitude of bioactivities. New work shows, surprisingly, that it is the loss of toxin-encoding genes that strongly influences venom function in rattlesnakes, highlighting how gene loss can underpin adaptive phenotypic change. PMID:27676304

  5. Pathogenesis and micro-anatomic characterization of a cell-adapted mutant foot-and-mouth disease virus in cattle: impact of the Jumonji C-domain containing protein 6 (JMJD6) and route of innoculation

    Science.gov (United States)

    In a companion study, we reported that the cellular Jumonji-C Domain containing Protein 6 (JMJD6) protein is involved in an alternate integrin- and HS-independent pathway of FMDV infection in CHO cells. Here, we investigated the JMJD6 localization in animal tissues from cattle infected with either ...

  6. Technology transfer for adaptation

    Science.gov (United States)

    Biagini, Bonizella; Kuhl, Laura; Gallagher, Kelly Sims; Ortiz, Claudia

    2014-09-01

    Technology alone will not be able to solve adaptation challenges, but it is likely to play an important role. As a result of the role of technology in adaptation and the importance of international collaboration for climate change, technology transfer for adaptation is a critical but understudied issue. Through an analysis of Global Environment Facility-managed adaptation projects, we find there is significantly more technology transfer occurring in adaptation projects than might be expected given the pessimistic rhetoric surrounding technology transfer for adaptation. Most projects focused on demonstration and early deployment/niche formation for existing technologies rather than earlier stages of innovation, which is understandable considering the pilot nature of the projects. Key challenges for the transfer process, including technology selection and appropriateness under climate change, markets and access to technology, and diffusion strategies are discussed in more detail.

  7. Diffusion Adaptation over Networks

    CERN Document Server

    Sayed, Ali H

    2012-01-01

    Adaptive networks are well-suited to perform decentralized information processing and optimization tasks and to model various types of self organized and complex behavior encountered in nature. Adaptive networks consist of a collection of agents with processing and learning abilities. The agents are linked together through a connection topology, and they cooperate with each other through local interactions to solve distributed inference problems in real-time. The continuous diffusion of information across the network enables agents to adapt their performance in relation to changing data and network conditions; it also results in improved adaptation and learning performance relative to non-cooperative networks. This article provides an overview of diffusion strategies for adaptation and learning over networks. The article is divided into several sections: 1. Motivation; 2. Mean-Square-Error Estimation; 3. Distributed Optimization via Diffusion Strategies; 4. Adaptive Diffusion Strategies; 5. Performance of Ste...

  8. Origins of adaptive immunity.

    Science.gov (United States)

    Liongue, Clifford; John, Liza B; Ward, Alister

    2011-01-01

    Adaptive immunity, involving distinctive antibody- and cell-mediated responses to specific antigens based on "memory" of previous exposure, is a hallmark of higher vertebrates. It has been argued that adaptive immunity arose rapidly, as articulated in the "big bang theory" surrounding its origins, which stresses the importance of coincident whole-genome duplications. Through a close examination of the key molecules and molecular processes underpinning adaptive immunity, this review suggests a less-extreme model, in which adaptive immunity emerged as part of longer evolutionary journey. Clearly, whole-genome duplications provided additional raw genetic materials that were vital to the emergence of adaptive immunity, but a variety of other genetic events were also required to generate some of the key molecules, whereas others were preexisting and simply co-opted into adaptive immunity.

  9. The Adaptive Organization

    DEFF Research Database (Denmark)

    Andersen, Torben Juul; Hallin, Carina Antonia

    2016-01-01

    Contemporary organizations operate under turbulent business conditions and must adapt their strategies to ongoing changes. This article argues that sustainable organizational performance is achieved when top management directs and coordinates interactive processes anchored in emerging organizatio......Contemporary organizations operate under turbulent business conditions and must adapt their strategies to ongoing changes. This article argues that sustainable organizational performance is achieved when top management directs and coordinates interactive processes anchored in emerging...... the adaptive organization....

  10. Human Adaptations: Free divers

    OpenAIRE

    Tournat, Troy Z.

    2014-01-01

    Freediving has been around for thousands of years and was only way to dive until the inventionof oxygen tanks in the 19th century. Around the world, people dove for goods such as pearls, andtoday people freedive for sport. Divers stretch the limit of their body and mind’s capabilitiesthrough psychological adaptations from thermal, respiratory, and cardiovascular responses.Findings conclude that thermal adaptations are a similar process to cold adaptive response. Withthe implementation of wets...

  11. Consciousness And Adaptive Behavior

    OpenAIRE

    Sieb, Richard/A.

    2005-01-01

    Consciousness has resisted scientific explanation for centuries. The main problem in explaining consciousness is its subjectivity. Subjective systems may be adaptive. Humans can produce voluntary new or novel intentional (adaptive) action and such action is always accompanied by consciousness. Action normally arises from perception. Perception must be rerepresented in order to produce new or novel adaptive action. The internal explicit states produced by a widespread nonlinear emergen...

  12. Quantifying the adaptive cycle

    Science.gov (United States)

    Angeler, David G.; Allen, Craig R.; Garmestani, Ahjond S.; Gunderson, Lance H.; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems.

  13. Adaptive Wireless Transceiver Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Wireless technologies are an increasingly attractive means for spatial data, input, manipulation, and distribution. Mobitrum is proposing an innovative Adaptive...

  14. Adaptive Multimedia Retrieval: Semantics, Context, and Adaptation

    DEFF Research Database (Denmark)

    This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on Adaptive Multimedia Retrieval, AMR 2012, held in Copenhagen, Denmark, in October 2012. The 17 revised full papers presented were carefully reviewed and selected from numerous submissi...

  15. Formation and Regulation of Adaptive Response in Nematode Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Y.-L. Zhao

    2012-01-01

    Full Text Available All organisms respond to environmental stresses (e.g., heavy metal, heat, UV irradiation, hyperoxia, food limitation, etc. with coordinated adjustments in order to deal with the consequences and/or injuries caused by the severe stress. The nematode Caenorhabditis elegans often exerts adaptive responses if preconditioned with low concentrations of agents or stressor. In C. elegans, three types of adaptive responses can be formed: hormesis, cross-adaptation, and dietary restriction. Several factors influence the formation of adaptive responses in nematodes, and some mechanisms can explain their response formation. In particular, antioxidation system, heat-shock proteins, metallothioneins, glutathione, signaling transduction, and metabolic signals may play important roles in regulating the formation of adaptive responses. In this paper, we summarize the published evidence demonstrating that several types of adaptive responses have converged in C. elegans and discussed some possible alternative theories explaining the adaptive response control.

  16. [Postvagotomy adaptation syndrome].

    Science.gov (United States)

    Shapovalov, V A

    1998-01-01

    It was established in experiment, that the changes of the natural resistance of organism indexes and of the peritoneal cavity cytology has compensatory-adaptational character while the denervation-adaptational syndrome occurrence and progress, which may be assessed as eustress. Vagotomy and operative trauma cause qualitatively different reactions of an organism.

  17. Adaptive Wavelet Transforms

    Energy Technology Data Exchange (ETDEWEB)

    Szu, H.; Hsu, C. [Univ. of Southwestern Louisiana, Lafayette, LA (United States)

    1996-12-31

    Human sensors systems (HSS) may be approximately described as an adaptive or self-learning version of the Wavelet Transforms (WT) that are capable to learn from several input-output associative pairs of suitable transform mother wavelets. Such an Adaptive WT (AWT) is a redundant combination of mother wavelets to either represent or classify inputs.

  18. Behavioral Adaptation and Acceptance

    NARCIS (Netherlands)

    Martens, M.H.; Jenssen, G.D.

    2012-01-01

    One purpose of Intelligent Vehicles is to improve road safety, throughput, and emissions. However, the predicted effects are not always as large as aimed for. Part of this is due to indirect behavioral changes of drivers, also called behavioral adaptation. Behavioral adaptation (BA) refers to uninte

  19. Behavioural adaptation and acceptance

    NARCIS (Netherlands)

    Martens, M.H.; Jenssen, G.D.; Eskandarian, A.

    2012-01-01

    One purpose of Intelligent Vehicles is to improve road safety, throughput, and emissions. However, the predicted effects are not always as large as aimed for. Part of this is due to indirect behavioral changes of drivers, also called behavioral adaptation. Behavioral adaptation (BA) refers to uninte

  20. Is There a Need for Protein Ingestion During Exercise?

    OpenAIRE

    Luc J. C. Van Loon

    2014-01-01

    Dietary protein ingestion following exercise increases muscle protein synthesis rates, stimulates net muscle protein accretion, and facilitates the skeletal muscle adaptive response to prolonged exercise training. Furthermore, recent studies show that protein ingestion before and during exercise also increases muscle protein synthesis rates during resistance- and endurance-type exercise. Therefore, protein ingestion before and during prolonged exercise may represent an effective dietary strat...

  1. Adaptive noise cancellation

    CERN Document Server

    Akram, N

    1999-01-01

    In this report we describe the concept of adaptive noise canceling, an alternative method of estimating signals corrupted by additive noise of interference. The method uses 'primary' input containing the corrupted signal and a 'reference' input containing noise correlated in some unknown way with the primary noise, the reference input is adaptively filtered and subtracted from the primary input to obtain the signal estimate. Adaptive filtering before subtraction allows the treatment of inputs that are deterministic or stochastic, stationary or time variable. When the reference input is free of signal and certain other conditions are met then noise in the primary input can be essentially eliminated without signal distortion. It is further shown that the adaptive filter also acts as notch filter. Simulated results illustrate the usefulness of the adaptive noise canceling technique.

  2. Appraising Adaptive Management

    Directory of Open Access Journals (Sweden)

    Kai N. Lee

    1999-12-01

    Full Text Available Adaptive management is appraised as a policy implementation approach by examining its conceptual, technical, equity, and practical strengths and limitations. Three conclusions are drawn: (1 Adaptive management has been more influential, so far, as an idea than as a practical means of gaining insight into the behavior of ecosystems utilized and inhabited by humans. (2 Adaptive management should be used only after disputing parties have agreed to an agenda of questions to be answered using the adaptive approach; this is not how the approach has been used. (3 Efficient, effective social learning, of the kind facilitated by adaptive management, is likely to be of strategic importance in governing ecosystems as humanity searches for a sustainable economy.

  3. Adaptive signal processor

    International Nuclear Information System (INIS)

    An experimental, general purpose adaptive signal processor system has been developed, utilizing a quantized (clipped) version of the Widrow-Hoff least-mean-square adaptive algorithm developed by Moschner. The system accommodates 64 adaptive weight channels with 8-bit resolution for each weight. Internal weight update arithmetic is performed with 16-bit resolution, and the system error signal is measured with 12-bit resolution. An adapt cycle of adjusting all 64 weight channels is accomplished in 8 μsec. Hardware of the signal processor utilizes primarily Schottky-TTL type integrated circuits. A prototype system with 24 weight channels has been constructed and tested. This report presents details of the system design and describes basic experiments performed with the prototype signal processor. Finally some system configurations and applications for this adaptive signal processor are discussed

  4. CRISPR adaptation in Escherichia coli subtypeI-E system.

    Science.gov (United States)

    Kiro, Ruth; Goren, Moran G; Yosef, Ido; Qimron, Udi

    2013-12-01

    The CRISPRs (clustered regularly interspaced short palindromic repeats) and their associated Cas (CRISPR-associated) proteins are a prokaryotic adaptive defence system against foreign nucleic acids. The CRISPR array comprises short repeats flanking short segments, called 'spacers', which are derived from foreign nucleic acids. The process of spacer insertion into the CRISPR array is termed 'adaptation'. Adaptation allows the system to rapidly evolve against emerging threats. In the present article, we review the most recent studies on the adaptation process, and focus primarily on the subtype I-E CRISPR-Cas system of Escherichia coli.

  5. Adapt or Become Extinct!

    DEFF Research Database (Denmark)

    Goumas, Georgios; McKee, Sally A.; Själander, Magnus;

    2011-01-01

    boundaries (walls) for applications which limit software development (parallel programming wall), performance (memory wall, communication wall) and viability (power wall). The only way to survive in such a demanding environment is by adaptation. In this paper we discuss how dynamic information collected...... static analysis (either during ahead-of-time or just-in-time) compilation. We extend the notion of information-driven adaptation and outline the architecture of an infrastructure designed to enable information ow and adaptation throughout the life-cycle of an application....

  6. Adaptation investments and homeownership

    DEFF Research Database (Denmark)

    Hansen, Jørgen Drud; Skak, Morten

    2008-01-01

    This article develops a model where ownership improves efficiency of the housing market as it enhances the utility of housing consumption for some consumers. The model is based on an extended Hotelling-Lancaster utility approach in which the ideal variant of housing is obtainable only by adapting...... the home through a supplementary investment. Ownership offers low costs of adaptation, but has high contract costs compared with renting. Consumers simultaneously decide housing demand and tenure, and because of the different cost structure only consumers with strong preferences for individual adaptation...

  7. [Adaptive optics for ophthalmology].

    Science.gov (United States)

    Saleh, M

    2016-04-01

    Adaptive optics is a technology enhancing the visual performance of an optical system by correcting its optical aberrations. Adaptive optics have already enabled several breakthroughs in the field of visual sciences, such as improvement of visual acuity in normal and diseased eyes beyond physiologic limits, and the correction of presbyopia. Adaptive optics technology also provides high-resolution, in vivo imaging of the retina that may eventually help to detect the onset of retinal conditions at an early stage and provide better assessment of treatment efficacy.

  8. Adaptive network countermeasures.

    Energy Technology Data Exchange (ETDEWEB)

    McClelland-Bane, Randy; Van Randwyk, Jamie A.; Carathimas, Anthony G.; Thomas, Eric D.

    2003-10-01

    This report describes the results of a two-year LDRD funded by the Differentiating Technologies investment area. The project investigated the use of countermeasures in protecting computer networks as well as how current countermeasures could be changed in order to adapt with both evolving networks and evolving attackers. The work involved collaboration between Sandia employees and students in the Sandia - California Center for Cyber Defenders (CCD) program. We include an explanation of the need for adaptive countermeasures, a description of the architecture we designed to provide adaptive countermeasures, and evaluations of the system.

  9. Introduction to adaptive arrays

    CERN Document Server

    Monzingo, Bob; Haupt, Randy

    2011-01-01

    This second edition is an extensive modernization of the bestselling introduction to the subject of adaptive array sensor systems. With the number of applications of adaptive array sensor systems growing each year, this look at the principles and fundamental techniques that are critical to these systems is more important than ever before. Introduction to Adaptive Arrays, 2nd Edition is organized as a tutorial, taking the reader by the hand and leading them through the maze of jargon that often surrounds this highly technical subject. It is easy to read and easy to follow as fundamental concept

  10. Resistance exercise and the mechanisms of muscle mass regulation in humans: acute effects on muscle protein turnover and the gaps in our understanding of chronic resistance exercise training adaptation.

    Science.gov (United States)

    Murton, A J; Greenhaff, P L

    2013-10-01

    Increasing muscle mass is important when attempting to maximize sports performance and achieve physique augmentation. However, the preservation of muscle mass is essential to maintaining mobility and quality of life with aging, and also impacts on our capacity to recover from illness. Nevertheless, our understanding of the processes that regulate muscle mass in humans during resistance exercise training, chronic disuse and rehabilitation training following atrophy remains very unclear. Here, we report on some of the recent developments in the study of those processes thought to be responsible for governing human muscle protein turnover in response to intense physical activity. Specifically, the effects of acute and chronic resistance exercise in healthy volunteers and also in response to rehabilitation resistance exercise training following muscle atrophy will be discussed, with discrepancies and gaps in our understanding highlighted. In particular, ubiquitin-proteasome mediated muscle proteolysis (Muscle Atrophy F-box/Atrogin-1 and Muscle RING Finger 1), translation initiation of muscle protein synthesis (mammalian target of rapamycin signaling), and satellite cell mediated myogenesis are highlighted as pathways of special relevance to muscle protein metabolism in response to acute resistance exercise. Furthermore, research focused on quantifying signaling and molecular events that modulate muscle protein synthesis and protein degradation under conditions of chronic resistance training is highlighted as being urgently needed to improve knowledge gaps. These studies need to include multiple time-point measurements over the course of any training intervention and must include dynamic measurements of muscle protein synthesis and degradation and sensitive measures of muscle mass. This article is part of a Directed Issue entitled Molecular basis of muscle wasting.

  11. The process of organisational adaptation through innovations, and organisational adaptability

    OpenAIRE

    Tikka, Tommi

    2010-01-01

    This study is about the process of organisational adaptation and organisational adaptability. The study generates a theoretical framework about organisational adaptation behaviour and conditions that have influence on success of organisational adaptation. The research questions of the study are: How does an organisation adapt through innovations, and which conditions enhance or impede organisational adaptation through innovations? The data were gathered from five case organisations withi...

  12. Adaptive functional evolution of leptin in cold-adaptive pika family

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Aresearch team led by Prof.ZHAO Xinquan with the CAS Northwest Institute of Plateau Biology has put forward the viewpoint for the first time that adaptive functional evolution may occur in the leptin protein of the pika (Ochotona) family, a typical coldadaptive mammal.

  13. Adapt or Die

    DEFF Research Database (Denmark)

    Brody, Joshua Eric; Larsen, Kasper Green

    2015-01-01

    In this paper, we study the role non-adaptivity plays in maintaining dynamic data structures. Roughly speaking, a data structure is non-adaptive if the memory locations it reads and/or writes when processing a query or update depend only on the query or update and not on the contents of previously...... read cells. We study such non-adaptive data structures in the cell probe model. This model is one of the least restrictive lower bound models and in particular, cell probe lower bounds apply to data structures developed in the popular word-RAM model. Unfortunately, this generality comes at a high cost...... several different notions of non-adaptivity and identify key properties that must be dealt with if we are to prove polynomial lower bounds without restrictions on the data structures. Finally, our results also unveil an interesting connection between data structures and depth-2 circuits. This allows us...

  14. Adaptations, exaptations, and spandrels.

    Science.gov (United States)

    Buss, D M; Haselton, M G; Shackelford, T K; Bleske, A L; Wakefield, J C

    1998-05-01

    Adaptation and natural selection are central concepts in the emerging science of evolutionary psychology. Natural selection is the only known causal process capable of producing complex functional organic mechanisms. These adaptations, along with their incidental by-products and a residue of noise, comprise all forms of life. Recently, S. J. Gould (1991) proposed that exaptations and spandrels may be more important than adaptations for evolutionary psychology. These refer to features that did not originally arise for their current use but rather were co-opted for new purposes. He suggested that many important phenomena--such as art, language, commerce, and war--although evolutionary in origin, are incidental spandrels of the large human brain. The authors outline the conceptual and evidentiary standards that apply to adaptations, exaptations, and spandrels and discuss the relative utility of these concepts for psychological science. PMID:9612136

  15. Adaptive Architectural Envelope

    DEFF Research Database (Denmark)

    Foged, Isak Worre; Kirkegaard, Poul Henning

    2010-01-01

    Recent years have seen an increasing variety of applications of adaptive architectural structures for improvement of structural performance by recognizing changes in their environments and loads, adapting to meet goals, and using past events to improve future performance or maintain serviceability....... The general scopes of this paper are to develop a new adaptive kinetic architectural structure, particularly a reconfigurable architectural structure which can transform body shape from planar geometries to hyper-surfaces using different control strategies, i.e. a transformation into more than one or two...... different shape alternatives. The adaptive structure is a proposal for a responsive building envelope which is an idea of a first level operational framework for present and future investigations towards performance based responsive architectures through a set of responsive typologies. A mock- up concept...

  16. Asimovian Adaptive Agents

    CERN Document Server

    Gordon, D F

    2011-01-01

    The goal of this research is to develop agents that are adaptive and predictable and timely. At first blush, these three requirements seem contradictory. For example, adaptation risks introducing undesirable side effects, thereby making agents' behavior less predictable. Furthermore, although formal verification can assist in ensuring behavioral predictability, it is known to be time-consuming. Our solution to the challenge of satisfying all three requirements is the following. Agents have finite-state automaton plans, which are adapted online via evolutionary learning (perturbation) operators. To ensure that critical behavioral constraints are always satisfied, agents' plans are first formally verified. They are then reverified after every adaptation. If reverification concludes that constraints are violated, the plans are repaired. The main objective of this paper is to improve the efficiency of reverification after learning, so that agents have a sufficiently rapid response time. We present two solutions: ...

  17. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

  18. Statistical Physics of Adaptation

    CERN Document Server

    Perunov, Nikolai; England, Jeremy

    2014-01-01

    All living things exhibit adaptations that enable them to survive and reproduce in the natural environment that they inhabit. From a biological standpoint, it has long been understood that adaptation comes from natural selection, whereby maladapted individuals do not pass their traits effectively to future generations. However, we may also consider the phenomenon of adaptation from the standpoint of physics, and ask whether it is possible to delineate what the difference is in terms of physical properties between something that is well-adapted to its surrounding environment, and something that is not. In this work, we undertake to address this question from a theoretical standpoint. Building on past fundamental results in far-from-equilibrium statistical mechanics, we demonstrate a generalization of the Helmholtz free energy for the finite-time stochastic evolution of driven Newtonian matter. By analyzing this expression term by term, we are able to argue for a general tendency in driven many-particle systems...

  19. Islands, resettlement and adaptation

    Science.gov (United States)

    Barnett, Jon; O'Neill, Saffron J.

    2012-01-01

    Resettlement of people living on islands in anticipation of climate impacts risks maladaptation, but some forms of population movement carry fewer risks and larger rewards in terms of adapting to climate change.

  20. Adaptive Heat Engine

    Science.gov (United States)

    Allahverdyan, A. E.; Babajanyan, S. G.; Martirosyan, N. H.; Melkikh, A. V.

    2016-07-01

    A major limitation of many heat engines is that their functioning demands on-line control and/or an external fitting between the environmental parameters (e.g., temperatures of thermal baths) and internal parameters of the engine. We study a model for an adaptive heat engine, where—due to feedback from the functional part—the engine's structure adapts to given thermal baths. Hence, no on-line control and no external fitting are needed. The engine can employ unknown resources; it can also adapt to results of its own functioning that make the bath temperatures closer. We determine resources of adaptation and relate them to the prior information available about the environment.

  1. Adaptive digital filters

    CERN Document Server

    Kovačević, Branko; Milosavljević, Milan

    2013-01-01

    Adaptive Digital Filters” presents an important discipline applied to the domain of speech processing. The book first makes the reader acquainted with the basic terms of filtering and adaptive filtering, before introducing the field of advanced modern algorithms, some of which are contributed by the authors themselves. Working in the field of adaptive signal processing requires the use of complex mathematical tools. The book offers a detailed presentation of the mathematical models that is clear and consistent, an approach that allows everyone with a college level of mathematics knowledge to successfully follow the mathematical derivations and descriptions of algorithms.   The algorithms are presented in flow charts, which facilitates their practical implementation. The book presents many experimental results and treats the aspects of practical application of adaptive filtering in real systems, making it a valuable resource for both undergraduate and graduate students, and for all others interested in m...

  2. Limits to adaptation

    Science.gov (United States)

    Dow, Kirstin; Berkhout, Frans; Preston, Benjamin L.; Klein, Richard J. T.; Midgley, Guy; Shaw, M. Rebecca

    2013-04-01

    An actor-centered, risk-based approach to defining limits to social adaptation provides a useful analytic framing for identifying and anticipating these limits and informing debates over society's responses to climate change.

  3. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation. PMID:23097510

  4. Adaptive quantum teleportation

    OpenAIRE

    Modlawska, Joanna; Grudka, Andrzej

    2008-01-01

    We consider multiple teleportation in the Knill-Laflamme-Milburn (KLM) scheme. We introduce adaptive teleportation, i.e., such that the choice of entangled state used in the next teleportation depends on the results of the measurements performed during the previous teleportations. We show that adaptive teleportation enables an increase in the probability of faithful multiple teleportation in the KLM scheme. In particular if a qubit is to be teleported more than once then it is better to use n...

  5. From equivalence to adaptation

    Directory of Open Access Journals (Sweden)

    Paulina Borowczyk

    2009-01-01

    Full Text Available The aim of this paper is to illustrate in which cases the translators use the adaptation when they are confronted with a term related to sociocultural aspects. We will discuss the notions of equivalence and adaptation and their limits in the translation. Some samples from Arte TV news and from the American film Shrek translated into Polish, German and French will be provided as a support for this article.

  6. Opportunistic Adaptation Knowledge Discovery

    OpenAIRE

    Badra, Fadi; Cordier, Amélie; Lieber, Jean

    2009-01-01

    The original publication is available at www.springerlink.com International audience Adaptation has long been considered as the Achilles' heel of case-based reasoning since it requires some domain-specific knowledge that is difficult to acquire. In this paper, two strategies are combined in order to reduce the knowledge engineering cost induced by the adaptation knowledge (CA) acquisition task: CA is learned from the case base by the means of knowledge discovery techniques, and the CA a...

  7. Frustratingly Easy Domain Adaptation

    CERN Document Server

    Daumé, Hal

    2009-01-01

    We describe an approach to domain adaptation that is appropriate exactly in the case when one has enough ``target'' data to do slightly better than just using only ``source'' data. Our approach is incredibly simple, easy to implement as a preprocessing step (10 lines of Perl!) and outperforms state-of-the-art approaches on a range of datasets. Moreover, it is trivially extended to a multi-domain adaptation problem, where one has data from a variety of different domains.

  8. Robust Adaptive Control

    Science.gov (United States)

    Narendra, K. S.; Annaswamy, A. M.

    1985-01-01

    Several concepts and results in robust adaptive control are are discussed and is organized in three parts. The first part surveys existing algorithms. Different formulations of the problem and theoretical solutions that have been suggested are reviewed here. The second part contains new results related to the role of persistent excitation in robust adaptive systems and the use of hybrid control to improve robustness. In the third part promising new areas for future research are suggested which combine different approaches currently known.

  9. Network and adaptive sampling

    CERN Document Server

    Chaudhuri, Arijit

    2014-01-01

    Combining the two statistical techniques of network sampling and adaptive sampling, this book illustrates the advantages of using them in tandem to effectively capture sparsely located elements in unknown pockets. It shows how network sampling is a reliable guide in capturing inaccessible entities through linked auxiliaries. The text also explores how adaptive sampling is strengthened in information content through subsidiary sampling with devices to mitigate unmanageable expanding sample sizes. Empirical data illustrates the applicability of both methods.

  10. The genomics of adaptation

    OpenAIRE

    Radwan, Jacek; Babik, Wiesław

    2012-01-01

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far ...

  11. Leak test adapter for containers

    Science.gov (United States)

    Hallett, Brian H.; Hartley, Michael S.

    1996-01-01

    An adapter is provided for facilitating the charging of containers and leak testing penetration areas. The adapter comprises an adapter body and stem which are secured to the container's penetration areas. The container is then pressurized with a tracer gas. Manipulating the adapter stem installs a penetration plug allowing the adapter to be removed and the penetration to be leak tested with a mass spectrometer. Additionally, a method is provided for using the adapter.

  12. Adaptation through proportion

    Science.gov (United States)

    Xiong, Liyang; Shi, Wenjia; Tang, Chao

    2016-08-01

    Adaptation is a ubiquitous feature in biological sensory and signaling networks. It has been suggested that adaptive systems may follow certain simple design principles across diverse organisms, cells and pathways. One class of networks that can achieve adaptation utilizes an incoherent feedforward control, in which two parallel signaling branches exert opposite but proportional effects on the output at steady state. In this paper, we generalize this adaptation mechanism by establishing a steady-state proportionality relationship among a subset of nodes in a network. Adaptation can be achieved by using any two nodes in the sub-network to respectively regulate the output node positively and negatively. We focus on enzyme networks and first identify basic regulation motifs consisting of two and three nodes that can be used to build small networks with proportional relationships. Larger proportional networks can then be constructed modularly similar to LEGOs. Our method provides a general framework to construct and analyze a class of proportional and/or adaptation networks with arbitrary size, flexibility and versatile functional features.

  13. Adaptation and perceptual norms

    Science.gov (United States)

    Webster, Michael A.; Yasuda, Maiko; Haber, Sara; Leonard, Deanne; Ballardini, Nicole

    2007-02-01

    We used adaptation to examine the relationship between perceptual norms--the stimuli observers describe as psychologically neutral, and response norms--the stimulus levels that leave visual sensitivity in a neutral or balanced state. Adapting to stimuli on opposite sides of a neutral point (e.g. redder or greener than white) biases appearance in opposite ways. Thus the adapting stimulus can be titrated to find the unique adapting level that does not bias appearance. We compared these response norms to subjectively defined neutral points both within the same observer (at different retinal eccentricities) and between observers. These comparisons were made for visual judgments of color, image focus, and human faces, stimuli that are very different and may depend on very different levels of processing, yet which share the property that for each there is a well defined and perceptually salient norm. In each case the adaptation aftereffects were consistent with an underlying sensitivity basis for the perceptual norm. Specifically, response norms were similar to and thus covaried with the perceptual norm, and under common adaptation differences between subjectively defined norms were reduced. These results are consistent with models of norm-based codes and suggest that these codes underlie an important link between visual coding and visual experience.

  14. Learning to Adapt. Organisational Adaptation to Climate Change Impacts

    International Nuclear Information System (INIS)

    Analysis of human adaptation to climate change should be based on realistic models of adaptive behaviour at the level of organisations and individuals. The paper sets out a framework for analysing adaptation to the direct and indirect impacts of climate change in business organisations with new evidence presented from empirical research into adaptation in nine case-study companies. It argues that adaptation to climate change has many similarities with processes of organisational learning. The paper suggests that business organisations face a number of obstacles in learning how to adapt to climate change impacts, especially in relation to the weakness and ambiguity of signals about climate change and the uncertainty about benefits flowing from adaptation measures. Organisations rarely adapt 'autonomously', since their adaptive behaviour is influenced by policy and market conditions, and draws on resources external to the organisation. The paper identifies four adaptation strategies that pattern organisational adaptive behaviour

  15. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... the vegetarian proteins, whether they have carbohydrate. Best Protein Choices The best choices are: Plant-based proteins ...

  16. Yeast Interacting Proteins Database: YMR025W, YGR120C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available or removal of the ubiquitin-like protein Rub1p from Cdc53p (cullin); involved in adaptation to pheromone sig... (cullin); involved in adaptation to pheromone signaling Rows with this bait as bait Rows with this bait as ...signalosome, which is required for deneddylation, or removal of the ubiquitin-like protein Rub1p from Cdc53p

  17. Solar tomography adaptive optics.

    Science.gov (United States)

    Ren, Deqing; Zhu, Yongtian; Zhang, Xi; Dou, Jiangpei; Zhao, Gang

    2014-03-10

    Conventional solar adaptive optics uses one deformable mirror (DM) and one guide star for wave-front sensing, which seriously limits high-resolution imaging over a large field of view (FOV). Recent progress toward multiconjugate adaptive optics indicates that atmosphere turbulence induced wave-front distortion at different altitudes can be reconstructed by using multiple guide stars. To maximize the performance over a large FOV, we propose a solar tomography adaptive optics (TAO) system that uses tomographic wave-front information and uses one DM. We show that by fully taking advantage of the knowledge of three-dimensional wave-front distribution, a classical solar adaptive optics with one DM can provide an extra performance gain for high-resolution imaging over a large FOV in the near infrared. The TAO will allow existing one-deformable-mirror solar adaptive optics to deliver better performance over a large FOV for high-resolution magnetic field investigation, where solar activities occur in a two-dimensional field up to 60'', and where the near infrared is superior to the visible in terms of magnetic field sensitivity.

  18. Solar Adaptive Optics

    Directory of Open Access Journals (Sweden)

    Thomas R. Rimmele

    2011-06-01

    Full Text Available Adaptive optics (AO has become an indispensable tool at ground-based solar telescopes. AO enables the ground-based observer to overcome the adverse effects of atmospheric seeing and obtain diffraction limited observations. Over the last decade adaptive optics systems have been deployed at major ground-based solar telescopes and revitalized ground-based solar astronomy. The relatively small aperture of solar telescopes and the bright source make solar AO possible for visible wavelengths where the majority of solar observations are still performed. Solar AO systems enable diffraction limited observations of the Sun for a significant fraction of the available observing time at ground-based solar telescopes, which often have a larger aperture than equivalent space based observatories, such as HINODE. New ground breaking scientific results have been achieved with solar adaptive optics and this trend continues. New large aperture telescopes are currently being deployed or are under construction. With the aid of solar AO these telescopes will obtain observations of the highly structured and dynamic solar atmosphere with unprecedented resolution. This paper reviews solar adaptive optics techniques and summarizes the recent progress in the field of solar adaptive optics. An outlook to future solar AO developments, including a discussion of Multi-Conjugate AO (MCAO and Ground-Layer AO (GLAO will be given.

  19. Evolution of adaptation mechanisms: Adaptation energy, stress, and oscillating death.

    Science.gov (United States)

    Gorban, Alexander N; Tyukina, Tatiana A; Smirnova, Elena V; Pokidysheva, Lyudmila I

    2016-09-21

    In 1938, Selye proposed the notion of adaptation energy and published 'Experimental evidence supporting the conception of adaptation energy.' Adaptation of an animal to different factors appears as the spending of one resource. Adaptation energy is a hypothetical extensive quantity spent for adaptation. This term causes much debate when one takes it literally, as a physical quantity, i.e. a sort of energy. The controversial points of view impede the systematic use of the notion of adaptation energy despite experimental evidence. Nevertheless, the response to many harmful factors often has general non-specific form and we suggest that the mechanisms of physiological adaptation admit a very general and nonspecific description. We aim to demonstrate that Selye׳s adaptation energy is the cornerstone of the top-down approach to modelling of non-specific adaptation processes. We analyze Selye׳s axioms of adaptation energy together with Goldstone׳s modifications and propose a series of models for interpretation of these axioms. Adaptation energy is considered as an internal coordinate on the 'dominant path' in the model of adaptation. The phenomena of 'oscillating death' and 'oscillating remission' are predicted on the base of the dynamical models of adaptation. Natural selection plays a key role in the evolution of mechanisms of physiological adaptation. We use the fitness optimization approach to study of the distribution of resources for neutralization of harmful factors, during adaptation to a multifactor environment, and analyze the optimal strategies for different systems of factors. PMID:26801872

  20. Symmetry Adapted Basis Sets

    DEFF Research Database (Denmark)

    Avery, John Scales; Rettrup, Sten; Avery, James Emil

    automatically with computer techniques. The method has a wide range of applicability, and can be used to solve difficult eigenvalue problems in a number of fields. The book is of special interest to quantum theorists, computer scientists, computational chemists and applied mathematicians....... eigenfunctions and eigenvalues for the Hamiltonian of a many-particle system is usually so difficult that it requires approximate methods, the most common of which is expansion of the eigenfunctions in terms of basis functions that obey the boundary conditions of the problem. The computational effort needed...... in such problems can be much reduced by making use of symmetry-adapted basis functions. The conventional method for generating symmetry-adapted basis sets is through the application of group theory, but this can be difficult. This book describes an easier method for generating symmetry-adapted basis sets...

  1. Adaptive Alternating Minimization Algorithms

    CERN Document Server

    Niesen, Urs; Wornell, Gregory

    2007-01-01

    The classical alternating minimization (or projection) algorithm has been successful in the context of solving optimization problems over two variables or equivalently of finding a point in the intersection of two sets. The iterative nature and simplicity of the algorithm has led to its application to many areas such as signal processing, information theory, control, and finance. A general set of sufficient conditions for the convergence and correctness of the algorithm is quite well-known when the underlying problem parameters are fixed. In many practical situations, however, the underlying problem parameters are changing over time, and the use of an adaptive algorithm is more appropriate. In this paper, we study such an adaptive version of the alternating minimization algorithm. As a main result of this paper, we provide a general set of sufficient conditions for the convergence and correctness of the adaptive algorithm. Perhaps surprisingly, these conditions seem to be the minimal ones one would expect in ...

  2. Adaptable Embedded Systems

    CERN Document Server

    Lisbôa, Carlos; Carro, Luigi

    2013-01-01

    As embedded systems become more complex, designers face a number of challenges at different levels: they need to boost performance, while keeping energy consumption as low as possible, they need to reuse existent software code, and at the same time they need to take advantage of the extra logic available in the chip, represented by multiple processors working together.  This book describes several strategies to achieve such different and interrelated goals, by the use of adaptability. Coverage includes reconfigurable systems, dynamic optimization techniques such as binary translation and trace reuse, new memory architectures including homogeneous and heterogeneous multiprocessor systems, communication issues and NOCs, fault tolerance against fabrication defects and soft errors, and finally, how one can combine several of these techniques together to achieve higher levels of performance and adaptability.  The discussion also includes how to employ specialized software to improve this new adaptive system, and...

  3. The PRE-Derived NMR Model of the 38.8-kDa Tri-Domain IsdH Protein from Staphylococcus aureus Suggests That It Adaptively Recognizes Human Hemoglobin.

    Science.gov (United States)

    Sjodt, Megan; Macdonald, Ramsay; Spirig, Thomas; Chan, Albert H; Dickson, Claire F; Fabian, Marian; Olson, John S; Gell, David A; Clubb, Robert T

    2016-03-27

    Staphylococcus aureus is a medically important bacterial pathogen that, during infections, acquires iron from human hemoglobin (Hb). It uses two closely related iron-regulated surface determinant (Isd) proteins to capture and extract the oxidized form of heme (hemin) from Hb, IsdH and IsdB. Both receptors rapidly extract hemin using a conserved tri-domain unit consisting of two NEAT (near iron transporter) domains connected by a helical linker domain. To gain insight into the mechanism of extraction, we used NMR to investigate the structure and dynamics of the 38.8-kDa tri-domain IsdH protein (IsdH(N2N3), A326-D660 with a Y642A mutation that prevents hemin binding). The structure was modeled using long-range paramagnetic relaxation enhancement (PRE) distance restraints, dihedral angle, small-angle X-ray scattering, residual dipolar coupling and inter-domain NOE nuclear Overhauser effect data. The receptor adopts an extended conformation wherein the linker and N3 domains pack against each other via a hydrophobic interface. In contrast, the N2 domain contacts the linker domain via a hydrophilic interface and, based on NMR relaxation data, undergoes inter-domain motions enabling it to reorient with respect to the body of the protein. Ensemble calculations were used to estimate the range of N2 domain positions compatible with the PRE data. A comparison of the Hb-free and Hb-bound forms reveals that Hb binding alters the positioning of the N2 domain. We propose that binding occurs through a combination of conformational selection and induced-fit mechanisms that may promote hemin release from Hb by altering the position of its F helix.

  4. Grit, a GTPase-Activating Protein for the Rho Family, Regulates Neurite Extension through Association with the TrkA Receptor and N-Shc and CrkL/Crk Adapter Molecules

    OpenAIRE

    Nakamura, Takeshi; Komiya, Misako; Sone, Kiyoaki; Hirose, Eiji; Gotoh, Noriko; Morii, Hiroshi; Ohta, Yasutaka; Mori, Nozomu

    2002-01-01

    Neurotrophins are key regulators of the fate and shape of neuronal cells and act as guidance cues for growth cones by remodeling the actin cytoskeleton. Actin dynamics is controlled by Rho GTPases. We identified a novel Rho GTPase-activating protein (Grit) for Rho/Rac/Cdc42 small GTPases. Grit was abundant in neuronal cells and directly interacted with TrkA, a high-affinity receptor for nerve growth factor (NGF). Another pool of Grit was recruited to the activated receptor tyrosine kinase thr...

  5. The Adaptability of Teams

    DEFF Research Database (Denmark)

    Jørgensen, Frances; Boer, Harry

    2006-01-01

    In this paper, data from a longitudinal case study in an organization attempting to adapt its internal work processes to changes in its external context are presented, analyzed and discussed. Specifically, functionally structured work teams in one department of a Danish production facility were...... on the proper alignment between the structuring of the work processes and characteristics of the external context (Lawrence & Lorsch, 1967) – it provides a unique opportunity to explore the adaptation process in practice. The paper contributes to the development of contingency theory by lending support...

  6. Adaptation investments and homeownership

    DEFF Research Database (Denmark)

    Hansen, Jørgen Drud; Skak, Morten

    2008-01-01

    This article develops a model where ownership improves the efficiency of the housing market as it enhances the utility of housing consumption for some consumers. The model is based on an extended Hotelling-Lancaster utility approach in which the ideal variant of housing is obtainable only...... by adapting the home through a supplementary investment. Ownership offers low costs of adaptation, but has high contract costs compared with renting. Consumers simultaneously choose housing demand and tenure, and because of the different cost structure only consumers with strong preferences for individual...

  7. Adaptive management: Chapter 1

    Science.gov (United States)

    Allen, Craig R.; Garmestani, Ahjond S.; Allen, Craig R.; Garmestani, Ahjond S.

    2015-01-01

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive management has explicit structure, including a careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. The process is iterative, and serves to reduce uncertainty, build knowledge and improve management over time in a goal-oriented and structured process.

  8. STUDYING COMPLEX ADAPTIVE SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    John H. Holland

    2006-01-01

    Complex adaptive systems (cas) - systems that involve many components that adapt or learn as they interact - are at the heart of important contemporary problems. The study of cas poses unique challenges: Some of our most powerful mathematical tools, particularly methods involving fixed points, attractors, and the like, are of limited help in understanding the development of cas. This paper suggests ways to modify research methods and tools, with an emphasis on the role of computer-based models, to increase our understanding of cas.

  9. Adaptive radar resource management

    CERN Document Server

    Moo, Peter

    2015-01-01

    Radar Resource Management (RRM) is vital for optimizing the performance of modern phased array radars, which are the primary sensor for aircraft, ships, and land platforms. Adaptive Radar Resource Management gives an introduction to radar resource management (RRM), presenting a clear overview of different approaches and techniques, making it very suitable for radar practitioners and researchers in industry and universities. Coverage includes: RRM's role in optimizing the performance of modern phased array radars The advantages of adaptivity in implementing RRMThe role that modelling and

  10. Intestinal mucosal adaptation

    Institute of Scientific and Technical Information of China (English)

    Laurie Drozdowski; Alan BR Thomson

    2006-01-01

    Intestinal failure is a condition characterized by malnutrition and/or dehydration as a result of the inadequate digestion and absorption of nutrients. The most common cause of intestinal failure is short bowel syndrome, which occurs when the functional gut mass is reduced below the level necessary for adequate nutrient and water absorption. This condition may be congenital, or may be acquired as a result of a massive resection of the small bowel. Following resection, the intestine is capable of adaptation in response to enteral nutrients as well as other trophic stimuli. Identifying factors that may enhance the process of intestinal adaptation is an exciting area of research with important potential clinical applications.

  11. Engineering Adaptive Web Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    2007-01-01

    . With the growing amount of information and services, the web applications become natural candidates to adopt the concepts of ambient intelligence. Such applications can deal with divers user intentions and actions based on the user profile and can suggest the combination of information content and services which...... suit the user profile the most. This paper summarizes the domain engineering framework for such adaptive web applications. The framework provides guidelines to develop adaptive web applications as members of a family. It suggests how to utilize the design artifacts as knowledge which can be used...

  12. Adaptive Metric Kernel Regression

    DEFF Research Database (Denmark)

    Goutte, Cyril; Larsen, Jan

    1998-01-01

    Kernel smoothing is a widely used nonparametric pattern recognition technique. By nature, it suffers from the curse of dimensionality and is usually difficult to apply to high input dimensions. In this paper, we propose an algorithm that adapts the input metric used in multivariate regression by...... minimising a cross-validation estimate of the generalisation error. This allows one to automatically adjust the importance of different dimensions. The improvement in terms of modelling performance is illustrated on a variable selection task where the adaptive metric kernel clearly outperforms the standard...

  13. Adaptive metric kernel regression

    DEFF Research Database (Denmark)

    Goutte, Cyril; Larsen, Jan

    2000-01-01

    Kernel smoothing is a widely used non-parametric pattern recognition technique. By nature, it suffers from the curse of dimensionality and is usually difficult to apply to high input dimensions. In this contribution, we propose an algorithm that adapts the input metric used in multivariate...... regression by minimising a cross-validation estimate of the generalisation error. This allows to automatically adjust the importance of different dimensions. The improvement in terms of modelling performance is illustrated on a variable selection task where the adaptive metric kernel clearly outperforms the...

  14. Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis in Both Haematological Malignancies and Solid Tumours: The Extraordinary Case of MYEOV Gene.

    Science.gov (United States)

    Papamichos, Spyros I; Margaritis, Dimitrios; Kotsianidis, Ioannis

    2015-01-01

    The incidence of cancer in human is high as compared to chimpanzee. However previous analysis has documented that numerous human cancer-related genes are highly conserved in chimpanzee. Till date whether human genome includes species-specific cancer-related genes that could potentially contribute to a higher cancer susceptibility remains obscure. This study focuses on MYEOV, an oncogene encoding for two protein isoforms, reported as causally involved in promoting cancer cell proliferation and metastasis in both haematological malignancies and solid tumours. First we document, via stringent in silico analysis, that MYEOV arose de novo in Catarrhini. We show that MYEOV short-isoform start codon was evolutionarily acquired after Catarrhini/Platyrrhini divergence. Throughout the course of Catarrhini evolution MYEOV acquired a gradually elongated translatable open reading frame (ORF), a gradually shortened translation-regulatory upstream ORF, and alternatively spliced mRNA variants. A point mutation introduced in human allowed for the acquisition of MYEOV long-isoform start codon. Second, we demonstrate the precious impact of exonized transposable elements on the creation of MYEOV gene structure. Third, we highlight that the initial part of MYEOV long-isoform coding DNA sequence was under positive selection pressure during Catarrhini evolution. MYEOV represents a Primate Orphan Gene that acquired, via ORF expansion, a human-protein-specific coding potential. PMID:26568894

  15. Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis in Both Haematological Malignancies and Solid Tumours: The Extraordinary Case of MYEOV Gene

    Directory of Open Access Journals (Sweden)

    Spyros I. Papamichos

    2015-01-01

    Full Text Available The incidence of cancer in human is high as compared to chimpanzee. However previous analysis has documented that numerous human cancer-related genes are highly conserved in chimpanzee. Till date whether human genome includes species-specific cancer-related genes that could potentially contribute to a higher cancer susceptibility remains obscure. This study focuses on MYEOV, an oncogene encoding for two protein isoforms, reported as causally involved in promoting cancer cell proliferation and metastasis in both haematological malignancies and solid tumours. First we document, via stringent in silico analysis, that MYEOV arose de novo in Catarrhini. We show that MYEOV short-isoform start codon was evolutionarily acquired after Catarrhini/Platyrrhini divergence. Throughout the course of Catarrhini evolution MYEOV acquired a gradually elongated translatable open reading frame (ORF, a gradually shortened translation-regulatory upstream ORF, and alternatively spliced mRNA variants. A point mutation introduced in human allowed for the acquisition of MYEOV long-isoform start codon. Second, we demonstrate the precious impact of exonized transposable elements on the creation of MYEOV gene structure. Third, we highlight that the initial part of MYEOV long-isoform coding DNA sequence was under positive selection pressure during Catarrhini evolution. MYEOV represents a Primate Orphan Gene that acquired, via ORF expansion, a human-protein-specific coding potential.

  16. How harmful are adaptation restrictions

    OpenAIRE

    Bruin, de, B.; Dellink, R.B.

    2009-01-01

    The dominant assumption in economic models of climate policy remains that adaptation will be implemented in an optimal manner. There are, however, several reasons why optimal levels of adaptation may not be attainable. This paper investigates the effects of suboptimal levels of adaptation, i.e. adaptation restrictions, on the composition and level of climate change costs and on welfare. Several adaptation restrictions are identified and then simulated in a revised DICE model, extended with ad...

  17. Robust Optimal Adaptive Control Method with Large Adaptive Gain

    Science.gov (United States)

    Nguyen, Nhan T.

    2009-01-01

    In the presence of large uncertainties, a control system needs to be able to adapt rapidly to regain performance. Fast adaptation is referred to the implementation of adaptive control with a large adaptive gain to reduce the tracking error rapidly. However, a large adaptive gain can lead to high-frequency oscillations which can adversely affect robustness of an adaptive control law. A new adaptive control modification is presented that can achieve robust adaptation with a large adaptive gain without incurring high-frequency oscillations as with the standard model-reference adaptive control. The modification is based on the minimization of the Y2 norm of the tracking error, which is formulated as an optimal control problem. The optimality condition is used to derive the modification using the gradient method. The optimal control modification results in a stable adaptation and allows a large adaptive gain to be used for better tracking while providing sufficient stability robustness. Simulations were conducted for a damaged generic transport aircraft with both standard adaptive control and the adaptive optimal control modification technique. The results demonstrate the effectiveness of the proposed modification in tracking a reference model while maintaining a sufficient time delay margin.

  18. ADAM: ADaptive Autonomous Machine

    NARCIS (Netherlands)

    Oosten, van Daan C.; Nijenhuis, Lucas F.J.; Bakkers, André W.P.; Vervoort, Wiek A.

    1996-01-01

    This paper describes a part of the development of an adaptive autonomous machine that is able to move in an unknown world extract knowledge out of the perceived data, has the possibility to reason, and finally has the capability to exchange experiences and knowledge with other agents. The agent is n

  19. Adaptive kernel density estimation

    OpenAIRE

    Philippe Van Kerm

    2003-01-01

    This insert describes the module akdensity. akdensity extends the official kdensity that estimates density functions by the kernel method. The extensions are of two types: akdensity allows the use of an "adaptive kernel" approach with varying, rather than fixed, bandwidths; and akdensity estimates pointwise variability bands around the estimated density functions. Copyright 2003 by Stata Corporation.

  20. Exploring Adaptive Program Behavior

    DEFF Research Database (Denmark)

    Bonnichsen, Lars Frydendal; Probst, Christian W.

    . Both solutions come at a cost; adaptivity issues a runtime overhead and requires more design effort, while dynamic recompilation takes time to perform. In this project, we plan to investigate the possibilities, limitations, and benefits of these techniques. This abstract covers our thoughts on how...

  1. Compiler Assisted Runtime Adaptation

    NARCIS (Netherlands)

    Sima, V.M.

    2012-01-01

    In this dissertation, we address the problem of runtime adaptation of the application to its execution environment. A typical example is changing theprocessing element on which a computation is executed, considering the available processing elements in the system. This is done based on the informati

  2. Engineering Adaptive Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    for a domain.In this book, we propose a new domain engineering framework which extends a development process of Web applications with techniques required when designing such adaptive customizable Web applications. The framework is provided with design abstractions which deal separately with information served...

  3. Complex adaptive systems ecology

    DEFF Research Database (Denmark)

    Sommerlund, Julie

    2003-01-01

    In the following, I will analyze two articles called Complex Adaptive Systems EcologyI & II (Molin & Molin, 1997 & 2000). The CASE-articles are some of the more quirkyarticles that have come out of the Molecular Microbial Ecology Group - a groupwhere I am currently making observational studies...

  4. Robust Adaptive Structural Control

    OpenAIRE

    Yang, Chi-Ming; Beck, James L.

    1995-01-01

    A new robust adaptive structural control design methodology is developed and presented which treats modeling uncertainties and limitations of control devices. Furthermore, no restriction is imposed on the structural models and the nature of the control devices so that the proposed method is very general. A simple linear single degree-of-freedom numerical example is presented to illustrate this approach.

  5. Prism Adaptation in Schizophrenia

    Science.gov (United States)

    Bigelow, Nirav O.; Turner, Beth M.; Andreasen, Nancy C.; Paulsen, Jane S.; O'Leary, Daniel S.; Ho, Beng-Choon

    2006-01-01

    The prism adaptation test examines procedural learning (PL) in which performance facilitation occurs with practice on tasks without the need for conscious awareness. Dynamic interactions between frontostriatal cortices, basal ganglia, and the cerebellum have been shown to play key roles in PL. Disruptions within these neural networks have also…

  6. Generalization of Prism Adaptation

    Science.gov (United States)

    Redding, Gordon M.; Wallace, Benjamin

    2006-01-01

    Prism exposure produces 2 kinds of adaptive response. Recalibration is ordinary strategic remapping of spatially coded movement commands to rapidly reduce performance error. Realignment is the extraordinary process of transforming spatial maps to bring the origins of coordinate systems into correspondence. Realignment occurs when spatial…

  7. Adapting Bulls to Florida

    Science.gov (United States)

    The adaptation of bulls used for natural breeding purposes to the Gulf Coast region of the United States including all of Florida is an important topic. Nearly 40% of the U.S. cow/calf population resides in the Gulf Coast and Southeast. Thus, as A.I. is relatively rare, the number of bulls used for ...

  8. Adaptive municipal electronic forms

    NARCIS (Netherlands)

    Kuiper, Pieter; Dijk, van Betsy; Bondarouk, Tanya; Ruël, Huub; Guiderdoni-Jourdain, Karine; Oiry, Ewan

    2009-01-01

    Adaptation of electronic forms (e-forms) seems to be a step forward to reduce the burden for people who fill in forms. Municipalities more and more offer e-forms online that can be used by citizens to request a municipal product or service or by municipal employees to place a request on behalf of a

  9. The adaptive evolution of the mammalian mitochondrial genome

    Directory of Open Access Journals (Sweden)

    O'Brien Stephen J

    2008-03-01

    Full Text Available Abstract Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas. Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.

  10. Exercise, PGC-1α and metabolic adaptation in skeletal muscle

    OpenAIRE

    Yan, Zhen

    2009-01-01

    Endurance exercise promotes skeletal muscle adaptation, and exercise-induced peroxisome proliferator-activated receptor γ co-activator-1α (Pgc-1α) gene expression may play a pivotal role in the adaptive processes. Recent applications of mouse genetic models and in vivo imaging in exercise studies started to delineate the signaling-transcription pathways that are involved in the regulation of the Pgc-1α gene. These studies revealed the importance of p38 mitogen-activated protein kinase (MAPK)/...

  11. Fine-scale recombination and adaptive radiation could be linked.

    Science.gov (United States)

    Bodilis, Josselin

    2013-09-15

    The difficult reconstruction of the evolutionary history of the major surface protein gene oprF highlighted an adaptive radiation in the Pseudomonas fluorescens group. The recent work of Hao (2013) showed that partial recombination events in oprF gene occurred specifically in a P. fluorescens lineage under ecological niche segregation. So, I suggest that identification of lineage-specific fine-scale recombination may be a way to detect putative adaptive radiation in bacteria. PMID:23774687

  12. Versatile protein tagging in cells with split fluorescent protein

    OpenAIRE

    Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A.; Ishikawa, Hiroaki; Leonetti, Manuel D.; Marshall, Wallace F.; Jonathan S Weissman; Huang, Bo

    2016-01-01

    In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respec...

  13. Lipid-transfer proteins.

    Science.gov (United States)

    Ng, Tzi Bun; Cheung, Randy Chi Fai; Wong, Jack Ho; Ye, Xiujuan

    2012-01-01

    Lipid-transfer proteins (LTPs) are basic proteins found in abundance in higher plants. LTPs play lots of roles in plants such as participation in cutin formation, embryogenesis, defense reactions against phytopathogens, symbiosis, and the adaptation of plants to various environmental conditions. In addition, LTPs from field mustard and Chinese daffodil exhibit antiproliferative activity against human cancer cells. LTPs from chili pepper and coffee manifest inhibitory activity against fungi pathogenic to humans such as Candida species. The intent of this article is to review LTPs in the plant kingdom. PMID:23193591

  14. Unraveling adaptation in eukaryotic pathways: lessons from protocells.

    Directory of Open Access Journals (Sweden)

    Giovanna De Palo

    2013-10-01

    Full Text Available Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption. Here, we present two minimal models showing that expenditure of energy by the cell is not essential for adaptation. Both models share important features with large eukaryotic cells: they employ small diffusible molecules and involve receptor subunits resembling highly conserved G-protein cascades. Analyzing the drawbacks of these models helps us understand the benefits of energy consumption, in terms of adjustability of response and adaptation times as well as separation of cell-external sensing and cell-internal signaling. Our work thus sheds new light on the evolution of adaptation mechanisms in complex systems.

  15. Unraveling adaptation in eukaryotic pathways: lessons from protocells.

    Science.gov (United States)

    De Palo, Giovanna; Endres, Robert G

    2013-10-01

    Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption. Here, we present two minimal models showing that expenditure of energy by the cell is not essential for adaptation. Both models share important features with large eukaryotic cells: they employ small diffusible molecules and involve receptor subunits resembling highly conserved G-protein cascades. Analyzing the drawbacks of these models helps us understand the benefits of energy consumption, in terms of adjustability of response and adaptation times as well as separation of cell-external sensing and cell-internal signaling. Our work thus sheds new light on the evolution of adaptation mechanisms in complex systems. PMID:24204235

  16. Adaptation: Needs, Financing and Institutions

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Richard J.T.; Kartha, Sivan; Persson, Aasa; Watkiss, Paul; Ackerman, Frank; Downing, Thomas E.; Kjellen, Bo; Schipper, Lisa (Stockholm Environment Institute, Stockholm (SE))

    2008-07-01

    Regardless of the efforts put into mitigation, some impacts of climate change are already unavoidable. Adaptation to climate change has therefore become a key component of domestic climate policy, along with mitigation. Adaptation has also become key to the success of global climate policy. Without an agreement on supporting adaptation in developing countries, there will be no agreement on mitigation. Strong mitigation efforts make it more likely that adaptation will be effective and affordable. The world cannot rely on adaptation alone: it would eventually lead to a level of climate change to which adaptation is no longer feasible. Government action is needed to create an enabling environment for adaptation. This includes removing existing financial, legal, institutional and knowledge barriers to adaptation, and strengthening the capacity of people and organisations to adapt. The success of adaptation relies on the success of development, and vice versa. Poverty reduction, good governance, education, environmental protection, health and gender equality all contribute to adaptive capacity. Substantially more money is needed to support adaptation in developing countries. Current levels of funding will soon have to be scaled up by two orders of magnitude (from US$ hundreds of million to US$ tens of billion per year). An agreement on adaptation in Copenhagen in 2009 will need to include concrete steps towards a strengthened knowledge base for adaptation, substantially more funding for developing countries, and enhanced adaptation planning and implementation at the national level. Recommendations: Developed countries should accept a transparent, principle-based allocation of responsibility for adaptation funding, resulting in adequate, new and additional money to support adaptation programmes in developing countries. Levies on carbon market transactions and auctioning emission permits are two existing mechanisms of generating new and additional funds consistent with

  17. Protein stress and stress proteins: implications in aging and disease

    Indian Academy of Sciences (India)

    C Sőti; Péter Csermely

    2007-04-01

    Environmantal stress induces damage that activates an adaptive response in any organism. The cellular stress response is based on the induction of cytoprotective proteins, the so called stress or heat shock proteins. The stress response as well as stress proteins are ubiquitous, highly conserved mechanism, and genes, respectively, already present in prokaryotes. Chaperones protect the proteome against conformational damage, promoting the function of protein networks. Protein damage takes place during aging and in several degenerative diseases, and presents a threat to overload the cellular defense mechanisms. The preservation of a robust stress response and protein disposal is indispensable for health and longevity. This review summarizes the present knowledge of protein damage, turnover, and the stress response in aging and degenerative diseases.

  18. AdaptME toolkit : adaptation monitoring and evaluation

    OpenAIRE

    Pringle, Patrick

    2011-01-01

    Organisations that have undertaken adaptation activities now face the challenge of evaluating what worked, what didn’t, how and why. This toolkit responds to a growing demand for practical support in evaluating adaptation progress and performance. AdaptME will help you to think through some of the factors that can make an evaluation of adaptation activities inherently challenging, and equip you to design a robust evaluation. You will be able to ‘tweak’ a single part of your evaluation des...

  19. Pathogenesis and micro-anatomic characterization of a cell-adapted mutant foot-and-mouth disease virus in cattle: Impact of the Jumonji C-domain containing protein 6 (JMJD6) and route of inoculation.

    Science.gov (United States)

    Lawrence, Paul; Pacheco, Juan; Stenfeldt, Carolina; Arzt, Jonathan; Rai, Devendra K; Rieder, Elizabeth

    2016-05-01

    A companion study reported Jumonji-C domain containing protein 6 (JMJD6) is involved in an integrin- and HS-independent pathway of FMDV infection in CHO cells. JMJD6 localization was investigated in animal tissues from cattle infected with either wild type A24-FMDV (A24-WT) or mutant FMDV (JMJD6-FMDV) carrying E95K/S96L and RGD to KGE mutations in VP1. Additionally, pathogenesis of mutant JMJD6-FMDV was investigated in cattle through aerosol and intraepithelial lingual (IEL) inoculation. Interestingly, JMJD6-FMDV pathogenesis was equivalent to A24-WT administered by IEL route. In contrast, JMJD6-FMDV aerosol-infected cattle did not manifest signs of FMD and animals showed no detectable viremia. Immunofluorescent microscopy of post-mortem tissue revealed JMJD6-FMDV exclusively co-localized with JMJD6(+) cells while A24-WT was occasionally found in JMJD6(+) cells. In vitro, chemical uptake inhibitors demonstrated JMJD6-FMDV entered cells via clathrin-coated pit endocytosis. In vivo, JMJD6-FMDV exhibited preference for JMJD6(+) cells, but availability of this alternative receptor likely depends on route of inoculation. PMID:26914509

  20. Pathogenesis and micro-anatomic characterization of a cell-adapted mutant foot-and-mouth disease virus in cattle: Impact of the Jumonji C-domain containing protein 6 (JMJD6) and route of inoculation.

    Science.gov (United States)

    Lawrence, Paul; Pacheco, Juan; Stenfeldt, Carolina; Arzt, Jonathan; Rai, Devendra K; Rieder, Elizabeth

    2016-05-01

    A companion study reported Jumonji-C domain containing protein 6 (JMJD6) is involved in an integrin- and HS-independent pathway of FMDV infection in CHO cells. JMJD6 localization was investigated in animal tissues from cattle infected with either wild type A24-FMDV (A24-WT) or mutant FMDV (JMJD6-FMDV) carrying E95K/S96L and RGD to KGE mutations in VP1. Additionally, pathogenesis of mutant JMJD6-FMDV was investigated in cattle through aerosol and intraepithelial lingual (IEL) inoculation. Interestingly, JMJD6-FMDV pathogenesis was equivalent to A24-WT administered by IEL route. In contrast, JMJD6-FMDV aerosol-infected cattle did not manifest signs of FMD and animals showed no detectable viremia. Immunofluorescent microscopy of post-mortem tissue revealed JMJD6-FMDV exclusively co-localized with JMJD6(+) cells while A24-WT was occasionally found in JMJD6(+) cells. In vitro, chemical uptake inhibitors demonstrated JMJD6-FMDV entered cells via clathrin-coated pit endocytosis. In vivo, JMJD6-FMDV exhibited preference for JMJD6(+) cells, but availability of this alternative receptor likely depends on route of inoculation.

  1. Extensive local adaptation within the chemosensory system following Drosophila melanogaster's global expansion.

    Science.gov (United States)

    Arguello, J Roman; Cardoso-Moreira, Margarida; Grenier, Jennifer K; Gottipati, Srikanth; Clark, Andrew G; Benton, Richard

    2016-01-01

    How organisms adapt to new environments is of fundamental biological interest, but poorly understood at the genetic level. Chemosensory systems provide attractive models to address this problem, because they lie between external environmental signals and internal physiological responses. To investigate how selection has shaped the well-characterized chemosensory system of Drosophila melanogaster, we have analysed genome-wide data from five diverse populations. By couching population genomic analyses of chemosensory protein families within parallel analyses of other large families, we demonstrate that chemosensory proteins are not outliers for adaptive divergence between species. However, chemosensory families often display the strongest genome-wide signals of recent selection within D. melanogaster. We show that recent adaptation has operated almost exclusively on standing variation, and that patterns of adaptive mutations predict diverse effects on protein function. Finally, we provide evidence that chemosensory proteins have experienced relaxed constraint, and argue that this has been important for their rapid adaptation over short timescales. PMID:27292132

  2. Adaptive Inflow Control System

    CERN Document Server

    Volkov, Vasily Y; Zhuravlev, Oleg N; Nukhaev, Marat T; Shchelushkin, Roman V

    2014-01-01

    This article presents the idea and realization for the unique Adaptive Inflow Control System being a part of well completion, able to adjust to the changing in time production conditions. This system allows to limit the flow rate from each interval at a certain level, which solves the problem of water and gas breakthroughs. We present the results of laboratory tests and numerical calculations obtaining the characteristics of the experimental setup with dual-in-position valves as parts of adaptive inflow control system, depending on the operating conditions. The flow distribution in the system was also studied with the help of three-dimensional computer model. The control ranges dependences are determined, an influence of the individual elements on the entire system is revealed.

  3. Unconsciously triggered conflict adaptation.

    Directory of Open Access Journals (Sweden)

    Simon van Gaal

    Full Text Available In conflict tasks such as the Stroop, the Eriksen flanker or the Simon task, it is generally observed that the detection of conflict in the current trial reduces the impact of conflicting information in the subsequent trial; a phenomenon termed conflict adaptation. This higher-order cognitive control function has been assumed to be restricted to cases where conflict is experienced consciously. In the present experiment we manipulated the awareness of conflict-inducing stimuli in a metacontrast masking paradigm to directly test this assumption. Conflicting response tendencies were elicited either consciously (through primes that were weakly masked or unconsciously (strongly masked primes. We demonstrate trial-by-trial conflict adaptation effects after conscious as well as unconscious conflict, which could not be explained by direct stimulus/response repetitions. These findings show that unconscious information can have a longer-lasting influence on our behavior than previously thought and further stretch the functional boundaries of unconscious cognition.

  4. Capabilities for Strategic Adaptation

    DEFF Research Database (Denmark)

    Distel, Andreas Philipp

    firms’ ability to absorb and leverage new knowledge. The third paper is an empirical study which conceptualizes top managers’ resource cognition as a managerial capability underlying firms’ resource adaptation; it empirically examines the performance implications of this capability and organizational......This dissertation explores capabilities that enable firms to strategically adapt to environmental changes and preserve competitiveness over time – often referred to as dynamic capabilities. While dynamic capabilities being a popular research domain, too little is known about what these capabilities...... empirical studies through the dynamic capabilities lens and develops propositions for future research. The second paper is an empirical study on the origins of firm-level absorptive capacity; it explores how organization-level antecedents, through their impact on individual-level antecedents, influence...

  5. Designing Adaptive Web Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    2008-01-01

    The unique characteristic of web applications is that they are supposed to be used by much bigger and diverse set of users and stakeholders. An example application area is e-Learning or business to business interaction. In eLearning environment, various users with different background use the e......Learning system to study a discipline. In business to business interaction, different requirements and parameters of exchanged business requests might be served by different services from third parties. Such applications require certain intelligence and a slightly different approach to design. Adpative web...... adaptation to the changed parameters of environments, user or context. Adaptation can be seen as an orthogonal concern or viewpoint in a design process. In this paper I will discuss design abstractions which are employed in current design methods for web applications. I will exemplify the use...

  6. Bacterial surface adaptation

    Science.gov (United States)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  7. Adaptive sensor fusion

    Science.gov (United States)

    Kadar, Ivan

    1995-07-01

    A perceptual reasoning system adaptively extracting, associating, and fusing information from multiple sources, at various levels of abstraction, is considered as the building block for the next generation of surveillance systems. A system architecture is presented which makes use of both centralized and distributed predetection fusion combined with intelligent monitor and control coupling both on-platform and off-board track and decision level fusion results. The goal of this system is to create a `gestalt fused sensor system' whose information product is greater than the sum of the information products from the individual sensors and has performance superior to either individual or a sub-group of combined sensors. The application of this architectural concept to the law enforcement arena (e.g. drug interdiction) utilizing multiple spatially and temporally diverse surveillance platforms and/or information sources, is used to illustrate the benefits of the adaptive perceptual reasoning system concept.

  8. Adaptive semantics visualization

    CERN Document Server

    Nazemi, Kawa

    2016-01-01

    This book introduces a novel approach for intelligent visualizations that adapts the different visual variables and data processing to human’s behavior and given tasks. Thereby a number of new algorithms and methods are introduced to satisfy the human need of information and knowledge and enable a usable and attractive way of information acquisition. Each method and algorithm is illustrated in a replicable way to enable the reproduction of the entire “SemaVis” system or parts of it. The introduced evaluation is scientifically well-designed and performed with more than enough participants to validate the benefits of the methods. Beside the introduced new approaches and algorithms, readers may find a sophisticated literature review in Information Visualization and Visual Analytics, Semantics and information extraction, and intelligent and adaptive systems. This book is based on an awarded and distinguished doctoral thesis in computer science.

  9. Adaptive method of lines

    CERN Document Server

    Saucez, Ph

    2001-01-01

    The general Method of Lines (MOL) procedure provides a flexible format for the solution of all the major classes of partial differential equations (PDEs) and is particularly well suited to evolutionary, nonlinear wave PDEs. Despite its utility, however, there are relatively few texts that explore it at a more advanced level and reflect the method''s current state of development.Written by distinguished researchers in the field, Adaptive Method of Lines reflects the diversity of techniques and applications related to the MOL. Most of its chapters focus on a particular application but also provide a discussion of underlying philosophy and technique. Particular attention is paid to the concept of both temporal and spatial adaptivity in solving time-dependent PDEs. Many important ideas and methods are introduced, including moving grids and grid refinement, static and dynamic gridding, the equidistribution principle and the concept of a monitor function, the minimization of a functional, and the moving finite elem...

  10. Adaptive Large Neighbourhood Search

    DEFF Research Database (Denmark)

    Røpke, Stefan

    Large neighborhood search is a metaheuristic that has gained popularity in recent years. The heuristic repeatedly moves from solution to solution by first partially destroying the solution and then repairing it. The best solution observed during this search is presented as the final solution....... This tutorial introduces the large neighborhood search metaheuristic and the variant adaptive large neighborhood search that dynamically tunes parameters of the heuristic while it is running. Both heuristics belong to a broader class of heuristics that are searching a solution space using very large...... neighborhoods. The tutorial also present applications of the adaptive large neighborhood search, mostly related to vehicle routing problems for which the heuristic has been extremely successful. We discuss how the heuristic can be parallelized and thereby take advantage of modern desktop computers...

  11. Semantische Adaption von Komponenten

    OpenAIRE

    Söldner, Guido

    2012-01-01

    Im Bereich der Informationstechnik ist die Adaption von Software an veränderte Gegebenheiten und Umgebungen ein wichtiges Thema. Dabei bestimmen vor allem die konkret verwendete Software-Programmiersprache, die benutzten Entwurfsmuster und die der Applikation zugrundeliegende Software-Architektur, mit welchem Aufwand eine Anwendung auf neue Anforderungen eingehen kann. Darüber hinaus war und ist es interessant, Mechanismen zu entwickeln, mit denen Applikationen selbst auf spontane Änderungen ...

  12. Traffic-Adaptive Routing

    OpenAIRE

    Kammenhuber, Nils

    2011-01-01

    Despite the bursty and highly volatile traffic, routing in the Internet today is optimised only on coarse time scales, as load-adaptive routing is known to induce performance deterioration by causing massive oscillations. We describe ReplEx, an universally applicable distributed algorithm for dynamic routing/traffic engineering, which is based on game theory. We show through extensive realistic simulations that ReplEx does not oscillate, and that it achieves performance gains comparable to tr...

  13. Reconfigurable environmentally adaptive computing

    Science.gov (United States)

    Coxe, Robin L. (Inventor); Galica, Gary E. (Inventor)

    2008-01-01

    Described are methods and apparatus, including computer program products, for reconfigurable environmentally adaptive computing technology. An environmental signal representative of an external environmental condition is received. A processing configuration is automatically selected, based on the environmental signal, from a plurality of processing configurations. A reconfigurable processing element is reconfigured to operate according to the selected processing configuration. In some examples, the environmental condition is detected and the environmental signal is generated based on the detected condition.

  14. Adaptive positioner; Posicionador adaptativo

    Energy Technology Data Exchange (ETDEWEB)

    Labrador Pavon, I.

    1993-07-01

    This paper describes the circuits and programs in assembly language, developed to control the two DC motors that give mobility to a mechanical arm with two degrees of freedom. As a whole, the system is based in a adaptable regulator designed around a 8 bit microprocessor that, starting from a mode of regulation based in the successive approximation method, evolve to another mode through which, only one approximation is sufficient to get the right position of each motor. (Author) 6 refs.

  15. Homeowiscous adaptation in fish

    OpenAIRE

    Flipiak, Anna; Gondko, Roman; Gabryelak, Teresa

    1997-01-01

    Homeowiscous adaptation is a common phenomenon observed in poikilotherms which remain active at different temperatures. It is usually caused by changes in fatty acids pool in cellular membranes, what enable to maintain the physical structure of their membranes within tolerable limits. The increased unsaturaition of membrane lipids has as its basis some changes in activity of the appropriate enzymes. Fluctuations in fluidity of membrame lipids activate transcription of the genes...

  16. Invited article: Adaptability

    Directory of Open Access Journals (Sweden)

    Olivia Parr Rud

    2011-01-01

    Full Text Available For the last several decades, organizations have dealt with economic shifts using change management. Based on the new science, there are two major flaws with this approach. First, the word change implies an event with an ending. Second, it implies that change can be managed. In a world of economic volatility, this approach is no longer viable. The continuous climate of uncertainty and volatility demands another view, one that supports adaptability and resilience.

  17. Improved Adaptive Fingerprint Binarization

    OpenAIRE

    Bartunek, Josef Ström; Nilsson, Mikael; Nordberg, Jörgen; Claesson, Ingvar

    2008-01-01

    In this paper improvements to a previous work are presented. Removing the redundant artifacts in the fingerprint mask is introduced enhancing the final result. The proposed method is entirely adaptive process adjusting to each fingerprint without any further supervision of the user. Hence, the algorithm is insensitive to the characteristics of the fingerprint sensor and the various physical appearances of the fingerprints. Further, a detailed description of fingerprint mask generation not ful...

  18. Stylistic Adaptation in Translation

    Institute of Scientific and Technical Information of China (English)

    孙芳

    2011-01-01

    <正>A translation criteria universally accepted is faithfulness, which can be examined from different dimensions of content, form and style.Among these three dimensions,faithfulness in content and form is easier to be noted,while the faithfulness in style is harder to judge.This paper will mainly focus on the study of stylistic features for the purpose of language providing methods to achieve stylistic adaptation in translation.

  19. Adaptive structures flight experiments

    Science.gov (United States)

    Martin, Maurice

    The topics are presented in viewgraph form and include the following: adaptive structures flight experiments; enhanced resolution using active vibration suppression; Advanced Controls Technology Experiment (ACTEX); ACTEX program status; ACTEX-2; ACTEX-2 program status; modular control patch; STRV-1b Cryocooler Vibration Suppression Experiment; STRV-1b program status; Precision Optical Bench Experiment (PROBE); Clementine Spacecraft Configuration; TECHSAT all-composite spacecraft; Inexpensive Structures and Materials Flight Experiment (INFLEX); and INFLEX program status.

  20. Adaptive Brain Interfaces

    OpenAIRE

    Millán, José del R.

    2003-01-01

    Severely disabled people are largely excluded from the benefits information and communication technologies have brought to our industries, economies, appliances, and general quality of life. But what if that technology would allow them to communicate their wishes or control electronic devices directly through their thoughts alone? This is the goal and promise of the Adaptive Brain Interfaces (ABI) project, which aims to augment natural human capabilities by enabling people to interact with co...

  1. Adaptive Consumption Behavior

    OpenAIRE

    Peter Howitt; Ömer Özak

    2009-01-01

    This paper proposes and studies a theory of adaptive consumption behavior under income uncertainty and liquidity constraints. We assume that consumption is governed by a linear function of wealth, whose coefficients are revised each period by a procedure, which, although sophisticated, places few informational or computational demands on the consumer. We show that under a variety of settings, our procedure converges quickly to a set of coefficients with low welfare cost relative to a fully op...

  2. Geometry-induced protein pattern formation

    OpenAIRE

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-01

    Biological cells need the ability to guide intracellular processes to specific spatial locations. This requires biochemical processes to sense and adapt to the geometry of the organism. Previously suggested mechanisms either assume proteins that are able to directly sense membrane curvature or are based on nonlinear diffusion–reaction systems that can generate geometry-adapted patterns. The latter, however, requires fine-tuning of the reaction rates. Here, we show that geometry adaption alrea...

  3. An Adaptive Robot Game

    DEFF Research Database (Denmark)

    Hansen, Søren Tranberg; Svenstrup, Mikael; Dalgaard, Lars

    2010-01-01

    The goal of this paper is to describe an adaptive robot game, which motivates elderly people to do a regular amount of physical exercise while playing. One of the advantages of robot based games is that the initiative to play can be taken autonomously by the robot. In this case, the goal is to im...... to the behavior of the interacting person. This paper presents a simple ball game between a single player and a mobile robot platform. The algorithm has been validated using simulation and real world experiments.......The goal of this paper is to describe an adaptive robot game, which motivates elderly people to do a regular amount of physical exercise while playing. One of the advantages of robot based games is that the initiative to play can be taken autonomously by the robot. In this case, the goal...... is to improve the mental and physical state of the user by playing a physical game with the robot. Ideally, a robot game should be simple to learn but difficult to master, providing an appropriate degree of challenge for players with different skills. In order to achieve that, the robot should be able to adapt...

  4. Adaptive colouration in amphibians.

    Science.gov (United States)

    Rudh, Andreas; Qvarnström, Anna

    2013-01-01

    Amphibians, i.e. salamanders, frogs and caecilians show a wide range of bright colours in combination with contrasting patterns. There is variation among species, populations and also within species and populations. Furthermore, individuals often change colours during developmental stages or in response to environmental factors. This extraordinary variation means that there are excellent opportunities to test hypotheses of the adaptive significance of colours using amphibian species as models. We review the present view of functions of colouration in amphibians with the main focus on relatively unexplored topics. Variation in colouration has been found to play a role in thermoregulation, UV protection, predator avoidance and sexual signalling. However, many proposed cases of adaptive functions of colouration in amphibians remain virtually scientifically unexplored and surprisingly few genes influencing pigmentation or patterning have been detected. We would like to especially encourage more studies that take advantage of recent developments in measurement of visual properties of several possible signalling receivers (e.g. predators, competitors or mates). Future investigations on interactions between behaviour, ecology and vision have the potential to challenge our current view of the adaptive function of colouration in amphibians.

  5. Scale adaptive compressive tracking.

    Science.gov (United States)

    Zhao, Pengpeng; Cui, Shaohui; Gao, Min; Fang, Dan

    2016-01-01

    Recently, the compressive tracking (CT) method (Zhang et al. in Proceedings of European conference on computer vision, pp 864-877, 2012) has attracted much attention due to its high efficiency, but it cannot well deal with the scale changing objects due to its constant tracking box. To address this issue, in this paper we propose a scale adaptive CT approach, which adaptively adjusts the scale of tracking box with the size variation of the objects. Our method significantly improves CT in three aspects: Firstly, the scale of tracking box is adaptively adjusted according to the size of the objects. Secondly, in the CT method, all the compressive features are supposed independent and equal contribution to the classifier. Actually, different compressive features have different confidence coefficients. In our proposed method, the confidence coefficients of features are computed and used to achieve different contribution to the classifier. Finally, in the CT method, the learning parameter λ is constant, which will result in large tracking drift on the occasion of object occlusion or large scale appearance variation. In our proposed method, a variable learning parameter λ is adopted, which can be adjusted according to the object appearance variation rate. Extensive experiments on the CVPR2013 tracking benchmark demonstrate the superior performance of the proposed method compared to state-of-the-art tracking algorithms. PMID:27386298

  6. Vestibulospinal adaptation to microgravity

    Science.gov (United States)

    Paloski, W. H.

    1998-01-01

    Human balance control is known to be transiently disrupted after spaceflight; however, the mechanisms responsible for postflight postural ataxia are still under investigation. In this report, we propose a conceptual model of vestibulospinal adaptation based on theoretical adaptive control concepts and supported by the results from a comprehensive study of balance control recovery after spaceflight. The conceptual model predicts that immediately after spaceflight the balance control system of a returning astronaut does not expect to receive gravity-induced afferent inputs and that descending vestibulospinal control of balance is disrupted until the central nervous system is able to cope with the newly available vestibular otolith information. Predictions of the model are tested using data from a study of the neurosensory control of balance in astronauts immediately after landing. In that study, the mechanisms of sensorimotor balance control were assessed under normal, reduced, and/or altered (sway-referenced) visual and somatosensory input conditions. We conclude that the adaptive control model accurately describes the neurobehavioral responses to spaceflight and that similar models of altered sensory, motor, or environmental constraints are needed clinically to predict responses that patients with sensorimotor pathologies may have to various visual-vestibular or changing stimulus environments.

  7. Adaptive Leadership in Digital Transformation

    DEFF Research Database (Denmark)

    Hansen, Anne Mette; Kræmmergaard, Pernille; Mathiassen, Lars

    2012-01-01

    Leaders’ ability to quickly adapt IT practices is especially critical in today’s increasingly turbulent environment with frequent changes in the competitive and technological landscape. However, developing such adaptive leadership is a difficult and complex process. Often, underlying assumptions...

  8. Adaptive Structural Mode Control Project

    Data.gov (United States)

    National Aeronautics and Space Administration — M4 Engineering proposes the development of an adaptive structural mode control system. The adaptive control system will begin from a "baseline" dynamic model of the...

  9. AdapterRemoval v2

    DEFF Research Database (Denmark)

    Schubert, Mikkel; Lindgreen, Stinus; Orlando, Ludovic Antoine Alexandre

    2016-01-01

    BACKGROUND: As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to...... process the growing amount of data generated per sequencing run. FINDINGS: We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi......-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and...

  10. The trypanocidal benznidazole promotes adaptive response to oxidative injury: Involvement of the nuclear factor-erythroid 2-related factor-2 (Nrf2) and multidrug resistance associated protein 2 (MRP2).

    Science.gov (United States)

    Rigalli, Juan Pablo; Perdomo, Virginia Gabriela; Ciriaci, Nadia; Francés, Daniel Eleazar Antonio; Ronco, María Teresa; Bataille, Amy Michele; Ghanem, Carolina Inés; Ruiz, María Laura; Manautou, José Enrique; Catania, Viviana Alicia

    2016-08-01

    Oxidative stress is a frequent cause underlying drug-induced hepatotoxicity. Benznidazole (BZL) is the only trypanocidal agent available for treatment of Chagas disease in endemic areas. Its use is associated with side effects, including increases in biomarkers of hepatotoxicity. However, BZL potential to cause oxidative stress has been poorly investigated. Here, we evaluated the effect of a pharmacologically relevant BZL concentration (200μM) at different time points on redox status and the counteracting mechanisms in the human hepatic cell line HepG2. BZL increased reactive oxygen species (ROS) after 1 and 3h of exposure, returning to normality at 24h. Additionally, BZL increased glutathione peroxidase activity at 12h and the oxidized glutathione/total glutathione (GSSG/GSSG+GSH) ratio that reached a peak at 24h. Thus, an enhanced detoxification of peroxide and GSSG formation could account for ROS normalization. GSSG/GSSG+GSH returned to control values at 48h. Expression of the multidrug resistance-associated protein 2 (MRP2) and GSSG efflux via MRP2 were induced by BZL at 24 and 48h, explaining normalization of GSSG/GSSG+GSH. BZL activated the nuclear erythroid 2-related factor 2 (Nrf2), already shown to modulate MRP2 expression in response to oxidative stress. Nrf2 participation was confirmed using Nrf2-knockout mice in which MRP2 mRNA expression was not affected by BZL. In summary, we demonstrated a ROS increase by BZL in HepG2 cells and a glutathione peroxidase- and MRP2 driven counteracting mechanism, being Nrf2 a key modulator of this response. Our results could explain hepatic alterations associated with BZL therapy. PMID:27180241

  11. Advanced Adaptive Optics Technology Development

    Energy Technology Data Exchange (ETDEWEB)

    Olivier, S

    2001-09-18

    The NSF Center for Adaptive Optics (CfAO) is supporting research on advanced adaptive optics technologies. CfAO research activities include development and characterization of micro-electro-mechanical systems (MEMS) deformable mirror (DM) technology, as well as development and characterization of high-resolution adaptive optics systems using liquid crystal (LC) spatial light modulator (SLM) technology. This paper presents an overview of the CfAO advanced adaptive optics technology development activities including current status and future plans.

  12. Strategy for Climate Change Adaptation

    DEFF Research Database (Denmark)

    Rasmussen, Torben Valdbjørn

    The absence of a global agreement on the reduction of greenhouse gas emissions calls for adaptation to climate change. The associated paper explains the need for climate change adaptation of the building stock and suggests a pattern for a strategic approach to how to reach the climate change...... adaptation needed. Issues that must be addressed in case a strategic approach is not developed, as the building sector is continuously investing in measures to adapt to climate change as impacts emerge are described....

  13. Attention modulates visual size adaptation.

    OpenAIRE

    Kreutzer, Sylvia; Fink, G R; R. Weidner

    2015-01-01

    The current study determined in healthy subjects (n = 16) whether size adaptation occurs at early, i.e., preattentive, levels of processing or whether higher cognitive processes such as attention can modulate the illusion. To investigate this issue, bottom-up stimulation was kept constant across conditions by using a single adaptation display containing both small and large adapter stimuli. Subjects' attention was directed to either the large or small adapter stimulus by means of a luminance ...

  14. Adaptation: A Partially Automated Approach

    OpenAIRE

    Manjing, Tham; Bukhsh, F.A.; Weigand, H.

    2014-01-01

    This paper showcases the possibility of creating an adaptive auditing system. Adaptation in an audit environment need human intervention at some point. Based on a case study this paper focuses on automation of adaptation process. It is divided into solution design and validation parts. The artifact design is developed around import procedures of M-company. An overview of the artefact is discussed in detail to fully describes the adaptation mechanism with automatic adjustment for compliance re...

  15. Chapter 17 - Economics of adaptation

    OpenAIRE

    Chambwera, M.; Heal, G.; Dubeux, C.; Hallegatte, S.; Leclerc, L.; Markandya, A.; McCarl, B.A.; Mechler, R; Neumann, J.E.

    2014-01-01

    This chapter assesses the literature on the economics of climate change adaptation, building on the Fourth Assessment Report (AR4) and the increasing role that economic considerations are playing in adaptation decisionmaking and policy. AR4 provided a limited assessment of the costs and benefits of adaptation, based on narrow and fragmented sectoral and regional literature (Adger et al, 2007). Substantial advances have been made in the economics of climate change adaptation after AR4.

  16. Mapping functional prion-prion protein interaction sites using prion protein based peptide-arrays

    NARCIS (Netherlands)

    Rigter, A.; Priem, J.; Timmers-Parohi, D.; Langeveld, J.; Bossers, A.

    2009-01-01

    Protein-protein interactions are at the basis of most if not all biological processes in living cells. Therefore, adapting existing techniques or developing new techniques to study interactions between proteins are of importance in elucidating which amino acid sequences contribute to these interacti

  17. Is The Ribosome Targeted By Adaptive Mutations

    DEFF Research Database (Denmark)

    Jimenez Fernandez, Alicia; Molin, Søren; Johansen, Helle Krogh

    2015-01-01

    degree of evolutionary conservation of the cellular MMSM tend to support this view. However, under certain selective conditions the machinery itself may be targeted by adaptive mutations, which result in fitness-increasing phenotypic changes. Here we investigate and characterize the role of ribosomal...... mutations in adaptive evolution. Methods: Several mutations in ribosomal genes have been identified in the genome analysis of nearly 700 Pseudomonas aeruginosa isolates from infected cystic fibrosis patients. Among these mutations we have repeatedly identified insertions, deletions and substitutions...... in specific ribosomal genes. The bacterial phenotypes of the mutated strains will be investigated. Results: Preliminary assays show that mutant strains have reduced growth rate and an altered antibiotic resistance pattern. The selection for mutations in ribosomal protein genes is partly explainable...

  18. Adaptation in Tourist Publicity Translation

    Institute of Scientific and Technical Information of China (English)

    谭娟

    2013-01-01

    This paper attempts to provide a preliminary study of adaptation adopted in the translation of tourist publicity and ex-plore the main reasons behind the adaptive techniques on the basis of functionalist theories of translation. It is found that cultural blanks, different linguistic conventions and also the intended functions of tourist publicity may all contribute to adaptation in translation.

  19. How Harmful are Adaptation Restrictions

    NARCIS (Netherlands)

    Bruin, de K.C.; Dellink, R.B.

    2009-01-01

    The dominant assumption in economic models of climate policy remains that adaptation will be implemented in an optimal manner. There are, however, several reasons why optimal levels of adaptation may not be attainable. This paper investigates the effects of suboptimal levels of adaptation, i.e. adap

  20. Evolving concepts of sensory adaptation

    OpenAIRE

    Webster, Michael A.

    2012-01-01

    Sensory systems constantly adapt their responses to match the current environment. These adjustments occur at many levels of the system and increasingly appear to calibrate even for highly abstract perceptual representations of the stimulus. The similar effects of adaptation across very different stimulus domains point to common design principles but also continue to raise questions about the purpose of adaptation.

  1. Evolutionary dynamics of metabolic adaptation

    NARCIS (Netherlands)

    van Hoek, M.J.A.

    2008-01-01

    In this thesis we study how organisms adapt their metabolism to a changing environment. Metabolic adaptation occurs at different timescales. Organisms adapt their metabolism via metabolic regulation, which happens in the order of minutes to hours and via evolution, which takes many generations. Here

  2. Adaptation : A Partially Automated Approach

    NARCIS (Netherlands)

    Manjing, Tham; Bukhsh, F.A.; Weigand, H.

    2014-01-01

    This paper showcases the possibility of creating an adaptive auditing system. Adaptation in an audit environment need human intervention at some point. Based on a case study this paper focuses on automation of adaptation process. It is divided into solution design and validation parts. The artifact

  3. On Adaptive vs. Non-adaptive Security of Multiparty Protocols

    DEFF Research Database (Denmark)

    Canetti, Ran; Damgård, Ivan Bjerre; Dziembowski, Stefan;

    2001-01-01

    Security analysis of multiparty cryptographic protocols distinguishes between two types of adversarialsettings: In the non-adaptive setting, the set of corrupted parties is chosen in advance, before the interaction begins. In the adaptive setting, the adversary chooses who to corrupt during...... the course of the computation. We study the relations between adaptive security (i.e., security in the adaptive setting) and non-adaptive security, according to two definitions and in several models of computation. While affirming some prevailing beliefs, we also obtain some unexpected results. Some...... highlights of our results are: – - According to the definition of Dodis-Micali-Rogaway (which is set in the information-theoretic model), adaptive and non-adaptive security are equivalent. This holds for both honest-but-curious and Byzantine adversaries, and for any number of parties. – - According...

  4. A generic mechanism for adaptive growth rate regulation.

    Directory of Open Access Journals (Sweden)

    Chikara Furusawa

    2008-01-01

    Full Text Available How can a microorganism adapt to a variety of environmental conditions despite the existence of a limited number of signal transduction mechanisms? We show that for any growing cells whose gene expression fluctuate stochastically, the adaptive cellular state is inevitably selected by noise, even without a specific signal transduction network for it. In general, changes in protein concentration in a cell are given by its synthesis minus dilution and degradation, both of which are proportional to the rate of cell growth. In an adaptive state with a higher growth speed, both terms are large and balanced. Under the presence of noise in gene expression, the adaptive state is less affected by stochasticity since both the synthesis and dilution terms are large, while for a nonadaptive state both the terms are smaller so that cells are easily kicked out of the original state by noise. Hence, escape time from a cellular state and the cellular growth rate are negatively correlated. This leads to a selection of adaptive states with higher growth rates, and model simulations confirm this selection to take place in general. The results suggest a general form of adaptation that has never been brought to light--a process that requires no specific mechanisms for sensory adaptation. The present scheme may help explain a wide range of cellular adaptive responses including the metabolic flux optimization for maximal cell growth.

  5. A generic mechanism for adaptive growth rate regulation.

    Science.gov (United States)

    Furusawa, Chikara; Kaneko, Kunihiko

    2008-01-01

    How can a microorganism adapt to a variety of environmental conditions despite the existence of a limited number of signal transduction mechanisms? We show that for any growing cells whose gene expression fluctuate stochastically, the adaptive cellular state is inevitably selected by noise, even without a specific signal transduction network for it. In general, changes in protein concentration in a cell are given by its synthesis minus dilution and degradation, both of which are proportional to the rate of cell growth. In an adaptive state with a higher growth speed, both terms are large and balanced. Under the presence of noise in gene expression, the adaptive state is less affected by stochasticity since both the synthesis and dilution terms are large, while for a nonadaptive state both the terms are smaller so that cells are easily kicked out of the original state by noise. Hence, escape time from a cellular state and the cellular growth rate are negatively correlated. This leads to a selection of adaptive states with higher growth rates, and model simulations confirm this selection to take place in general. The results suggest a general form of adaptation that has never been brought to light--a process that requires no specific mechanisms for sensory adaptation. The present scheme may help explain a wide range of cellular adaptive responses including the metabolic flux optimization for maximal cell growth.

  6. Adaptability Responding Effectively to Change

    CERN Document Server

    (CCL), Center for Creative Leadership; Calarco, Allan

    2011-01-01

    In today's business world, the complexity and pace of change can be daunting. Adaptability has become recognized as a necessary skill for leaders to develop to be effective in this environment. Even so, leaders rarely know what they can do to become more adaptable and foster adaptability in others. This guidebook contributes to a greater understanding of adaptability and the cognitive, emotional, and dispositional flexibility it requires. Leaders will learn how to develop their adaptability and to become more effective for themselves, the people they lead, and their organizations.

  7. Adaptive filtering prediction and control

    CERN Document Server

    Goodwin, Graham C

    2009-01-01

    Preface1. Introduction to Adaptive TechniquesPart 1. Deterministic Systems2. Models for Deterministic Dynamical Systems3. Parameter Estimation for Deterministic Systems4. Deterministic Adaptive Prediction5. Control of Linear Deterministic Systems6. Adaptive Control of Linear Deterministic SystemsPart 2. Stochastic Systems7. Optimal Filtering and Prediction8. Parameter Estimation for Stochastic Dynamic Systems9. Adaptive Filtering and Prediction10. Control of Stochastic Systems11. Adaptive Control of Stochastic SystemsAppendicesA. A Brief Review of Some Results from Systems TheoryB. A Summary o

  8. Adaptive Optical Scanning Holography

    Science.gov (United States)

    Tsang, P. W. M.; Poon, Ting-Chung; Liu, J.-P.

    2016-01-01

    Optical Scanning Holography (OSH) is a powerful technique that employs a single-pixel sensor and a row-by-row scanning mechanism to capture the hologram of a wide-view, three-dimensional object. However, the time required to acquire a hologram with OSH is rather lengthy. In this paper, we propose an enhanced framework, which is referred to as Adaptive OSH (AOSH), to shorten the holographic recording process. We have demonstrated that the AOSH method is capable of decreasing the acquisition time by up to an order of magnitude, while preserving the content of the hologram favorably. PMID:26916866

  9. Adaptive Spectral Doppler Estimation

    DEFF Research Database (Denmark)

    Gran, Fredrik; Jakobsson, Andreas; Jensen, Jørgen Arendt

    2009-01-01

    of matched filters (one for each veloc- ity component of interest) and filtering the blood process over slow-time and averaging over depth to find the PSD. The methods are tested using various experiments and simulations. First, controlled flow-rig experiments with steady laminar flow are carried out....... Simulations in Field II for pul- sating flow resembling the femoral artery are also analyzed. The simulations are followed by in vivo measurement on the common carotid artery. In all simulations and experiments it was concluded that the adaptive methods display superior per- formance for short observation...

  10. Reentry vehicle adaptive telemetry

    Energy Technology Data Exchange (ETDEWEB)

    Kidner, R.E.

    1993-09-01

    In RF telemetry (TM) the allowable RF bandwidth limits the amount of data in the telemetered data set. Typically the data set is less than ideal to accommodate all aspects of a test. In the case of diagnostic data, the compromise often leaves insufficient diagnostic data when problems occur. As a solution, intelligence was designed into a TM, allowing it to adapt to changing data requirements. To minimize the computational requirements for an intelligent TM, a fuzzy logic inference engine was developed. This reference engine was simulated on a PC and then loaded into a TM hardware package for final testing.

  11. An Adaptive TVD Limiter

    Science.gov (United States)

    Jeng, Yih Nen; Payne, Uon Jan

    1995-05-01

    An adaptive TVD limiter, based on a limiter approximating the upper boundary of the TVD range and that of the third-order upwind TVD scheme, is developed in this work. The limiter switches to the comprressive limiter near a discontinuity, to the third-order TVD scheme's limiter in the smooth region, and to a weighted averaged scheme in the transition region between smooth and high gradient solutions. Numerical experiments show that the proposed scheme works very well for one-dimensional scalar equation problems but becomes less effective in one- and two-dimensional Euler equation problems. Further study is required for the two-dimensional scalar equation problems.

  12. Adopting an Adaptive Architecture

    DEFF Research Database (Denmark)

    Ayres, Phil

    2009-01-01

    This thesis grounds itself upon two implicitly time-based assumptions: 1. Change is inevitable 2. Design is an iterative process Herbert Simon posits design as an engine of change. He states that design activity is the devising of ‘courses of action aimed at changing existing situations into pref...... particular time-based attributes can be exhibited – most notably, adaptation. The implementation of this framework necessitates a re-examination of the process and concerns of architectural design. The sub-text of the thesis is to remember that the activity of design is itself designed....

  13. Adaptive antennas and receivers

    CERN Document Server

    Weiner, Melvin M

    2005-01-01

    In our modern age of remote sensing, wireless communication, and the nearly endless list of other antenna-based applications, complex problems require increasingly sophisticated solutions. Conventional antenna systems are no longer suited to high-noise or low-signal applications such as intrusion detection. Detailing highly effective approaches to non-Gaussian weak signal detection, Adaptive Antennas and Receivers provides an authoritative introduction to state-of-the-art research on the modeling, testing, and application of these technologies.Edited by innovative researcher and eminent expert

  14. Adaptation in Collaborative Governance Regimes

    Science.gov (United States)

    Emerson, Kirk; Gerlak, Andrea K.

    2014-10-01

    Adaptation and the adaptive capacity of human and environmental systems have been of central concern to natural and social science scholars, many of whom characterize and promote the need for collaborative cross-boundary systems that are seen as flexible and adaptive by definition. Researchers who study collaborative governance systems in the public administration, planning and policy literature have paid less attention to adaptive capacity specifically and institutional adaptation in general. This paper bridges the two literatures and finds four common dimensions of capacity, including structural arrangements, leadership, knowledge and learning, and resources. In this paper, we focus on institutional adaptation in the context of collaborative governance regimes and try to clarify and distinguish collaborative capacity from adaptive capacity and their contributions to adaptive action. We posit further that collaborative capacities generate associated adaptive capacities thereby enabling institutional adaptation within collaborative governance regimes. We develop these distinctions and linkages between collaborative and adaptive capacities with the help of an illustrative case study in watershed management within the National Estuary Program.

  15. Adaptation dynamics in densely clustered chemoreceptors.

    Directory of Open Access Journals (Sweden)

    William Pontius

    Full Text Available In many sensory systems, transmembrane receptors are spatially organized in large clusters. Such arrangement may facilitate signal amplification and the integration of multiple stimuli. However, this organization likely also affects the kinetics of signaling since the cytoplasmic enzymes that modulate the activity of the receptors must localize to the cluster prior to receptor modification. Here we examine how these spatial considerations shape signaling dynamics at rest and in response to stimuli. As a model system, we use the chemotaxis pathway of Escherichia coli, a canonical system for the study of how organisms sense, respond, and adapt to environmental stimuli. In bacterial chemotaxis, adaptation is mediated by two enzymes that localize to the clustered receptors and modulate their activity through methylation-demethylation. Using a novel stochastic simulation, we show that distributive receptor methylation is necessary for successful adaptation to stimulus and also leads to large fluctuations in receptor activity in the steady state. These fluctuations arise from noise in the number of localized enzymes combined with saturated modification kinetics between the localized enzymes and the receptor substrate. An analytical model explains how saturated enzyme kinetics and large fluctuations can coexist with an adapted state robust to variation in the expression levels of the pathway constituents, a key requirement to ensure the functionality of individual cells within a population. This contrasts with the well-mixed covalent modification system studied by Goldbeter and Koshland in which mean activity becomes ultrasensitive to protein abundances when the enzymes operate at saturation. Large fluctuations in receptor activity have been quantified experimentally and may benefit the cell by enhancing its ability to explore empty environments and track shallow nutrient gradients. Here we clarify the mechanistic relationship of these large

  16. Adaptation dynamics in densely clustered chemoreceptors.

    Science.gov (United States)

    Pontius, William; Sneddon, Michael W; Emonet, Thierry

    2013-01-01

    In many sensory systems, transmembrane receptors are spatially organized in large clusters. Such arrangement may facilitate signal amplification and the integration of multiple stimuli. However, this organization likely also affects the kinetics of signaling since the cytoplasmic enzymes that modulate the activity of the receptors must localize to the cluster prior to receptor modification. Here we examine how these spatial considerations shape signaling dynamics at rest and in response to stimuli. As a model system, we use the chemotaxis pathway of Escherichia coli, a canonical system for the study of how organisms sense, respond, and adapt to environmental stimuli. In bacterial chemotaxis, adaptation is mediated by two enzymes that localize to the clustered receptors and modulate their activity through methylation-demethylation. Using a novel stochastic simulation, we show that distributive receptor methylation is necessary for successful adaptation to stimulus and also leads to large fluctuations in receptor activity in the steady state. These fluctuations arise from noise in the number of localized enzymes combined with saturated modification kinetics between the localized enzymes and the receptor substrate. An analytical model explains how saturated enzyme kinetics and large fluctuations can coexist with an adapted state robust to variation in the expression levels of the pathway constituents, a key requirement to ensure the functionality of individual cells within a population. This contrasts with the well-mixed covalent modification system studied by Goldbeter and Koshland in which mean activity becomes ultrasensitive to protein abundances when the enzymes operate at saturation. Large fluctuations in receptor activity have been quantified experimentally and may benefit the cell by enhancing its ability to explore empty environments and track shallow nutrient gradients. Here we clarify the mechanistic relationship of these large fluctuations to well

  17. AdapterRemoval v2

    DEFF Research Database (Denmark)

    Schubert, Mikkel; Lindgreen, Stinus; Orlando, Ludovic

    2016-01-01

    process the growing amount of data generated per sequencing run. FINDINGS: We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi......-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and...... bzip2 support. CONCLUSIONS: We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations....

  18. The Adaptation Finance Gap Report

    DEFF Research Database (Denmark)

    Environment Programme (UNEP), which laid out the concept of ‘adaptation gaps’ and outlined three such gaps: technology, finance and knowledge. The 2016 Adaptation Gap Report assesses the difference between the financial costs of adapting to climate change in developing countries and the amount of money......UNEP’s Adaptation Gap Report series focuses on Finance, Technology and Knowledge gaps in climate change adaptation. It compliments the Emissions Gap Report series, and explores the implications of failing to close the emissions gap. The report builds on a 2014 assessment by the United Nations...... actually available to meet these costs – a difference known as the “adaptation finance gap”. Like the 2014 report, the 2016 report focuses on developing countries, where adaptation capacity is often the lowest and needs the highest, and concentrates on the period up to 2050. The report identifies trends...

  19. Classifying climate change adaptation frameworks

    Science.gov (United States)

    Armstrong, Jennifer

    2014-05-01

    Complex socio-ecological demographics are factors that must be considered when addressing adaptation to the potential effects of climate change. As such, a suite of deployable climate change adaptation frameworks is necessary. Multiple frameworks that are required to communicate the risks of climate change and facilitate adaptation. Three principal adaptation frameworks have emerged from the literature; Scenario - Led (SL), Vulnerability - Led (VL) and Decision - Centric (DC). This study aims to identify to what extent these adaptation frameworks; either, planned or deployed are used in a neighbourhood vulnerable to climate change. This work presents a criterion that may be used as a tool for identifying the hallmarks of adaptation frameworks and thus enabling categorisation of projects. The study focussed on the coastal zone surrounding the Sizewell nuclear power plant in Suffolk in the UK. An online survey was conducted identifying climate change adaptation projects operating in the study area. This inventory was analysed to identify the hallmarks of each adaptation project; Levels of dependency on climate model information, Metrics/units of analysis utilised, Level of demographic knowledge, Level of stakeholder engagement, Adaptation implementation strategies and Scale of adaptation implementation. The study found that climate change adaptation projects could be categorised, based on the hallmarks identified, in accordance with the published literature. As such, the criterion may be used to establish the matrix of adaptation frameworks present in a given area. A comprehensive summary of the nature of adaptation frameworks in operation in a locality provides a platform for further comparative analysis. Such analysis, enabled by the criterion, may aid the selection of appropriate frameworks enhancing the efficacy of climate change adaptation.

  20. Adaptive Robust Variable Selection

    CERN Document Server

    Fan, Jianqing; Barut, Emre

    2012-01-01

    Heavy-tailed high-dimensional data are commonly encountered in various scientific fields and pose great challenges to modern statistical analysis. A natural procedure to address this problem is to use penalized least absolute deviation (LAD) method with weighted $L_1$-penalty, called weighted robust Lasso (WR-Lasso), in which weights are introduced to ameliorate the bias problem induced by the $L_1$-penalty. In the ultra-high dimensional setting, where the dimensionality can grow exponentially with the sample size, we investigate the model selection oracle property and establish the asymptotic normality of the WR-Lasso. We show that only mild conditions on the model error distribution are needed. Our theoretical results also reveal that adaptive choice of the weight vector is essential for the WR-Lasso to enjoy these nice asymptotic properties. To make the WR-Lasso practically feasible, we propose a two-step procedure, called adaptive robust Lasso (AR-Lasso), in which the weight vector in the second step is c...

  1. Bayesian Adaptive Exploration

    Science.gov (United States)

    Loredo, Thomas J.

    2004-04-01

    I describe a framework for adaptive scientific exploration based on iterating an Observation-Inference-Design cycle that allows adjustment of hypotheses and observing protocols in response to the results of observation on-the-fly, as data are gathered. The framework uses a unified Bayesian methodology for the inference and design stages: Bayesian inference to quantify what we have learned from the available data and predict future data, and Bayesian decision theory to identify which new observations would teach us the most. When the goal of the experiment is simply to make inferences, the framework identifies a computationally efficient iterative ``maximum entropy sampling'' strategy as the optimal strategy in settings where the noise statistics are independent of signal properties. Results of applying the method to two ``toy'' problems with simulated data-measuring the orbit of an extrasolar planet, and locating a hidden one-dimensional object-show the approach can significantly improve observational efficiency in settings that have well-defined nonlinear models. I conclude with a list of open issues that must be addressed to make Bayesian adaptive exploration a practical and reliable tool for optimizing scientific exploration.

  2. Protein Detection with Aptamer Biosensors

    Directory of Open Access Journals (Sweden)

    Regina Stoltenburg

    2008-07-01

    Full Text Available Aptamers have been developed for different applications. Their use as new biological recognition elements in biosensors promises progress for fast and easy detection of proteins. This new generation of biosensor (aptasensors will be more stable and well adapted to the conditions of real samples because of the specific properties of aptamers.

  3. An adaptive algorithm for pass adaptation in plate rolling

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new algorithm for pass adaptation in plate rolling is developed to improve thickness accuracy of plate products. The feature of the algorithm is that it uses the measured data rather than the schedule calculated data in adaptation, which leads to notable improvementin prediction accuracy of the rolling parameters and thickness accuracy of products can be improved accordingly. Results show that this adaptive algorithm is effective in practice.

  4. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  5. Insights Into Quantitative Biology: analysis of cellular adaptation

    OpenAIRE

    Agoni, Valentina

    2013-01-01

    In the last years many powerful techniques have emerged to measure protein interactions as well as gene expression. Many progresses have been done since the introduction of these techniques but not toward quantitative analysis of data. In this paper we show how to study cellular adaptation and how to detect cellular subpopulations. Moreover we go deeper in analyzing signal transduction pathways dynamics.

  6. Adaptive immunity to fungi.

    Science.gov (United States)

    Verma, Akash; Wüthrich, Marcel; Deepe, George; Klein, Bruce

    2014-11-06

    Life-threatening fungal infections have risen sharply in recent years, owing to the advances and intensity of medical care that may blunt immunity in patients. This emerging crisis has created the growing need to clarify immune defense mechanisms against fungi with the ultimate goal of therapeutic intervention. We describe recent insights in understanding the mammalian immune defenses that are deployed against pathogenic fungi. We focus on adaptive immunity to the major medically important fungi and emphasize three elements that coordinate the response: (1) dendritic cells and subsets that are mobilized against fungi in various anatomical compartments; (2) fungal molecular patterns and their corresponding receptors that signal responses and shape the differentiation of T-cell subsets and B cells; and, ultimately (3) the effector and regulatory mechanisms that eliminate these invaders while constraining collateral damage to vital tissue. These insights create a foundation for the development of new, immune-based strategies for prevention or enhanced clearance of systemic fungal diseases.

  7. Climate Change Adaptation

    DEFF Research Database (Denmark)

    Hudecz, Adriána

    -operation and research into the common problems of the Northern Periphery. This report is an output of the ROADEX “Implementing Accessibility” project (2009-2012). It gives a summary of the results of research into adaptation measures to combat climate change effects on low volume roads in the Northern Periphery....... The research was carried out between January 2000 and March 2012. One of the biggest challenges that mankind has to face is the prospect of climate change resulting from emissions of greenhouse gases. These gases trap energy in the atmosphere and cause global surface temperatures to rise. This warming in turn...... causes changes in other climatic variables such as rainfall, humidity and wind speed that impact on the functioning of infrastructure such road networks. This paper discusses the climate changes predicted by the world’s meteorological organisations and considers how these may impact on the public...

  8. Adapting to climate change

    DEFF Research Database (Denmark)

    Arndt, Channing; Strzepek, Kenneth; Tarp, Finn;

    2011-01-01

    Mozambique, like many African countries, is already highly susceptible to climate variability and extreme weather events. Climate change threatens to heighten this vulnerability. In order to evaluate potential impacts and adaptation options for Mozambique, we develop an integrated modeling...... framework that translates atmospheric changes from general circulation model projections into biophysical outcomes via detailed hydrologic, crop, hydropower and infrastructure models. These sector models simulate a historical baseline and four extreme climate change scenarios. Sector results are then passed...... down to a dynamic computable general equilibrium model, which is used to estimate economy-wide impacts on national welfare, as well as the total cost of damages caused by climate change. Potential damages without changes in policy are significant; our discounted estimates range from US2.3 to US2.3toUS7...

  9. Bayesian Adaptive Exploration

    CERN Document Server

    Loredo, T J

    2004-01-01

    I describe a framework for adaptive scientific exploration based on iterating an Observation--Inference--Design cycle that allows adjustment of hypotheses and observing protocols in response to the results of observation on-the-fly, as data are gathered. The framework uses a unified Bayesian methodology for the inference and design stages: Bayesian inference to quantify what we have learned from the available data and predict future data, and Bayesian decision theory to identify which new observations would teach us the most. When the goal of the experiment is simply to make inferences, the framework identifies a computationally efficient iterative ``maximum entropy sampling'' strategy as the optimal strategy in settings where the noise statistics are independent of signal properties. Results of applying the method to two ``toy'' problems with simulated data--measuring the orbit of an extrasolar planet, and locating a hidden one-dimensional object--show the approach can significantly improve observational eff...

  10. Adaptive Sentence Boundary Disambiguation

    CERN Document Server

    Palmer, D D; Palmer, David D.; Hearst, Marti A.

    1994-01-01

    Labeling of sentence boundaries is a necessary prerequisite for many natural language processing tasks, including part-of-speech tagging and sentence alignment. End-of-sentence punctuation marks are ambiguous; to disambiguate them most systems use brittle, special-purpose regular expression grammars and exception rules. As an alternative, we have developed an efficient, trainable algorithm that uses a lexicon with part-of-speech probabilities and a feed-forward neural network. After training for less than one minute, the method correctly labels over 98.5\\% of sentence boundaries in a corpus of over 27,000 sentence-boundary marks. We show the method to be efficient and easily adaptable to different text genres, including single-case texts.

  11. Adaptively Compressed Exchange Operator

    CERN Document Server

    Lin, Lin

    2016-01-01

    The Fock exchange operator plays a central role in modern quantum chemistry. The large computational cost associated with the Fock exchange operator hinders Hartree-Fock calculations and Kohn-Sham density functional theory calculations with hybrid exchange-correlation functionals, even for systems consisting of hundreds of atoms. We develop the adaptively compressed exchange operator (ACE) formulation, which greatly reduces the computational cost associated with the Fock exchange operator without loss of accuracy. The ACE formulation does not depend on the size of the band gap, and thus can be applied to insulating, semiconducting as well as metallic systems. In an iterative framework for solving Hartree-Fock-like systems, the ACE formulation only requires moderate modification of the code, and can be potentially beneficial for all electronic structure software packages involving exchange calculations. Numerical results indicate that the ACE formulation can become advantageous even for small systems with tens...

  12. Adaptive compressive sensing camera

    Science.gov (United States)

    Hsu, Charles; Hsu, Ming K.; Cha, Jae; Iwamura, Tomo; Landa, Joseph; Nguyen, Charles; Szu, Harold

    2013-05-01

    We have embedded Adaptive Compressive Sensing (ACS) algorithm on Charge-Coupled-Device (CCD) camera based on the simplest concept that each pixel is a charge bucket, and the charges comes from Einstein photoelectric conversion effect. Applying the manufactory design principle, we only allow altering each working component at a minimum one step. We then simulated what would be such a camera can do for real world persistent surveillance taking into account of diurnal, all weather, and seasonal variations. The data storage has saved immensely, and the order of magnitude of saving is inversely proportional to target angular speed. We did design two new components of CCD camera. Due to the matured CMOS (Complementary metal-oxide-semiconductor) technology, the on-chip Sample and Hold (SAH) circuitry can be designed for a dual Photon Detector (PD) analog circuitry for changedetection that predicts skipping or going forward at a sufficient sampling frame rate. For an admitted frame, there is a purely random sparse matrix [Φ] which is implemented at each bucket pixel level the charge transport bias voltage toward its neighborhood buckets or not, and if not, it goes to the ground drainage. Since the snapshot image is not a video, we could not apply the usual MPEG video compression and Hoffman entropy codec as well as powerful WaveNet Wrapper on sensor level. We shall compare (i) Pre-Processing FFT and a threshold of significant Fourier mode components and inverse FFT to check PSNR; (ii) Post-Processing image recovery will be selectively done by CDT&D adaptive version of linear programming at L1 minimization and L2 similarity. For (ii) we need to determine in new frames selection by SAH circuitry (i) the degree of information (d.o.i) K(t) dictates the purely random linear sparse combination of measurement data a la [Φ]M,N M(t) = K(t) Log N(t).

  13. Adaptive Playware in Physical Games

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop; Thorsteinsson, Arnar Tumi

    2011-01-01

    that the activity automatically will match the capability of the individual user. With small test groups, we investigate how different age groups and gender groups physically interact with some playware games, and find indications of differences between the groups. Despite the small test set, the results......We describe how playware and games may adapt to the interaction of the individual user. We hypothesize that in physical games there are individual differences in user interaction capabilities and styles, and that adaptive playware may adapt to the individual user’s capabilities, so...... are a proof of existence of differences and of the need for adaptation, and therefore we investigate adaptation as an important issue for playware. With simple playware games, we show that the adaptation will speed the physical game up and down to find the appropriate level that matches the reaction speed...

  14. Intestinal mucosal atrophy and adaptation

    Institute of Scientific and Technical Information of China (English)

    Darcy Shaw; Kartik Gohil; Marc D Basson

    2012-01-01

    Mucosal adaptation is an essential process in gut homeostasis.The intestinal mucosa adapts to a range of pathological conditions including starvation,short-gut syndrome,obesity,and bariatric surgery.Broadly,these adaptive functions can be grouped into proliferation and differentiation.These are influenced by diverse interactions with hormonal,immune,dietary,nervous,and mechanical stimuli.It seems likely that clinical outcomes can be improved by manipulating the physiology of adaptation.This review will summarize current understanding of the basic science surrounding adaptation,delineate the wide range of potential targets for therapeutic intervention,and discuss how these might be incorporated into an overall treatment plan.Deeper insight into the physiologic basis of adaptation will identify further targets for intervention to improve clinical outcomes.

  15. Adaptive resummation of Markovian quantum dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lucas, Felix

    2014-08-06

    In this thesis we derive a highly convergent, nonperturbative expansion of Markovian open quantum dynamics. It is based on a splitting of the incoherent dynamics into periods of continuous evolution and abrupt jumps and attains its favorable convergence properties from an adaptive resummation of this so-called jump expansion. By means of the long-standing problems of spatial particle detection and Landau-Zener tunneling in the presence of dephasing, we show that this adaptive resummation technique facilitates new highly accurate analytic approximations of Markovian open systems. The open Landau-Zener model leads us to propose an efficient and robust incoherent control technique for the isomerization reaction of the visual pigment protein rhodopsin. Besides leading to approximate analytic descriptions of Markovian open quantum dynamics, the adaptive resummation of the jump expansion implies an efficient numerical simulation method. We spell out the corresponding numerical algorithm by means of Monte Carlo integration of the relevant terms in the jump expansion and demonstrate it in a set of paradigmatic open quantum systems.

  16. Adaptive resummation of Markovian quantum dynamics

    International Nuclear Information System (INIS)

    In this thesis we derive a highly convergent, nonperturbative expansion of Markovian open quantum dynamics. It is based on a splitting of the incoherent dynamics into periods of continuous evolution and abrupt jumps and attains its favorable convergence properties from an adaptive resummation of this so-called jump expansion. By means of the long-standing problems of spatial particle detection and Landau-Zener tunneling in the presence of dephasing, we show that this adaptive resummation technique facilitates new highly accurate analytic approximations of Markovian open systems. The open Landau-Zener model leads us to propose an efficient and robust incoherent control technique for the isomerization reaction of the visual pigment protein rhodopsin. Besides leading to approximate analytic descriptions of Markovian open quantum dynamics, the adaptive resummation of the jump expansion implies an efficient numerical simulation method. We spell out the corresponding numerical algorithm by means of Monte Carlo integration of the relevant terms in the jump expansion and demonstrate it in a set of paradigmatic open quantum systems.

  17. Information diffusion on adaptive network

    Institute of Scientific and Technical Information of China (English)

    Hu Ke; Tang Yi

    2008-01-01

    Based on the adaptive network,the feedback mechanism and interplay between the network topology and the diffusive process of information are studied.The results reveal that the adaptation of network topology can drive systems into the scale-free one with the assortative or disassortative degree correlations,and the hierarchical clustering.Meanwhile,the processes of the information diffusion are extremely speeded up by the adaptive changes of network topology.

  18. Adaptive designs for sequential experiments

    Institute of Scientific and Technical Information of China (English)

    林正炎; 张立新

    2003-01-01

    Various adaptive designs have been proposed and applied to clinical trials, bioassay, psychophysics, etc.Adaptive designs are also useful in high cost engineering trials.More and more people have been paying attention to these design methods. This paper introduces several broad families of designs, such as the play-the-winner rule, randomized play-the-winner rule and its generalization to the multi-arm case, doubly biased coin adaptive design, Markov chain model.

  19. Adaptive Mesh Refinement in CTH

    International Nuclear Information System (INIS)

    This paper reports progress on implementing a new capability of adaptive mesh refinement into the Eulerian multimaterial shock- physics code CTH. The adaptivity is block-based with refinement and unrefinement occurring in an isotropic 2:1 manner. The code is designed to run on serial, multiprocessor and massive parallel platforms. An approximate factor of three in memory and performance improvements over comparable resolution non-adaptive calculations has-been demonstrated for a number of problems

  20. Content adaptive screen image scaling

    OpenAIRE

    Zhai, Yao; Wang, Qifei; Lu, Yan; Li, Shipeng

    2015-01-01

    This paper proposes an efficient content adaptive screen image scaling scheme for the real-time screen applications like remote desktop and screen sharing. In the proposed screen scaling scheme, a screen content classification step is first introduced to classify the screen image into text and pictorial regions. Afterward, we propose an adaptive shift linear interpolation algorithm to predict the new pixel values with the shift offset adapted to the content type of each pixel. The shift offse...

  1. Staff Adaptation in Selected Company

    OpenAIRE

    Štolcová, Jana

    2011-01-01

    The work focuses on personnel actions of employee adaptation as, nowadays, it is very important to maintain a good and skilled staff. The main aim of this work is to analyze and evaluate the process of adaptation of new employees at the headquarters of the BILLA, Ltd., which operates more than 200 supermarkets around the Czech Republic,. Another task is to propose partial measures which would improve the process of adaptation in the society. The literature review discusses the importance of ...

  2. PCMAT, an adaptive learning platform

    OpenAIRE

    Couto, Paulo; Fernandes, Marta; Martins, Constantino; Faria, Luiz

    2013-01-01

    This paper is about PCMAT, an adaptive learning platform for Mathematics in Basic Education schools. Based on a constructivist approach, PCMAT aims at verifying how techniques from adaptive hypermedia systems can improve e-learning based systems. To achieve this goal, PCMAT includes a Pedagogical Model that contains a set of adaptation rules that influence the student-platform interaction. PCMAT was subject to a preliminary testing with students aged between 12 and 14 years old on th...

  3. Understanding Adaptation in Large Populations

    OpenAIRE

    Talia Karasov; Messer, Philipp W.; Petrov, Dmitri A.

    2010-01-01

    Adaptation in eukaryotes is generally assumed to be mutation-limited because of small effective population sizes. This view is difficult to reconcile, however, with the observation that adaptation to anthropogenic changes, such as the introduction of pesticides, can occur very rapidly. Here we investigate adaptation at a key insecticide resistance locus (Ace) in Drosophila melanogaster and show that multiple simple and complex resistance alleles evolved quickly and repeatedly within individua...

  4. Adaptive Motion Compensation in Radiotherapy

    CERN Document Server

    Murphy, Martin J

    2011-01-01

    External-beam radiotherapy has long been challenged by the simple fact that patients can (and do) move during the delivery of radiation. Recent advances in imaging and beam delivery technologies have made the solution--adapting delivery to natural movement--a practical reality. Adaptive Motion Compensation in Radiotherapy provides the first detailed treatment of online interventional techniques for motion compensation radiotherapy. This authoritative book discusses: Each of the contributing elements of a motion-adaptive system, including target detection and tracking, beam adaptation, and pati

  5. Adaptive filtering and change detection

    CERN Document Server

    Gustafsson, Fredrik

    2003-01-01

    Adaptive filtering is a classical branch of digital signal processing (DSP). Industrial interest in adaptive filtering grows continuously with the increase in computer performance that allows ever more conplex algorithms to be run in real-time. Change detection is a type of adaptive filtering for non-stationary signals and is also the basic tool in fault detection and diagnosis. Often considered as separate subjects Adaptive Filtering and Change Detection bridges a gap in the literature with a unified treatment of these areas, emphasizing that change detection is a natural extensi

  6. Immunologic mechanisms in the adaptation of swine farm workers to their work environment

    DEFF Research Database (Denmark)

    Bønløkke, Jakob Hjort; Cormier, Yvon; Veillette, Marc;

    2013-01-01

    Swine building exposure causes inflammatory reactions that appear to be attenuated with prolonged periods of contact. The mechanisms behind this adaptation to a dusty and endotoxin-rich environment are poorly understood. Our aim was to compare levels of selected inflammatory mediators in swine farm...... for these proteins in adaptation to the swine building environment after repeated exposures....

  7. Adaptive Behaviour Assessment System: Indigenous Australian Adaptation Model (ABAS: IAAM)

    Science.gov (United States)

    du Plessis, Santie

    2015-01-01

    The study objectives were to develop, trial and evaluate a cross-cultural adaptation of the Adaptive Behavior Assessment System-Second Edition Teacher Form (ABAS-II TF) ages 5-21 for use with Indigenous Australian students ages 5-14. This study introduced a multiphase mixed-method design with semi-structured and informal interviews, school…

  8. Molecular adaptations in psychrophilic bacteria: potential for biotechnological applications.

    Science.gov (United States)

    Russell, N J

    1998-01-01

    Bacteria which live in cold conditions are known as psychrophiles. Since so much of our planet is generally cold, i.e. below 5 degrees C, it is not surprising that they are very common amongst a wide variety of habitats. To enable them to survive and grow in cold environments, psychrophilic bacteria have evolved a complex range of adaptations to all of their cellular components, including their membranes, energy-generating systems, protein synthesis machinery, biodegradative enzymes and the components responsible for nutrient uptake. Whilst such a systems approach to the topic has its advantages, all of the changes can be described in terms of adaptive alterations in the proteins and lipids of the bacterial cell. The present review adopts the latter approach and, following a brief consideration of the definition of psychrophiles and description of their habitats, focuses on those adaptive changes in proteins and lipids, especially those which are either currently being explored for their biotechnological potential or might be so in the future. Such applications for proteins range from the use of cold-active enzymes in the detergent and food industries, in specific biotransformations and environmental bioremediations, to specialised uses in contact lens cleaning fluids and reducing the lactose content of milk; ice-nucleating proteins have potential uses in the manufacture of ice cream or artificial snow; for lipids, the uses include dietary supplements in the form of polyunsaturated fatty acids from some Antarctic marine psychrophiles.

  9. Europe adapts to climate change: Comparing National Adaptation Strategies

    DEFF Research Database (Denmark)

    Biesbroek, G. Robbert; Swart, Rob J.; Carter, Timothy R.;

    2010-01-01

    For the last two decades, European climate policy has focused almost exclusively on mitigation of climate change. It was only well after the turn of the century, with impacts of climate change increasingly being observed, that adaptation was added to the policy agenda and EU Member States started...... to develop National Adaptation Strategies (NASs). This paper reviews seven National Adaptation Strategies that were either formally adopted or under development by Member States at the end of 2008. The strategies are analysed under the following six themes. Firstly, the factors motivating and facilitating...... the development of a national adaptation strategy. Secondly, the scientific and technical support needed for the development and implementation of such a strategy. Thirdly, the role of the strategy in information, communication and awareness-raising of the adaptation issue. Fourthly, new or existing forms...

  10. Smartphone adapters for digital photomicrography

    Directory of Open Access Journals (Sweden)

    Somak Roy

    2014-01-01

    Full Text Available Background: Photomicrographs in Anatomic Pathology provide a means of quickly sharing information from a glass slide for consultation, education, documentation and publication. While static image acquisition historically involved the use of a permanently mounted camera unit on a microscope, such cameras may be expensive, need to be connected to a computer, and often require proprietary software to acquire and process images. Another novel approach for capturing digital microscopic images is to use smartphones coupled with the eyepiece of a microscope. Recently, several smartphone adapters have emerged that allow users to attach mobile phones to the microscope. The aim of this study was to test the utility of these various smartphone adapters. Materials and Methods: We surveyed the market for adapters to attach smartphones to the ocular lens of a conventional light microscope. Three adapters (Magnifi, Skylight and Snapzoom were tested. We assessed the designs of these adapters and their effectiveness at acquiring static microscopic digital images. Results: All adapters facilitated the acquisition of digital microscopic images with a smartphone. The optimal adapter was dependent on the type of phone used. The Magnifi adapters for iPhone were incompatible when using a protective case. The Snapzoom adapter was easiest to use with iPhones and other smartphones even with protective cases. Conclusions: Smartphone adapters are inexpensive and easy to use for acquiring digital microscopic images. However, they require some adjustment by the user in order to optimize focus and obtain good quality images. Smartphone microscope adapters provide an economically feasible method of acquiring and sharing digital pathology photomicrographs.

  11. Epistatic adaptive evolution of human color vision.

    Directory of Open Access Journals (Sweden)

    Shozo Yokoyama

    2014-12-01

    Full Text Available Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV-free retinal environment, the short wavelength-sensitive (SWS1 visual pigment in human (human S1 switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45-30 million years ago, the middle and long wavelength-sensitive (MWS/LWS pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments.

  12. Structural disorder provides increased adaptability for vesicle trafficking pathways.

    Directory of Open Access Journals (Sweden)

    Natalia Pietrosemoli

    Full Text Available Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (~23% than the other two, COPI (~9% and COPII (~8%. We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking

  13. Structural disorder provides increased adaptability for vesicle trafficking pathways.

    Science.gov (United States)

    Pietrosemoli, Natalia; Pancsa, Rita; Tompa, Peter

    2013-01-01

    Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (~23%) than the other two, COPI (~9%) and COPII (~8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest

  14. Stimuli-Adaptable Materials

    DEFF Research Database (Denmark)

    Frankær, Sarah Maria Grundahl

    The work presented in this Thesis deals with the development of a stimuli-adaptable polymer material based on the UV-induced dimerisation of cinnamic acid and its derivatives. It is in the nature of an adhesive to adhere very well to its substrate and therefore problems can arise upon removal...... of the adhesive. This is also known from skin adhesives where it is very undesirable to cause damage to the skin. The overall idea of this project was to resolve this problem by developing a material which could switch between an adhesive and a non-adhesive state. Switchable adhesion is known in the literature...... but the presented work has a new approach to the field by basing itself on the idea of developing a network into which a photo-active polymer is mixed and which function as an adhesive. Upon irradiation with UV-light for a short time a non-adhering inter-penetrating network material would be formed. Two simple...

  15. Statistical Physics of Adaptation

    Science.gov (United States)

    Perunov, Nikolay; Marsland, Robert A.; England, Jeremy L.

    2016-04-01

    Whether by virtue of being prepared in a slowly relaxing, high-free energy initial condition, or because they are constantly dissipating energy absorbed from a strong external drive, many systems subject to thermal fluctuations are not expected to behave in the way they would at thermal equilibrium. Rather, the probability of finding such a system in a given microscopic arrangement may deviate strongly from the Boltzmann distribution, raising the question of whether thermodynamics still has anything to tell us about which arrangements are the most likely to be observed. In this work, we build on past results governing nonequilibrium thermodynamics and define a generalized Helmholtz free energy that exactly delineates the various factors that quantitatively contribute to the relative probabilities of different outcomes in far-from-equilibrium stochastic dynamics. By applying this expression to the analysis of two examples—namely, a particle hopping in an oscillating energy landscape and a population composed of two types of exponentially growing self-replicators—we illustrate a simple relationship between outcome-likelihood and dissipative history. In closing, we discuss the possible relevance of such a thermodynamic principle for our understanding of self-organization in complex systems, paying particular attention to a possible analogy to the way evolutionary adaptations emerge in living things.

  16. Adaptive sharpening of photos

    Science.gov (United States)

    Safonov, Ilia V.; Rychagov, Michael N.; Kang, KiMin; Kim, Sang Ho

    2008-01-01

    Sharpness is an important attribute that contributes to the overall impression of printed photo quality. Often it is impossible to estimate sharpness prior to printing. Sometimes it is a complex task for a consumer to obtain accurate sharpening results by editing a photo on a computer. The novel method of adaptive sharpening aimed for photo printers is proposed. Our approach includes 3 key techniques: sharpness level estimation, local tone mapping and boosting of local contrast. Non-reference automatic sharpness level estimation is based on analysis of variations of edges histograms, where edges are produced by high-pass filters with various kernel sizes, array of integrals of logarithm of edges histograms characterizes photo sharpness, machine learning is applied to choose optimal parameters for given printing size and resolution. Local tone mapping with ordering is applied to decrease edge transition slope length without noticeable artifacts and with some noise suppression. Unsharp mask via bilateral filter is applied for boosting of local contrast. This stage does not produce strong halo artifact which is typical for the traditional unsharp mask filter. The quality of proposed approach is evaluated by surveying observer's opinions. According to obtained replies the proposed method enhances the majority of photos.

  17. Adapting to an aftereffect.

    Science.gov (United States)

    Sheth, Bhavin R; Shimojo, Shinsuke

    2008-01-01

    We report a new type of orientation-contingent color aftereffect in which the color aftereffect is opposite to the classical McCollough effect, i.e., the perceived color of the aftereffect is the same as the inducer's color. Interleaved exposure to red, horizontal and achromatic (gray), horizontal gratings led to a long-lasting aftereffect in which achromatic horizontal gratings appeared reddish. The effect, termed the anti-McCollough effect, although weaker than the classical aftereffect, remained stable for a moderate duration of time (24 hours). Unlike the classical aftereffect, which is known to not transfer interocularly, the new after-aftereffect transferred 100%, suggesting that its locus in the brain was downstream of the classical effect. It is likely that neurons in a higher-order area adapted to the classical color aftereffect that was represented in a lower-order area, thus forming an aftereffect of an aftereffect, i.e., an after-aftereffect. Our finding has implications as to how neural activity in lower- and higher-level areas in the brain interacts to yield conscious visual experience. PMID:18484835

  18. Success and adaptation

    CERN Multimedia

    2013-01-01

    Yesterday morning, the last colliding proton beams of 2013 were extracted from the LHC, heralding the start of the machine’s first long shutdown (LS1) and crowning its first three glorious years of running. I hardly need to tell the CERN community what a fabulous performance all the people running the machine, the experiments, the computing and all supporting infrastructures put in. Those people are you, and you all know very well what a great job everyone did.   Nevertheless, I would like to express my thanks to all the people who made this first LHC run such a success. Re-measuring the whole Standard Model in such a short period, and then completing it with the discovery of what looks increasingly like the Higgs boson, is no mean feat. What I’d like to focus on today is another aspect of our field: its remarkable ability to adapt. When I started out in research, experiments involved a handful of people and lasted a few years at most. The timescale for the development of ...

  19. Interdisciplinarity in Adapted Physical Activity

    Science.gov (United States)

    Bouffard, Marcel; Spencer-Cavaliere, Nancy

    2016-01-01

    It is commonly accepted that inquiry in adapted physical activity involves the use of different disciplines to address questions. It is often advanced today that complex problems of the kind frequently encountered in adapted physical activity require a combination of disciplines for their solution. At the present time, individual research…

  20. Codon Adaptation of Plastid Genes

    Science.gov (United States)

    Suzuki, Haruo; Morton, Brian R.

    2016-01-01

    Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes. PMID:27196606

  1. Codon Adaptation of Plastid Genes.

    Directory of Open Access Journals (Sweden)

    Haruo Suzuki

    Full Text Available Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes.

  2. Adaptive Cartography and Geographical Education

    Science.gov (United States)

    Konecny, Milan; Stanek, Karel

    2010-01-01

    The article focuses on adaptive cartography and its potential for geographical education. After briefly describing the wider context of adaptive cartography, it is suggested that this new cartographic approach establishes new demands and benefits for geographical education, especially in offering the possibility for broader individual…

  3. Adaptive Regularization of Neural Classifiers

    DEFF Research Database (Denmark)

    Andersen, Lars Nonboe; Larsen, Jan; Hansen, Lars Kai;

    1997-01-01

    We present a regularization scheme which iteratively adapts the regularization parameters by minimizing the validation error. It is suggested to use the adaptive regularization scheme in conjunction with optimal brain damage pruning to optimize the architecture and to avoid overfitting. Furthermore...

  4. The adaptation to climate change

    International Nuclear Information System (INIS)

    The authors address the issue of adaptation to climate change. They first address the physical aspects related to this issue: scenarios of temperature evolution, main possible impacts. Then, they address the social impacts related to climate risks, and the adaptation strategies which aim at reducing the exposure and vulnerability of human societies, or at increasing their resilience. Some examples of losses of human lives and of economic damages due to recent catastrophes related to climate change are evoked. The authors address the international framework, the emergence of an international regime on climate, the quite recent emergence of adaptation within international negotiations in 2001, the emergence of the idea of a support to developing countries. National and local policies are presented in the next chapter (in the European Union, the Netherlands which are faced with the issue of sea level rise, programs in developing countries) and their limitations are also outlined. The next chapter addresses the adaptation actions performed by private actors (enterprises, households, associations, civil society, and so on) with example of vulnerability, and adaptation opportunities and possibilities in some specific sectors. The last chapter presents a typology of actions of adaptation, indicators of adaptation to climate change, and examples of mistaken adaptation

  5. fMRI adaptation revisited.

    Science.gov (United States)

    Larsson, Jonas; Solomon, Samuel G; Kohn, Adam

    2016-07-01

    Adaptation has been widely used in functional magnetic imaging (fMRI) studies to infer neuronal response properties in human cortex. fMRI adaptation has been criticized because of the complex relationship between fMRI adaptation effects and the multiple neuronal effects that could underlie them. Many of the longstanding concerns about fMRI adaptation have received empirical support from neurophysiological studies over the last decade. We review these studies here, and also consider neuroimaging studies that have investigated how fMRI adaptation effects are influenced by high-level perceptual processes. The results of these studies further emphasize the need to interpret fMRI adaptation results with caution, but they also provide helpful guidance for more accurate interpretation and better experimental design. In addition, we argue that rather than being used as a proxy for measurements of neuronal stimulus selectivity, fMRI adaptation may be most useful for studying population-level adaptation effects across cortical processing hierarchies.

  6. Adaptive Assessments Using Open Specifications

    Science.gov (United States)

    Leon, Hector Barbosa; Garcia-Penalvo, Francisco J.; Rodriguez-Conde, Maria Jose; Morales, Erla M.; de Pablos, Patricia Ordonez

    2012-01-01

    Evaluation is a key element in formal education processes; it must be constructed in a way that the item questions within help students understand by adapting them to the learning style as well. The focus of the present research work specifically in the convenience to adapt an associated multimedia material in each single question besides the…

  7. Multi-Directional Motion Adaptation

    Directory of Open Access Journals (Sweden)

    David Patrick McGovern

    2012-05-01

    Full Text Available The direction aftereffect (DAE is a phenomenon whereby prolonged exposure to a moving stimulus biases the perceived direction of subsequent stimuli. It is believed to arise through a selective suppression of directionally tuned neurons in the visual cortex, causing shifts in the population response away from the adapted direction. Whereas most studies consider only unidirectional adaptation, here we examine how concurrent adaptation to multiple directions affects the DAE. Observers were required to judge whether a random dot kinematogram (RDK moved clockwise or counter-clockwise relative to upwards. In different conditions, observers adapted to a stimulus comprised of directions drawn from a distribution or to bidirectional motion. Increasing the variance of normally distributed directions reduced the magnitude of the peak DAE and broadened its tuning profile. Asymmetric sampling of Gaussian and uniform distributions resulted in shifts of DAE tuning profiles consistent with changes in the perceived global direction of the adapting stimulus. Discrimination thresholds were elevated by an amount that related to the magnitude of the bias. For bidirectional adaptors, adding dots in directions away from the adapting motion led to a pronounced reduction in the DAE. This reduction was observed when dots were added in opposite or orthogonal directions to the adaptor suggesting that it may arise via inhibition from a broadly tuned normalisation pool. Preliminary simulations with a population coding model, where the gain of a direction-selective neuron is inversely proportional to its response to the adapting stimulus, suggest that it provides a parsimonious account of these adaptation effects.

  8. Adapting agriculture to climate change

    NARCIS (Netherlands)

    Howden, S.M.; Soussana, J.F.; Tubiello, F.N.; Chhetri, N.; Dunlop, M.; Meinke, H.B.

    2007-01-01

    The strong trends in climate change already evident, the likelihood of further changes occurring, and the increasing scale of potential climate impacts give urgency to addressing agricultural adaptation more coherently. There are many potential adaptation options available for marginal change of exi

  9. Techniques of English Textbooks Adaptation

    Institute of Scientific and Technical Information of China (English)

    张婧雯; 杨竞欧

    2014-01-01

    This essay attempts to aim English teachers to evaluate and adapt the current English textbooks.According to different levels and majors of the students,English teachers can enhance the teaching materials and their teaching skills.This paper would provide several useful techniques for teachers to make evaluations and adaptations of using teaching materials.

  10. Tracking adaptation and measuring development

    Energy Technology Data Exchange (ETDEWEB)

    Brooks, Nick; Anderson, Simon; Ayers, Jessica; Burton, Ian; Tellam, Ian

    2011-11-15

    This is the first paper in the new IIED Climate Change Working Paper series. As adaptation to climate change becomes the focus of increasing attention and the target of significant spending, there is a growing need for frameworks and tools that enable organisations to track and assess the outcomes of adaptation interventions. This paper presents a coherent framework for climate change adaptation programming, including potential indicators, or indicator categories/types, for tracking and evaluating the success of adaptation support and adaptation interventions. The paper begins with a discussion of some of the key issues related to the evaluation of adaptation, and outlines some of the main difficulties and constraints with respect to the development of adaptation indicators. Next, an evaluation framework is proposed and indicator categories or 'domains' are identified. Lastly, key conclusions are provided and a theory of change is outlined that shows how development and use of the framework could lead to more effective adaptation investments for climate resilient development.

  11. Dynamic adaption of vascular morphology

    DEFF Research Database (Denmark)

    Okkels, Fridolin; Jacobsen, Jens Christian Brings

    2012-01-01

    The structure of vascular networks adapts continuously to meet changes in demand of the surrounding tissue. Most of the known vascular adaptation mechanisms are based on local reactions to local stimuli such as pressure and flow, which in turn reflects influence from the surrounding tissue. Here ...

  12. Codon Adaptation of Plastid Genes.

    Science.gov (United States)

    Suzuki, Haruo; Morton, Brian R

    2016-01-01

    Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes. PMID:27196606

  13. Career adaptability and career entrenchment

    NARCIS (Netherlands)

    Zacher, Hannes; Ambiel, Rodolfo A.M.; Noronha, Ana Paula Porto

    2015-01-01

    Career adaptability constitutes a resource that can help employees to effectively manage career changes and challenges. The goal of this study was to investigate the relationship between the two higher-order constructs of career adaptability and career entrenchment (i.e., the perceived inability and

  14. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  15. Strategy for Climate Change Adaptation

    DEFF Research Database (Denmark)

    Rasmussen, Torben Valdbjørn

    2013-01-01

    . This absence of an agreement calls for adaptation to climate change. Emphasis should be put on buildings, as they play a vital economic and social role in society and are vulnerable to climate change. Therefore, the building stock deserves its own policy and implementation plans as well as tools that enable...... adequate and cost-efficient adaptation to climate change. This paper explains the need for climate change adaptation of the building stock and suggests a pattern for a strategic approach to how to reach the climate change adaptation needed. The suggested and presented need of a strategic approach is based...... on three main initiatives consisting of the need to examine the potential impacts of climate change on the building stock, the need to assess and develop a roadmap of current and future adaptation measures that can withstand the effects of climate change, and the need to engage relevant stakeholders...

  16. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    Science.gov (United States)

    He, Yi-Ming; Ma, Bin-Guang

    2016-05-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

  17. Tree Adapt: Web Content Adaptation for Mobile Devices

    Directory of Open Access Journals (Sweden)

    Rajibul Anam

    2014-08-01

    Full Text Available Mobile web browsing usually becomes time-consuming since currently it requires horizontal and vertical scrolling in addition to this, users interested in only a section of a web page are often burdened with cumbersome whole web pages that not only do not properly fit their mobile screens but also require a lot of delivery time. This problem can be addressed and resolved with the help of a mobile web content adaptation system. Existing web content adaptation systems focus on resizing contents to fit a mobile device and removing unnecessary contents from the adapted web page. This paper’s aim is to address the gap by proposing the TreeAdapt which provides a condensed view of an adapted web page. This condensed view consists of only block headers which users can then expand for complete content. In order to achieve this, the proposed algorithm will first categorize an HTML object as menu, block title or the main content. A depth-first traversal algorithm is then used to select the sequence of blocks to be displayed on a mobile device. Usability studies were performed to evaluate the usability of the adapted contents against other deployed systems. Results from the usability studies indicate that the adapted contents produced by the proposed techniques enabled users to locate targeted information within a web page in a shorter span of time.

  18. Protein Structure

    Science.gov (United States)

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  19. Lessons in Protein Design from Combined Evolution and Conformational Dynamics

    OpenAIRE

    Swarnendu Tripathi; M Neal Waxham; Cheung, Margaret S.; Yin Liu

    2015-01-01

    Protein-protein interactions play important roles in the control of every cellular process. How natural selection has optimized protein design to produce molecules capable of binding to many partner proteins is a fascinating problem but not well understood. Here, we performed a combinatorial analysis of protein sequence evolution and conformational dynamics to study how calmodulin (CaM), which plays essential roles in calcium signaling pathways, has adapted to bind to a large number of partne...

  20. Formation of functional cell membrane domains: the interplay of lipid- and protein-mediated interactions.

    OpenAIRE

    Harder, Thomas

    2003-01-01

    Numerous cell membrane associated processes, including signal transduction, membrane sorting, protein processing and virus trafficking take place in membrane subdomains. Protein-protein interactions provide the frameworks necessary to generate biologically functional membrane domains. For example, coat proteins define membrane areas destined for sorting processes, viral proteins self-assemble to generate a budding virus, and adapter molecules organize multimolecular signalling assemblies, whi...

  1. Investigation of the parallel tempering method for protein folding

    Science.gov (United States)

    Schug, Alexander; Herges, Thomas; Verma, Abhinav; Wenzel, Wolfgang

    2005-05-01

    We investigate the suitability and efficiency of an adapted version of the parallel tempering method for all-atom protein folding. We have recently developed an all-atom free energy force field (PFF01) for protein structure prediction with stochastic optimization methods. Here we report reproducible folding of the 20-amino-acid trp-cage protein and the conserved 40-amino-acid three-helix HIV accessory protein with an adapted parallel tempering method. We find that the native state, for both proteins, is correctly predicted to 2 Å backbone root mean square deviation and analyse the efficiency of the simulation approach.

  2. Parallel Adaptive Mesh Refinement

    Energy Technology Data Exchange (ETDEWEB)

    Diachin, L; Hornung, R; Plassmann, P; WIssink, A

    2005-03-04

    As large-scale, parallel computers have become more widely available and numerical models and algorithms have advanced, the range of physical phenomena that can be simulated has expanded dramatically. Many important science and engineering problems exhibit solutions with localized behavior where highly-detailed salient features or large gradients appear in certain regions which are separated by much larger regions where the solution is smooth. Examples include chemically-reacting flows with radiative heat transfer, high Reynolds number flows interacting with solid objects, and combustion problems where the flame front is essentially a two-dimensional sheet occupying a small part of a three-dimensional domain. Modeling such problems numerically requires approximating the governing partial differential equations on a discrete domain, or grid. Grid spacing is an important factor in determining the accuracy and cost of a computation. A fine grid may be needed to resolve key local features while a much coarser grid may suffice elsewhere. Employing a fine grid everywhere may be inefficient at best and, at worst, may make an adequately resolved simulation impractical. Moreover, the location and resolution of fine grid required for an accurate solution is a dynamic property of a problem's transient features and may not be known a priori. Adaptive mesh refinement (AMR) is a technique that can be used with both structured and unstructured meshes to adjust local grid spacing dynamically to capture solution features with an appropriate degree of resolution. Thus, computational resources can be focused where and when they are needed most to efficiently achieve an accurate solution without incurring the cost of a globally-fine grid. Figure 1.1 shows two example computations using AMR; on the left is a structured mesh calculation of a impulsively-sheared contact surface and on the right is the fuselage and volume discretization of an RAH-66 Comanche helicopter [35]. Note the

  3. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    OpenAIRE

    Yi-Ming He; Bin-Guang Ma

    2016-01-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophil...

  4. Extremophilic adaptations and biotechnological applications in diverse environments

    Directory of Open Access Journals (Sweden)

    Brendan P. Burns

    2016-07-01

    Full Text Available Extremophiles are organisms that tolerate and thrive in the most extreme and challenging conditions to life. As a result of these extreme environmental insults extremophiles have developed a number of interesting adaptations to cellular membranes, proteins and extracellular metabolites. These uniquely adapted biological molecules and systems already have roles in a number of biotechnological fields. In this review we give a brief overview of a number of different extreme environments and the potential for biotechnological innovation from the microbes which inhabit them.

  5. The yak genome and adaptation to life at high altitude

    DEFF Research Database (Denmark)

    Qiu, Qiang; Zhang, Guojie; Ma, Tao;

    2012-01-01

    Domestic yaks (Bos grunniens) provide meat and other necessities for Tibetans living at high altitude on the Qinghai-Tibetan Plateau and in adjacent regions. Comparison between yak and the closely related low-altitude cattle (Bos taurus) is informative in studying animal adaptation to high altitude...... of protein domains involved in sensing the extracellular environment and hypoxic stress. Positively selected and rapidly evolving genes in the yak lineage are also found to be significantly enriched in functional categories and pathways related to hypoxia and nutrition metabolism. These findings may have...... important implications for understanding adaptation to high altitude in other animal species and for hypoxia-related diseases in humans....

  6. Cognitive and adaptive behavior profiles of children with Angelman syndrome.

    Science.gov (United States)

    Peters, Sarika U; Goddard-Finegold, Jan; Beaudet, Arthur L; Madduri, Niru; Turcich, Marie; Bacino, Carlos A

    2004-07-15

    Angelman syndrome (AS) is a neurodevelopmental disorder caused by maternal deficiency of the UBE3A gene that encodes E6-AP ubiquitin-protein ligase. Expression of the UBE3A gene from the maternal chromosome is essential to prevent AS. AS is characterized by severe mental retardation, ataxia, and a defined behavioral pattern characterized mainly by happy/sociable disposition. This study used the Bayley Scales of Infant Development and the Vineland Adaptive Behavior Scales to examine the cognitive abilities and adaptive behavior of children (n = 20) with the four known molecular classes of AS, including patterns of strengths and weaknesses across adaptive behavior domains, and the relationship between adaptive behavior and overall cognitive abilities. Cognitive skills fell within the severe to profound range of mental deficiency. Differences in cognitive skills according to genetic subtype only partially supported previous research and suggest that there is overlap in abilities across genetic subtypes of AS. Adaptive behavior skills were also significantly delayed, with participants demonstrating a significant strength in socialization, and a weakness in motor skills. Strong, positive correlations emerge between cognitive ability scores and adaptive behaviors scores. These results provide further delineation of a cognitive/behavioral phenotype in AS.

  7. Simultaneous expression of regulatory genes associated with specific drought-adaptive traits improves drought adaptation in peanut.

    Science.gov (United States)

    Ramu, Vemanna S; Swetha, Thavarekere N; Sheela, Shekarappa H; Babitha, Chandrashekar K; Rohini, Sreevathsa; Reddy, Malireddy K; Tuteja, Narendra; Reddy, Chandrashekar P; Prasad, Trichi Ganesh; Udayakumar, Makarla

    2016-03-01

    Adaptation of crops to drought-prone rain-fed conditions can be achieved by improving plant traits such as efficient water mining (by superior root characters) and cellular-level tolerance mechanisms. Pyramiding these drought-adaptive traits by simultaneous expression of genes regulating drought-adaptive mechanisms has phenomenal relevance in improving stress tolerance. In this study, we provide evidence that peanut transgenic plants expressing Alfalfa zinc finger 1 (Alfin1), a root growth-associated transcription factor gene, Pennisetum glaucum heat-shock factor (PgHSF4) and Pea DNA helicase (PDH45) involved in protein turnover and protection showed improved tolerance, higher growth and productivity under drought stress conditions. Stable integration of all the transgenes was noticed in transgenic lines. The transgenic lines showed higher root growth, cooler crop canopy air temperature difference (less CCATD) and higher relative water content (RWC) under drought stress. Low proline levels in transgenic lines substantiate the maintenance of higher water status. The survival and recovery of transgenic lines was significantly higher under gradual moisture stress conditions with higher biomass. Transgenic lines also showed significant tolerance to ethrel-induced senescence and methyl viologen-induced oxidative stress. Several stress-responsive genes such as heat-shock proteins (HSPs), RING box protein-1 (RBX1), Aldose reductase, late embryogenesis abundant-5 (LEA5) and proline-rich protein-2 (PRP2), a gene involved in root growth, showed enhanced expression under stress in transgenic lines. Thus, the simultaneous expression of regulatory genes contributing for drought-adaptive traits can improve crop adaptation and productivity under water-limited conditions. PMID:26383697

  8. Molecular mechanisms underlying thermal adaptation of xeric animals

    Indian Academy of Sciences (India)

    M B Evgen'Ev; D G Garbuz; V Y Shilova; O G Zatsepina

    2007-04-01

    For many years, we and our collaborators have investigated the adaptive role of heat shock proteins in different animals, including the representatives of homothermic and poikilothermic species that inhabit regions with contrasting thermal conditions. Adaptive evolution of the response to hyperthermia has led to different results depending upon the species. The thermal threshold of induction of heat shock proteins in desert thermophylic species is, as a rule, higher than in the species from less extreme climates. In addition, thermoresistant poikilothermic species often exhibit a certain level of heat shock proteins in cells even at a physiologically normal temperature. Furthermore, there is often a positive correlation between the characteristic temperature of the ecological niche of a given species and the amount of Hsp70-like proteins in the cells at normal temperature. Although in most cases adaptation to hyperthermia occurs without changes in the number of heat shock genes, these genes can be amplified in some xeric species. It was shown that mobile genetic elements may play an important role in the evolution and fine-tuning of the heat shock response system, and can be used for direct introduction of mutations in the promoter regions of these genes.

  9. Protein intrinsic disorder in plants

    Directory of Open Access Journals (Sweden)

    Florencio ePazos

    2013-09-01

    Full Text Available To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously with different partners. Similarly, they also serve as signal integrators in signalling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms can not escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  10. Adaptive designs for sequential experiments

    Institute of Scientific and Technical Information of China (English)

    林正炎; 张立新

    2003-01-01

    Various adaptive designe have been proposed and applied to clinical trials,bioassay,psycho-physics,etc.Adaptive designs are also useful in high cost engineering trials.More and More people have been paying attention to these desing methods.This paper introduces several broad families of designs,such as the play-the-winner rele,randomized play-the-winner rule and its generalization to the multi-arm case,doubly bi-ased coin adaptive design,Markov chain model.

  11. Livelihood Resilience and Adaptive Capacity

    DEFF Research Database (Denmark)

    Thulstrup, Andreas Waaben

    2015-01-01

    This article analyses the implementation and outcomes of national development programs in a mountainous commune in Vietnam. The article traces the history of State intervention and the capacity of households and the community to adapt to change. The assessment reveals unintended consequences...... of the programs which strongly influence the ability of households to adapt to change. Some households possess more adaptive capacity given their better access to capital while others remain vulnerable because they are constrained in accessing resources and engage in nondiversified livelihoods. If shock events...

  12. Racism in America through adaptation

    OpenAIRE

    Munk, Jakob; Jakobsen, Sebastian; Chung, Jacinta; Schulze, Anja; Papakonstantinou, Vaitza

    2015-01-01

    This study examines the adaptation of the movie 12 Years a Slave from the memoir of Solomon Northup. In order to analyse the adaptation, several theories will be used as guidelines for our research such as adaptation theories and film techniques. The analysis will lead through the different chapters of the book focusing on atmosphere, characters and religion. The main themes dealt with in the book as well as the movie will be linked with the events which unfolded in Ferguson and Baltimore. In...

  13. Adaptive stochastic cellular automata: Applications

    Science.gov (United States)

    Qian, S.; Lee, Y. C.; Jones, R. D.; Barnes, C. W.; Flake, G. W.; O'Rourke, M. K.; Lee, K.; Chen, H. H.; Sun, G. Z.; Zhang, Y. Q.; Chen, D.; Giles, C. L.

    1990-09-01

    The stochastic learning cellular automata model has been applied to the problem of controlling unstable systems. Two example unstable systems studied are controlled by an adaptive stochastic cellular automata algorithm with an adaptive critic. The reinforcement learning algorithm and the architecture of the stochastic CA controller are presented. Learning to balance a single pole is discussed in detail. Balancing an inverted double pendulum highlights the power of the stochastic CA approach. The stochastic CA model is compared to conventional adaptive control and artificial neural network approaches.

  14. Resource-adaptive cognitive processes

    CERN Document Server

    Crocker, Matthew W

    2010-01-01

    This book investigates the adaptation of cognitive processes to limited resources. The central topics of this book are heuristics considered as results of the adaptation to resource limitations, through natural evolution in the case of humans, or through artificial construction in the case of computational systems; the construction and analysis of resource control in cognitive processes; and an analysis of resource-adaptivity within the paradigm of concurrent computation. The editors integrated the results of a collaborative 5-year research project that involved over 50 scientists. After a mot

  15. Characterization of bortezomib-adapted I-45 mesothelioma cells

    Directory of Open Access Journals (Sweden)

    Peddaboina Chander

    2010-05-01

    Full Text Available Abstract Background Bortezomib, a proteasome-specific inhibitor, has emerged as a promising cancer therapeutic agent. However, development of resistance to bortezomib may pose a challenge to effective anticancer therapy. Therefore, characterization of cellular mechanisms involved in bortezomib resistance and development of effective strategies to overcome this resistance represent important steps in the advancement of bortezomib-mediated cancer therapy. Results The present study reports the development of I-45-BTZ-R, a bortezomib-resistant cell line, from the bortezomib-sensitive mesothelioma cell line I-45. I-45-BTZ-R cells showed no cross-resistance to the chemotherapeutic drugs cisplatin, 5-fluorouracil, and doxorubicin. Moreover, the bortezomib-adapted I-45-BTZ-R cells had decreased growth kinemics and did not over express proteasome subunit β5 (PSMB5 as compared to parental I-45 cells. I-45-BTZ-R cells and parental I-45 cells showed similar inhibition of proteasome activity, but I-45-BTZ-R cells exhibited much less accumulation of ubiquitinated proteins following exposure to 40 nm bortezomib. Further studies revealed that relatively low doses of bortezomib did not induce an unfolded protein response (UPR in the bortezomib-adapted cells, while higher doses induced UPR with concomitant cell death, as evidenced by higher expression of the mitochondrial chaperone protein Bip and the endoplasmic reticulum (ER stress-related pro-apoptotic protein CHOP. In addition, bortezomib exposure did not induce the accumulation of the pro-apoptotic proteins p53, Mcl-1S, and noxa in the bortezomib-adapted cells. Conclusion These results suggest that UPR evasion, together with reduced pro-apoptotic gene induction, accounts for bortezomib resistance in the bortezomib-adapted mesothelioma cell line I-45-BTZ-R.

  16. Adapting playware to multiple players

    DEFF Research Database (Denmark)

    Þorsteinsson, Arnar Tumi; Lund, Henrik Hautop; Mastorakis, Nikos;

    2011-01-01

    With the creation of playware as intelligent hardware and software that creates play, it is possible to adapt the play tool to the individual user, and even to multiple users playing at the same time with the play tool. In this paper, we show how it is possible to implement adaptivity in modular...... to such differences, and argues that adaptivity is needed to make games fit to the individual users in both single-player games and multi-player games. As a case study, we implemented such adaptivity on modular interactive tiles for the single-user game ColorTimer, and for the multiple-user games PingPong, in which...

  17. Viewer preferences for adaptive playout

    Science.gov (United States)

    Deshpande, Sachin

    2013-03-01

    Adaptive media playout techniques are used to avoid buffer underflow in a dynamic streaming environment where the available bandwidth may be fluctuating. In this paper we report human perceptions from audio quality studies that we performed on speech and music samples for adaptive audio playout. Test methods based on ITU-R BS. 1534-1 recommendation were used. Studies were conducted for both slow playout and fast playout. Two scales - a coarse scale and a finer scale was used for the slow and fast audio playout factors. Results from our study can be used to determine acceptable slow and fast playout factors for speech and music content. An adaptive media playout algorithm could use knowledge of these upper and lower bounds on playback speeds to decide its adaptive playback schedule.

  18. Genetic Algorithms for Case Adaptation

    International Nuclear Information System (INIS)

    Case based reasoning (CBR) paradigm has been widely used to provide computer support for recalling and adapting known cases to novel situations. Case adaptation algorithms generally rely on knowledge based and heuristics in order to change the past solutions to solve new problems. However, case adaptation has always been a difficult process to engineers within (CBR) cycle. Its difficulties can be referred to its domain dependency; and computational cost. In an effort to solve this problem, this research explores a general-purpose method that applying a genetic algorithm (GA) to CBR adaptation. Therefore, it can decrease the computational complexity of the search space in the problems having a great dependency on their domain knowledge. The proposed model can be used to perform a variety of design tasks on a broad set of application domains. However, it has been implemented for the tablet formulation as a domain of application. The proposed system has improved the performance of the CBR design systems

  19. Face Adaptation Without a Face

    OpenAIRE

    Ghuman, Avniel Singh; McDaniel, Jonathan R.; Martin, Alex

    2010-01-01

    Prolonged viewing of a stimulus results in a subsequent perceptual bias [1], [2] and [3]. This perceptual adaptation and the resulting aftereffect reveal important characteristics regarding how perceptual systems are tuned [2], [4], [5] and [6]. These aftereffects occur not only for simple stimulus features but also for high-level stimulus properties [7], [8], [9] and [10]. Here we report a novel cross-category adaptation aftereffect demonstrating that prolonged viewing of a human body withou...

  20. Film Adaptation on Othello (1995)

    Institute of Scientific and Technical Information of China (English)

    辛世博

    2012-01-01

      Othello is one of the four Shakespeare's famous tragedies. It is an adaptation of the Italian writer Cinthio's tale,“Un Capitano Moro”. Shakespeare re-arranges the entire story in a relatively short time and limited space. It also attracts many directors to adapt the drama for film. The essay will indicate how directors use skills and cinematic techniques to portray the characters,push the plot forward and increase the tragic effect in the film Othello(1995).

  1. Climate change adaptation in Ethiopia

    DEFF Research Database (Denmark)

    Weldegebriel, Zerihun Berhane; Prowse, Martin

    Ethiopia is vulnerable to climate change due to its limited development and dependence on agriculture. Social protection schemes like the Productive Safety Net Programme (PSNP) can play a positive role in promoting livelihoods and enhancing households’ risk management. This article examines......, they suggest the PSNP may not be helping smallholders diversify income sources in a positive manner for climate adaptation. The article concludes by arguing for further investigation of the PSNP’s influence on smallholders’ adaptation strategies....

  2. Adaptive Liquid Crystal Windows

    Energy Technology Data Exchange (ETDEWEB)

    Taheri, Bahman; Bodnar, Volodymyr

    2011-12-31

    Energy consumption by private and commercial sectors in the U.S. has steadily grown over the last decade. The uncertainty in future availability of imported oil, on which the energy consumption relies strongly, resulted in a dramatic increase in the cost of energy. About 20% of this consumption are used to heat and cool houses and commercial buildings. To reduce dependence on the foreign oil and cut down emission of greenhouse gases, it is necessary to eliminate losses and reduce total energy consumption by buildings. To achieve this goal it is necessary to redefine the role of the conventional windows. At a minimum, windows should stop being a source for energy loss. Ideally, windows should become a source of energy, providing net gain to reduce energy used to heat and cool homes. It is possible to have a net energy gain from a window if its light transmission can be dynamically altered, ideally electronically without the need of operator assistance, providing optimal control of the solar gain that varies with season and climate in the U.S. In addition, the window must not require power from the building for operation. Resolution of this problem is a societal challenge and of national interest and will have a broad global impact. For this purpose, the year-round, allclimate window solution to provide an electronically variable solar heat gain coefficient (SHGC) with a wide dynamic range is needed. AlphaMicron, Inc. (AMI) developed and manufactured 1ft × 1ft prototype panels for the world’s first auto-adjusting Adaptive Liquid Crystal Windows (ALCWs) that can operate from sunlight without the need for external power source and demonstrate an electronically adjustable SHGC. This novel windows are based on AlphaMicron’s patented e-Tint® technology, a guesthost liquid crystal system implemented on flexible, optically clear plastic films. This technology is suitable both for OEM and aftermarket (retro-fitting) lamination to new and existing windows. Low level of

  3. The Geobiochemistry of Methanogen Proteins

    Science.gov (United States)

    Prasad, A.; Shock, E.

    2013-12-01

    A principle of geobiochemistry is that adaptation over evolutionary time includes a thermodynamic drive to minimize costs of making biomolecules like proteins and lipids. If so, then biomolecule abundances will reflect, at least in part, their relative stabilities at the conditions imposed by external environments. We tested this hypothesis by comparing relative stabilities of 138 orthologous proteins between a representative lake-sediment methanogen (Methanoculleus marisnigri) and a representative rumen methanogen (Methanospirillum hungatei) at the compositional constraints of their respective environments. Chemical affinities of the proteins were calculated based on pH, temperature, and concentrations of dissolved hydrogen, bicarbonate, ammonia, and hydrogen sulfide, together with standard Gibbs energies of formation of proteins from the elements predicted with a group additivity algorithm for unfolded proteins [1]. Methanogens were chosen as they are chemoautotrophs and their metabolism proceeds at relatively small affinities. Also, they are found in a variety of compositionally varying habitats like rumen, sediments, hydrothermal systems and sewage. The methanogens selected belong to the same order of taxonomy and are closely related. Preliminary results show that a majority of the proteins belonging to the rumen methanogen (66%) are more stable in the rumen environment, while a majority of the proteins belonging to the lake-sediment methanogen (58%) are more stable at sediment conditions. In a separate observation, it was noted that while the complete protein ';proteasome subunit alpha' of another rumen methanogen (Methanobrevibacter smithii) was less stable in its more reducing habitat as compared to a sewage methanogen (Methanothermobacter thermoautotophicus), its first 26 amino acid residues (N terminal) were in fact more stable in its own environment. These 26 residues are reported to be unique as compared to other proteasome proteins and are suggested to

  4. Adaptive capture of expert knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Barrett, C.L.; Jones, R.D. [Los Alamos National Lab., NM (United States); Hand, Un Kyong [Los Alamos National Lab., NM (United States)]|[US Navy (United States)

    1995-05-01

    A method is introduced that can directly acquire knowledge-engineered, rule-based logic in an adaptive network. This adaptive representation of the rule system can then replace the rule system in simulated intelligent agents and thereby permit further performance-based adaptation of the rule system. The approach described provides both weight-fitting network adaptation and potentially powerful rule mutation and selection mechanisms. Nonlinear terms are generated implicitly in the mutation process through the emergent interaction of multiple linear terms. By this method it is possible to acquire nonlinear relations that exist in the training data without addition of hidden layers or imposition of explicit nonlinear terms in the network. We smoothed and captured a set of expert rules with an adaptive network. The motivation for this was to (1) realize a speed advantage over traditional rule-based simulations; (2) have variability in the intelligent objects not possible by rule-based systems but provided by adaptive systems: and (3) maintain the understandability of rule-based simulations. A set of binary rules was smoothed and converted into a simple set of arithmetic statements, where continuous, non-binary rules are permitted. A neural network, called the expert network, was developed to capture this rule set, which it was able to do with zero error. The expert network is also capable of learning a nonmonotonic term without a hidden layer. The trained network in feedforward operation is fast running, compact, and traceable to the rule base.

  5. Mechanisms of temperature adaptation in poikilotherms.

    Science.gov (United States)

    Guschina, Irina A; Harwood, John L

    2006-10-01

    For good function, membrane lipids have to be arranged appropriately and be in the correct physical state. In poikilotherms, exposure to cold stress or heat shock can alter membrane properties such that, unless they are corrected quickly, damage and, possibly, death can result. Low temperature stress is countered by modifying membrane lipids such that their average transition temperature is lowered. There are various ways in which this can be achieved but an increase in fatty acid unsaturation is the most common. For heat shock, various changes in lipids have been noted and some defensive strategies involving heat shock proteins noted. In this short review, we will describe recent results where adaptive lipid changes, as a result of temperature stress, have been found. Mechanisms for bringing about such alterations are discussed, together with the contrasting data for different organisms. PMID:16824520

  6. Principles of protein-protein interactions.

    OpenAIRE

    Jones, S; Thornton, J. M.

    1996-01-01

    This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The factors that influence the formation of protein-protein complexes are explored in four different types of protein-protein complexes--homodimeric proteins, heterodimeric proteins, enzyme-inhibitor complexes, and antibody-protein complexes. The comparison between the complexes highlights differences tha...

  7. Sequencing of 50 human exomes reveals adaptation to high altitude

    DEFF Research Database (Denmark)

    Yi, Xin; Liang, Yu; Huerta-Sanchez, Emilia;

    2010-01-01

    Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which...... represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency...... difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus...

  8. Fitness seascapes and adaptive evolution of the influenza virus

    Science.gov (United States)

    Lassig, Michael

    2014-03-01

    The seasonal human influenza A virus undergoes rapid genome evolution. This process is triggered by interactions with the host immune system and produces significant year-to-year sequence turnover in the population of circulating viral strains. We develop a dynamical fitness model that predicts the evolution of the viral population from one year to the next. Two factors are shown to determine the fitness of a viral strain: adaptive changes, which are under positive selection, and deleterious mutations, which affect conserved viral functions such as protein stability. Combined with the influenza strain tree, this fitness model maps the adaptive history of influenza A. We discuss the implications of our results for the statistical theory of adaptive evolution in asexual populations. Based on this and related systems, we touch upon the fundamental question of when evolution can be predicted. Joint work with Marta Luksza, Columbia University.

  9. How seabirds adapt to ocean processes

    Energy Technology Data Exchange (ETDEWEB)

    Powers, K.D.

    A general review is presented of the adaptations made by seabirds to their environments. Included in the discussion are behavioral, morphological and physiological adaptation to the ocean environment.

  10. Burkholderia pseudomallei transcriptional adaptation in macrophages

    Directory of Open Access Journals (Sweden)

    Chieng Sylvia

    2012-07-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a facultative intracellular pathogen of phagocytic and non-phagocytic cells. How the bacterium interacts with host macrophage cells is still not well understood and is critical to appreciate the strategies used by this bacterium to survive and how intracellular survival leads to disease manifestation. Results Here we report the expression profile of intracellular B. pseudomallei following infection of human macrophage-like U937 cells. During intracellular growth over the 6 h infection period, approximately 22 % of the B. pseudomallei genome showed significant transcriptional adaptation. B. pseudomallei adapted rapidly to the intracellular environment by down-regulating numerous genes involved in metabolism, cell envelope, motility, replication, amino acid and ion transport system and regulatory function pathways. Reduced expression in catabolic and housekeeping genes suggested lower energy requirement and growth arrest during macrophage infection, while expression of genes encoding anaerobic metabolism functions were up regulated. However, whilst the type VI secretion system was up regulated, expression of many known virulence factors was not significantly modulated over the 6hours of infection. Conclusions The transcriptome profile described here provides the first comprehensive view of how B. pseudomallei survives within host cells and will help identify potential virulence factors and proteins that are important for the survival and growth of B. pseudomallei within human cells.

  11. Protein breakdown in cancer cachexia.

    Science.gov (United States)

    Sandri, Marco

    2016-06-01

    Skeletal muscle is a highly adaptive tissue, capable of altering muscle fiber size, functional capacity and metabolism in response to physiological stimuli. However, pathological conditions such as cancer growth compromise the mechanisms that regulate muscle homeostasis, resulting in loss of muscle mass, functional impairment and compromised metabolism. This tumor-induced condition is characterized by enhanced muscle protein breakdown and amino acids release that sustain liver gluconeogenesis and tissue protein synthesis. Proteolysis is controlled by the two most important cellular degradation systems, the ubiquitin proteasome and autophagy lysosome. These systems are carefully regulated by different signalling pathways that determine protein and organelle turnover. In this review we will describe the involvement of the ubiquitin proteasome and autophagy lysosome systems in cancer cachexia and the principal signalling pathways that regulate tumor-induced protein breakdown in muscle. PMID:26564688

  12. Adaptive control with aerospace applications

    Science.gov (United States)

    Gadient, Ross

    Robust and adaptive control techniques have a rich history of theoretical development with successful application. Despite the accomplishments made, attempts to combine the best elements of each approach into robust adaptive systems has proven challenging, particularly in the area of application to real world aerospace systems. In this research, we investigate design methods for general classes of systems that may be applied to representative aerospace dynamics. By combining robust baseline control design with augmentation designs, our work aims to leverage the advantages of each approach. This research contributes the development of robust model-based control design for two classes of dynamics: 2nd order cascaded systems, and a more general MIMO framework. We present a theoretically justified method for state limiting via augmentation of a robust baseline control design. Through the development of adaptive augmentation designs, we are able to retain system performance in the presence of uncertainties. We include an extension that combines robust baseline design with both state limiting and adaptive augmentations. In addition we develop an adaptive augmentation design approach for a class of dynamic input uncertainties. We present formal stability proofs and analyses for all proposed designs in the research. Throughout the work, we present real world aerospace applications using relevant flight dynamics and flight test results. We derive robust baseline control designs with application to both piloted and unpiloted aerospace system. Using our developed methods, we add a flight envelope protecting state limiting augmentation for piloted aircraft applications and demonstrate the efficacy of our approach via both simulation and flight test. We illustrate our adaptive augmentation designs via application to relevant fixed-wing aircraft dynamics. Both a piloted example combining the state limiting and adaptive augmentation approaches, and an unpiloted example with

  13. Hydrolyzed Proteins in Preterm Infants.

    Science.gov (United States)

    Senterre, Thibault; Rigo, Jacques

    2016-01-01

    Milk proteins are an essential component of the diet of preterm infants who have high requirements. Hydrolyzed proteins (HPs) have been introduced in infants' formulas (HPFs) to treat gastrointestinal disorders and to prevent allergic diseases. Several studies have evaluated the adequacy of HPs in preterm infants. Protein source significantly influences plasma amino acid concentrations. Protein utilization and efficiency are usually lower with HPFs compared to formulas with intact proteins. When protein intake is similar, a lower weight gain is generally observed with HPFs and a 10% increase in protein content is usually necessary to compensate for this reduction in protein utilization. Mineral absorption may also be reduced and no data exist for trace elements and vitamins. Most HPFs are associated with accelerated gastrointestinal transit time and softer stools but without clear benefit on feeding tolerance. Preterm infants seem to be at similar risk of allergic diseases than term infants, but the preventive effect of HPFs has not been sufficiently explored in preterm infants. Most modern HPFs designed for preterm infants are well tolerated and have adapted their nutrient content to improve nutrient absorption and retention. However, their benefits and safety have not been demonstrated and, therefore, further high-quality studies are needed. PMID:27336633

  14. Human Protein and Amino Acid Requirements.

    Science.gov (United States)

    Hoffer, L John

    2016-05-01

    Human protein and amino acid nutrition encompasses a wide, complex, frequently misunderstood, and often contentious area of clinical research and practice. This tutorial explains the basic biochemical and physiologic principles that underlie our current understanding of protein and amino acid nutrition. The following topics are discussed: (1) the identity, measurement, and essentiality of nutritional proteins; (2) the definition and determination of minimum requirements; (3) nutrition adaptation; (4) obligatory nitrogen excretion and the minimum protein requirement; (5) minimum versus optimum protein intakes; (6) metabolic responses to surfeit and deficient protein intakes; (7) body composition and protein requirements; (8) labile protein; (9) N balance; (10) the principles of protein and amino acid turnover, including an analysis of the controversial indicator amino acid oxidation technique; (11) general guidelines for evaluating protein turnover articles; (12) amino acid turnover versus clearance; (13) the protein content of hydrated amino acid solutions; (14) protein requirements in special situations, including protein-catabolic critical illness; (15) amino acid supplements and additives, including monosodium glutamate and glutamine; and (16) a perspective on the future of protein and amino acid nutrition research. In addition to providing practical information, this tutorial aims to demonstrate the importance of rigorous physiologic reasoning, stimulate intellectual curiosity, and encourage fresh ideas in this dynamic area of human nutrition. In general, references are provided only for topics that are not well covered in modern textbooks. PMID:26796095

  15. A new experimental system for study on adaptive mutations

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A super-repressed mutant of purR (purRS), which encodes arepressor protein controlling expression of purine biosynthetic genes in Salmonella typhimurium, grew very slowly on NCE medium with 10 mg / mL Ade and lactose as sole carbon source (cannot form colonies). However, a phenomenon of late-arising mutations was observed when purRS mutants were spread on NCE+lactose plates and subjected to a prolonged non-lethal selection. The reconstruction experiments of revertants showed that the late-arising "lac+" mutants are not slow growing mutants. Statistical analysis indicated that the distribution of late-arising mutants is Poisson distribution, showing that reversion occurred after plating. The result of co-transductional analysis preliminarily showed that late-arising mutation occurred at selected gene purR or 16 bp PUR box, cis element of structural gene purD. The above results suggest that the phenomenon of late-arising mutation observed by our system is a result of adaptive mutations which are different from random mutations. This is the first time to extend target genes at which adaptive mutations could occur from structural genes involved in carbon metabolism and amino acid biosynthesis to trans regulatory gene coding repressor protein. Our results have provided not only a new proof for generality of adaptive mutations but also a new system for study on adaptive mutations.

  16. 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.

  17. Adaptive Multilevel Monte Carlo Simulation

    KAUST Repository

    Hoel, H

    2011-08-23

    This work generalizes a multilevel forward Euler Monte Carlo method introduced in Michael B. Giles. (Michael Giles. Oper. Res. 56(3):607–617, 2008.) for the approximation of expected values depending on the solution to an Itô stochastic differential equation. The work (Michael Giles. Oper. Res. 56(3):607– 617, 2008.) proposed and analyzed a forward Euler multilevelMonte Carlo method based on a hierarchy of uniform time discretizations and control variates to reduce the computational effort required by a standard, single level, Forward Euler Monte Carlo method. This work introduces an adaptive hierarchy of non uniform time discretizations, generated by an adaptive algorithmintroduced in (AnnaDzougoutov et al. Raùl Tempone. Adaptive Monte Carlo algorithms for stopped diffusion. In Multiscale methods in science and engineering, volume 44 of Lect. Notes Comput. Sci. Eng., pages 59–88. Springer, Berlin, 2005; Kyoung-Sook Moon et al. Stoch. Anal. Appl. 23(3):511–558, 2005; Kyoung-Sook Moon et al. An adaptive algorithm for ordinary, stochastic and partial differential equations. In Recent advances in adaptive computation, volume 383 of Contemp. Math., pages 325–343. Amer. Math. Soc., Providence, RI, 2005.). This form of the adaptive algorithm generates stochastic, path dependent, time steps and is based on a posteriori error expansions first developed in (Anders Szepessy et al. Comm. Pure Appl. Math. 54(10):1169– 1214, 2001). Our numerical results for a stopped diffusion problem, exhibit savings in the computational cost to achieve an accuracy of ϑ(TOL),from(TOL−3), from using a single level version of the adaptive algorithm to ϑ(((TOL−1)log(TOL))2).

  18. Low dose effects. Adaptive response

    International Nuclear Information System (INIS)

    The purpose of this work was to evaluate if there are disturbancies in adaptive response when lymphocytes of people living on the polluted with radionuclides area after Chernobyl disaster and liquidators suffered from accident have been investigated. The level of lymphocytes with micronuclei have been scored in Moscow donors and people living in Bryansk region with the degree of contamination 15 - 40 Ci/km. The doses that liquidators have been obtained were not higher then 25 cGy. The mean spontaneous level of MN in control people and people from Chernobyl zones does't differ significantly but the individual variability in the mean value between two populations does not differ significantly too. And in this case it seems that persons of exposed areas. Then another important fact in lymphocytes of people living on polluted areas the chronic low dose irradiation does not induce the adaptive response. In Moscow people in most cases (≅ 59 %) the adaptive response is observed and in some cases the demonstration of adaptive response is not significant (≅1%). In Chernobyl population exposed to chronic low level, low dose rate irradiation there are fewer people here with distinct adaptive response (≅38%). And there appear beings with increased radiosensitivity after conditioned dose. Such population with enhanced radiosensitivity have not observed in Moscow. In liquidators the same types of effects have been registered. These results have been obtained on adults. Adaptive response in children 8 - 14 old population living in Moscow and in Chernobyl zone have been investigated too. In this case the spontaneous level of MN is higher in children living in polluted areas, after the 1.0 Gy irradiation the individual variability is very large. Only 5 % of children have distinct is very large. Only 5 % of children have distinct adaptive response, the enhancement of radiosensitivity after conditioned dose is observed. (authors)

  19. Tau protein

    DEFF Research Database (Denmark)

    Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc;

    2011-01-01

    Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14......-3-3 protein in the cerebrospinal fluid (CSF) of patients with monosymptomatic optic neuritis (ON) versus patients with monosymptomatic onset who progressed to multiple sclerosis (MS). To evaluate results against data found in a complete literature review. Methods: A total of 66 patients with MS and/or ON from...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased concentration of tau...

  20. Evolution or adaptation? What do heritable adaptive changes imply?

    Directory of Open Access Journals (Sweden)

    M. Kemal Irmak

    2014-02-01

    Full Text Available Interactions between environmental factors and epigenetic inheritance system produce a great deal of variation from one geographic region to another in human craniofacial morphology, skin color, hair form, stature and body proportions. In this system, while environmental factors produce modifications in the body, they simultaneously induce long-term epigenetic modifications in the germ cells that are inherited to offspring. This kind of heritable changes is called biological adaptation. It was previously reported that biological adaptation is limited to neural crest derivatives such as craniofacial tissues, melanocytes, and structures related to hair form, stature and body proportions. Thus, inheritance of adaptive changes is limited to a number of traits and species-to-species evolution seems unlikely. [J Exp Integr Med 2014; 4(1.000: 13-16

  1. Genomics of local adaptation with gene flow.

    Science.gov (United States)

    Tigano, Anna; Friesen, Vicki L

    2016-05-01

    Gene flow is a fundamental evolutionary force in adaptation that is especially important to understand as humans are rapidly changing both the natural environment and natural levels of gene flow. Theory proposes a multifaceted role for gene flow in adaptation, but it focuses mainly on the disruptive effect that gene flow has on adaptation when selection is not strong enough to prevent the loss of locally adapted alleles. The role of gene flow in adaptation is now better understood due to the recent development of both genomic models of adaptive evolution and genomic techniques, which both point to the importance of genetic architecture in the origin and maintenance of adaptation with gene flow. In this review, we discuss three main topics on the genomics of adaptation with gene flow. First, we investigate selection on migration and gene flow. Second, we discuss the three potential sources of adaptive variation in relation to the role of gene flow in the origin of adaptation. Third, we explain how local adaptation is maintained despite gene flow: we provide a synthesis of recent genomic models of adaptation, discuss the genomic mechanisms and review empirical studies on the genomics of adaptation with gene flow. Despite predictions on the disruptive effect of gene flow in adaptation, an increasing number of studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow.

  2. Adaptations to chronic rapamycin in mice

    Directory of Open Access Journals (Sweden)

    Sherry G. Dodds

    2016-05-01

    Full Text Available Rapamycin inhibits mechanistic (or mammalian target of rapamycin (mTOR that promotes protein production in cells by facilitating ribosome biogenesis (RiBi and eIF4E-mediated 5'cap mRNA translation. Chronic treatment with encapsulated rapamycin (eRapa extended health and life span for wild-type and cancer-prone mice. Yet, the long-term consequences of chronic eRapa treatment are not known at the organ level. Here, we report our observations of chronic eRapa treatment on mTORC1 signaling and RiBi in mouse colon and visceral adipose. As expected, chronic eRapa treatment decreased detection of phosphorylated mTORC1/S6K substrate, ribosomal protein (rpS6 in colon and fat. However, in colon, contrary to expectations, there was an upregulation of 18S rRNA and some ribosomal protein genes (RPGs suggesting increased RiBi. Among RPGs, eRapa increases rpl22l1 mRNA but not its paralog rpl22. Furthermore, there was an increase in the cap-binding protein, eIF4E relative to its repressor 4E-BP1 suggesting increased translation. By comparison, in fat, there was a decrease in the level of 18S rRNA (opposite to colon, while overall mRNAs encoding ribosomal protein genes appeared to increase, including rpl22, but not rpl22l1 (opposite to colon. In fat, there was a decrease in eIF4E relative to actin (opposite to colon but also an increase in the eIF4E/4E-BP1 ratio likely due to reductions in 4E-BP1 at our lower eRapa dose (similar to colon. Thus, in contrast to predictions of decreased protein production seen in cell-based studies, we provide evidence that colon from chronically treated mice exhibited an adaptive ‘pseudo-anabolic’ state, which is only partially present in fat, which might relate to differing tissue levels of rapamycin, cell-type-specific responses, and/or strain differences.

  3. Coping with thermal challenges: physiological adaptations to environmental temperatures.

    Science.gov (United States)

    Tattersall, Glenn J; Sinclair, Brent J; Withers, Philip C; Fields, Peter A; Seebacher, Frank; Cooper, Christine E; Maloney, Shane K

    2012-07-01

    Temperature profoundly influences physiological responses in animals, primarily due to the effects on biochemical reaction rates. Since physiological responses are often exemplified by their rate dependency (e.g., rate of blood flow, rate of metabolism, rate of heat production, and rate of ion pumping), the study of temperature adaptations has a long history in comparative and evolutionary physiology. Animals may either defend a fairly constant temperature by recruiting biochemical mechanisms of heat production and utilizing physiological responses geared toward modifying heat loss and heat gain from the environment, or utilize biochemical modifications to allow for physiological adjustments to temperature. Biochemical adaptations to temperature involve alterations in protein structure that compromise the effects of increased temperatures on improving catalytic enzyme function with the detrimental influences of higher temperature on protein stability. Temperature has acted to shape the responses of animal proteins in manners that generally preserve turnover rates at animals' normal, or optimal, body temperatures. Physiological responses to cold and warmth differ depending on whether animals maintain elevated body temperatures (endothermic) or exhibit minimal internal heat production (ectothermic). In both cases, however, these mechanisms involve regulated neural and hormonal over heat flow to the body or heat flow within the body. Examples of biochemical responses to temperature in endotherms involve metabolic uncoupling mechanisms that decrease metabolic efficiency with the outcome of producing heat, whereas ectothermic adaptations to temperature are best exemplified by the numerous mechanisms that allow for the tolerance or avoidance of ice crystal formation at temperatures below 0°C.

  4. Numerosity perception after size adaptation

    Science.gov (United States)

    Zimmermann, Eckart; Fink, Gereon R.

    2016-01-01

    While some researchers propose the existence of a special numerosity sense, others challenge this view and argue that numerosity is derived from low-level features as density information. Here, we used size adaptation to manipulate the apparent area size of an object set without changing its physical density. After size adaptation, two probe patches were shown, each of which contained a specific numerosity of dots. Subjects were required to report, which probe patch contained more dots. Numerosity perception was compared between conditions where probe patches were adapted to appear smaller or larger. Size adaptation affected numerosity perception in a logarithmic fashion, increasing with the numerosity in the probe patch. No changes in density perception were found after size adaptation. Data suggest that size and density information play only a minor role in the estimation of low numerosities. In stark contrast, high numerosities strongly depend on size and density information. The data reinforce recent claims of separate mechanism for the perception of low and high numerosities. PMID:27650296

  5. Adaptive evolution in ecological communities.

    Directory of Open Access Journals (Sweden)

    Martin M Turcotte

    Full Text Available Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.

  6. Numerosity perception after size adaptation.

    Science.gov (United States)

    Zimmermann, Eckart; Fink, Gereon R

    2016-01-01

    While some researchers propose the existence of a special numerosity sense, others challenge this view and argue that numerosity is derived from low-level features as density information. Here, we used size adaptation to manipulate the apparent area size of an object set without changing its physical density. After size adaptation, two probe patches were shown, each of which contained a specific numerosity of dots. Subjects were required to report, which probe patch contained more dots. Numerosity perception was compared between conditions where probe patches were adapted to appear smaller or larger. Size adaptation affected numerosity perception in a logarithmic fashion, increasing with the numerosity in the probe patch. No changes in density perception were found after size adaptation. Data suggest that size and density information play only a minor role in the estimation of low numerosities. In stark contrast, high numerosities strongly depend on size and density information. The data reinforce recent claims of separate mechanism for the perception of low and high numerosities. PMID:27650296

  7. Adaptive evolution of molecular phenotypes

    Science.gov (United States)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-09-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.

  8. Ecological adaptation of diverse honey bee (Apis mellifera populations.

    Directory of Open Access Journals (Sweden)

    Robert Parker

    Full Text Available BACKGROUND: Honey bees are complex eusocial insects that provide a critical contribution to human agricultural food production. Their natural migration has selected for traits that increase fitness within geographical areas, but in parallel their domestication has selected for traits that enhance productivity and survival under local conditions. Elucidating the biochemical mechanisms of these local adaptive processes is a key goal of evolutionary biology. Proteomics provides tools unique among the major 'omics disciplines for identifying the mechanisms employed by an organism in adapting to environmental challenges. RESULTS: Through proteome profiling of adult honey bee midgut from geographically dispersed, domesticated populations combined with multiple parallel statistical treatments, the data presented here suggest some of the major cellular processes involved in adapting to different climates. These findings provide insight into the molecular underpinnings that may confer an advantage to honey bee populations. Significantly, the major energy-producing pathways of the mitochondria, the organelle most closely involved in heat production, were consistently higher in bees that had adapted to colder climates. In opposition, up-regulation of protein metabolism capacity, from biosynthesis to degradation, had been selected for in bees from warmer climates. CONCLUSIONS: Overall, our results present a proteomic interpretation of expression polymorphisms between honey bee ecotypes and provide insight into molecular aspects of local adaptation or selection with consequences for honey bee management and breeding. The implications of our findings extend beyond apiculture as they underscore the need to consider the interdependence of animal populations and their agro-ecological context.

  9. Aneuploidy as a mechanism of adaptation to telomerase insufficiency.

    Science.gov (United States)

    Millet, Caroline; Makovets, Svetlana

    2016-08-01

    Cells' survival is determined by their ability to adapt to constantly changing environment. Adaptation responses involve global changes in transcription, translation, and posttranslational modifications of proteins. In recent years, karyotype changes in adapting populations of single cell organisms have been reported in a number of studies. More recently, we have described aneuploidy as an adaptation mechanism used by populations of budding yeast Saccharomyces cerevisiae to survive telomerase insufficiency induced by elevated growth temperature. Genetic evidence suggests that telomerase insufficiency is caused by decreased levels of the telomerase catalytic subunit Est2. Here, we present experiments arguing that the underlying cause of this phenomenon may be within the telomerase RNA TLC1: changes in the expression of TLC1 as well as mutations in the TLC1 template region affect telomere length equilibrium and the temperature threshold for the induction of telomerase insufficiency. We discuss what lies at the root of telomerase insufficiency, how cell populations overcome it through aneuploidy and whether reversible aneuploidy could be an adaptation mechanism for a variety of environmental stresses. PMID:26758992

  10. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

    of research are explored. Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware...

  11. Dietas com nitrogênio não-proteico para fêmeas bovinas superovuladas sem prévia adaptação durante curto tempo e em diferentes fases do ciclo estral Effect of short term non-protein nitrogen feeding for superovulated beef cows without previous adaptation and at different periods of the oestrus cycle

    Directory of Open Access Journals (Sweden)

    Flávio Rocha Alves

    2010-09-01

    effects of short term non-protein nitrogen feeding at different periods of the oestrus cycle in superovulated cows, without previous adaptation, on yield, quality and development degree of recovered embryos. A total of sixty-eight Nelore cows were distributed in three groups: the control group (C and two groups with urea supply before (UB; urea supply from day -5 to day 0 and after (UA; supply from day 0 to day 5 artificial insemination. Animals were kept grazing and received 3.0 kg/animal/day of concentrate during 16 days. Two concentrates were formulated and the total diets (concentrate and estimate forage intake showed 12.0% (control diet and 14.6% (non-protein diet of crude protein. Animals were synchronized, superovulated and inseminated. The embryos were collected and analysed seven days (day 7 after insemination (day 0. Blood samples were collected on days -5, 0 and 5 to determine concentration of plasmatic urea nitrogen, glucose, insulin and progesterone. The time of urea supply affected average plasmatic urea nitrogen concentration on days -5, 0 5 but it did not affect concetrations of glucose, insulin and progesterone. The moment of urea inclusion had effect on compact morula percentage in relation to the total number of structures (UB = 51.4 vs. UA = 15.3%, to the total number of fertilized oocytes (UB = 62.5 vs. UA = 30.6% and to the total number of viable embryos (UB = 68.8 vs. UA = 38.6%. In the after insemination group of urea supply there was 70.2% of reduction on compact morula proportion over the total structures in relation to the group that received urea before insemination. Non-protein nitrogen feeding immediately after insemination promotes faster rates of embryo development.

  12. Adaptive dynamics of saturated polymorphisms.

    Science.gov (United States)

    Kisdi, Éva; Geritz, Stefan A H

    2016-03-01

    We study the joint adaptive dynamics of n scalar-valued strategies in ecosystems where n is the maximum number of coexisting strategies permitted by the (generalized) competitive exclusion principle. The adaptive dynamics of such saturated systems exhibits special characteristics, which we first demonstrate in a simple example of a host-pathogen-predator model. The main part of the paper characterizes the adaptive dynamics of saturated polymorphisms in general. In order to investigate convergence stability, we give a new sufficient condition for absolute stability of an arbitrary (not necessarily saturated) polymorphic singularity and show that saturated evolutionarily stable polymorphisms satisfy it. For the case [Formula: see text], we also introduce a method to construct different pairwise invasibility plots of the monomorphic population without changing the selection gradients of the saturated dimorphism. PMID:26676357

  13. Training Adaptive Decision-Making.

    Energy Technology Data Exchange (ETDEWEB)

    Abbott, Robert G.; Forsythe, James C.

    2014-10-01

    Adaptive Thinking has been defined here as the capacity to recognize when a course of action that may have previously been effective is no longer effective and there is need to adjust strategy. Research was undertaken with human test subjects to identify the factors that contribute to adaptive thinking. It was discovered that those most effective in settings that call for adaptive thinking tend to possess a superior capacity to quickly and effectively generate possible courses of action, as measured using the Category Generation test. Software developed for this research has been applied to develop capabilities enabling analysts to identify crucial factors that are predictive of outcomes in fore-on-force simulation exercises.

  14. Error signals driving locomotor adaptation

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo;

    2016-01-01

    perturbations. Forces were applied to the ankle joint during the early swing phase using an electrohydraulic ankle-foot orthosis. Repetitive 80 Hz electrical stimulation was applied to disrupt cutaneous feedback from the superficial peroneal nerve (foot dorsum) and medial plantar nerve (foot sole) during...... walking (Choi et al. 2013). Sensory tests were performed to measure cutaneous touch threshold and perceptual threshold of force perturbations. Ankle movement were measured while subjects walked on the treadmill over three periods: baseline (1 min), adaptation (1 min) and post-adaptation (3 min). Subjects...... (n = 10) showed increased touch thresholds measured with Von Frey monofilaments and increased force perception thresholds with stimulation. Stimulation reduced the magnitude of walking adaptation to force perturbation. In addition, we compared the effects of interrupting cutaneous feedback using...

  15. Adaptive sampling for noisy problems

    Energy Technology Data Exchange (ETDEWEB)

    Cantu-Paz, E

    2004-03-26

    The usual approach to deal with noise present in many real-world optimization problems is to take an arbitrary number of samples of the objective function and use the sample average as an estimate of the true objective value. The number of samples is typically chosen arbitrarily and remains constant for the entire optimization process. This paper studies an adaptive sampling technique that varies the number of samples based on the uncertainty of deciding between two individuals. Experiments demonstrate the effect of adaptive sampling on the final solution quality reached by a genetic algorithm and the computational cost required to find the solution. The results suggest that the adaptive technique can effectively eliminate the need to set the sample size a priori, but in many cases it requires high computational costs.

  16. Adaptive Radiation for Lung Cancer

    Directory of Open Access Journals (Sweden)

    Daniel R. Gomez

    2011-01-01

    need to spare surrounding critical structures. Evolving radiotherapy technologies, such as four-dimensional (4D image-based motion management, daily on-board imaging and adaptive radiotherapy based on volumetric images over the course of radiotherapy, have enabled us to deliver higher dose to target while minimizing normal tissue toxicities. The image-guided radiotherapy adapted to changes of motion and anatomy has made the radiotherapy more precise and allowed ablative dose delivered to the target using novel treatment approaches such as intensity-modulated radiation therapy, stereotactic body radiation therapy, and proton therapy in lung cancer, techniques used to be considered very sensitive to motion change. Future clinical trials using real time tracking and biological adaptive radiotherapy based on functional images are proposed.

  17. 3D Structured Grid Adaptation

    Science.gov (United States)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  18. Adaptive Sampling in Hierarchical Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Knap, J; Barton, N R; Hornung, R D; Arsenlis, A; Becker, R; Jefferson, D R

    2007-07-09

    We propose an adaptive sampling methodology for hierarchical multi-scale simulation. The method utilizes a moving kriging interpolation to significantly reduce the number of evaluations of finer-scale response functions to provide essential constitutive information to a coarser-scale simulation model. The underlying interpolation scheme is unstructured and adaptive to handle the transient nature of a simulation. To handle the dynamic construction and searching of a potentially large set of finer-scale response data, we employ a dynamic metric tree database. We study the performance of our adaptive sampling methodology for a two-level multi-scale model involving a coarse-scale finite element simulation and a finer-scale crystal plasticity based constitutive law.

  19. Adaptive Optics for Large Telescopes

    Energy Technology Data Exchange (ETDEWEB)

    Olivier, S

    2008-06-27

    The use of adaptive optics was originally conceived by astronomers seeking to correct the blurring of images made with large telescopes due to the effects of atmospheric turbulence. The basic idea is to use a device, a wave front corrector, to adjust the phase of light passing through an optical system, based on some measurement of the spatial variation of the phase transverse to the light propagation direction, using a wave front sensor. Although the original concept was intended for application to astronomical imaging, the technique can be more generally applied. For instance, adaptive optics systems have been used for several decades to correct for aberrations in high-power laser systems. At Lawrence Livermore National Laboratory (LLNL), the world's largest laser system, the National Ignition Facility, uses adaptive optics to correct for aberrations in each of the 192 beams, all of which must be precisely focused on a millimeter scale target in order to perform nuclear physics experiments.

  20. Rapid Adaptation in Digital Transformation

    DEFF Research Database (Denmark)

    Hansen, Anne Mette; Kræmmergaard, Pernille; Mathiassen, Lars

    2011-01-01

    In today’s highly dynamic environments, organizational leaders need to quickly adapt existing approaches to digital transformation. However, without a shared mindset between IS and business leaders, it is difficult to adopt new approaches in response to changes in the competitive and technology...... landscape. In this article, we share insights gained from two public sector organizations in which IS and business leaders used the Participatory Process Model (PPM) designed by the authors to share their assumptions about IS leadership, challenge existing IT strategies and collaboration patterns and adapt...... the organization’s digitization approach. We demonstrate in detail how the leaders within these two organizations were engaged and offer recommendations for how other organizations can use the PPM to rapidly adapt their approaches to digital transformation through more effective IS leadership roles....

  1. Toward Adaptability: Where to from Here?

    Science.gov (United States)

    Parsons, Seth A.; Vaughn, Margaret

    2016-01-01

    In this article, the collection of articles in this issue are synthesized to discuss conceptualizations of adaptive teaching as a means to foster spaces for adaptive teaching in today's complex educational system. Themes that exist across this collection of articles include adaptive teachers as constructivists, adaptive teachers as knowledgeable…

  2. The Adaptive Immune System of Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Lisa-Katharina Maier

    2015-02-01

    Full Text Available To fight off invading genetic elements, prokaryotes have developed an elaborate defence system that is both adaptable and heritable—the CRISPR-Cas system (CRISPR is short for: clustered regularly interspaced short palindromic repeats and Cas: CRISPR associated. Comprised of proteins and multiple small RNAs, this prokaryotic defence system is present in 90% of archaeal and 40% of bacterial species, and enables foreign intruders to be eliminated in a sequence-specific manner. There are three major types (I–III and at least 14 subtypes of this system, with only some of the subtypes having been analysed in detail, and many aspects of the defence reaction remaining to be elucidated. Few archaeal examples have so far been analysed. Here we summarize the characteristics of the CRISPR-Cas system of Haloferax volcanii, an extremely halophilic archaeon originally isolated from the Dead Sea. It carries a single CRISPR-Cas system of type I-B, with a Cascade like complex composed of Cas proteins Cas5, Cas6b and Cas7. Cas6b is essential for CRISPR RNA (crRNA maturation but is otherwise not required for the defence reaction. A systematic search revealed that six protospacer adjacent motif (PAM sequences are recognised by the Haloferax defence system. For successful invader recognition, a non-contiguous seed sequence of 10 base-pairs between the crRNA and the invader is required.

  3. Pressure adaptive honeycomb: a new adaptive structure for aerospace applications

    NARCIS (Netherlands)

    Vos, R.; Barrett, R.

    2010-01-01

    A new type of adaptive structure is presented that relies on pressurized honeycomb cells that extent a significant length with respect to the plane of the hexagons. By varying the pressure inside each of the cells, the stiffness can be altered. A variable stiffness in combination with an externally

  4. Model reference adaptive control and adaptive stability augmentation

    DEFF Research Database (Denmark)

    Henningsen, Arne; Ravn, Ole

    1993-01-01

    A comparison of the standard concepts in MRAC design suggests that a combination of the implicit and the explicit design techniques may lead to an improvement of the overall system performance in the presence of unmodelled dynamics. Using the ideas of adaptive stability augmentation a combined...

  5. Adapting Books: Ready, Set, Read!: EAT: Equipment, Adaptations, and Technology

    Science.gov (United States)

    Schoonover, Judith; Norton-Darr, Sally

    2016-01-01

    Developing multimodal materials to introduce or extend literacy experiences sets the stage for literacy success. Alternative ways to organize, display and arrange, interact and respond to information produces greater understanding of concepts. Adaptations include making books easier to use (turning pages or holding), and text easier to read…

  6. ADAPTER: Analysing & Developing Adaptability & Performance in Teams to Enhance Resilience

    NARCIS (Netherlands)

    Beek, F.A. van der; Schraagen, J.M.C.

    2015-01-01

    In the current study, the concept of team resilience was operationalized by developing a first version of a questionnaire (ADAPTER) driven by the four essential abilities of resilience (Hollnagel, 2011) and expanded with more relation-oriented abilities of leadership and cooperation. The development

  7. Adaptation, Bacteria and Maxwell's Demons

    Science.gov (United States)

    Galajda, Peter; Keymer, Juan E.; Austin, Robert H.

    2007-03-01

    We propose a method to study the adaptation of bacterial populations with an asymmetric wall of Maxwell Demon openings. A Maxwell Demon opening is a funnel which is easier to enter than to leave. The interaction of swimming cells with such a Maxwell Demon Wall results in a population density separation, in apparent (but not real) violation of the Second Law of Thermodynamics, as we will show. Bacteria can be exposed to spatial challenges in order to move to e. g. higher food levels. The question we address in these experiments is: do the bacteria adapt and overcome the Maxwell Demon Wall?

  8. Time-adaptive quantile regression

    DEFF Research Database (Denmark)

    Møller, Jan Kloppenborg; Nielsen, Henrik Aalborg; Madsen, Henrik

    2008-01-01

    An algorithm for time-adaptive quantile regression is presented. The algorithm is based on the simplex algorithm, and the linear optimization formulation of the quantile regression problem is given. The observations have been split to allow a direct use of the simplex algorithm. The simplex method...... and an updating procedure are combined into a new algorithm for time-adaptive quantile regression, which generates new solutions on the basis of the old solution, leading to savings in computation time. The suggested algorithm is tested against a static quantile regression model on a data set with wind power...

  9. Adaptive approaches to biosecurity governance.

    Science.gov (United States)

    Cook, David C; Liu, Shuang; Murphy, Brendan; Lonsdale, W Mark

    2010-09-01

    This article discusses institutional changes that may facilitate an adaptive approach to biosecurity risk management where governance is viewed as a multidisciplinary, interactive experiment acknowledging uncertainty. Using the principles of adaptive governance, evolved from institutional theory, we explore how the concepts of lateral information flows, incentive alignment, and policy experimentation might shape Australia's invasive species defense mechanisms. We suggest design principles for biosecurity policies emphasizing overlapping complementary response capabilities and the sharing of invasive species risks via a polycentric system of governance. PMID:20561262

  10. Micro Evolutionary Processes and Adaptation

    Institute of Scientific and Technical Information of China (English)

    SHADMANOV R K; RUBAN I N; VOROPAEVA N L; SHADMANOVA A R

    2008-01-01

    @@ It would be well to note that in the absence of clear data about the formation of adaptation systems,or mechanisms of their occurrence,all that is recognized is the realization of the micro evolutionary processes.There is no well-defined connection between information exchange and formation of adaptation systems.Obviously,it occurs because mechanisms and systems reacting to any external actions are not considered from the point of view of "coexistence" of dynamic and static processes and structures.

  11. Adaptive critics for dynamic optimization.

    Science.gov (United States)

    Kulkarni, Raghavendra V; Venayagamoorthy, Ganesh Kumar

    2010-06-01

    A novel action-dependent adaptive critic design (ACD) is developed for dynamic optimization. The proposed combination of a particle swarm optimization-based actor and a neural network critic is demonstrated through dynamic sleep scheduling of wireless sensor motes for wildlife monitoring. The objective of the sleep scheduler is to dynamically adapt the sleep duration to node's battery capacity and movement pattern of animals in its environment in order to obtain snapshots of the animal on its trajectory uniformly. Simulation results show that the sleep time of the node determined by the actor critic yields superior quality of sensory data acquisition and enhanced node longevity. PMID:20223635

  12. Adapting agriculture with traditional knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Swiderska, Krystyna; Reid, Hannah [IIED, London (United Kingdom); Song, Yiching; Li, Jingsong [Centre for Chinese Agriculutral Policy (China); Mutta, Doris [Kenya Forestry Research Institute (Kenya)

    2011-10-15

    Over the coming decades, climate change is likely to pose a major challenge to agriculture; temperatures are rising, rainfall is becoming more variable and extreme weather is becoming a more common event. Researchers and policymakers agree that adapting agriculture to these impacts is a priority for ensuring future food security. Strategies to achieve that in practice tend to focus on modern science. But evidence, both old and new, suggests that the traditional knowledge and crop varieties of indigenous peoples and local communities could prove even more important in adapting agriculture to climate change.

  13. Protein intake in renal disease.

    Science.gov (United States)

    Pollock, C A; Ibels, L S; Zhu, F Y; Warnant, M; Caterson, R J; Waugh, D A; Mahony, J F

    1997-05-01

    The dietary protein intake (DPI) of 766 patients (aged 7 to 88 yr) was determined from 24-h urinary urea and protein excretion by urea kinetic modelling. Five hundred sixty-five patients had a normal serum creatinine concentration, and of these 565, 385 patients had no dietary modification advised and 180 were advised to follow a low-protein diet. The remaining 201 patients had an increased serum creatinine concentration; 148 of these 201 patients had been advised to restrict their DPI. Patients with a normal serum creatinine concentration who had no dietary restriction had a significantly higher DPI than those advised to restrict their protein intake (1.08 +/- 0.01 versus 0.96 +/- 0.02 g/kg per day (mean +/- SEM), P level of renal dysfunction, independent of dietary advice (P level (P level (P levels (P Adaptation to a high-protein diet after instigation of dialysis is unsuccessful in the short term, irrespective of whether or not advice is given regarding a low-protein diet before dialysis is initiated. However, 6 to 9 months after the commencement of dialysis, a significant increase in protein intake occurs, which in the hemodialysis population correlates with dialysis delivery.

  14. Comparison of Adaptive Information Security Approaches

    OpenAIRE

    Antti Evesti; Eila Ovaska

    2013-01-01

    Dynamically changing environments and threat landscapes require adaptive information security. Adaptive information security makes it possible to change and modify security mechanisms at runtime. Hence, all security decisions are not enforced at design-time. This paper builds a framework to compare security adaptation approaches. The framework contains three viewpoints, that is, adaptation, security, and lifecycle. Furthermore, the paper describes five security adaptation approaches and compa...

  15. Sleep facilitates long-term face adaptation

    OpenAIRE

    Ditye, T.; A.H Javadi; Carbon, C.C.; Walsh, V

    2013-01-01

    Adaptation is an automatic neural mechanism supporting the optimization of visual processing on the basis of previous experiences. While the short-term effects of adaptation on behaviour and physiology have been studied extensively, perceptual long-term changes associated with adaptation are still poorly understood. Here, we show that the integration of adaptation-dependent long-term shifts in neural function is facilitated by sleep. Perceptual shifts induced by adaptation to a distorted imag...

  16. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Sandip Chakraborty

    2016-01-01

    Full Text Available Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes’ adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

  17. Geometry-induced protein pattern formation.

    Science.gov (United States)

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-19

    Protein patterns are known to adapt to cell shape and serve as spatial templates that choreograph downstream processes like cell polarity or cell division. However, how can pattern-forming proteins sense and respond to the geometry of a cell, and what mechanistic principles underlie pattern formation? Current models invoke mechanisms based on dynamic instabilities arising from nonlinear interactions between proteins but neglect the influence of the spatial geometry itself. Here, we show that patterns can emerge as a direct result of adaptation to cell geometry, in the absence of dynamical instability. We present a generic reaction module that allows protein densities robustly to adapt to the symmetry of the spatial geometry. The key component is an NTPase protein that cycles between nucleotide-dependent membrane-bound and cytosolic states. For elongated cells, we find that the protein dynamics generically leads to a bipolar pattern, which vanishes as the geometry becomes spherically symmetrical. We show that such a reaction module facilitates universal adaptation to cell geometry by sensing the local ratio of membrane area to cytosolic volume. This sensing mechanism is controlled by the membrane affinities of the different states. We apply the theory to explain AtMinD bipolar patterns in [Formula: see text] EcMinDE Escherichia coli. Due to its generic nature, the mechanism could also serve as a hitherto-unrecognized spatial template in many other bacterial systems. Moreover, the robustness of the mechanism enables self-organized optimization of protein patterns by evolutionary processes. Finally, the proposed module can be used to establish geometry-sensitive protein gradients in synthetic biological systems. PMID:26739566

  18. Geometry-induced protein pattern formation.

    Science.gov (United States)

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-19

    Protein patterns are known to adapt to cell shape and serve as spatial templates that choreograph downstream processes like cell polarity or cell division. However, how can pattern-forming proteins sense and respond to the geometry of a cell, and what mechanistic principles underlie pattern formation? Current models invoke mechanisms based on dynamic instabilities arising from nonlinear interactions between proteins but neglect the influence of the spatial geometry itself. Here, we show that patterns can emerge as a direct result of adaptation to cell geometry, in the absence of dynamical instability. We present a generic reaction module that allows protein densities robustly to adapt to the symmetry of the spatial geometry. The key component is an NTPase protein that cycles between nucleotide-dependent membrane-bound and cytosolic states. For elongated cells, we find that the protein dynamics generically leads to a bipolar pattern, which vanishes as the geometry becomes spherically symmetrical. We show that such a reaction module facilitates universal adaptation to cell geometry by sensing the local ratio of membrane area to cytosolic volume. This sensing mechanism is controlled by the membrane affinities of the different states. We apply the theory to explain AtMinD bipolar patterns in [Formula: see text] EcMinDE Escherichia coli. Due to its generic nature, the mechanism could also serve as a hitherto-unrecognized spatial template in many other bacterial systems. Moreover, the robustness of the mechanism enables self-organized optimization of protein patterns by evolutionary processes. Finally, the proposed module can be used to establish geometry-sensitive protein gradients in synthetic biological systems.

  19. Perfect NIZK with Adaptive Soundness

    NARCIS (Netherlands)

    Abe, M.; Fehr, S.

    2007-01-01

    This paper presents a very simple and efficient adaptively-sound perfect NIZK argument system for any NP-language. In contrast to recently proposed schemes by Groth, Ostrovsky and Sahai, our scheme does not pose any restriction on the statements to be proven. Besides, it enjoys a number of desirable

  20. Micro Evolutionary Processes and Adaptation

    Institute of Scientific and Technical Information of China (English)

    SHADMANOV; R; K; RUBAN; I; N; VOROPAEVA; N; L; SHADMANOVA; A; R

    2008-01-01

    It would be well to note that in the absence of clear data about the formation of adaptation systems,or mechanisms of their occurrence,all that is recognized is the realization of the micro evolutionary processes.There is no well-defined connection between information exchange and formation of

  1. Future trends in adaptive Optics

    Science.gov (United States)

    Le Louarn, Miska

    2001-05-01

    In this talk, I will summarize the limitations of current adaptive optics systems (cone effect, anisoplanatism) and I will show what methods can be used to overcome them. I will focus on Multi-Conjugate AO and the polychromatic laser guide star. I will also address AO for Extremely Large Telescopes (ELTs), such as OWL (ESO) and CELT (University of California / Caltech).

  2. Reward Modulates Adaptations to Conflict

    Science.gov (United States)

    Braem, Senne; Verguts, Tom; Roggeman, Chantal; Notebaert, Wim

    2012-01-01

    Both cognitive conflict (e.g. Verguts & Notebaert, 2009) and reward signals (e.g. Waszak & Pholulamdeth, 2009) have been proposed to enhance task-relevant associations. Bringing these two notions together, we predicted that reward modulates conflict-based sequential adaptations in cognitive control. This was tested combining either a single…

  3. Adaptive and integrated water management

    NARCIS (Netherlands)

    Pahl-Wostl, C.; Kabat, P.; Möltgen, J.

    2007-01-01

    Sustainable water management is a key environmental challenge of the 21st century. Developing and implementing innovative management approaches and how to cope with the increasing complexity and uncertainties was the theme of the first International Conference on Adaptive and Integrated Water Manage

  4. Adaptable typologies for active roofs

    NARCIS (Netherlands)

    Quanjel, E.M.C.J.; Zeiler, W.

    2006-01-01

    The main objective of this part of the 6th framework Pan-European EUR-ACTIVE ROOF-er project is to improve the interaction between design participants of dynamic adaptable Active Roofs in product development and Active Roofs from an architects/ customers perspective. Improvements in Active Roof desi

  5. Aesthetic Adaptation in Translating Poetry

    Institute of Scientific and Technical Information of China (English)

    周丽艳

    2008-01-01

    This paper attempts to explore the strategy of adaptation,in particular,the method of naturalizing and historicizing,in the translation of poetry to maintain the aesthetic meaning.Theoretical support from Susan Bassnett,James Holmes and others is applied and example lines from both Chinese and English verses are given.

  6. Adaptive protection algorithm and system

    Science.gov (United States)

    Hedrick, Paul [Pittsburgh, PA; Toms, Helen L [Irwin, PA; Miller, Roger M [Mars, PA

    2009-04-28

    An adaptive protection algorithm and system for protecting electrical distribution systems traces the flow of power through a distribution system, assigns a value (or rank) to each circuit breaker in the system and then determines the appropriate trip set points based on the assigned rank.

  7. Physiological adaptation in desert birds

    NARCIS (Netherlands)

    Williams, JB; Tieleman, BI; Williams, Joseph B.

    2005-01-01

    We call into question the idea that birds have not evolved unique physiological adaptations to desert environments. The rate at which desert larks metabolize energy is lower than in mesic species within the same family, and this lower rate of living translates into a lower overall energy requirement

  8. Adaptive wiener image restoration kernel

    Science.gov (United States)

    Yuan, Ding

    2007-06-05

    A method and device for restoration of electro-optical image data using an adaptive Wiener filter begins with constructing imaging system Optical Transfer Function, and the Fourier Transformations of the noise and the image. A spatial representation of the imaged object is restored by spatial convolution of the image using a Wiener restoration kernel.

  9. Adaptive instruction and pupil achievement

    NARCIS (Netherlands)

    Houtveen, A.A M; Booy, N; de Jong, Robert (Rob); van de Grift, W.J C M

    1999-01-01

    In this article the results are reported of a quasi-experiment on effects of adaptive instruction on reading results of children in the first year of reading instruction in Dutch primary schools. The research involved 456 pupils from 23 schools (12 experimental and 11 control group schools). Teacher

  10. Continuous-time adaptive critics.

    Science.gov (United States)

    Hanselmann, Thomas; Noakes, Lyle; Zaknich, Anthony

    2007-05-01

    A continuous-time formulation of an adaptive critic design (ACD) is investigated. Connections to the discrete case are made, where backpropagation through time (BPTT) and real-time recurrent learning (RTRL) are prevalent. Practical benefits are that this framework fits in well with plant descriptions given by differential equations and that any standard integration routine with adaptive step-size does an adaptive sampling for free. A second-order actor adaptation using Newton's method is established for fast actor convergence for a general plant and critic. Also, a fast critic update for concurrent actor-critic training is introduced to immediately apply necessary adjustments of critic parameters induced by actor updates to keep the Bellman optimality correct to first-order approximation after actor changes. Thus, critic and actor updates may be performed at the same time until some substantial error build up in the Bellman optimality or temporal difference equation, when a traditional critic training needs to be performed and then another interval of concurrent actor-critic training may resume. PMID:17526332

  11. Inducible competitors and adaptive diversification

    Directory of Open Access Journals (Sweden)

    Beren W. ROBINSON, David W. PFENNIG

    2013-08-01

    Full Text Available Identifying the causes of diversification is central to evolutionary biology. The ecological theory of adaptive diversification holds that the evolution of phenotypic differences between populations and species––and the formation of new species––stems from divergent natural selection, often arising from competitive interactions. Although increasing evidence suggests that phenotypic plasticity can facilitate this process, it is not generally appreciated that competitively mediated selection often also provides ideal conditions for phenotypic plasticity to evolve in the first place. Here, we discuss how competition plays at least two key roles in adaptive diversification depending on its pattern. First, heterogenous competition initially generates heterogeneity in resource use that favors adaptive plasticity in the form of “inducible competitors”. Second, once such competitively induced plasticity evolves, its capacity to rapidly generate phenotypic variation and expose phenotypes to alternate selective regimes allows populations to respond readily to selection favoring diversification, as may occur when competition generates steady diversifying selection that permanently drives the evolutionary divergence of populations that use different resources. Thus, competition plays two important roles in adaptive diversification––one well-known and the other only now emerging––mediated through its effect on the evolution of phenotypic plasticity [Current Zoology 59 (4: 537–552, 2013].

  12. Adaptive representations for reinforcement learning

    NARCIS (Netherlands)

    S. Whiteson

    2010-01-01

    This book presents new algorithms for reinforcement learning, a form of machine learning in which an autonomous agent seeks a control policy for a sequential decision task. Since current methods typically rely on manually designed solution representations, agents that automatically adapt their own r

  13. Pseudomonas genomes: diverse and adaptable.

    Science.gov (United States)

    Silby, Mark W; Winstanley, Craig; Godfrey, Scott A C; Levy, Stuart B; Jackson, Robert W

    2011-07-01

    Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.

  14. Adaptive Clustering of Hypermedia Documents.

    Science.gov (United States)

    Johnson, Andrew; Fotouhi, Farshad

    1996-01-01

    Discussion of hypermedia systems focuses on a comparison of two types of adaptive algorithm (genetic algorithm and neural network) in clustering hypermedia documents. These clusters allow the user to index into the nodes to find needed information more quickly, since clustering is "personalized" based on the user's paths rather than representing…

  15. Inducible competitors and adaptive diversification

    Institute of Scientific and Technical Information of China (English)

    Beren W.ROBINSON; David W.PFENNIG

    2013-01-01

    Identifying the causes of diversification is central to evolutionary biology.The ecological theory of adaptive diversification holds that the evolution of phenotypic differences between populations and species-and the formation of new species-stems from divergent natural selection,often arising from competitive interactions.Although increasing evidence suggests that phenotypic plasticity can facilitate this process,it is not generally appreciated that competitively mediated selection often also provides ideal conditions for phenotypic plasticity to evolve in the first place.Here,we discuss how competition plays at least two key roles in adaptive diversification depending on its pattern.First,heterogenous competition initially generates heterogeneity in resource use that favors adaptive plasticity in the form of"inducible competitors".Second,once such competitively induced plasticity evolves,its capacity to rapidly generate phenotypic variation and expose phenotypes to alternate selective regimes allows populations to respond readily to selection favoring diversification,as may occur when competition generates steady diversifying selection that permanently drives the evolutionary divergence of populations that use different resources.Thus,competition plays two important roles in adaptive diversification--one well-known and the other only now emerging-mediated through its effect on the evolution of phenotypic plasticity.

  16. Private sector finance for adaptation

    NARCIS (Netherlands)

    Atteridge, A.; Pauw, W.P.; Terpstra, P.; Bedini, F.; Bosi, L; Costella, C.

    2016-01-01

    An emphasis on private finance has emerged in climate finance discussions, particularly in the context of international climate change negotiations. This is partly because the overall volume of finance needed to support adaptation in developing countries is beyond what many expect public finance to

  17. Human whole body cold adaptation.

    Science.gov (United States)

    Daanen, Hein A M; Van Marken Lichtenbelt, Wouter D

    2016-01-01

    Reviews on whole body human cold adaptation generally do not distinguish between population studies and dedicated acclimation studies, leading to confusing results. Population studies show that indigenous black Africans have reduced shivering thermogenesis in the cold and poor cold induced vasodilation in fingers and toes compared to Caucasians and Inuit. About 40,000 y after humans left Africa, natives in cold terrestrial areas seems to have developed not only behavioral adaptations, but also physiological adaptations to cold. Dedicated studies show that repeated whole body exposure of individual volunteers, mainly Caucasians, to severe cold results in reduced cold sensation but no major physiological changes. Repeated cold water immersion seems to slightly reduce metabolic heat production, while repeated exposure to milder cold conditions shows some increase in metabolic heat production, in particular non-shivering thermogenesis. In conclusion, human cold adaptation in the form of increased metabolism and insulation seems to have occurred during recent evolution in populations, but cannot be developed during a lifetime in cold conditions as encountered in temperate and arctic regions. Therefore, we mainly depend on our behavioral skills to live in and survive the cold. PMID:27227100

  18. The Adaptation of Migrant Children

    Science.gov (United States)

    Portes, Alejandro; Rivas, Alejandro

    2011-01-01

    Alejandro Portes and Alejandro Rivas examine how young immigrants are adapting to life in the United States. They begin by noting the existence of two distinct pan-ethnic populations: Asian Americans, who tend to be the offspring of high-human-capital migrants, and Hispanics, many of whose parents are manual workers. Vast differences in each, both…

  19. Economics of adaptation to climate change

    International Nuclear Information System (INIS)

    This report proposes a general economic framework for the issue of adaptation to climate change in order to help public and private actors to build up efficient adaptation strategies. It proposes a general definition of adaptation, identifies the major stakes for these strategies, and discusses the assessment of global costs of adaptation to climate change. It discusses the role and modalities of public action and gives some examples of possible adaptation measures in some important sectors (building and town planning, energy and transport infrastructures, water and agriculture, ecosystems, insurance). It examines the regional and national dimensions of adaptation and their relationship, and defines steps for implementing an adaptation strategy. It describes and discusses the use of economic tools in the elaboration of an adaptation strategy, i.e. how to take uncertainties into account, which scenarios to choose, how to use economic calculations to assess adaptation policies

  20. Suppression of mutants aberrant in light intensity responses of complementary chromatic adaptation.

    OpenAIRE

    Casey, E S; Kehoe, D M; Grossman, A R

    1997-01-01

    Complementary chromatic adaptation is a process in which cyanobacteria alter the pigment protein (phycocyanin and phycoerythrin) composition of their light-harvesting complexes, the phycobilisomes, to help optimize the absorbance of prevalent wavelengths of light in the environment. Several classes of mutants that display aberrant complementary chromatic adaptation have been isolated. One of the mutant classes, designated "blue" or FdB, accumulates high levels of the blue chromoprotein phycoc...