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Sample records for adapter protein tsad

  1. Protein Adaptations in Archaeal Extremophiles

    Science.gov (United States)

    Reed, Christopher J.; Lewis, Hunter; Trejo, Eric; Winston, Vern; Evilia, Caryn

    2013-01-01

    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. PMID:24151449

  2. 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.

  3. ADAPTATION TO PROTEIN DEFICIENCY: CORTISOL, THYROXINE ...

    African Journals Online (AJOL)

    Sci.6, I0I- 104 (1976). ADAPTATION TO PROTEIN DEFICIENCY: CORTISOL, THYROXINE,. INSULIN AND GLUCOSE IN YOUNG PIGS. J.M. van der Westhuysen*, P.C. Belonje**. A.P.D. de Satge*** & D.H. Holness***. Nutritional deficiencies place stress on the body. To maintain metabolic integrity. the body adapts by re-.

  4. Pervasive adaptive evolution in primate seminal proteins.

    Directory of Open Access Journals (Sweden)

    Nathaniel L Clark

    2005-09-01

    Full Text Available Seminal fluid proteins show striking effects on reproduction, involving manipulation of female behavior and physiology, mechanisms of sperm competition, and pathogen defense. Strong adaptive pressures are expected for such manifestations of sexual selection and host defense, but the extent of positive selection in seminal fluid proteins from divergent taxa is unknown. We identified adaptive evolution in primate seminal proteins using genomic resources in a tissue-specific study. We found extensive signatures of positive selection when comparing 161 human seminal fluid proteins and 2,858 prostate-expressed genes to those in chimpanzee. Seven of eight outstanding genes yielded statistically significant evidence of positive selection when analyzed in divergent primates. Functional clues were gained through divergent analysis, including several cases of species-specific loss of function in copulatory plug genes, and statistically significant spatial clustering of positively selected sites near the active site of kallikrein 2. This study reveals previously unidentified positive selection in seven primate seminal proteins, and when considered with findings in Drosophila, indicates that extensive positive selection is found in seminal fluid across divergent taxonomic groups.

  5. Pervasive Adaptive Evolution in Primate Seminal Proteins.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available Seminal fluid proteins show striking effects on reproduction, involving manipulation of female behavior and physiology, mechanisms of sperm competition, and pathogen defense. Strong adaptive pressures are expected for such manifestations of sexual selection and host defense, but the extent of positive selection in seminal fluid proteins from divergent taxa is unknown. We identified adaptive evolution in primate seminal proteins using genomic resources in a tissue-specific study. We found extensive signatures of positive selection when comparing 161 human seminal fluid proteins and 2,858 prostate-expressed genes to those in chimpanzee. Seven of eight outstanding genes yielded statistically significant evidence of positive selection when analyzed in divergent primates. Functional clues were gained through divergent analysis, including several cases of species-specific loss of function in copulatory plug genes, and statistically significant spatial clustering of positively selected sites near the active site of kallikrein 2. This study reveals previously unidentified positive selection in seven primate seminal proteins, and when considered with findings in Drosophila, indicates that extensive positive selection is found in seminal fluid across divergent taxonomic groups.

  6. 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

  7. Protein Supplementation Does Not Affect Myogenic Adaptations to Resistance Training.

    Science.gov (United States)

    Reidy, Paul T; Fry, Christopher S; Igbinigie, Sherry; Deer, Rachel R; Jennings, Kristofer; Cope, Mark B; Mukherjea, Ratna; Volpi, Elena; Rasmussen, Blake B

    2017-06-01

    It has been proposed that protein supplementation during resistance exercise training enhances muscle hypertrophy. The degree of hypertrophy during training is controlled in part through the activation of satellite cells and myonuclear accretion. This study aimed to determine the efficacy of protein supplementation (and the type of protein) during traditional resistance training on myofiber cross-sectional area, satellite cell content, and myonuclear addition. Healthy young men participated in supervised whole-body progressive resistance training 3 d·wk for 12 wk. Participants were randomized to one of three groups ingesting a daily 22-g macronutrient dose of soy-dairy protein blend (PB, n = 22), whey protein isolate (WP, n = 15), or an isocaloric maltodextrin placebo (MDP, n = 17). Lean mass, vastus lateralis myofiber-type-specific cross-sectional area, satellite cell content, and myonuclear addition were assessed before and after resistance training. PB and the pooled protein treatments (PB + WP = PRO) exhibited a greater whole-body lean mass %change compared with MDP (P = 0.057 for PB) and (P = 0.050 for PRO), respectively. All treatments demonstrated similar leg muscle hypertrophy and vastus lateralis myofiber-type-specific cross-sectional area (P supplementation during resistance training has a modest effect on whole-body lean mass as compared with exercise training without protein supplementation, and there was no effect on any outcome between protein supplement types (blend vs whey). However, protein supplementation did not enhance resistance exercise-induced increases in myofiber hypertrophy, satellite cell content, or myonuclear addition in young healthy men. We propose that as long as protein intake is adequate during muscle overload, the adaptations in muscle growth and function will not be influenced by protein supplementation.

  8. Adaptive response in Drosophila melanogaster heat shock proteins mutant strains

    International Nuclear Information System (INIS)

    Shaposhnikov, M.V.; Moskalev, A.A.; Turysheva, E.V.

    2007-01-01

    Complete text of publication follows. The members of the heat shock proteins (Hsp) family function as molecular chaperones and assist intracellular folding of newly synthesized proteins. Also it is possible that molecular chaperones are induced during adaptive response to oxidative stress and radiation. The aim of our research was to exam the role of heat shock proteins in adaptive response to oxidative stress after low dose rate gamma-irradiation in Drosophila melanogaster. Drosophilamelanogaster strains were kindly provided by Bloomington Drosophila Stock Center (University of state of Indiana, Bloomington, USA). We used wild type strain (CS), heat shock protein mutant strains (Hsp22, Hsp70, Hsp83), and heat shock factor mutant strain (Hsf). Strains were chronically exposured to adaptive dose of gamma-irradiation in dose rate of 0.17 cGy/h during all stages of life history (from the embrional stage to the stage of matured imago). The rate of absorbed dose was 60 cGy. For oxidative-stress challenge twodays old flies were starved in empty vials for 6 h and then transferred to vials containing only filter paper soaked with 20 mM paraquat in 5% sucrose solution. Survival data were collected after 26 h of treatment. Dead flies were counted daily. The obtained data were subjected to survival analysis by Kaplan and Meier method and presented as survival curves. Statistical analysis was held by non-parametric methods. To test the significance of the difference between the two age distributions Kolmogorov-Smirnov test was applied. Gehan-Braslow- Wilcoxon and Cox-Mantel tests were used for estimation of median life span differences. In addition the minimal and maximal life span, time of 90% death, and mortality rate doubling time (MRDT) were estimated. The obtained results will be discussed in presentation.

  9. Structural adaptations of proteins to different biological membranes

    Science.gov (United States)

    Pogozheva, Irina D.; Tristram-Nagle, Stephanie; Mosberg, Henry I.; Lomize, Andrei L.

    2013-01-01

    To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31 Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5 Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22 Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4 Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8 Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds. PMID:23811361

  10. The immunoreceptor adapter protein DAP12 suppresses B lymphocyte?driven adaptive immune responses

    OpenAIRE

    Nakano-Yokomizo, Takako; Tahara-Hanaoka, Satoko; Nakahashi-Oda, Chigusa; Nabekura, Tsukasa; Tchao, Nadia K.; Kadosaki, Momoko; Totsuka, Naoya; Kurita, Naoki; Nakamagoe, Kiyotaka; Tamaoka, Akira; Takai, Toshiyuki; Yasui, Teruhito; Kikutani, Hitoshi; Honda, Shin-ichiro; Shibuya, Kazuko

    2011-01-01

    DAP12, an immunoreceptor tyrosine-based activation motif?bearing adapter protein, is involved in innate immunity mediated by natural killer cells and myeloid cells. We show that DAP12-deficient mouse B cells and B cells from a patient with Nasu-Hakola disease, a recessive genetic disorder resulting from loss of DAP12, showed enhanced proliferation after stimulation with anti-IgM or CpG. Myeloid-associated immunoglobulin-like receptor (MAIR) II (Cd300d) is a DAP12-associated immune receptor. L...

  11. Protein and DNA sequence determinants of thermophilic adaptation.

    Directory of Open Access Journals (Sweden)

    Konstantin B Zeldovich

    2007-01-01

    Full Text Available There have been considerable attempts in the past to relate phenotypic trait--habitat temperature of organisms--to their genotypes, most importantly compositions of their genomes and proteomes. However, despite accumulation of anecdotal evidence, an exact and conclusive relationship between the former and the latter has been elusive. We present an exhaustive study of the relationship between amino acid composition of proteomes, nucleotide composition of DNA, and optimal growth temperature (OGT of prokaryotes. Based on 204 complete proteomes of archaea and bacteria spanning the temperature range from -10 degrees C to 110 degrees C, we performed an exhaustive enumeration of all possible sets of amino acids and found a set of amino acids whose total fraction in a proteome is correlated, to a remarkable extent, with the OGT. The universal set is Ile, Val, Tyr, Trp, Arg, Glu, Leu (IVYWREL, and the correlation coefficient is as high as 0.93. We also found that the G + C content in 204 complete genomes does not exhibit a significant correlation with OGT (R = -0.10. On the other hand, the fraction of A + G in coding DNA is correlated with temperature, to a considerable extent, due to codon patterns of IVYWREL amino acids. Further, we found strong and independent correlation between OGT and the frequency with which pairs of A and G nucleotides appear as nearest neighbors in genome sequences. This adaptation is achieved via codon bias. These findings present a direct link between principles of proteins structure and stability and evolutionary mechanisms of thermophylic adaptation. On the nucleotide level, the analysis provides an example of how nature utilizes codon bias for evolutionary adaptation to extreme conditions. Together these results provide a complete picture of how compositions of proteomes and genomes in prokaryotes adjust to the extreme conditions of the environment.

  12. A Drosophila protein-tyrosine phosphatase associates with an adapter protein required for axonal guidance.

    Science.gov (United States)

    Clemens, J C; Ursuliak, Z; Clemens, K K; Price, J V; Dixon, J E

    1996-07-19

    We have used the yeast two-hybrid system to isolate a novel Drosophila adapter protein, which interacts with the Drosophila protein-tyrosine phosphatase (PTP) dPTP61F. Absence of this protein in Drosophila causes the mutant photoreceptor axon phenotype dreadlocks (dock) (Garrity, P. A., Rao, Y., Salecker, I., and Zipursky, S. L.(1996) Cell 85, 639-650). Dock is similar to the mammalian oncoprotein Nck and contains three Src homology 3 (SH3) domains and one Src homology 2 (SH2) domain. The interaction of dPTP61F with Dock was confirmed in vivo by immune precipitation experiments. A sequence containing five PXXP motifs from the non-catalytic domain of the PTP is sufficient for interaction with Dock. This suggests that binding to the PTP is mediated by one or more of the SH3 domains of Dock. Immune precipitations of Dock also co-precipitate two tyrosine-phosphorylated proteins having molecular masses of 190 and 145 kDa. Interactions between Dock and these tyrosine-phosphorylated proteins are likely mediated by the Dock SH2 domain. These findings identify potential signal-transducing partners of Dock and propose a role for dPTP61F and the unidentified phosphoproteins in axonal guidance.

  13. Staphylococcal Immune Evasion Proteins: Structure, Function, and Host Adaptation.

    Science.gov (United States)

    Koymans, Kirsten J; Vrieling, Manouk; Gorham, Ronald D; van Strijp, Jos A G

    2017-01-01

    Staphylococcus aureus is a successful human and animal pathogen. Its pathogenicity is linked to its ability to secrete a large amount of virulence factors. These secreted proteins interfere with many critical components of the immune system, both innate and adaptive, and hamper proper immune functioning. In recent years, numerous studies have been conducted in order to understand the molecular mechanism underlying the interaction of evasion molecules with the host immune system. Structural studies have fundamentally contributed to our understanding of the mechanisms of action of the individual factors. Furthermore, such studies revealed one of the most striking characteristics of the secreted immune evasion molecules: their conserved structure. Despite high-sequence variability, most immune evasion molecules belong to a small number of structural categories. Another remarkable characteristic is that S. aureus carries most of these virulence factors on mobile genetic elements (MGE) or ex-MGE in its accessory genome. Coevolution of pathogen and host has resulted in immune evasion molecules with a highly host-specific function and prevalence. In this review, we explore how these shared structures and genomic locations relate to function and host specificity. This is discussed in the context of therapeutic options for these immune evasion molecules in infectious as well as in inflammatory diseases.

  14. Gab Adapter Proteins as Therapeutic Targets for Hematologic Disease

    Directory of Open Access Journals (Sweden)

    Sheetal Verma

    2012-01-01

    Full Text Available The Grb-2 associated binder (Gab family of scaffolding/adaptor/docking proteins is a group of three molecules with significant roles in cytokine receptor signaling. Gabs possess structural motifs for phosphorylation-dependent receptor recruitment, Grb2 binding, and activation of downstream signaling pathways through p85 and SHP-2. In addition, Gabs participate in hematopoiesis and regulation of immune response which can be aberrantly activated in cancer and inflammation. The multifunctionality of Gab adapters might suggest that they would be too difficult to consider as candidates for “targeted” therapy. However, the one drug/one target approach is giving way to the concept of one drug/multiple target approach since few cancers are addicted to a single signaling molecule for survival and combination drug therapies can be problematic. In this paper, we cover recent findings on Gab multi-functionality, binding partners, and their role in hematological malignancy and examine the concept of Gab-targeted therapy.

  15. Proteins induced during adaptation of Acetobacter aceti to high acetate concentrations.

    Science.gov (United States)

    Steiner, P; Sauer, U

    2001-12-01

    As a typical product of microbial metabolism, the weak acid acetate is well known for its cytotoxic effects. In contrast to most other microbes, the so-called acetic acid bacteria can acquire significant resistance to high acetate concentrations when properly adapted to such hostile conditions. To characterize the molecular events that are associated with this adaptation, we analyzed global protein expression levels during adaptation of Acetobacter aceti by two-dimensional gel electrophoresis. Adaptation was achieved by using serial batch and continuous cultivations with increasing acetate supplementation. Computer-aided analysis revealed a complex proteome response with at least 50 proteins that are specifically induced by adaptation to acetate but not by other stress conditions, such as heat or oxidative or osmotic stress. Of these proteins, 19 were significantly induced in serial batch and continuous cultures and were thus noted as acetate adaptation proteins (Aaps). Here we present first microsequence information on such Aaps from A. aceti. Membrane-associated processes appear to be of major importance for adaptation, because some of the Aap bear N-terminal sequence homology to membrane proteins and 11 of about 40 resolved proteins from membrane protein-enriched fractions are significantly induced.

  16. The limits of adaptation of functional protein synthesis to severe undernutrition

    International Nuclear Information System (INIS)

    Forrester, T.; Jahoor, F.; Reeds, P.

    1996-01-01

    This project was designed to investigate the limits of adaptation of protein metabolism in the stree of severe childhood malnutrition, representing as it does chronic dietary insufficiency of macronutrients and superimposed infection. The tasks included measurement of concentrations and rates of synthesis of nutrient transport proteins and hepatic acute phase proteins inseverely malnourished children during their acute illness and a recovery

  17. Pre-Sleep Protein Ingestion to Improve the Skeletal Muscle Adaptive Response to Exercise Training.

    Science.gov (United States)

    Trommelen, Jorn; van Loon, Luc J C

    2016-11-28

    Protein ingestion following resistance-type exercise stimulates muscle protein synthesis rates, and enhances the skeletal muscle adaptive response to prolonged resistance-type exercise training. As the adaptive response to a single bout of resistance exercise extends well beyond the first couple of hours of post-exercise recovery, recent studies have begun to investigate the impact of the timing and distribution of protein ingestion during more prolonged recovery periods. Recent work has shown that overnight muscle protein synthesis rates are restricted by the level of amino acid availability. Protein ingested prior to sleep is effectively digested and absorbed, and thereby stimulates muscle protein synthesis rates during overnight recovery. When applied during a prolonged period of resistance-type exercise training, protein supplementation prior to sleep can further augment gains in muscle mass and strength. Recent studies investigating the impact of pre-sleep protein ingestion suggest that at least 40 g of protein is required to display a robust increase in muscle protein synthesis rates throughout overnight sleep. Furthermore, prior exercise allows more of the pre-sleep protein-derived amino acids to be utilized for de novo muscle protein synthesis during sleep. In short, pre-sleep protein ingestion represents an effective dietary strategy to improve overnight muscle protein synthesis, thereby improving the skeletal muscle adaptive response to exercise training.

  18. Pre-Sleep Protein Ingestion to Improve the Skeletal Muscle Adaptive Response to Exercise Training

    Science.gov (United States)

    Trommelen, Jorn; van Loon, Luc J. C.

    2016-01-01

    Protein ingestion following resistance-type exercise stimulates muscle protein synthesis rates, and enhances the skeletal muscle adaptive response to prolonged resistance-type exercise training. As the adaptive response to a single bout of resistance exercise extends well beyond the first couple of hours of post-exercise recovery, recent studies have begun to investigate the impact of the timing and distribution of protein ingestion during more prolonged recovery periods. Recent work has shown that overnight muscle protein synthesis rates are restricted by the level of amino acid availability. Protein ingested prior to sleep is effectively digested and absorbed, and thereby stimulates muscle protein synthesis rates during overnight recovery. When applied during a prolonged period of resistance-type exercise training, protein supplementation prior to sleep can further augment gains in muscle mass and strength. Recent studies investigating the impact of pre-sleep protein ingestion suggest that at least 40 g of protein is required to display a robust increase in muscle protein synthesis rates throughout overnight sleep. Furthermore, prior exercise allows more of the pre-sleep protein-derived amino acids to be utilized for de novo muscle protein synthesis during sleep. In short, pre-sleep protein ingestion represents an effective dietary strategy to improve overnight muscle protein synthesis, thereby improving the skeletal muscle adaptive response to exercise training. PMID:27916799

  19. Pre-Sleep Protein Ingestion to Improve the Skeletal Muscle Adaptive Response to Exercise Training

    Directory of Open Access Journals (Sweden)

    Jorn Trommelen

    2016-11-01

    Full Text Available Protein ingestion following resistance-type exercise stimulates muscle protein synthesis rates, and enhances the skeletal muscle adaptive response to prolonged resistance-type exercise training. As the adaptive response to a single bout of resistance exercise extends well beyond the first couple of hours of post-exercise recovery, recent studies have begun to investigate the impact of the timing and distribution of protein ingestion during more prolonged recovery periods. Recent work has shown that overnight muscle protein synthesis rates are restricted by the level of amino acid availability. Protein ingested prior to sleep is effectively digested and absorbed, and thereby stimulates muscle protein synthesis rates during overnight recovery. When applied during a prolonged period of resistance-type exercise training, protein supplementation prior to sleep can further augment gains in muscle mass and strength. Recent studies investigating the impact of pre-sleep protein ingestion suggest that at least 40 g of protein is required to display a robust increase in muscle protein synthesis rates throughout overnight sleep. Furthermore, prior exercise allows more of the pre-sleep protein-derived amino acids to be utilized for de novo muscle protein synthesis during sleep. In short, pre-sleep protein ingestion represents an effective dietary strategy to improve overnight muscle protein synthesis, thereby improving the skeletal muscle adaptive response to exercise training.

  20. High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites.

    Science.gov (United States)

    Ebel, Emily R; Telis, Natalie; Venkataram, Sandeep; Petrov, Dmitri A; Enard, David

    2017-09-01

    Plasmodium parasites, along with their Piroplasm relatives, have caused malaria-like illnesses in terrestrial mammals for millions of years. Several Plasmodium-protective alleles have recently evolved in human populations, but little is known about host adaptation to blood parasites over deeper evolutionary timescales. In this work, we analyze mammalian adaptation in ~500 Plasmodium- or Piroplasm- interacting proteins (PPIPs) manually curated from the scientific literature. We show that (i) PPIPs are enriched for both immune functions and pleiotropy with other pathogens, and (ii) the rate of adaptation across mammals is significantly elevated in PPIPs, compared to carefully matched control proteins. PPIPs with high pathogen pleiotropy show the strongest signatures of adaptation, but this pattern is fully explained by their immune enrichment. Several pieces of evidence suggest that blood parasites specifically have imposed selection on PPIPs. First, even non-immune PPIPs that lack interactions with other pathogens have adapted at twice the rate of matched controls. Second, PPIP adaptation is linked to high expression in the liver, a critical organ in the parasite life cycle. Finally, our detailed investigation of alpha-spectrin, a major red blood cell membrane protein, shows that domains with particularly high rates of adaptation are those known to interact specifically with P. falciparum. Overall, we show that host proteins that interact with Plasmodium and Piroplasm parasites have experienced elevated rates of adaptation across mammals, and provide evidence that some of this adaptation has likely been driven by blood parasites.

  1. 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...

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

    Directory of Open Access Journals (Sweden)

    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

  3. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    Directory of Open Access Journals (Sweden)

    Murat Cetinbaş

    Full Text Available Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.

  4. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

    Directory of Open Access Journals (Sweden)

    Daniel L Halligan

    Full Text Available The contribution of regulatory versus protein change to adaptive evolution has long been controversial. In principle, the rate and strength of adaptation within functional genetic elements can be quantified on the basis of an excess of nucleotide substitutions between species compared to the neutral expectation or from effects of recent substitutions on nucleotide diversity at linked sites. Here, we infer the nature of selective forces acting in proteins, their UTRs and conserved noncoding elements (CNEs using genome-wide patterns of diversity in wild house mice and divergence to related species. By applying an extension of the McDonald-Kreitman test, we infer that adaptive substitutions are widespread in protein-coding genes, UTRs and CNEs, and we estimate that there are at least four times as many adaptive substitutions in CNEs and UTRs as in proteins. We observe pronounced reductions in mean diversity around nonsynonymous sites (whether or not they have experienced a recent substitution. This can be explained by selection on multiple, linked CNEs and exons. We also observe substantial dips in mean diversity (after controlling for divergence around protein-coding exons and CNEs, which can also be explained by the combined effects of many linked exons and CNEs. A model of background selection (BGS can adequately explain the reduction in mean diversity observed around CNEs. However, BGS fails to explain the wide reductions in mean diversity surrounding exons (encompassing ~100 Kb, on average, implying that there is a substantial role for adaptation within exons or closely linked sites. The wide dips in diversity around exons, which are hard to explain by BGS, suggest that the fitness effects of adaptive amino acid substitutions could be substantially larger than substitutions in CNEs. We conclude that although there appear to be many more adaptive noncoding changes, substitutions in proteins may dominate phenotypic evolution.

  5. Adaptive changes of duodenal iron transport proteins in celiac disease.

    Science.gov (United States)

    Barisani, Donatella; Parafioriti, Antonina; Bardella, Maria Teresa; Zoller, Heinz; Conte, Dario; Armiraglio, Elisabetta; Trovato, Cristina; Koch, Robert O; Weiss, Günter

    2004-05-19

    Iron deficiency is a manifestation of celiac disease (CD) usually attributed to a decreased absorptive surface, although no data on the regulation of iron transport under these conditions are currently available. Our aim was to evaluate divalent metal transporter 1 (DMT1), duodenal cytochrome b (Dcytb), ferroportin 1 (FP1), hephaestin, and transferrin receptor 1 (TfR1) expression, as well as iron regulatory protein (IRP) activity in duodenal biopsies from control, anemic, and CD patients. We studied 10 subjects with dyspepsia, 6 with iron-deficiency anemia, and 25 with CD. mRNA levels were determined by real-time PCR, protein expression by Western blotting or immunohistochemistry, and IRP activity by gel shift assay. Our results showed that DMT1, FP1, hephaestin, and TfR1 mRNA levels were significantly increased in CD patients with reduced body iron stores compared with controls, similar to what was observed in anemic patients. Protein expression paralleled the mRNAs changes. DMT1 protein expression was localized in differentiated enterocytes at the villi tips in controls, whereas with iron deficiency it was observed throughout the villi. FP1 expression was localized on the basolateral membrane of enterocytes and increased with low iron stores. TfR1 was localized in the crypts in controls but also in the villi with iron deficiency. These changes were paralleled by IRP activity, which increased in all iron-deficient subjects. We conclude that duodenal DMT1, FP1, hephaestin, and TfR1 expression and IRP activity, thus the iron absorption capacity, are upregulated in CD patients as a consequence of iron deficiency, whereas the increased enterocyte proliferation observed in CD has no effect on iron uptake regulation.

  6. Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.

    Directory of Open Access Journals (Sweden)

    Nicolas Galtier

    2016-01-01

    Full Text Available The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila experiencing a very high adaptive rate, while other (e.g. humans are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla-with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed.

  7. Thioredoxin binding protein-2 mediates metabolic adaptation in response to lipopolysaccharide in vivo.

    OpenAIRE

    Oka, Shin-ichi; Liu, Wenrui; Yoshihara, Eiji; Ahsan, Md Kaimul; Ramos, Dorys Adriana Lopez; Son, Aoi; Okuyama, Hiroaki; Zhang, Li; Masutani, Hiroshi; Nakamura, Hajime; Yodoi, Junji

    2010-01-01

    Endotoxin triggers a reorganization of the energy metabolic pathway, including the promotion of fatty acid utilization to adapt to a high energy demand during endotoxemia. However, the factors responsible for the metabolic adaptation and characteristic pathologies resulting from defective utilization fatty acids during endotoxin response have not been fully clarified. The thioredoxin binding protein-2 (TBP-2) knockout (TBP-2) mouse is an animal model of fatty acid oxidation disorder. The aim ...

  8. Domain requirements for the Dock adapter protein in growth- cone signaling

    OpenAIRE

    Rao, Yong; Zipursky, S. Lawrence

    1998-01-01

    Tyrosine phosphorylation has been implicated in growth-cone guidance through genetic, biochemical, and pharmacological studies. Adapter proteins containing src homology 2 (SH2) domains and src homology 3 (SH3) domains provide a means of linking guidance signaling through phosphotyrosine to downstream effectors regulating growth-cone motility. The Drosophila adapter, Dreadlocks (Dock), the homolog of mammalian Nck containing three N-terminal SH3 domains and a single SH2 domain, is highly speci...

  9. Role of X-ray-inducible genes and proteins in adaptive survival responses

    International Nuclear Information System (INIS)

    Meyers, M.; Schea, R.A.; Petrowski, A.E.; Seabury, H.; McLaughlin, P.W.; Lee, I.; Lee, S.W.; Boothman, D.A.

    1992-01-01

    Certain X-ray-inducible genes and their corresponding protein products, appearing following low priming doses of ionizing radiation may subsequently give rise to an adaptive survival response, ultimately leading to increased radioresistance. Further, this adaptive radioresistance may be due to increased DNA repair (or misrepair) processes. Ultimately, the function of low-dose-induced cDNA clones within the cell is hoped to elucidate to follow the effects of specific gene turn-off on adaptive responses. Future research must determine the various functions of adaptive response gene products so that the beneficial or deleterious consequences of adaptive responses, which increases resistance to ionizing radiation, can be determined. (author). 19 refs., 1 fig

  10. Proteomic study on X-irradiation-responsive proteins and ageing. Search for responsible proteins for radiation adaptive response

    International Nuclear Information System (INIS)

    Miura, Yuri; Kano, Mayumi; Suzuki, Shozo; Endo, Tamao; Toda, Tosifusa; Yamada, Masaki; Nishine, Tsutomu; Urano, Shiro

    2007-01-01

    We investigated high- or low-dose irradiation-responsive proteins using proteomics on two-dimensional (2D) polyacrylamide gel electrophoresis (PAGE), and the effects of ageing on cell responses to radiation in variously aged rat astrocytes. After 5 Gy irradiation, the relative abundance of peroxiredoxin 2, an antioxidant enzyme, and latexin, an inhibitor of carboxypeptidase, increased. The induction of these proteins was suppressed by ageing, suggesting that the response to high-dose radiation decreased with ageing. The relative abundance of elongation factor 2 (EF-2) fragment increased 3 h and reduced 24 h after 0.1 Gy irradiation. Temporal enhancement of the EF-2 fragment due to low-dose irradiation was suppressed by ageing. Since radiation adaptive response in cultured astrocytes was observed 3 h but not 24 h after 0.1 Gy irradiation and suppressed by ageing as previously reported, alteration of the EF-2 fragment corresponded to the radiation adaptive response. We also examined phospho-protein profiles, resulting in the relative abundance of phospho-EF-1β and phospho-β-actin being altered by 0.1 Gy irradiation; however, ageing did not affect the alteration of phospho-EF-1β and phospho-β-actin, unlike the EF-2 fragment. The results suggested that the EF-2 fragment was a possible candidate for the protein responsible for the radiation adaptive response in cultured astrocytes. (author)

  11. Protein loss during long-distance migratory flight in passerine birds: adaptation and constraint.

    Science.gov (United States)

    Schwilch, Regine; Grattarola, Alessandra; Spina, Fernando; Jenni, Lukas

    2002-03-01

    During long-distance flights, birds catabolize not only fat but also protein. Because there is no storage form of protein, protein catabolism entails a structural or functional loss. In this study, we investigated which organs were most reduced in lean mass during different phases of fat store loss and whether protein loss can be regarded as adaptive or as a constraint. Body and organ composition were analysed both during the autumn migration over continental Europe (sample from Switzerland) and after a long-distance flight over the Sahara and the Mediterranean Sea in spring (sample from Ventotene, Italy) in four species of passerine bird: pied flycatcher Ficedula hypoleuca, willow warbler Phylloscopus trochilus, garden warbler Sylvia borin and barn swallow Hirundo rustica. Large variations in protein mass occurred when long non-stop flights were performed. After a long-distance flight, birds showed a marked increase in net protein loss when fat stores were nearing depletion (analogous to the late phase of endurance fasting when the rate of protein catabolism is increased). When fat reserves were above approximately 5-10 %, protein was derived from all organs, but particularly from the breast muscles. When fat stores diminished further and protein catabolism increased, the mass of the digestive organs was reduced fastest. When the decrease in breast muscle mass during flight was regarded in terms of potential flight performance, it appeared that the use of breast muscle protein with decreasing body mass can be regarded as adaptive as long as fat stores did not reach a critical level. Below approximately 5-10 % body fat, however, protein loss reduced flight performance. This demonstrates that the phase of fasting (the size of the remaining fat stores) is an important condition for understanding the occurrence and effects of protein loss during endurance flights.

  12. First Experimental Assessment of Protein Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process.

    Science.gov (United States)

    Charon, Justine; Barra, Amandine; Walter, Jocelyne; Millot, Pauline; Hébrard, Eugénie; Moury, Benoît; Michon, Thierry

    2018-01-01

    Intrinsic disorder (ID) in proteins is defined as a lack of stable structure in physiological conditions. Intrinsically disordered regions (IDRs) are highly abundant in some RNA virus proteomes. Low topological constraints exerted on IDRs are expected to buffer the effect of numerous deleterious mutations and could be related to the remarkable adaptive potential of RNA viruses to overcome resistance of their host. To experimentally test this hypothesis in a natural pathosystem, a set of four variants of Potato virus Y (PVY; Potyvirus genus) containing various ID degrees in the Viral genome-linked (VPg) protein, a key determinant of potyvirus adaptation, was designed. To estimate the ID contribution to the VPg-based PVY adaptation, the adaptive ability of the four PVY variants was monitored in the pepper host (Capsicum annuum) carrying a recessive resistance gene. Intriguingly, the two mutants with the highest ID content displayed a significantly higher ability to restore infection in the resistant host, whereas the less intrinsically disordered mutant was unable to restore infection. The role of ID on virus adaptation may be due either to a larger exploration of evolutionary pathways or the minimization of fitness penalty caused by resistance-breaking mutations. This pioneering study strongly suggests the positive impact of ID in an RNA virus adaptive capacity. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Neutron scattering reveals the dynamic basis of protein adaptation to extreme temperature.

    Science.gov (United States)

    Tehei, Moeava; Madern, Dominique; Franzetti, Bruno; Zaccai, Giuseppe

    2005-12-09

    To explore protein adaptation to extremely high temperatures, two parameters related to macromolecular dynamics, the mean square atomic fluctuation and structural resilience, expressed as a mean force constant, were measured by neutron scattering for hyperthermophilic malate dehydrogenase from Methanococcus jannaschii and a mesophilic homologue, lactate dehydrogenase from Oryctolagus cunniculus (rabbit) muscle. The root mean square fluctuations, defining flexibility, were found to be similar for both enzymes (1.5 A) at their optimal activity temperature. Resilience values, defining structural rigidity, are higher by an order of magnitude for the high temperature-adapted protein (0.15 Newtons/meter for O. cunniculus lactate dehydrogenase and 1.5 Newtons/meter for M. jannaschii malate dehydrogenase). Thermoadaptation appears to have been achieved by evolution through selection of appropriate structural rigidity in order to preserve specific protein structure while allowing the conformational flexibility required for activity.

  14. GTPase-activating protein oligophrenin 1 is a new partner of multifunctional adapter protein intersectin 1

    Directory of Open Access Journals (Sweden)

    Gasman S.

    2012-09-01

    Full Text Available Intersectin 1 (ITSN1 is a multifunctional adaptor protein which is involved in endocytosis, exocytosis and cellular signaling and it is also associated with such pathologies as Down syndrome and Alzheimer’s disease. The aim of this study was to identify new ITSN1 protein partners which are implicated in membrane trafficking. Methods. In silico analysis by Scansite online resource had identified a GTPase activating protein oligophrenin 1 (OPHN1 as a potential partner of ITSN1 SH3A domain. GST pull-down and immunoprecipitation were used to prove complex formation between ITSN1 and OPHN1. Subcellular protein localization was determined by immunofluorescence and confocal microscopy. Results. We have shown that brain-specific and ubiquitously expressed SH3A domain isoforms of ITSN1 interact with OPHN1. ITSN1 and OPHN1 form complexes in both resting and stimulated to exocytosis PC12 cell line. Conclusions. GTPase activating protein OPHN1 and adaptor protein ITSN1 interact in PC12 cell line independently of exocytosis stimulation.

  15. Intra-plastid protein trafficking: how plant cells adapted prokaryotic mechanisms to the eukaryotic condition.

    Science.gov (United States)

    Celedon, Jose M; Cline, Kenneth

    2013-02-01

    Protein trafficking and localization in plastids involve a complex interplay between ancient (prokaryotic) and novel (eukaryotic) translocases and targeting machineries. During evolution, ancient systems acquired new functions and novel translocation machineries were developed to facilitate the correct localization of nuclear encoded proteins targeted to the chloroplast. Because of its post-translational nature, targeting and integration of membrane proteins posed the biggest challenge to the organelle to avoid aggregation in the aqueous compartments. Soluble proteins faced a different kind of problem since some had to be transported across three membranes to reach their destination. Early studies suggested that chloroplasts addressed these issues by adapting ancient-prokaryotic machineries and integrating them with novel-eukaryotic systems, a process called 'conservative sorting'. In the last decade, detailed biochemical, genetic, and structural studies have unraveled the mechanisms of protein targeting and localization in chloroplasts, suggesting a highly integrated scheme where ancient and novel systems collaborate at different stages of the process. In this review we focus on the differences and similarities between chloroplast ancestral translocases and their prokaryotic relatives to highlight known modifications that adapted them to the eukaryotic situation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Adaptation.

    Science.gov (United States)

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  17. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment.

    Directory of Open Access Journals (Sweden)

    David F Gruber

    Full Text Available We report the identification and characterization of two new members of a family of bilirubin-inducible fluorescent proteins (FPs from marine chlopsid eels and demonstrate a key region of the sequence that serves as an evolutionary switch from non-fluorescent to fluorescent fatty acid-binding proteins (FABPs. Using transcriptomic analysis of two species of brightly fluorescent Kaupichthys eels (Kaupichthys hyoproroides and Kaupichthys n. sp., two new FPs were identified, cloned and characterized (Chlopsid FP I and Chlopsid FP II. We then performed phylogenetic analysis on 210 FABPs, spanning 16 vertebrate orders, and including 163 vertebrate taxa. We show that the fluorescent FPs diverged as a protein family and are the sister group to brain FABPs. Our results indicate that the evolution of this family involved at least three gene duplication events. We show that fluorescent FABPs possess a unique, conserved tripeptide Gly-Pro-Pro sequence motif, which is not found in non-fluorescent fatty acid binding proteins. This motif arose from a duplication event of the FABP brain isoforms and was under strong purifying selection, leading to the classification of this new FP family. Residues adjacent to the motif are under strong positive selection, suggesting a further refinement of the eel protein's fluorescent properties. We present a phylogenetic reconstruction of this emerging FP family and describe additional fluorescent FABP members from groups of distantly related eels. The elucidation of this class of fish FPs with diverse properties provides new templates for the development of protein-based fluorescent tools. The evolutionary adaptation from fatty acid-binding proteins to fluorescent fatty acid-binding proteins raises intrigue as to the functional role of bright green fluorescence in this cryptic genus of reclusive eels that inhabit a blue, nearly monochromatic, marine environment.

  18. 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.

  19. Comparative Proteomics of Mouse Tears and Saliva: Evidence from Large Protein Families for Functional Adaptation

    Directory of Open Access Journals (Sweden)

    Robert C. Karn

    2015-09-01

    Full Text Available We produced a tear proteome of the genome mouse, C57BL/6, that contained 139 different protein identifications: 110 from a two-dimensional (2D gel with subsequent trypsin digestion, 19 from a one-dimensional (1D gel with subsequent trypsin digestion and ten from a 1D gel with subsequent Asp-N digestion. We compared this tear proteome with a C57BL/6 mouse saliva proteome produced previously. Sixteen of the 139 tear proteins are shared between the two proteomes, including six proteins that combat microbial growth. Among the 123 other tear proteins, were members of four large protein families that have no counterparts in humans: Androgen-binding proteins (ABPs with different members expressed in the two proteomes, Exocrine secreted peptides (ESPs expressed exclusively in the tear proteome, major urinary proteins (MUPs expressed in one or both proteomes and the mouse-specific Kallikreins (subfamily b KLKs expressed exclusively in the saliva proteome. All four families have members with suggested roles in mouse communication, which may influence some aspect of reproductive behavior. We discuss this in the context of functional adaptation involving tear and saliva proteins in the secretions of mouse lacrimal and salivary glands, respectively.

  20. Kinetic Stability of Proteins in Beans and Peas: Implications for Protein Digestibility, Seed Germination, and Plant Adaptation.

    Science.gov (United States)

    Xia, Ke; Pittelli, Sandy; Church, Jennifer; Colón, Wilfredo

    2016-10-12

    Kinetically stable proteins (KSPs) are resistant to the denaturing detergent sodium dodecyl sulfate (SDS). Such resilience makes KSPs resistant to proteolytic degradation and may have arisen in nature as a mechanism for organismal adaptation and survival against harsh conditions. Legumes are well-known for possessing degradation-resistant proteins that often diminish their nutritional value. Here we applied diagonal two-dimensional (D2D) SDS-polyacrylamide gel electrophoresis (PAGE), a method that allows for the proteomics-level identification of KSPs, to a group of 12 legumes (mostly beans and peas) of agricultural and nutritional importance. Our proteomics results show beans that are more difficult to digest, such as soybean, lima beans, and various common beans, have high contents of KSPs. In contrast, mung bean, red lentil, and various peas that are highly digestible contain low amounts of KSPs. Identified proteins with high kinetic stability are associated with warm-season beans, which germinate at higher temperatures. In contrast, peas and red lentil, which are cool-season legumes, contain low levels of KSPs. Thus, our results show protein kinetic stability is an important factor in the digestibility of legume proteins and may relate to nutrition efficiency, timing of seed germination, and legume resistance to biotic stressors. Furthermore, we show D2D SDS-PAGE is a powerful method that could be applied for determining the abundance and identity of KSPs in engineered and wild legumes and for advancing basic research and associated applications.

  1. Live imaging using adaptive optics with fluorescent protein guide-stars.

    Science.gov (United States)

    Tao, Xiaodong; Crest, Justin; Kotadia, Shaila; Azucena, Oscar; Chen, Diana C; Sullivan, William; Kubby, Joel

    2012-07-02

    Spatially and temporally dependent optical aberrations induced by the inhomogeneous refractive index of live samples limit the resolution of live dynamic imaging. We introduce an adaptive optical microscope with a direct wavefront sensing method using a Shack-Hartmann wavefront sensor and fluorescent protein guide-stars for live imaging. The results of imaging Drosophila embryos demonstrate its ability to correct aberrations and achieve near diffraction limited images of medial sections of large Drosophila embryos. GFP-polo labeled centrosomes can be observed clearly after correction but cannot be observed before correction. Four dimensional time lapse images are achieved with the correction of dynamic aberrations. These studies also demonstrate that the GFP-tagged centrosome proteins, Polo and Cnn, serve as excellent biological guide-stars for adaptive optics based microscopy.

  2. Adaptive optics microscopy with direct wavefront sensing using fluorescent protein guide stars.

    Science.gov (United States)

    Tao, Xiaodong; Azucena, Oscar; Fu, Min; Zuo, Yi; Chen, Diana C; Kubby, Joel

    2011-09-01

    We introduce a direct wavefront sensing method using structures labeled with fluorescent proteins in tissues as guide stars. An adaptive optics confocal microscope using this method is demonstrated for imaging of mouse brain tissue. A dendrite and a cell body of a neuron labeled with yellow fluorescent protein are tested as guide stars without injection of other fluorescent labels. Photobleaching effects are also analyzed. The results shows increased image contrast and 3× improvement in the signal intensity for fixed mouse tissues at depths of 70 μm.

  3. Nonrandom allele associations between unlinked protein loci: are the polymorphisms of the immunoglobulin constant regions adaptive?

    OpenAIRE

    van der Loo, W; Arthur, C P; Richardson, B J; Wallage-Drees, M; Hamers, R

    1987-01-01

    Consistent linkage disequilibrium was observed between independently segregating protein loci. In natural populations of the European rabbit Oryctolagus cuniculus, highly significant, nonrandom associations between alleles of the constant regions of the immunoglobulin light and heavy chains were found, both within localities and between localities. We suggest that the population genetic data presented here are relevant to the adaptive significance of the genetic polymorphisms of the antibody ...

  4. REEPs are membrane shaping adapter proteins that modulate specific g protein-coupled receptor trafficking by affecting ER cargo capacity.

    Directory of Open Access Journals (Sweden)

    Susann Björk

    proteins. Therefore, some REEPs can be further described as ER membrane shaping adapter proteins.

  5. 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.

  6. Adaptation

    International Development Research Centre (IDRC) Digital Library (Canada)

    . Dar es Salaam. Durban. Bloemfontein. Antananarivo. Cape Town. Ifrane ... program strategy. A number of CCAA-supported projects have relevance to other important adaptation-related themes such as disaster preparedness and climate.

  7. The effects of whey protein with or without carbohydrates on resistance training adaptations.

    Science.gov (United States)

    Hulmi, Juha J; Laakso, Mia; Mero, Antti A; Häkkinen, Keijo; Ahtiainen, Juha P; Peltonen, Heikki

    2015-01-01

    Nutrition intake in the context of a resistance training (RT) bout may affect body composition and muscle strength. However, the individual and combined effects of whey protein and carbohydrates on long-term resistance training adaptations are poorly understood. A four-week preparatory RT period was conducted in previously untrained males to standardize the training background of the subjects. Thereafter, the subjects were randomized into three groups: 30 g of whey proteins (n = 22), isocaloric carbohydrates (maltodextrin, n = 21), or protein + carbohydrates (n = 25). Within these groups, the subjects were further randomized into two whole-body 12-week RT regimens aiming either for muscle hypertrophy and maximal strength or muscle strength, hypertrophy and power. The post-exercise drink was always ingested immediately after the exercise bout, 2-3 times per week depending on the training period. Body composition (by DXA), quadriceps femoris muscle cross-sectional area (by panoramic ultrasound), maximal strength (by dynamic and isometric leg press) and serum lipids as basic markers of cardiovascular health, were analysed before and after the intervention. Twelve-week RT led to increased fat-free mass, muscle size and strength independent of post-exercise nutrient intake (P whey protein group reduced more total and abdominal area fat when compared to the carbohydrate group independent of the type of RT (P protein vs. carbohydrate group (P whey proteins when compared to carbohydrates or combination of proteins and carbohydrates did not have a major effect on muscle size or strength when ingested two to three times a week. However, whey proteins may increase abdominal fat loss and relative fat-free mass adaptations in response to resistance training when compared to fast-acting carbohydrates.

  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

  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

    KAUST Repository

    Martinez, N.

    2016-09-06

    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.

  11. 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.

    2016-09-01

    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.

  12. 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

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

    International Nuclear Information System (INIS)

    Jahoor, F.; Bhattiprolu, S.; Reeds, P.; Forrester, T.; Boyne, M.

    1994-01-01

    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

  14. Adaptation of proteomic techniques for the identification and characterization of protein species from murine heart.

    Science.gov (United States)

    Schwab, Karima; Neumann, Boris; Scheler, Christian; Jungblut, Peter R; Theuring, Franz

    2011-07-01

    Disturbed energy metabolism with impaired fatty acid oxidation, ATP synthesis and changing levels of contractile proteins has been observed during the development and manifestation of cardiovascular diseases, with the latter showing sexual differences in terms of onset, manifestation and progress. Estrogenic compounds, such as estrogens and phytoestrogens, are known to exert beneficial effects on several cardiovascular parameters. However, global studies implying the normal, non-failing myocardium are rare. Thus, identifying and characterizing protein patterns involved in the maintenance of normal heart physiology at the protein species level will help understanding disease conditions. In this study, we performed an adapted 2-DE/MS approach in order to identify and characterize post-translational modified and truncated protein species from murine heart. Female and male animals of different age were receiving the phytoestrogen genistein and comparative analyses were performed to identify sex and genistein treatment-related effects. Selected 2-DE spots that exposed varying abundance between animal groups and identified as identical proteins were subject to multi-protease cleavage to generate an elevated sequence coverage enabling characterization of post-translational modifications and truncation loci via high-resolution MS. Several truncated, phosphorylated and acetylated species were identified for mitochondrial ATP synthase, malate dehydrogenase and trifunctional enzyme subunit alpha. However, confirmation of several of these modifications by manual spectra interpretation failed. Thus, our results warrant caution for the blind trust in software output. For the regulatory light chain of myosin, we identified an N-terminal processed species, which so far has been related to ischemic conditions only. We tried to unravel the information content of protein species separated by high-resolution 2-DE as an alternative to high-throughput proteomics, which mainly is

  15. Adaptation

    International Development Research Centre (IDRC) Digital Library (Canada)

    Nairobi, Kenya. 28 Adapting Fishing Policy to Climate Change with the Aid of Scientific and Endogenous Knowledge. Cap Verde, Gambia,. Guinea, Guinea Bissau,. Mauritania and Senegal. Environment and Development in the Third World. (ENDA-TM). Dakar, Senegal. 29 Integrating Indigenous Knowledge in Climate Risk ...

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

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    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.

  17. Domain requirements for the Dock adapter protein in growth- cone signaling.

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    Rao, Y; Zipursky, S L

    1998-03-03

    Tyrosine phosphorylation has been implicated in growth-cone guidance through genetic, biochemical, and pharmacological studies. Adapter proteins containing src homology 2 (SH2) domains and src homology 3 (SH3) domains provide a means of linking guidance signaling through phosphotyrosine to downstream effectors regulating growth-cone motility. The Drosophila adapter, Dreadlocks (Dock), the homolog of mammalian Nck containing three N-terminal SH3 domains and a single SH2 domain, is highly specialized for growth-cone guidance. In this paper, we demonstrate that Dock can couple signals in either an SH2-dependent or an SH2-independent fashion in photoreceptor (R cell) growth cones, and that Dock displays different domain requirements in different neurons.

  18. Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation.

    Science.gov (United States)

    Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto; Pazos, Florencio

    2013-01-01

    Intrinsically disordered proteins/regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in Arabidopsis thaliana, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.

  19. 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.

  20. Reciprocal influence of protein domains in the cold-adapted acyl aminoacyl peptidase from Sporosarcina psychrophila.

    Science.gov (United States)

    Parravicini, Federica; Natalello, Antonino; Papaleo, Elena; De Gioia, Luca; Doglia, Silvia Maria; Lotti, Marina; Brocca, Stefania

    2013-01-01

    Acyl aminoacyl peptidases are two-domain proteins composed by a C-terminal catalytic α/β-hydrolase domain and by an N-terminal β-propeller domain connected through a structural element that is at the N-terminus in sequence but participates in the 3D structure of the C-domain. We investigated about the structural and functional interplay between the two domains and the bridge structure (in this case a single helix named α1-helix) in the cold-adapted enzyme from Sporosarcina psychrophila (SpAAP) using both protein variants in which entire domains were deleted and proteins carrying substitutions in the α1-helix. We found that in this enzyme the inter-domain connection dramatically affects the stability of both the whole enzyme and the β-propeller. The α1-helix is required for the stability of the intact protein, as in other enzymes of the same family; however in this psychrophilic enzyme only, it destabilizes the isolated β-propeller. A single charged residue (E10) in the α1-helix plays a major role for the stability of the whole structure. Overall, a strict interaction of the SpAAP domains seems to be mandatory for the preservation of their reciprocal structural integrity and may witness their co-evolution.

  1. Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation

    Science.gov (United States)

    Peter, Emanuel K.

    2017-12-01

    In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

  2. Aerobic Exercise Training Adaptations Are Increased by Postexercise Carbohydrate-Protein Supplementation

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    Lisa Ferguson-Stegall

    2011-01-01

    Full Text Available Carbohydrate-protein supplementation has been found to increase the rate of training adaptation when provided postresistance exercise. The present study compared the effects of a carbohydrate and protein supplement in the form of chocolate milk (CM, isocaloric carbohydrate (CHO, and placebo on training adaptations occurring over 4.5 weeks of aerobic exercise training. Thirty-two untrained subjects cycled 60 min/d, 5 d/wk for 4.5 wks at 75–80% of maximal oxygen consumption (VO2 max. Supplements were ingested immediately and 1 h after each exercise session. VO2 max and body composition were assessed before the start and end of training. VO2 max improvements were significantly greater in CM than CHO and placebo. Greater improvements in body composition, represented by a calculated lean and fat mass differential for whole body and trunk, were found in the CM group compared to CHO. We conclude supplementing with CM postexercise improves aerobic power and body composition more effectively than CHO alone.

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

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    Yoojin Hong

    2010-10-01

    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

  4. Assisted protein folding at low temperature: evolutionary adaptation of the Antarctic fish chaperonin CCT and its client proteins

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    Jorge Cuellar

    2014-03-01

    Full Text Available Eukaryotic ectotherms of the Southern Ocean face energetic challenges to protein folding assisted by the cytosolic chaperonin CCT. We hypothesize that CCT and its client proteins (CPs have co-evolved molecular adaptations that facilitate CCT–CP interaction and the ATP-driven folding cycle at low temperature. To test this hypothesis, we compared the functional and structural properties of CCT–CP systems from testis tissues of an Antarctic fish, Gobionotothen gibberifrons (Lönnberg (habitat/body T = −1.9 to +2°C, and of the cow (body T = 37°C. We examined the temperature dependence of the binding of denatured CPs (β-actin, β-tubulin by fish and bovine CCTs, both in homologous and heterologous combinations and at temperatures between −4°C and 20°C, in a buffer conducive to binding of the denatured CP to the open conformation of CCT. In homologous combination, the percentage of G. gibberifrons CCT bound to CP declined linearly with increasing temperature, whereas the converse was true for bovine CCT. Binding of CCT to heterologous CPs was low, irrespective of temperature. When reactions were supplemented with ATP, G. gibberifrons CCT catalyzed the folding and release of actin at 2°C. The ATPase activity of apo-CCT from G. gibberifrons at 4°C was ∼2.5-fold greater than that of apo-bovine CCT, whereas equivalent activities were observed at 20°C. Based on these results, we conclude that the catalytic folding cycle of CCT from Antarctic fishes is partially compensated at their habitat temperature, probably by means of enhanced CP-binding affinity and increased flexibility of the CCT subunits.

  5. Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells.

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    Bozhena Jhas

    Full Text Available Recently, we demonstrated that the anti-bacterial agent tigecycline preferentially induces death in leukemia cells through the inhibition of mitochondrial protein synthesis. Here, we sought to understand mechanisms of resistance to tigecycline by establishing a leukemia cell line resistant to the drug. TEX leukemia cells were treated with increasing concentrations of tigecycline over 4 months and a population of cells resistant to tigecycline (RTEX+TIG was selected. Compared to wild type cells, RTEX+TIG cells had undetectable levels of mitochondrially translated proteins Cox-1 and Cox-2, reduced oxygen consumption and increased rates of glycolysis. Moreover, RTEX+TIG cells were more sensitive to inhibitors of glycolysis and more resistant to hypoxia. By electron microscopy, RTEX+TIG cells had abnormally swollen mitochondria with irregular cristae structures. RNA sequencing demonstrated a significant over-representation of genes with binding sites for the HIF1α:HIF1β transcription factor complex in their promoters. Upregulation of HIF1α mRNA and protein in RTEX+TIG cells was confirmed by Q-RTPCR and immunoblotting. Strikingly, upon removal of tigecycline from RTEX+TIG cells, the cells re-established aerobic metabolism. Levels of Cox-1 and Cox-2, oxygen consumption, glycolysis, mitochondrial mass and mitochondrial membrane potential returned to wild type levels, but HIF1α remained elevated. However, upon re-treatment with tigecycline for 72 hours, the glycolytic phenotype was re-established. Thus, we have generated cells with a reversible metabolic phenotype by chronic treatment with an inhibitor of mitochondrial protein synthesis. These cells will provide insight into cellular adaptations used to cope with metabolic stress.

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

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    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.

  7. Changes in protein synthesis during thermal adaptation of Propionibacterium freudenreichii subsp. shermanii.

    Science.gov (United States)

    Anastasiou, Rania; Leverrier, Pauline; Krestas, Ioannis; Rouault, Annette; Kalantzopoulos, George; Boyaval, Patrick; Tsakalidou, Effie; Jan, Gwénaël

    2006-05-01

    Dairy propionibacteria are present in Graviera Kritis, a traditional Gruyère-type cheese made without added propionic starter. Ten isolated strains were identified by a combination of SDS-PAGE, species-specific PCR and according to their ability to ferment lactose. They were all found to belong to the Propionibacterium freudenreichii subsp. shermanii species. Because of the stressing Gruyère technology, which includes cooking at 52 to 53 degrees C their thermotolerance was investigated at 55 degrees C. Thermotolerant and thermosensitive strains were clearly discriminated. Interestingly, the reference strain CIP 103027 belongs to the sensitive subset. One sensitive strain, ACA-DC 1305 and one tolerant, ACA-DC 1451, were selected for further study and compared to CIP 103027. For the sensitive strains ACA-DC 1305 and CIP 103027, heat pre-treatment at 42 degrees C conferred thermoprotection of cells at the lethal temperature of 55 degrees C, while there was less effect on the tolerant ACA-DC 1451. No cross-protection of salt-adapted cells against heat stress was observed for none of the strains. Differential proteomic analysis revealed distinct but overlapping cell responses to heat stress between sensitive and tolerant strains. Thermal adaptation upregulated typical HSPs involved in protein repair or turnover in the sensitive one. In the tolerant one, a distinct subset of proteins was overexpressed, whatever the temperature used, in addition to HSPs. This included enzymes involved in propionic fermentation, amino acid metabolism, oxidative stress remediation and nucleotide phosphorylation. These results bring new insights into thermoprotection in propionibacteria and the occurrence of divergent phenotypes within a same subspecies.

  8. Phospholipids and protein adaptation of Pseudomonas sp. to the xenoestrogen tributyltin chloride (TBT).

    Science.gov (United States)

    Bernat, Przemysław; Siewiera, Paulina; Soboń, Adrian; Długoński, Jerzy

    2014-09-01

    A tributyltin (TBT)-resistant strain of Pseudomonas sp. isolated from an overworked car filter was tested for its adaptation to TBT. The isolate was checked for organotin degradation ability, as well as membrane lipid and cellular protein composition in the presence of TBT. The phospholipid profiles of bacteria, grown with and without increased amounts of TBT, were characterized using liquid chromatography/electrospray ionization/mass spectrometry. The strain reacted to the biocide by changing the composition of its phospholipids. TBT induced a twofold decline in the amounts of many molecular species of phosphatidylglycerol and an increase in the levels of phosphatidic acid (by 58%) and phosphatidylethanolamine (by 70%). An increase in the degree of saturation of phospholipid fatty acids of TBT exposed Pseudomonas sp. was observed. These changes in the phospholipid composition and concentration reflect the mechanisms which support optimal lipid ordering in the presence of toxic xenobiotic. In the presence of TBT the abundances of 16 proteins, including TonB-dependent receptors, porins and peroxidases were modified, which could indicate a contribution of some enzymes to TBT resistance.

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

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    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.

  10. 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. © 2013.

  11. Structural adaptation of tooth enamel protein amelogenin in the presence of SDS micelles.

    Science.gov (United States)

    Chandrababu, Karthik Balakrishna; Dutta, Kaushik; Lokappa, Sowmya Bekshe; Ndao, Moise; Evans, John Spencer; Moradian-Oldak, Janet

    2014-05-01

    Amelogenin, the major extracellular matrix protein of developing tooth enamel is intrinsically disordered. Through its interaction with other proteins and mineral, amelogenin assists enamel biomineralization by controlling the formation of highly organized enamel crystal arrays. We used circular dichroism (CD), dynamic light scattering (DLS), fluorescence, and NMR spectroscopy to investigate the folding propensity of recombinant porcine amelogenin rP172 following its interaction with SDS, at levels above critical micelle concentration. The rP172-SDS complex formation was confirmed by DLS, while an increase in the structure moiety of rP172 was noted through CD and fluorescence experiments. Fluorescence quenching analyses performed on several rP172 mutants where all but one Trp was replaced by Tyr at different sequence regions confirmed that the interaction of amelogenin with SDS micelles occurs via the N-terminal region close to Trp25 where helical segments can be detected by NMR. NMR spectroscopy and structural refinement calculations using CS-Rosetta modeling confirm that the highly conserved N-terminal domain is prone to form helical structure when bound to SDS micelles. Our findings reported here reveal interactions leading to significant changes in the secondary structure of rP172 upon treatment with SDS. These interactions may reflect the physiological relevance of the flexible nature of amelogenin and its sequence specific helical propensity that might enable it to structurally adapt with charged and potential targets such as cell surface, mineral, and other proteins during enamel biomineralization. Copyright © 2013 Wiley Periodicals, Inc.

  12. Laboratory adaptation of Bactrocera tryoni (Diptera: Tephritidae) decreases mating age and increases protein consumption and number of eggs produced per milligram of protein.

    Science.gov (United States)

    Meats, A; Holmes, H M; Kelly, G L

    2004-12-01

    A significant reduction in age of mating occurred during the first four generations (G1-G4) of laboratory adaptation of wild Bactrocera tryoni (Froggatt) and this was associated with the earlier attainment of peak egg load although no significant differences were detected in the peak egg load itself. A long term laboratory (LTL) strain had a significantly earlier mating age and higher peak egg load than flies of wild origin or those from the first four laboratory generations. The amount of protein consumed by females in the first week of adult life was significantly higher in the LTL strain than in flies of wild origin or G1-G4 but there were no significant changes (or only slight changes) with laboratory adaptation in the amounts of protein consumed up to the ages of mating and peak egg load. Laboratory adaptation resulted in no significant changes in egg size, egg dry weight, puparial fresh weight and the dry weight of newly emerged females. The large increase in fecundity with laboratory adaptation is associated with a 4- to 5-fold increase in the rate of conversion of dietary protein to eggs (i.e. eggs produced per mg of protein consumed).

  13. Adaptive Assembly: Maximizing the Potential of a Given Functional Peptide with a Tailor-Made Protein Scaffold.

    Science.gov (United States)

    Watanabe, Hideki; Honda, Shinya

    2015-09-17

    Protein engineering that exploits known functional peptides holds great promise for generating novel functional proteins. Here we propose a combinatorial approach, termed adaptive assembly, which provides a tailor-made protein scaffold for a given functional peptide. A combinatorial library was designed to create a tailor-made scaffold, which was generated from β hairpins derived from a 10-residue minimal protein "chignolin" and randomized amino acid sequences. We applied adaptive assembly to a peptide with low affinity for the Fc region of human immunoglobulin G, generating a 54-residue protein AF.p17 with a 40,600-fold enhanced affinity. The crystal structure of AF.p17 complexed with the Fc region revealed that the scaffold fixed the active conformation with a unique structure composed of a short α helix, β hairpins, and a loop-like structure. Adaptive assembly can take full advantage of known peptides as assets for generating novel functional proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Pseudomonas aeruginosa Cell Membrane Protein Expression from Phenotypically Diverse Cystic Fibrosis Isolates Demonstrates Host-Specific Adaptations.

    Science.gov (United States)

    Kamath, Karthik Shantharam; Pascovici, Dana; Penesyan, Anahit; Goel, Apurv; Venkatakrishnan, Vignesh; Paulsen, Ian T; Packer, Nicolle H; Molloy, Mark P

    2016-07-01

    Pseudomonas aeruginosa is a Gram-negative, nosocomial, highly adaptable opportunistic pathogen especially prevalent in immuno-compromised cystic fibrosis (CF) patients. The bacterial cell surface proteins are important contributors to virulence, yet the membrane subproteomes of phenotypically diverse P. aeruginosa strains are poorly characterized. We carried out mass spectrometry (MS)-based proteome analysis of the membrane proteins of three novel P. aeruginosa strains isolated from the sputum of CF patients and compared protein expression to the widely used laboratory strain, PAO1. Microbes were grown in planktonic growth condition using minimal M9 media, and a defined synthetic lung nutrient mimicking medium (SCFM) limited passaging. Two-dimensional LC-MS/MS using iTRAQ labeling enabled quantitative comparisons among 3171 and 2442 proteins from the minimal M9 medium and in the SCFM, respectively. The CF isolates showed marked differences in membrane protein expression in comparison with PAO1 including up-regulation of drug resistance proteins (MexY, MexB, MexC) and down-regulation of chemotaxis and aerotaxis proteins (PA1561, PctA, PctB) and motility and adhesion proteins (FliK, FlgE, FliD, PilJ). Phenotypic analysis using adhesion, motility, and drug susceptibility assays confirmed the proteomics findings. These results provide evidence of host-specific microevolution of P. aeruginosa in the CF lung and shed light on the adaptation strategies used by CF pathogens.

  15. Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis).

    Science.gov (United States)

    Saarman, Norah P; Kober, Kord M; Simison, W Brian; Pogson, Grant H

    2017-10-01

    Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M. trossulus. Such thermal adaptations might help to explain, mechanistically, the success with which the invasive marine mussel M. galloprovincialis has displaced native species in contact zones in the eastern (California) and western (Japan) Pacific. We tested for stabilizing amino acid substitutions in warm tolerant M. galloprovincialis relative to cold tolerant M. trossulus with a generalized linear model that compares in silico estimates of recent changes in protein stability among closely related congeners. Fixed substitutions in M. galloprovincialis were 3,180.0 calories per mol per substitution more stabilizing at genes with both elevated dN/dS ratios and transcriptional responses to heat stress, and 705.8 calories per mol per substitution more stabilizing across all 2,770 loci investigated. Amino acid substitutions concentrated in a small number of genes were more stabilizing in M. galloprovincialis compared with cold tolerant M. trossulus. We also tested for, but did not find, enrichment of a priori GO terms in genes with elevated dN/dS ratios in M. galloprovincialis. This might indicate that selection for thermodynamic stability is generic across all lineages, and suggests that the high change in estimated protein stability that we observed in M. galloprovincialis is driven by selection for extra stabilizing substitutions, rather than by higher incidence of selection in a greater number of genes in this lineage

  16. Electrochemical Characterization of Escherichia coli Adaptive Response Protein AidB

    Directory of Open Access Journals (Sweden)

    Sean J. Elliott

    2012-12-01

    Full Text Available When exposed to known DNA-damaging alkylating agents, Escherichia coli cells increase production of four DNA repair enzymes: Ada, AlkA, AlkB, and AidB. The role of three enzymes (Ada, AlkA, and AlkB in repairing DNA lesions has been well characterized, while the function of AidB is poorly understood. AidB has a distinct cofactor that is potentially related to the elusive role of AidB in adaptive response: a redox active flavin adenine dinucleotide (FAD. In this study, we report the thermodynamic redox properties of the AidB flavin for the first time, both for free protein and in the presence of potential substrates. We find that the midpoint reduction potential of the AidB flavin is within a biologically relevant window for redox chemistry at −181 mV, that AidB significantly stabilizes the flavin semiquinone, and that small molecule binding perturbs the observed reduction potential. Our electrochemical results combined with structural analysis allow for fresh comparisons between AidB and the homologous acyl-coenzyme A dehydrogenase (ACAD family of enzymes. AidB exhibits several discrepancies from ACADs that suggest a novel catalytic mechanism distinct from that of the ACAD family enzymes.

  17. Cth2 Protein Mediates Early Adaptation of Yeast Cells to Oxidative Stress Conditions.

    Directory of Open Access Journals (Sweden)

    Laia Castells-Roca

    Full Text Available Cth2 is an mRNA-binding protein that participates in remodeling yeast cell metabolism in iron starvation conditions by promoting decay of the targeted molecules, in order to avoid excess iron consumption. This study shows that in the absence of Cth2 immediate upregulation of expression of several of the iron regulon genes (involved in high affinity iron uptake and intracellular iron redistribution upon oxidative stress by hydroperoxide is more intense than in wild type conditions where Cth2 is present. The oxidative stress provokes a temporary increase in the levels of Cth2 (itself a member of the iron regulon. In such conditions Cth2 molecules accumulate at P bodies-like structures when the constitutive mRNA decay machinery is compromised. In addition, a null Δcth2 mutant shows defects, in comparison to CTH2 wild type cells, in exit from α factor-induced arrest at the G1 stage of the cell cycle when hydroperoxide treatment is applied. The cell cycle defects are rescued in conditions that compromise uptake of external iron into the cytosol. The observations support a role of Cth2 in modulating expression of diverse iron regulon genes, excluding those specifically involved in the reductive branch of the high-affinity transport. This would result in immediate adaptation of the yeast cells to an oxidative stress, by controlling uptake of oxidant-promoting iron cations.

  18. Efficient expression of codon-adapted affinity tagged super folder green fluorescent protein for synchronous protein localization and affinity purification studies in Tetrahymena thermophila.

    Science.gov (United States)

    Yilmaz, Gürkan; Arslanyolu, Muhittin

    2015-03-25

    A superior Green Fluorescent Protein (GFP) mutant, known as superfolder GFP (sfGFP), is more soluble, faster folding, and is the brightest of the known GFP mutants. This study aimed to create a codon-adapted sfGFP tag (TtsfGFP) for simultaneous protein localization and affinity purification in Tetrahymena thermophila. In vivo fluorescence spectroscopic analyses of clones carrying a codon-adapted and 6 × His tagged TtsfGFP cassette showed approximately 2-4-fold increased fluorescence emission compared with the control groups at 3 h. Fluorescence microscopy also revealed that TtsfGFP reached its emission maxima at 100 min, which was much earlier than controls expressing EGFP and sfGFP (240 min). A T. thermophila ATP-dependent DNA ligase domain containing hypothetical gene (H) was cloned into the 3' end of 6 × His-TtsfGFP to assess the affinity/localization dual tag feature. Fluorescence microscopy of the 6 × His-TtsfGFP-H clone confirmed its localization in the macro- and micronucleus of vegetative T. thermophila. Simultaneous affinity purification of TtsfGFP and TtsfGFP-H with Ni-NTA beads was feasible, as shown by Ni-NTA purified proteins analysis by SDS-PAGE and western blotting. We successfully codon adapted the N-terminal 6 × His-TtsfGFP tag and showed that it could be used for protein localization and affinity purification simultaneously in T. thermophila. We believe that this dual tag will advance T. thermophila studies by providing strong visual traceability of the target protein in vivo and in vitro during recombinant production of heterologous and homologous proteins.

  19. 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.

  20. 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.

  1. Protein translocation across the endoplasmic reticulum membrane in cold-adapted organisms

    NARCIS (Netherlands)

    Römisch, Karin; Collie, Nicola; Soto, Nelyn; Logue, James; Lindsay, Margaret; Scheper, Wiep; Cheng, Chi-Hing C.

    2003-01-01

    Secretory proteins enter the secretory pathway by translocation across the membrane of the endoplasmic reticulum (ER) via a channel formed primarily by the Sec61 protein. Protein translocation is highly temperature dependent in mesophilic organisms. We asked whether the protein translocation

  2. The histone-like protein HU has a role in gene expression during the acid adaptation response in Helicobacter pylori.

    Science.gov (United States)

    Álvarez, Alhejandra; Toledo, Héctor

    2017-08-01

    Gastritis, ulcers, and gastric malignancy have been linked to human gastric epithelial colonization by Helicobacter pylori. Characterization of the mechanisms by which H. pylori adapts to the human stomach environment is of crucial importance to understand H. pylori pathogenesis. In an effort to extend our knowledge of these mechanisms, we used proteomic analysis and qRT-PCR to characterize the role of the histone-like protein HU in the response of H. pylori to low pH. Proteomic analysis revealed that genes involved in chemotaxis, oxidative stress, or metabolism are under control of the HU protein. Also, expression of the virulence factors Ggt and NapA is affected by the null mutation of hup gene both at neutral and acid pH, as evidenced by qRT-PCR analysis. Those results showed that H. pylori gene expression is altered by shift to low pH, thus confirming that acid exposure leads to profound changes in genomic expression, and suggest that the HU protein is a regulator that may help the bacterium adapt to the acid stress. In accordance with previous reports, we found that the HU protein participates in gene expression regulation when the microorganism is exposed to acid stress. Such transcriptional regulation underlies protein accumulation in the H. pylori cell. © 2017 John Wiley & Sons Ltd.

  3. 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

    SUMMARY Human skeletal muscle has a remarkable capability of adapting to a change in demands. The preservation of this adaptability relies partly on a pool of resident myogenic stem cells (satellite cells, SCs). Extrinsic factors such as mechanical load (e.g. resistance exercise) and dietary...... recovery from eccentric exercise In paper I, we evaluated the effect of a single bout of unaccustomed eccentric exercise on fiber type specific SC content by immunohistochemistry. Subjects received either hydrolysed whey protein (Whey) or iso-caloric carbohydrate (Placebo) in the days post eccentric...... the effect of contraction mode specific resistance training and protein supplementation on whole muscle and tendon hypertrophy. Quadriceps muscle and patellar tendon cross-sectional area (CSA) was quantified using magnetic resonance imaging pre and post 12 weeks of eccentric (Ecc) or concentric (Conc...

  4. Effects of heat, cold, acid and bile salt adaptations on the stress tolerance and protein expression of kefir-isolated probiotic Lactobacillus kefiranofaciens M1.

    Science.gov (United States)

    Chen, Ming-Ju; Tang, Hsin-Yu; Chiang, Ming-Lun

    2017-09-01

    Lactobacillus kefiranofaciens M1 is a probiotic strain isolated from Taiwanese kefir grains. The present study evaluated the effects of heat, cold, acid and bile salt adaptations on the stress tolerance of L. kefiranofaciens M1. The regulation of protein expression of L. kefiranofaciens M1 under these adaptation conditions was also investigated. The results showed that adaptation of L. kefiranofaciens M1 to heat, cold, acid and bile salts induced homologous tolerance and cross-protection against heterologous challenge. The extent of induced tolerance varied depending on the type and condition of stress. Proteomic analysis revealed that 27 proteins exhibited differences in expression between non-adapted and stress-adapted L. kefiranofaciens M1 cells. Among these proteins, three proteins involved in carbohydrate metabolism (triosephosphate isomerase, enolase and NAD-dependent glycerol-3-phosphate dehydrogenase), two proteins involved in pH homeostasis (ATP synthase subunits AtpA and AtpB), two stress response proteins (chaperones DnaK and GroEL) and one translation-related protein (30S ribosomal protein S2) were up-regulated by three of the four adaptation treatments examined. The increased synthesis of these stress proteins might play a critical protective role in the cellular defense against heat, cold, acid and bile salt stresses. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    OpenAIRE

    Jansen, Gert; Weinkove, David; Plasterk, Ronald H.A.

    2002-01-01

    Caenorhabditis elegans has two heterotrimeric G-protein γ 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 developed a water soluble compound adaptation assay. The behaviour of wild-type animals in this assay confirms that prolonged exposure to salts can abolish chemo-attraction to these compounds. This process is time and concentration...

  6. 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.

  7. Differential compartmentalization of Streptococcus pyogenes virulence factors and host protein binding properties as a mechanism for host adaptation.

    Science.gov (United States)

    Kilsgård, Ola; Karlsson, Christofer; Malmström, Erik; Malmström, Johan

    2016-11-01

    Streptococcus pyogenes is an important human pathogen responsible for substantial morbidity and mortality worldwide. Although S. pyogenes is a strictly human pathogen with no other known animal reservoir, several murine infection models exist to explore different aspects of the bacterial pathogenesis. Inoculating mice with wild-type S. pyogenes strains can result in the generation of new bacterial phenotypes that are hypervirulent compared to the original inoculum. In this study, we used a serial mass spectrometry based proteomics strategy to investigate if these hypervirulent strains have an altered distribution of virulence proteins across the intracellular, surface associated and secreted bacterial compartments and if any change in compartmentalization can alter the protein-protein interaction network between bacteria and host proteins. Quantitative analysis of the S. pyogenes surface and secreted proteomes revealed that animal passaged strains are associated with significantly higher amount of virulence factors on the bacterial surface and in the media. This altered virulence factor compartmentalization results in increased binding of several mouse plasma proteins to the bacterial surface, a trend that was consistent for mouse plasma from several different mouse strains. In general, both the wild-type strain and animal passaged strain were capable of binding high amounts of human plasma proteins. However, compared to the non-passaged strains, the animal passaged strains displayed an increased ability to bind mouse plasma proteins, in particular for M protein binders, indicating that the increased affinity for mouse blood plasma proteins is a consequence of host adaptation of this pathogen to a new host. In conclusion, plotting the total amount of virulence factors against the total amount of plasma proteins associated to the bacterial surface could clearly separate out animal passaged strains from wild type strains indicating a virulence model that could

  8. A Comparative Pan-Genome Perspective of Niche-Adaptable Cell-Surface Protein Phenotypes in Lactobacillus rhamnosus

    Science.gov (United States)

    Kant, Ravi; Sigvart-Mattila, Pia; Paulin, Lars; Mecklin, Jukka-Pekka; Saarela, Maria; Palva, Airi; von Ossowski, Ingemar

    2014-01-01

    Lactobacillus rhamnosus is a ubiquitously adaptable Gram-positive bacterium and as a typical commensal can be recovered from various microbe-accessible bodily orifices and cavities. Then again, other isolates are food-borne, with some of these having been long associated with naturally fermented cheeses and yogurts. Additionally, because of perceived health benefits to humans and animals, numerous L. rhamnosus strains have been selected for use as so-called probiotics and are often taken in the form of dietary supplements and functional foods. At the genome level, it is anticipated that certain genetic variances will have provided the niche-related phenotypes that augment the flexible adaptiveness of this species, thus enabling its strains to grow and survive in their respective host environments. For this present study, we considered it functionally informative to examine and catalogue the genotype-phenotype variation existing at the cell surface between different L. rhamnosus strains, with the presumption that this might be relatable to habitat preferences and ecological adaptability. Here, we conducted a pan-genomic study involving 13 genomes from L. rhamnosus isolates with various origins. In using a benchmark strain (gut-adapted L. rhamnosus GG) for our pan-genome comparison, we had focused our efforts on a detailed examination and description of gene products for certain functionally relevant surface-exposed proteins, each of which in effect might also play a part in niche adaptability among the other strains. Perhaps most significantly of the surface protein loci we had analyzed, it would appear that the spaCBA operon (known to encode SpaCBA-called pili having a mucoadhesive phenotype) is a genomic rarity and an uncommon occurrence in L. rhamnosus. However, for any of the so-piliated L. rhamnosus strains, they will likely possess an increased niche-specific fitness, which functionally might presumably be manifested by a protracted transient colonization of

  9. A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus.

    Directory of Open Access Journals (Sweden)

    Ravi Kant

    Full Text Available Lactobacillus rhamnosus is a ubiquitously adaptable Gram-positive bacterium and as a typical commensal can be recovered from various microbe-accessible bodily orifices and cavities. Then again, other isolates are food-borne, with some of these having been long associated with naturally fermented cheeses and yogurts. Additionally, because of perceived health benefits to humans and animals, numerous L. rhamnosus strains have been selected for use as so-called probiotics and are often taken in the form of dietary supplements and functional foods. At the genome level, it is anticipated that certain genetic variances will have provided the niche-related phenotypes that augment the flexible adaptiveness of this species, thus enabling its strains to grow and survive in their respective host environments. For this present study, we considered it functionally informative to examine and catalogue the genotype-phenotype variation existing at the cell surface between different L. rhamnosus strains, with the presumption that this might be relatable to habitat preferences and ecological adaptability. Here, we conducted a pan-genomic study involving 13 genomes from L. rhamnosus isolates with various origins. In using a benchmark strain (gut-adapted L. rhamnosus GG for our pan-genome comparison, we had focused our efforts on a detailed examination and description of gene products for certain functionally relevant surface-exposed proteins, each of which in effect might also play a part in niche adaptability among the other strains. Perhaps most significantly of the surface protein loci we had analyzed, it would appear that the spaCBA operon (known to encode SpaCBA-called pili having a mucoadhesive phenotype is a genomic rarity and an uncommon occurrence in L. rhamnosus. However, for any of the so-piliated L. rhamnosus strains, they will likely possess an increased niche-specific fitness, which functionally might presumably be manifested by a protracted transient

  10. A dynamic and adaptive network of cytosolic interactions governs protein export by the T3SS injectisome.

    Science.gov (United States)

    Diepold, Andreas; Sezgin, Erdinc; Huseyin, Miles; Mortimer, Thomas; Eggeling, Christian; Armitage, Judith P

    2017-06-27

    Many bacteria use a type III secretion system (T3SS) to inject effector proteins into host cells. Selection and export of the effectors is controlled by a set of soluble proteins at the cytosolic interface of the membrane spanning type III secretion 'injectisome'. Combining fluorescence microscopy, biochemical interaction studies and fluorescence correlation spectroscopy, we show that in live Yersinia enterocolitica bacteria these soluble proteins form complexes both at the injectisome and in the cytosol. Binding to the injectisome stabilizes these cytosolic complexes, whereas the free cytosolic complexes, which include the type III secretion ATPase, constitute a highly dynamic and adaptive network. The extracellular calcium concentration, which triggers activation of the T3SS, directly influences the cytosolic complexes, possibly through the essential component SctK/YscK, revealing a potential mechanism involved in the regulation of type III secretion.

  11. 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.

  12. Proteins associated with adaptation of cultured tobacco cells to NaCl

    International Nuclear Information System (INIS)

    Singh, N.K.; Handa, A.K.; Hasegawa, P.M.; Bressan, R.A.

    1985-01-01

    Cultured tobacco cells (Nicotiana tabacum L. cv Wisconsin 38) adapted to grow in medium containing high levels of NaCl or polyethylene glycol (PEG) produce several new or enhanced polypeptide bands on sodium dodecyl sulfate-polyarylamide gel electrophoresis. The intensities of some of the polypeptide bands increase with increasing levels of NaCl adaptation, while the intensities of other polypeptide bands are reduced. Synthesis of 26-kilodalton polypeptide(s) occurs at two different periods during culture growth of NaCl adapted cells. Unadapted cells also incorporate 35 S into a 26-kilodalton polypeptide during the later stage of culture growth beginning at midlog phase. The 26-kilodalton polypeptides from adapted and unadapted cells have similar partial proteolysis peptide maps and are immunologically cross-reactive. During adaptation to NaCl, unadapted cells synthesize and accumulate a major 26-kilodalton polypeptide, and the beginning of synthesis corresponds to the period of osmotic adjustment and culture growth. From their results, the authors suggest an involvement of the 26-kilodalton polypeptide in the adaptation of cultured tobacco cells to NaCl and water stress. 38 references, 11 figures, 2 tables

  13. Intra-plastid protein trafficking: How plant cells adapted prokaryotic mechanisms to the eukaryotic condition

    OpenAIRE

    Celedon, Jose M.; Cline, Kenneth

    2013-01-01

    Protein trafficking and localization in plastids involves a complex interplay between ancient (prokaryotic) and novel (eukaryotic) translocases and targeting machineries. During evolution, ancient systems acquired new functions and novel translocation machineries were developed to facilitate the correct localization of nuclear encoded proteins targeted to the chloroplast. Because of its post-translational nature, targeting and integration of membrane proteins posed the biggest challenge to th...

  14. AptRank: an adaptive PageRank model for protein function prediction on   bi-relational graphs.

    Science.gov (United States)

    Jiang, Biaobin; Kloster, Kyle; Gleich, David F; Gribskov, Michael

    2017-06-15

    Diffusion-based network models are widely used for protein function prediction using protein network data and have been shown to outperform neighborhood-based and module-based methods. Recent studies have shown that integrating the hierarchical structure of the Gene Ontology (GO) data dramatically improves prediction accuracy. However, previous methods usually either used the GO hierarchy to refine the prediction results of multiple classifiers, or flattened the hierarchy into a function-function similarity kernel. No study has taken the GO hierarchy into account together with the protein network as a two-layer network model. We first construct a Bi-relational graph (Birg) model comprised of both protein-protein association and function-function hierarchical networks. We then propose two diffusion-based methods, BirgRank and AptRank, both of which use PageRank to diffuse information on this two-layer graph model. BirgRank is a direct application of traditional PageRank with fixed decay parameters. In contrast, AptRank utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. We evaluate the ability of both methods to predict protein function on yeast, fly and human protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design four different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly discovered function prediction to comprehensively evaluate predictability of all six methods. We find that both BirgRank and AptRank outperform the previous methods, especially in missing function prediction when using only 10% of the data for training. The MATLAB code is available at https://github.rcac.purdue.edu/mgribsko/aptrank . gribskov@purdue.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  15. Signal regulatory protein alpha (SIRPalpha cells in the adaptive response to ESAT-6/CFP-10 protein of tuberculous mycobacteria.

    Directory of Open Access Journals (Sweden)

    W Ray Waters

    2009-07-01

    Full Text Available Early secretory antigenic target-6 (ESAT-6 and culture filtrate protein-10 (CFP-10 are co-secreted proteins of Mycobacterium tuberculosis complex mycobacteria (includes M. bovis, the zoonotic agent of bovine tuberculosis involved in phagolysosome escape of the bacillus and, potentially, in the efficient induction of granulomas. Upon tuberculosis infection, multi-nucleate giant cells are elicited, likely as a response aimed at containing mycobacteria. In tissue culture models, signal regulatory protein (SIRPalpha (also referred to as macrophage fusion receptor or CD172a is essential for multi-nucleate giant cell formation.In the present study, ESAT-6/CFP-10 complex and SIRPalpha interactions were evaluated with samples obtained from calves experimentally infected with M. bovis. Peripheral blood CD172a(+ (SIRPalpha-expressing cells from M. bovis-infected calves proliferated upon in vitro stimulation with ESAT-6/CFP-10 (either as a fusion protein or a peptide cocktail, but not with cells from animals receiving M. bovis strains lacking ESAT-6/CFP-10 (i.e, M. bovis BCG or M. bovis DeltaRD1. Sorted CD172a(+ cells from these cultures had a dendritic cell/macrophage morphology, bound fluorescently-tagged rESAT-6:CFP-10, bound and phagocytosed live M. bovis BCG, and co-expressed CD11c, DEC-205, CD44, MHC II, CD80/86 (a subset also co-expressed CD11b or CD8alpha. Intradermal administration of rESAT-6:CFP-10 into tuberculous calves elicited a delayed type hypersensitive response consisting of CD11c(+, CD172a(+, and CD3(+ cells, including CD172a-expressing multi-nucleated giant cells.These findings demonstrate the ability of ESAT-6/CFP-10 to specifically expand CD172a(+ cells, bind to CD172a(+ cells, and induce multi-nucleated giant cells expressing CD172a.

  16. Protein evaluation of four oat (Avena sativa L.) cultivars adapted for cultivation in the south of Brazil.

    Science.gov (United States)

    Pedó, I; Sgarbieri, V C; Gutkoski, L C

    1999-01-01

    Four oat cultivars adapted for soil and climate conditions in the southern region of Brazil were evaluated for protein nutritive value. Evaluations were done both in vitro and in vivo. In vitro evaluation was done by essential amino acid profile, available lysine, amino acid scoring, and protein digestibility corrected amino acid-scoring (PDCAAS). Nitrogen balance indices and PER were determined in vivo with rats. In all four cultivars (UFP-15, UFP-16, CTC-03, UFRGS-14), lysine was the most limiting amino acid. Available lysine, amino acid score and PDCAAS were highest for cultivar UFRGS-14 and lowest for CTC-03. When compared to casein, only nitrogen retention for UFRGS-14 did not differ statistically (p>0.05); all other indices of protein quality were inferior to casein for the oat cultivars. The oat cultivars tended to be identical among themselves, except for apparent protein digestibility which was significantly higher in the UFRGS-14 and CTC-03 cultivars. On average, the PER values of the oat cultivars were 82% of casein; the net protein utilization was 88% of casein as determined in vivo and 49% by the estimation in vitro (PDCAAS).

  17. Involvement of skeletal muscle protein, glycogen, and fat metabolism in the adaptation on early lactation of dairy cows.

    Science.gov (United States)

    Kuhla, Björn; Nürnberg, Gerd; Albrecht, Dirk; Görs, Solvig; Hammon, Harald M; Metges, Cornelia C

    2011-09-02

    During early lactation, high-yielding dairy cows cannot consume enough feed to meet nutrient requirements. As a consequence, animals drop into negative energy balance and mobilize body reserves including muscle protein and glycogen for milk production, direct oxidation, and hepatic gluconeogenesis. To examine which muscle metabolic processes contribute to the adaptation during early lactation, six German Holstein cows were blood sampled and muscle biopsied throughout the periparturient period. From pregnancy to lactation, the free plasma amino acid pattern imbalanced and plasma glucose decreased. Several muscle amino acids, as well as total muscle protein, fat, and glycogen, and the expression of glucose transporter-4 were reduced within the first 4 weeks of lactation. The 2-DE and MALDI-TOF-MS analysis identified 43 differentially expressed muscle protein spots throughout the periparturient period. In early lactation, expression of cytoskeletal proteins and enzymes involved in glycogen synthesis and in the TCA cycle was decreased, whereas proteins related to glycolysis, fatty acid degradation, lactate, and ATP production were increased. On the basis of these results, we propose a model in which the muscle breakdown in early lactation provides substrates for milk production by a decoupled Cori cycle favoring hepatic gluconeogenesis and by interfering with feed intake signaling.

  18. Amino acid substitutions in cold-adapted proteins from Halorubrum lacusprofundi, an extremely halophilic microbe from antarctica.

    Directory of Open Access Journals (Sweden)

    Shiladitya Dassarma

    Full Text Available The halophilic Archaeon Halorubrum lacusprofundi, isolated from the perennially cold and hypersaline Deep Lake in Antarctica, was recently sequenced and compared to 12 Haloarchaea from temperate climates by comparative genomics. Amino acid substitutions for 604 H. lacusprofundi proteins belonging to conserved haloarchaeal orthologous groups (cHOGs were determined and found to occur at 7.85% of positions invariant in proteins from mesophilic Haloarchaea. The following substitutions were observed most frequently: (a glutamic acid with aspartic acid or alanine; (b small polar residues with other small polar or non-polar amino acids; (c small non-polar residues with other small non-polar residues; (d aromatic residues, especially tryptophan, with other aromatic residues; and (e some larger polar residues with other similar residues. Amino acid substitutions for a cold-active H. lacusprofundi β-galactosidase were then examined in the context of a homology modeled structure at residues invariant in homologous enzymes from mesophilic Haloarchaea. Similar substitutions were observed as in the genome-wide approach, with the surface accessible regions of β-galactosidase displaying reduced acidity and increased hydrophobicity, and internal regions displaying mainly subtle changes among smaller non-polar and polar residues. These findings are consistent with H. lacusprofundi proteins displaying amino acid substitutions that increase structural flexibility and protein function at low temperature. We discuss the likely mechanisms of protein adaptation to a cold, hypersaline environment on Earth, with possible relevance to life elsewhere.

  19. Reversal of charge selectivity in transmembrane protein pores by using noncovalent molecular adapters

    Science.gov (United States)

    Gu, Li-Qun; Dalla Serra, Mauro; Vincent, J. Bryan; Vigh, Gyula; Cheley, Stephen; Braha, Orit; Bayley, Hagan

    2000-01-01

    In this study, the charge selectivity of staphylococcal α-hemolysin (αHL), a bacterial pore-forming toxin, is manipulated by using cyclodextrins as noncovalent molecular adapters. Anion-selective versions of αHL, including the wild-type pore and various mutants, become more anion selective when β-cyclodextrin (βCD) is lodged within the channel lumen. By contrast, the negatively charged adapter, hepta-6-sulfato-β-cyclodextrin (s7βCD), produces cation selectivity. The cyclodextrin adapters have similar effects when placed in cation-selective mutant αHL pores. Most probably, hydrated Cl− ions partition into the central cavity of βCD more readily than K+ ions, whereas s7βCD introduces a charged ring near the midpoint of the channel lumen and confers cation selectivity through electrostatic interactions. The molecular adapters generate permeability ratios (PK+/PCl−) over a 200-fold range and should be useful in the de novo design of membrane channels both for basic studies of ion permeation and for applications in biotechnology. PMID:10760267

  20. Chromosome locations of genes encoding human signal transduction adapter proteins, Nck (NCK), Shc (SHC1), and Grb2 (GRB2)

    DEFF Research Database (Denmark)

    Huebner, K; Kastury, K; Druck, T

    1994-01-01

    Abnormalities due to chromosomal aberration or point mutation in gene products of growth factor receptors or in ras gene products, which lie on the same signaling pathway, can cause disease in animals and humans. Thus, it can be important to determine chromosomal map positions of genes encoding...... "adapter" proteins, which are involved in transducing signals from receptor tyrosine kinases to downstream signal recipients such as ras, because adaptor protein genes could also, logically, serve as targets of mutation, rearrangement, or other aberration in disease. Therefore, DNAs from panels of rodent...... hybridization. The NCK locus is at chromosome region 3q21, a region involved in neoplasia-associated changes; the SHC cognate locus, SHC1, is at 1q21, and the GRB2 locus is at 17q22-qter telomeric to the HOXB and NGFR loci. Both SHC1 and GRB2 are in chromosome regions that may be duplicated in some tumor types....

  1. Redox stress proteins are involved in adaptation response of the hyperthermoacidophilic archaeon Sulfolobus solfataricus to nickel challenge

    Directory of Open Access Journals (Sweden)

    Scaloni Andrea

    2007-08-01

    Full Text Available Abstract Background Exposure to nickel (Ni and its chemical derivatives has been associated with severe health effects in human. On the contrary, poor knowledge has been acquired on target physiological processes or molecular mechanisms of this metal in model organisms, including Bacteria and Archaea. In this study, we describe an analysis focused at identifying proteins involved in the recovery of the archaeon Sulfolobus solfataricus strain MT4 from Ni-induced stress. Results To this purpose, Sulfolobus solfataricus was grown in the presence of the highest nickel sulphate concentration still allowing cells to survive; crude extracts from treated and untreated cells were compared at the proteome level by using a bi-dimensional chromatography approach. We identified several proteins specifically repressed or induced as result of Ni treatment. Observed up-regulated proteins were largely endowed with the ability to trigger recovery from oxidative and osmotic stress in other biological systems. It is noteworthy that most of the proteins induced following Ni treatment perform similar functions and a few have eukaryal homologue counterparts. Conclusion These findings suggest a series of preferential gene expression pathways activated in adaptation response to metal challenge.

  2. Accumulation of small heat shock proteins, including mitochondrial HSP22, induced by oxidative stress and adaptive response in tomato cells

    International Nuclear Information System (INIS)

    Banzet, N.; Richaud, C.; Deveaux, Y.; Kazmaier, M.; Gagnon, J.; Triantaphylides, C.

    1998-01-01

    Changes in gene expression, by application of H2O2, O2.- generating agents (methyl viologen, digitonin) and gamma irradiation to tomato suspension cultures, were investigated and compared to the well-described heat shock response. Two-dimensional gel protein mapping analyses gave the first indication that at least small heat shock proteins (smHSP) accumulated in response to application of H2O2 and gamma irradiation, but not to O2.- generating agents. While some proteins seemed to be induced specifically by each treatment, only part of the heat shock response was observed. On the basis of Northern hybridization experiments performed with four heterologous cDNA, corresponding to classes I-IV of pea smHSP, it could be concluded that significant amounts of class I and II smHSP mRNA are induced by H2O2 and by irradiation. Taken together, these results demonstrate that in plants some HSP genes are inducible by oxidative stresses, as in micro-organisms and other eukaryotic cells. HSP22, the main stress protein that accumulates following H2O2 action or gamma irradiation, was also purified. Sequence homology of amino terminal and internal sequences, and immunoreactivity with Chenopodium rubrum mitochondrial smHSP antibody, indicated that the protein belongs to the recently discovered class of plant mitochondrial smHSP. Heat shock or a mild H2O2 pretreatment was also shown to lead to plant cell protection against oxidative injury. Therefore, the synthesis of these stress proteins can be considered as an adaptive mechanism in which mitochondrial protection could be essential

  3. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

    Science.gov (United States)

    Haney, P. J.; Badger, J. H.; Buldak, G. L.; Reich, C. I.; Woese, C. R.; Olsen, G. J.

    1999-01-01

    The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P < 0.01) preferred direction of replacement.

  4. 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......High altitude hypoxia is a paraphysiological condition triggering redox status disturbances of cell organization leading, via oxidative stress, to proteins, lipids, and DNA damage. In man, skeletal muscle, after prolonged exposure to hypoxia, undergoes mass reduction and alterations at the cellular...... level featuring a reduction of mitochondrial volume density, accumulation of lipofuscin, a product of lipid peroxidation, and dysregulation of enzymes whose time course is unknown. The effects of 7-9 days exposure to 4559 m (Margherita Hut, Monte Rosa, Italy) on the muscle proteins pattern were...

  5. 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

    level featuring a reduction of mitochondrial volume density, accumulation of lipofuscin, a product of lipid peroxidation, and dysregulation of enzymes whose time course is unknown. The effects of 7-9 days exposure to 4559 m (Margherita Hut, Monte Rosa, Italy) on the muscle proteins pattern were...... 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...

  6. Effect of adaptation to ethanol on cytoplasmic and membrane protein profiles of Oenococcus oeni

    NARCIS (Netherlands)

    Silveira, da M.G.; Baumgärtner, M.; Rombouts, F.M.; Abee, T.

    2004-01-01

    The practical application of commercial malolactic starter cultures of Oenococcus oeni surviving direct inoculation in wine requires insight into mechanisms of ethanol toxicity and of acquired ethanol tolerance in this organism. Therefore, the site-specific location of proteins involved in ethanol

  7. Pre- versus post-exercise protein intake has similar effects on muscular adaptations

    Directory of Open Access Journals (Sweden)

    Brad Jon Schoenfeld

    2017-01-01

    Full Text Available The purpose of this study was to test the anabolic window theory by investigating muscle strength, hypertrophy, and body composition changes in response to an equal dose of protein consumed either immediately pre- versus post-resistance training (RT in trained men. Subjects were 21 resistance-trained men (>1 year RT experience recruited from a university population. After baseline testing, participants were randomly assigned to 1 of 2 experimental groups: a group that consumed a supplement containing 25 g protein and 1 g carbohydrate immediately prior to exercise (PRE-SUPP (n = 9 or a group that consumed the same supplement immediately post-exercise (POST-SUPP (n = 12. The RT protocol consisted of three weekly sessions performed on non-consecutive days for 10 weeks. A total-body routine was employed with three sets of 8–12 repetitions for each exercise. Results showed that pre- and post-workout protein consumption had similar effects on all measures studied (p > 0.05. These findings refute the contention of a narrow post-exercise anabolic window to maximize the muscular response and instead lends support to the theory that the interval for protein intake may be as wide as several hours or perhaps more after a training bout depending on when the pre-workout meal was consumed.

  8. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes

    NARCIS (Netherlands)

    Kalodimos, Ch.; Biris, N.; Bonvin, A.M.J.J.; Levandoski, M.M.; Guennuegues, M.; Boelens, R.; Kaptein, R.

    2004-01-01

    Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding

  9. Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts

    Science.gov (United States)

    Yilmaz, Lutfu Safak; Atilgan, Ali Rana

    2000-09-01

    A low-resolution structural model based on the packing geometry of α-carbons is utilized to establish a connection between the flexible and rigid parts of a folded protein. The former commonly recognizes a complementing molecule for making a complex, while the latter manipulates the necessary conformational change for binding. We attempt analytically to distinguish this control architecture that intrinsically exists in globular proteins. First with two-dimensional simple models, then for a native protein, bovine pancreatic trypsin inhibitor, we explicitly demonstrate that inserting fluctuations in tertiary contacts supported by the stable core, one can regulate the displacement of residues on loop regions. The positional fluctuations of the flexible regions are annihilated by the rest of the protein in conformity with the Le Chatelier-Braun principle. The results indicate that the distortion of the principal nonbonded contacts between highly packed residues is accompanied by that of the slavery fluctuations that are widely distributed over the native structure. These positional arrangements do not appear in a reciprocal relation between a perturbation and the associated response; the effect of a movement of residue i on residue j is not equal to that of the same movement of residue j on residue i.

  10. Dancing to a Different Tune: Adaptive Evolution Fine-Tunes Protein Dynamics

    Science.gov (United States)

    2015-09-01

    Biosyst. 5, 207-216. [14] Fuentes , EJ, Gilmore, SA, Mauldin, RV, and Lee, AL. (2006) Evaluation of energetic and dynamic coupling networks in a PDZ...studies, including those by Fuentes et al.35 Fuentes et al., demonstrated that mutations in the PDZ (second postsynaptic density-95/discs large/zonula... Fuentes , EJ, Gilmore, SA, Mauldin, RV, and Lee, AL. (2006) Evaluation of energetic and dynamic coupling networks in a PDZ domain protein, J. Mol. Biol

  11. Adaptive local learning in sampling based motion planning for protein folding.

    Science.gov (United States)

    Ekenna, Chinwe; Thomas, Shawna; Amato, Nancy M

    2016-08-01

    Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms, such as Probabilistic Roadmap Methods, have been successful in modeling the folding landscape. Probabilistic Roadmap Methods and variants contain several phases (i.e., sampling, connection, and path extraction). Most of the time is spent in the connection phase and selecting which variant to employ is a difficult task. Global machine learning has been applied to the connection phase but is inefficient in situations with varying topology, such as those typical of folding landscapes. We develop a local learning algorithm that exploits the past performance of methods within the neighborhood of the current connection attempts as a basis for learning. It is sensitive not only to different types of landscapes but also to differing regions in the landscape itself, removing the need to explicitly partition the landscape. We perform experiments on 23 proteins of varying secondary structure makeup with 52-114 residues. We compare the success rate when using our methods and other methods. We demonstrate a clear need for learning (i.e., only learning methods were able to validate against all available experimental data) and show that local learning is superior to global learning producing, in many cases, significantly higher quality results than the other methods. We present an algorithm that uses local learning to select appropriate connection methods in the context of roadmap construction for protein folding. Our method removes the burden of deciding which method to use, leverages the strengths of the individual input methods, and it is extendable to include other future connection methods.

  12. Protein surface softness is the origin of enzyme cold-adaptation of trypsin.

    Directory of Open Access Journals (Sweden)

    Geir Villy Isaksen

    2014-08-01

    Full Text Available Life has effectively colonized most of our planet and extremophilic organisms require specialized enzymes to survive under harsh conditions. Cold-loving organisms (psychrophiles express heat-labile enzymes that possess a high specific activity and catalytic efficiency at low temperatures. A remarkable universal characteristic of cold-active enzymes is that they show a reduction both in activation enthalpy and entropy, compared to mesophilic orthologs, which makes their reaction rates less sensitive to falling temperature. Despite significant efforts since the early 1970s, the important question of the origin of this effect still largely remains unanswered. Here we use cold- and warm-active trypsins as model systems to investigate the temperature dependence of the reaction rates with extensive molecular dynamics free energy simulations. The calculations quantitatively reproduce the catalytic rates of the two enzymes and further yield high-precision Arrhenius plots, which show the characteristic trends in activation enthalpy and entropy. Detailed structural analysis indicates that the relationship between these parameters and the 3D structure is reflected by significantly different internal protein energy changes during the reaction. The origin of this effect is not localized to the active site, but is found in the outer regions of the protein, where the cold-active enzyme has a higher degree of softness. Several structural mechanisms for softening the protein surface are identified, together with key mutations responsible for this effect. Our simulations further show that single point-mutations can significantly affect the thermodynamic activation parameters, indicating how these can be optimized by evolution.

  13. Drosophila photoreceptor axon guidance and targeting requires the dreadlocks SH2/SH3 adapter protein.

    Science.gov (United States)

    Garrity, P A; Rao, Y; Salecker, I; McGlade, J; Pawson, T; Zipursky, S L

    1996-05-31

    Mutations in the Drosophila gene dreadlocks (dock) disrupt photoreceptor cell (R cell) axon guidance and targeting. Genetic mosaic analysis and cell-type-specific expression of dock transgenes demonstrate dock is required in R cells for proper innervation. Dock protein contains one SH2 and three SH3 domains, implicating it in tyrosine kinase signaling, and is highly related to the human proto-oncogene Nck. Dock expression is detected in R cell growth cones in the target region. We propose Dock transmits signals in the growth cone in response to guidance and targeting cues. These findings provide an important step for dissection of signaling pathways regulating growth cone motility.

  14. "Adapted Linear Interaction Energy": A Structure-Based LIE Parametrization for Fast Prediction of Protein-Ligand Affinities.

    Science.gov (United States)

    Linder, Mats; Ranganathan, Anirudh; Brinck, Tore

    2013-02-12

    We present a structure-based parametrization of the Linear Interaction Energy (LIE) method and show that it allows for the prediction of absolute protein-ligand binding energies. We call the new model "Adapted" LIE (ALIE) because the α and β coefficients are defined by system-dependent descriptors and do therefore not require any empirical γ term. The best formulation attains a mean average deviation of 1.8 kcal/mol for a diverse test set and depends on only one fitted parameter. It is robust with respect to additional fitting and cross-validation. We compare this new approach with standard LIE by Åqvist and co-workers and the LIE + γSASA model (initially suggested by Jorgensen and co-workers) against in-house and external data sets and discuss their applicabilities.

  15. KAT2B Is Required for Pancreatic Beta Cell Adaptation to Metabolic Stress by Controlling the Unfolded Protein Response.

    Science.gov (United States)

    Rabhi, Nabil; Denechaud, Pierre-Damien; Gromada, Xavier; Hannou, Sarah Anissa; Zhang, Hongbo; Rashid, Talha; Salas, Elisabet; Durand, Emmanuelle; Sand, Olivier; Bonnefond, Amélie; Yengo, Loic; Chavey, Carine; Bonner, Caroline; Kerr-Conte, Julie; Abderrahmani, Amar; Auwerx, Johan; Fajas, Lluis; Froguel, Philippe; Annicotte, Jean-Sébastien

    2016-05-03

    The endoplasmic reticulum (ER) unfolded protein response (UPR(er)) pathway plays an important role in helping pancreatic β cells to adapt their cellular responses to environmental cues and metabolic stress. Although altered UPR(er) gene expression appears in rodent and human type 2 diabetic (T2D) islets, the underlying molecular mechanisms remain unknown. We show here that germline and β cell-specific disruption of the lysine acetyltransferase 2B (Kat2b) gene in mice leads to impaired insulin secretion and glucose intolerance. Genome-wide analysis of Kat2b-regulated genes and functional assays reveal a critical role for Kat2b in maintaining UPR(er) gene expression and subsequent β cell function. Importantly, Kat2b expression is decreased in mouse and human diabetic β cells and correlates with UPR(er) gene expression in normal human islets. In conclusion, Kat2b is a crucial transcriptional regulator for adaptive β cell function during metabolic stress by controlling UPR(er) and represents a promising target for T2D prevention and treatment. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  16. HTLV-1 Tax-mediated TAK1 activation involves TAB2 adapter protein

    International Nuclear Information System (INIS)

    Yu Qingsheng; Minoda, Yasumasa; Yoshida, Ryoko; Yoshida, Hideyuki; Iha, Hidekatsu; Kobayashi, Takashi; Yoshimura, Akihiko; Takaesu, Giichi

    2008-01-01

    Human T cell leukemia virus type 1 (HTLV-1) Tax is an oncoprotein that plays a crucial role in the proliferation and transformation of HTLV-1-infected T lymphocytes. It has recently been reported that Tax activates a MAPKKK family, TAK1. However, the molecular mechanism of Tax-mediated TAK1 activation is not well understood. In this report, we investigated the role of TAK1-binding protein 2 (TAB2) in Tax-mediated TAK1 activation. We found that TAB2 physically interacts with Tax and augments Tax-induced NF-κB activity. Tax and TAB2 cooperatively activate TAK1 when they are coexpressed. Furthermore, TAK1 activation by Tax requires TAB2 binding as well as ubiquitination of Tax. We also found that the overexpression of TRAF2, 5, or 6 strongly induces Tax ubiquitination. These results suggest that TAB2 may be critically involved in Tax-mediated activation of TAK1 and that NF-κB-activating TRAF family proteins are potential cellular E3 ubiquitin ligases toward Tax

  17. 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.

  18. TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA targeting proteins

    Science.gov (United States)

    Doyle, Erin L.; Stoddard, Barry L.; Voytas, Daniel F.; Bogdanove, Adam J.

    2013-01-01

    Transcription activator-like (TAL) effectors are transcription factors injected into plant cells by pathogenic bacteria in the genus Xanthomonas. They function as virulence factors by activating host genes important for disease, or as avirulence factors by turning on genes that provide resistance. DNA binding specificity is encoded by polymorphic repeats in each protein that correspond one-to-one with different nucleotides. This code has facilitated target identification and opened new avenues for engineering disease resistance. It has also enabled TAL effector customization for targeted gene control, genome editing, and other applications. This article reviews the structural basis for TAL effector-DNA specificity, the impact of the TAL effector-DNA code on plant pathology and engineered resistance, and recent accomplishments and future challenges in TAL effector-based DNA targeting. PMID:23707478

  19. 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.

  20. Evidence of a New Role for the High-Osmolarity Glycerol Mitogen-Activated Protein Kinase Pathway in Yeast: Regulating Adaptation to Citric Acid Stress†

    OpenAIRE

    Lawrence, Clare L.; Botting, Catherine H.; Antrobus, Robin; Coote, Peter J.

    2004-01-01

    Screening the Saccharomyces cerevisiae disruptome, profiling transcripts, and determining changes in protein expression have identified an important new role for the high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway in the regulation of adaptation to citric acid stress. Deletion of HOG1, SSK1, PBS2, PTC2, PTP2, and PTP3 resulted in sensitivity to citric acid. Furthermore, citric acid resulted in the dual phosphorylation, and thus activation, of Hog1p. Despite mino...

  1. Influence of training intensity on adaptations in acid/base transport proteins, muscle buffer capacity, and repeated-sprint ability in active men.

    Science.gov (United States)

    McGinley, Cian; Bishop, David J

    2016-12-01

    McGinley C, Bishop DJ. Influence of training intensity on adaptations in acid/base transport proteins, muscle buffer capacity, and repeated-sprint ability in active men. J Appl Physiol 121: 1290-1305, 2016. First published October 14, 2016; doi:10.1152/japplphysiol.00630.2016-This study measured the adaptive response to exercise training for each of the acid-base transport protein families, including providing isoform-specific evidence for the monocarboxylate transporter (MCT)1/4 chaperone protein basigin and for the electrogenic sodium-bicarbonate cotransporter (NBCe)1. We investigated whether 4 wk of work-matched, high-intensity interval training (HIIT), performed either just above the lactate threshold (HIITΔ20; n = 8), or close to peak aerobic power (HIITΔ90; n = 8), influenced adaptations in acid-base transport protein abundance, nonbicarbonate muscle buffer capacity (βm in vitro ), and exercise capacity in active men. Training intensity did not discriminate between adaptations for most proteins measured, with abundance of MCT1, sodium/hydrogen exchanger (NHE) 1, NBCe1, carbonic anhydrase (CA) II, and CAXIV increasing after 4 wk, whereas there was little change in CAIII and CAIV abundance. βm in vitro also did not change. However, MCT4 protein content only increased for HIITΔ20 [effect size (ES): 1.06, 90% confidence limits × / ÷ 0.77], whereas basigin protein content only increased for HIITΔ90 (ES: 1.49, × / ÷ 1.42). Repeated-sprint ability (5 × 6-s sprints; 24 s passive rest) improved similarly for both groups. Power at the lactate threshold only improved for HIITΔ20 (ES: 0.49; 90% confidence limits ± 0.38), whereas peak O 2 uptake did not change for either group. Detraining was characterized by the loss of adaptations for all of the proteins measured and for repeated-sprint ability 6 wk after removing the stimulus of HIIT. In conclusion, 4 wk of HIIT induced improvements in each of the acid-base transport protein families, but, remarkably, a 40

  2. Microchidia protein 2, MORC2, downregulates the cytoskeleton adapter protein, ArgBP2, via histone methylation in gastric cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Yuxin; Li, Yan [Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, Liaoning 110122 (China); Gu, Hui [Department of Key Laboratory of Health Ministry for Congenital Malformation Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004 (China); Wang, Chunyu [Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, Liaoning 110122 (China); Liu, Funan [Department of Surgical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning 110001 (China); Shao, Yangguang; Li, Jiabin; Cao, Liu [Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, Liaoning 110122 (China); Li, Feng, E-mail: fli@mail.cmu.edu.cn [Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, Liaoning 110122 (China)

    2015-11-27

    ArgBP2 is an adapter protein that plays an important role in actin-dependent processes such as cell adhesion and migration. However, its function and regulation mechanisms in gastric cancer have not yet been investigated. Here, we showed the low expression of ArgBP2 mRNA level in gastric tumor samples and its repressive function in the proliferation, migration, and invasion of gastric cancer cells. Then, we cloned and identified ArgBP2 promoter and verified that MORC2 bound to the promoter. Moreover, we demonstrated that MORC2 enhanced the recruitment of EZH2, which promoted the tri-methylation of H3K27, leading to the transcriptional repression of ArgBP2. Our results might thus contribute to understanding the molecular mechanisms of ArgBP2 regulation and suggesting ArgBP2 as a potential therapeutic target for gastric cancer. - Highlights: • ArgBP2 inhibits proliferation, migration, and invasion of gastric cancer cells. • Identification of ArgBP2 promoter and its transcription factor MORC2. • EZH2 is required in MORC2 down-regulating ArgBP2 via histone methylation.

  3. Microchidia protein 2, MORC2, downregulates the cytoskeleton adapter protein, ArgBP2, via histone methylation in gastric cancer cells

    International Nuclear Information System (INIS)

    Tong, Yuxin; Li, Yan; Gu, Hui; Wang, Chunyu; Liu, Funan; Shao, Yangguang; Li, Jiabin; Cao, Liu; Li, Feng

    2015-01-01

    ArgBP2 is an adapter protein that plays an important role in actin-dependent processes such as cell adhesion and migration. However, its function and regulation mechanisms in gastric cancer have not yet been investigated. Here, we showed the low expression of ArgBP2 mRNA level in gastric tumor samples and its repressive function in the proliferation, migration, and invasion of gastric cancer cells. Then, we cloned and identified ArgBP2 promoter and verified that MORC2 bound to the promoter. Moreover, we demonstrated that MORC2 enhanced the recruitment of EZH2, which promoted the tri-methylation of H3K27, leading to the transcriptional repression of ArgBP2. Our results might thus contribute to understanding the molecular mechanisms of ArgBP2 regulation and suggesting ArgBP2 as a potential therapeutic target for gastric cancer. - Highlights: • ArgBP2 inhibits proliferation, migration, and invasion of gastric cancer cells. • Identification of ArgBP2 promoter and its transcription factor MORC2. • EZH2 is required in MORC2 down-regulating ArgBP2 via histone methylation.

  4. Distinct domains within the NITROGEN LIMITATION ADAPTATION protein mediate its subcellular localization and function in the nitrate-dependent phosphate homeostasis pathway

    Science.gov (United States)

    The NITROGEN LIMITATION ADAPTATION (NLA) protein is a RING-type E3 ubiquitin ligase that plays an essential role in the regulation of nitrogen and phosphate homeostasis. NLA is localized to two distinct subcellular sites, the plasma membrane and nucleus, and contains four distinct domains: i) a RING...

  5. The p36 Isoform of Murine Cytomegalovirus m152 Protein Suffices for Mediating Innate and Adaptive Immune Evasion

    Science.gov (United States)

    Fink, Annette; Renzaho, Angeliqué; Reddehase, Matthias J.; Lemmermann, Niels A. W.

    2013-01-01

    The MHC-class I (MHC-I)-like viral (MHC-Iv) m152 gene product of murine cytomegalovirus (mCMV) was the first immune evasion molecule described for a member of the β-subfamily of herpesviruses as a paradigm for analogous functions of human cytomegalovirus proteins. Notably, by interacting with classical MHC-I molecules and with MHC-I-like RAE1 family ligands of the activatory natural killer (NK) cell receptor NKG2D, it inhibits presentation of antigenic peptides to CD8 T cells and the NKG2D-dependent activation of NK cells, respectively, thus simultaneously interfering with adaptive and innate immune recognition of infected cells. Although the m152 gene product exists in differentially glycosylated isoforms whose individual contributions to immune evasion are unknown, it has entered the scientific literature as m152/gp40, based on the quantitatively most prominent isoform but with no functional justification. By construction of a recombinant mCMV in which all three N-glycosylation sites are mutated (N61Q, N208Q, and N241Q), we show here that N-linked glycosylation is not essential for functional interaction of the m152 immune evasion protein with either MHC-I or RAE1. These data add an important functional detail to recent structural analysis of the m152/RAE1γ complex that has revealed N-glycosylations at positions Asn61 and Asn208 of m152 distant from the m152/RAE1γ interface. PMID:24351798

  6. The p36 isoform of murine cytomegalovirus m152 protein suffices for mediating innate and adaptive immune evasion.

    Science.gov (United States)

    Fink, Annette; Renzaho, Angeliqué; Reddehase, Matthias J; Lemmermann, Niels A W

    2013-12-16

    The MHC-class I (MHC-I)-like viral (MHC-Iv) m152 gene product of murine cytomegalovirus (mCMV) was the first immune evasion molecule described for a member of the β-subfamily of herpesviruses as a paradigm for analogous functions of human cytomegalovirus proteins. Notably, by interacting with classical MHC-I molecules and with MHC-I-like RAE1 family ligands of the activatory natural killer (NK) cell receptor NKG2D, it inhibits presentation of antigenic peptides to CD8 T cells and the NKG2D-dependent activation of NK cells, respectively, thus simultaneously interfering with adaptive and innate immune recognition of infected cells. Although the m152 gene product exists in differentially glycosylated isoforms whose individual contributions to immune evasion are unknown, it has entered the scientific literature as m152/gp40, based on the quantitatively most prominent isoform but with no functional justification. By construction of a recombinant mCMV in which all three N-glycosylation sites are mutated (N61Q, N208Q, and N241Q), we show here that N-linked glycosylation is not essential for functional interaction of the m152 immune evasion protein with either MHC-I or RAE1. These data add an important functional detail to recent structural analysis of the m152/RAE1g complex that has revealed N-glycosylations at positions Asn61 and Asn208 of m152 distant from the m152/RAE1g interface.

  7. 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.

  8. Prolyl isomerization as a molecular memory in the allosteric regulation of the signal adapter protein c-CrkII.

    Science.gov (United States)

    Schmidpeter, Philipp A M; Schmid, Franz X

    2015-01-30

    c-CrkII is a central signal adapter protein. A domain opening/closing reaction between its N- and C-terminal Src homology 3 domains (SH3N and SH3C, respectively) controls signal propagation from upstream tyrosine kinases to downstream targets. In chicken but not in human c-CrkII, opening/closing is coupled with cis/trans isomerization at Pro-238 in SH3C. Here, we used advanced double-mixing experiments and kinetic simulations to uncover dynamic domain interactions in c-CrkII and to elucidate how they are linked with cis/trans isomerization and how this regulates substrate binding to SH3N. Pro-238 trans → cis isomerization is not a simple on/off switch but converts chicken c-CrkII from a high affinity to a low affinity form. We present a double-box model that describes c-CrkII as an allosteric system consisting of an open, high affinity R state and a closed, low affinity T state. Coupling of the T-R transition with an intrinsically slow prolyl isomerization provides c-CrkII with a kinetic memory and possibly functions as a molecular attenuator during signal transduction. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Chromosome locations of genes encoding human signal transduction adapter proteins, Nck (NCK), Shc (SHC1), and Grb2 (GRB2)

    DEFF Research Database (Denmark)

    Huebner, K; Kastury, K; Druck, T

    1994-01-01

    -human hybrids carrying defined complements of human chromosomes were assayed for the presence of the cognate genes for NCK, SHC, and GRB2, three SH2 or SH2/SH3 (Src homology 2 and 3) domain-containing adapter proteins. Additionally, NCK and SHC genes were more narrowly localized by chromosomal in situ...... hybridization. The NCK locus is at chromosome region 3q21, a region involved in neoplasia-associated changes; the SHC cognate locus, SHC1, is at 1q21, and the GRB2 locus is at 17q22-qter telomeric to the HOXB and NGFR loci. Both SHC1 and GRB2 are in chromosome regions that may be duplicated in some tumor types.......Abnormalities due to chromosomal aberration or point mutation in gene products of growth factor receptors or in ras gene products, which lie on the same signaling pathway, can cause disease in animals and humans. Thus, it can be important to determine chromosomal map positions of genes encoding...

  10. Small but crucial: the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans.

    Directory of Open Access Journals (Sweden)

    François L Mayer

    Full Text Available Small heat shock proteins (sHsps have multiple cellular functions. However, the biological function of sHsps in pathogenic microorganisms is largely unknown. In the present study we identified and characterized the novel sHsp Hsp21 of the human fungal pathogen Candida albicans. Using a reverse genetics approach we demonstrate the importance of Hsp21 for resistance of C. albicans to specific stresses, including thermal and oxidative stress. Furthermore, a hsp21Δ/Δ mutant was defective in invasive growth and formed significantly shorter filaments compared to the wild type under various filament-inducing conditions. Although adhesion to and invasion into human-derived endothelial and oral epithelial cells was unaltered, the hsp21Δ/Δ mutant exhibited a strongly reduced capacity to damage both cell lines. Furthermore, Hsp21 was required for resisting killing by human neutrophils. Measurements of intracellular levels of stress protective molecules demonstrated that Hsp21 is involved in both glycerol and glycogen regulation and plays a major role in trehalose homeostasis in response to elevated temperatures. Mutants defective in trehalose and, to a lesser extent, glycerol synthesis phenocopied HSP21 deletion in terms of increased susceptibility to environmental stress, strongly impaired capacity to damage epithelial cells and increased sensitivity to the killing activities of human primary neutrophils. Via systematic analysis of the three main C. albicans stress-responsive kinases (Mkc1, Cek1, Hog1 under a range of stressors, we demonstrate Hsp21-dependent phosphorylation of Cek1 in response to elevated temperatures. Finally, the hsp21Δ/Δ mutant displayed strongly attenuated virulence in two in vivo infection models. Taken together, Hsp21 mediates adaptation to specific stresses via fine-tuning homeostasis of compatible solutes and activation of the Cek1 pathway, and is crucial for multiple stages of C. albicans pathogenicity. Hsp21 therefore

  11. A modular and adaptive mass spectrometry-based platform for support of bioprocess development toward optimal host cell protein clearance

    Science.gov (United States)

    Yang, Feng; Carver, Joseph; Joe, Koman; Michels, David A.

    2017-01-01

    ABSTRACT A modular and adaptive mass spectrometry (MS)-based platform was developed to provide fast, robust and sensitive host cell protein (HCP) analytics to support process development. This platform relies on one-dimensional ultra-high performance liquid chromatography (1D UHPLC) combined with several different MS data acquisition strategies to meet the needs of purification process development. The workflow was designed to allow HCP composition and quantitation for up to 20 samples per day, a throughput considered essential for real time bioprocess development support. With data-dependent acquisition (DDA), the 1D UHPLC-MS/MS method had excellent speed and demonstrated robustness in detecting unknown HCPs at ≥ 50 ng/mg (ppm) level. Combining 1D UHPLC with sequential window acquisition of all theoretical spectra (SWATH) MS enabled simultaneous detection and quantitation of all HCPs in single-digit ng/mg range within 1 hour, demonstrating for the first time the benefit of SWATH MS as a technique for HCP analysis. As another alternative, a targeted MS approach can be used to track the clearance of specific known HCP under various process conditions. This study highlights the importance of designing a robust LC-MS/MS workflow that not only allows HCP discovery, but also affords greatly improved process knowledge and capability in HCP removal. As an orthogonal and complementary detection approach to traditional HCP analysis by enzyme-linked immunosorbent assay, the reported LC-MS/MS workflow supports the development of bioprocesses with optimal HCP clearance and the production of safe and high quality therapeutic biopharmaceuticals. PMID:28346045

  12. Glucagon-Like Peptide 2 Stimulates Postresection Intestinal Adaptation in Preterm Pigs by Affecting Proteins Related to Protein, Carbohydrate, and Sulphur Metabolism

    DEFF Research Database (Denmark)

    Jiang, Pingping; Vegge, Andreas; Thymann, Thomas

    2017-01-01

    BACKGROUND: Exogenous glucagon-like peptide 2 (GLP-2) stimulates intestinal adaptation after resection in animal models of pediatric short bowel syndrome (SBS). It is unknown whether the molecular mechanisms of such GLP-2 effects are similar to those of postresection spontaneous adaptation. Using...... affected by the spontaneous intestinal adaptation following resection alone. Whether more long-term GLP-2 treatment may affect the intestinal proteome following intestinal resection remains unknown.......BACKGROUND: Exogenous glucagon-like peptide 2 (GLP-2) stimulates intestinal adaptation after resection in animal models of pediatric short bowel syndrome (SBS). It is unknown whether the molecular mechanisms of such GLP-2 effects are similar to those of postresection spontaneous adaptation. Using...

  13. Reflections on: "A general role for adaptations in G-Proteins and the cyclic AMP system in mediating the chronic actions of morphine and cocaine on neuronal function".

    Science.gov (United States)

    Nestler, Eric J

    2016-08-15

    In 1991 we demonstrated that chronic morphine exposure increased levels of adenylyl cyclase and protein kinase A (PKA) in several regions of the rat central nervous system as inferred from measures of enzyme activity in crude extracts (Terwilliger et al., 1991). These findings led us to hypothesize that a concerted upregulation of the cAMP pathway is a general mechanism of opiate tolerance and dependence. Moreover, in the same study we showed similar induction of adenylyl cyclase and PKA activity in nucleus accumbens (NAc) in response to chronic administration of cocaine, but not of several non-abused psychoactive drugs. Morphine and cocaine also induced equivalent changes in inhibitory G protein subunits in this brain region. We thus extended our hypothesis to suggest that, particularly within brain reward regions such as NAc, cAMP pathway upregulation represents a common mechanism of reward tolerance and dependence shared by several classes of drugs of abuse. Research since that time, by many laboratories, has provided substantial support for these hypotheses. Specifically, opiates in several CNS regions including NAc, and cocaine more selectively in NAc, induce expression of certain adenylyl cyclase isoforms and PKA subunits via the transcription factor, CREB, and these transcriptional adaptations serve a homeostatic function to oppose drug action. In certain brain regions, such as locus coeruleus, these adaptations mediate aspects of physical opiate dependence and withdrawal, whereas in NAc they mediate reward tolerance and dependence that drives increased drug self-administration. This work has had important implications for understanding the molecular basis of addiction. "A general role for adaptations in G-proteins and the cyclic AMP system in mediating the chronic actions of morphine and cocaine on neuronal function". Previous studies have shown that chronic morphine increases levels of the G-protein subunits Giα and Goα, adenylate cyclase, cyclic AMP

  14. SNP analysis of the inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP gene by a fluorescence-adapted SSCP method

    Directory of Open Access Journals (Sweden)

    Taniyama Matsuo

    2002-07-01

    Full Text Available Abstract Background Single-nucleotide polymorphisms (SNPs are considered to be useful polymorphic markers for genetic studies of polygenic traits. Single-stranded conformational polymorphism (SSCP analysis has been widely applied to detect SNPs, including point mutations in cancer and congenital diseases. In this study, we describe an application of the fluorescent labeling of PCR fragments using a fluorescent-adapted primer for SSCP analysis as a novel method. Methods Single-nucleotide polymorphisms (SNPs of the inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP gene were analyzed using a fluorescence-adapted SSCP method. The method was constructed from two procedures: 1 a fluorescent labeling reaction of PCR fragments using fluorescence-adapted primers in a single tube, and 2 electrophoresis on a non-denaturing polyacrylamide gel. Results This method was more economical and convenient than the single-stranded conformational polymorphism (SSCP methods previously reported in the detection of the labeled fragments obtained. In this study, eight SNPs of the IHRP gene were detected by the fluorescence-adapted SSCP. One of the SNPs was a new SNP resulting in an amino acid substitution, while the other SNPs have already been reported in the public databases. Six SNPs of the IHRP were associated with two haplotypes. Conclusions The fluorescence-adapted SSCP was useful for detecting and genotyping SNPs.

  15. 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).

  16. 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.

  17. IR-inducible clusterin gene expression: a protein with potential roles in ionizing radiation-induced adaptive responses, genomic instability, and bystander effects

    Energy Technology Data Exchange (ETDEWEB)

    Klokov, Dmitry [Laboratory of Molecular Stress Responses, Department of Radiation Oncology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building 3-531, Cleveland, OH 44106-4942 (United States); Criswell, Tracy [Laboratory of Molecular Stress Responses, Department of Radiation Oncology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building 3-531, Cleveland, OH 44106-4942 (United States); Program in Molecular and Cellular Basis of Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4942 (United States); Leskov, Konstantin S. [Laboratory of Molecular Stress Responses, Department of Radiation Oncology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building 3-531, Cleveland, OH 44106-4942 (United States); Araki, Shinako [Laboratory of Molecular Stress Responses, Department of Radiation Oncology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building 3-531, Cleveland, OH 44106-4942 (United States); Mayo, Lindsey [Laboratory of Molecular Stress Responses, Department of Radiation Oncology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building 3-531, Cleveland, OH 44106-4942 (United States); Boothman, David A. [Laboratory of Molecular Stress Responses, Department of Radiation Oncology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building 3-531, Cleveland, OH 44106-4942 (United States) and Program in Molecular and Cellular Basis of Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4942 (United States)]. E-mail: dab30@po.cwru.edu

    2004-12-02

    Clusterin (CLU) plays numerous roles in mammalian cells after stress. A review of the recent literature strongly suggests potential roles for CLU proteins in low dose ionizing radiation (IR)-inducible adaptive responses, bystander effects, and delayed death and genomic instability. Its most striking and evident feature is the inducibility of the CLU promoter after low, as well as high, doses of IR. Two major forms of CLU, secreted (sCLU) and nuclear (nCLU), possess opposite functions in cellular responses to IR: sCLU is cytoprotective, whereas nCLU (a byproduct of alternative splicing) is a pro-death factor. Recent studies from our laboratory and others demonstrated that down-regulation of sCLU by specific siRNA increased cytotoxic responses to chemotherapy and IR. sCLU was induced after low non-toxic doses of IR (0.02-0.5 Gy) in human cultured cells and in mice in vivo. The low dose inducibility of this survival protein suggests a possible role for sCLU in radiation adaptive responses, characterized by increased cell radioresistance after exposure to low adapting IR doses. Although it is still unclear whether the adaptive response is beneficial or not to cells, survival of damaged cells after IR may lead to genomic instability in the descendants of surviving cells. Recent studies indicate a link between sCLU accumulation and cancer incidence, as well as aging, supporting involvement of the protein in the development of genomic instability. Secreted after IR, sCLU may also alter intracellular communication due to its ability to bind cell surface receptors, such as the TGF-{beta} receptors (types I and II). This interference with signaling pathways may contribute to IR-induced bystander effects. We hypothesize that activation of the TGF-{beta} signaling pathway, which often occurs after IR exposure, can in turn activate the CLU promoter. TGF-{beta} and IR-inducible de novo synthesized sCLU may then bind the TGF-{beta} receptors and suppress downstream growth arrest

  18. Adaptation and cultivation of permanent fish cell line CCO in serum-free medium and influence of protein hydrolysates on growth performance.

    Science.gov (United States)

    Radošević, Kristina; Dukić, Bogdanka; Andlar, Martina; Slivac, Igor; Gaurina Srček, Višnja

    2016-01-01

    In this work we describe the adaptation of channel catfish ovary (CCO) cell line to commercially available Ultra Culture serum-free medium by gradual reduction of serum concentration from 10 to 0 %. With this approach we obtained CCO cells fully adapted to serum-free conditions in 32 days. Growth, nutritional and morphological characteristics of these cells remained unchanged when compared to the control group kept in the presence of serum. Additionally, three commercially available protein hydrolysates were tested for the effects on growth performance of the newly serum-free adapted CCO cells. Supplementation with wheat gluten hydrolysate resulted in growth similar to serum free medium solely, while yeast and soy hydrolysates showed inhibitory effects on the cell growth. Taken together, the successful adaptation of CCO cells to serum-free conditions indicates their potential to be used in cytotoxicity assays when serum omission is demanded or for developing serum free bioprocesses using CCO cells. However, a more extended study on nutrient supplementation is still required to further boost the cell growth in a serum free culture.

  19. 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.

  20. 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...

  1. Systematic evaluation of the adaptability of the non-radioactive SUnSET assay to measure cardiac protein synthesis.

    Science.gov (United States)

    Ravi, Venkatraman; Jain, Aditi; Ahamed, Faiz; Fathma, Nowrin; Desingu, Perumal Arumugam; Sundaresan, Nagalingam R

    2018-03-15

    Heart is a dynamic organ that undergoes remodeling in response to both physiological and pathological stimuli. One of the fundamental cellular processes that facilitates changes in the size and shape of this muscular organ is the protein synthesis. Traditionally changes in cardiac protein synthesis levels were measured by radiolabeled tracers. However, these methods are often cumbersome and suffer from radioactive risk. Recently a nonradioactive method for detecting protein synthesis under in vitro conditions called the Surface Sensing of Translation (SUnSET) was described in cell lines of mouse dendrites and T cells. In this work, we provide multiple lines of evidence that the SUnSET assay can be applied to reliably detect changes in protein synthesis both in isolated neonatal primary cardiomyocytes and heart. We successfully tracked the changes in protein synthesis by western blotting as well as immunohistochemical variants of the SUnSET assay. Applying the SUnSET assay, we measured the cardiac protein synthesis during the different ages of mice. Further, we successfully tracked the increase in cardiac protein synthesis during different stages of a well-established model for pathological hypertrophy. Overall, we propose SUnSET assay as a simple, reliable and robust method to measure protein synthesis in the cardiac milieu.

  2. 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

    The acyl-CoA binding protein/diazepam binding inhibitor (ACBP/DBI) is an evolutionary conserved intracellular protein that binds C14-C22 acyl-CoA esters with very high affinity. ACBP is thought to act as an acyl-CoA transporter, and in vitro analyses have indicated that ACBP can transport acyl...

  3. 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

    The acyl-CoA binding protein/diazepam binding inhibitor (ACBP/DBI) is an intracellular protein that binds C14-C22 acyl-CoA esters and is thought to act as an acyl-CoA transporter. In vitro analyses have indicated that ACBP can transport acyl-CoA esters between different enzymatic systems; however...

  4. Postprandial oxidative losses of free and protein-bound amino acids in the diet: interactions and adaptation

    NARCIS (Netherlands)

    Nolles, J.A.; Verreijen, A.M.; Koopmanschap, R.E.; Verstegen, M.W.A.; Schreurs, V.V.A.M.

    2009-01-01

    Postprandial oxidation of dietary free amino acids or egg white protein was studied using the [13CO2] breath test in rats, as well as in humans. Thirty-eight male rats were assigned to four dietary test groups. Two diets only differed in their protein fraction. Diet I contained 21% egg white

  5. 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

    . 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...... the effect of contraction mode specific resistance training and protein supplementation on whole muscle and tendon hypertrophy. Quadriceps muscle and patellar tendon cross-sectional area (CSA) was quantified using magnetic resonance imaging pre and post 12 weeks of eccentric (Ecc) or concentric (Conc...... compared to Placebo. Exercise contraction mode did not influence muscle or tendon hypertrophy. In conclusion, hydrolysed whey protein may augment both muscle and tendon hypertrophy independently of exercise contraction mode during training. Paper III. Influence of exercise contraction mode and protein...

  6. 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

  7. Relative importance of sympathetic outflow and insulin in the reactivation of brown adipose tissue lipogenesis in rats adapted to a high-protein diet.

    Science.gov (United States)

    Kawashita, N H; Moura, M A F; Brito, M N; Brito, S M R C; Garofalo, M A R; Kettelhut, I C; Migliorini, R H

    2002-03-01

    The effect of denervation or acute insulin deficiency on brown adipose tissue lipogenesis was investigated in rats adapted to a high-protein diet before and after diet reversion to a balanced diet. Denervation of rats fed the balanced diet induced a 50% reduction in in vivo rates of brown adipose tissue fatty acid synthesis, with decreased activities of acetyl-CoA carboxylase and adenosine triphosphate (ATP)-citrate lyase. The markedly (80%) reduced fatty acid synthesis and enzyme activities in brown adipose tissue from rats adapted to the high-protein diet were not affected by denervation. Replacement of the high-protein diet by the balanced diet for 24 hours restored fatty acid synthesis to normal levels, but recovery of enzyme activities was only partial. Lipogenesis restoration and partial recovery of enzyme activities were impaired in denervated tissue from high-protein diet-fed rats. In all experimental conditions, the activities of acetyl-CoA carboxylase and ATP-citrate lyase showed a better correlation with brown adipose tissue lipogenesis than the generators of H(+), glucose-6-P dehydrogenase, and malic enzyme. Anti-insulin serum administration during the 12- to 24-hour period after diet reversion completely blocked lipogenesis recovery in innervated and denervated tissues and drastically reduced brown adipose tissue lipogenesis of concomitantly injected rats fed the balanced diet. The data suggest that efficient and rapid adjustments of brown adipose tissue lipogenesis require sympathetic activation, and that this tissue can maintain significant, albeit reduced, rates of lipogenesis in the absence of sympathetic activation, but not in the absence of insulin. Copyright 2002 by W.B. Saunders Company

  8. Adaptation of Tri-molecular fluorescence complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria.

    Science.gov (United States)

    Gelderman, Grant; Sivakumar, Anusha; Lipp, Sarah; Contreras, Lydia

    2015-02-01

    sRNAs play a significant role in controlling and regulating cellular metabolism. One of the more interesting aspects of certain sRNAs is their ability to make global changes in the cell by interacting with regulatory proteins. In this work, we demonstrate the use of an in vivo Tri-molecular Fluorescence Complementation assay to detect and visualize the central regulatory sRNA-protein interaction of the Carbon Storage Regulatory system in E. coli. The Carbon Storage Regulator consists primarily of an RNA binding protein, CsrA, that alters the activity of mRNA targets and of an sRNA, CsrB, that modulates the activity of CsrA. We describe the construction of a fluorescence complementation system that detects the interactions between CsrB and CsrA. Additionally, we demonstrate that the intensity of the fluorescence of this system is able to detect changes in the affinity of the CsrB-CsrA interaction, as caused by mutations in the protein sequence of CsrA. While previous methods have adopted this technique to study mRNA or RNA localization, this is the first attempt to use this technique to study the sRNA-protein interaction directly in bacteria. This method presents a potentially powerful tool to study complex bacterial RNA protein interactions in vivo. © 2014 Wiley Periodicals, Inc.

  9. Protein Supplementation Has Minimal Effects on Muscle Adaptations during Resistance Exercise Training in Young Men: A Double-Blind Randomized Clinical Trial.

    Science.gov (United States)

    Reidy, Paul T; Borack, Michael S; Markofski, Melissa M; Dickinson, Jared M; Deer, Rachel R; Husaini, Syed H; Walker, Dillon K; Igbinigie, Sherry; Robertson, Shay M; Cope, Mark B; Mukherjea, Ratna; Hall-Porter, Janine M; Jennings, Kristofer; Volpi, Elena; Rasmussen, Blake B

    2016-09-01

    To our knowledge the efficacy of soy-dairy protein blend (PB) supplementation with resistance exercise training (RET) has not been evaluated in a longitudinal study. Our aim was to determine the effect of PB supplementation during RET on muscle adaptation. In this double-blind randomized clinical trial, healthy young men [18-30 y; BMI (in kg/m(2)): 25 ± 0.5] participated in supervised whole-body RET at 60-80% 1-repetition maximum (1-RM) for 3 d/wk for 12 wk with random assignment to daily receive 22 g PB (n = 23), whey protein (WP) isolate (n = 22), or an isocaloric maltodextrin (carbohydrate) placebo [(MDP) n = 23]. Serum testosterone, muscle strength, thigh muscle thickness (MT), myofiber cross-sectional area (mCSA), and lean body mass (LBM) were assessed before and after 6 and 12 wk of RET. All treatments increased LBM (P 0.10) between treatments. Testosterone was not altered. PB supplementation during 3 mo of RET tended to slightly enhance gains in whole-body and arm LBM, but not leg muscle mass, compared with RET without protein supplementation. Although protein supplementation minimally enhanced gains in LBM of healthy young men, there was no enhancement of gains in strength. This trial was registered at clinicaltrials.gov as NCT01749189. © 2016 American Society for Nutrition.

  10. 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)

    Calligari, Paolo

    2008-01-01

    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) [fr

  11. Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution.

    Science.gov (United States)

    Modahl, Cassandra M; Mackessy, Stephen P

    2016-06-01

    Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides

  12. Yeast hEST1A/B (SMG5/6)–Like Proteins Contribute to Environment-Sensing Adaptive Gene Expression Responses

    Science.gov (United States)

    Lai, Xianning; Beilharz, Traude; Au, Wei-Chun; Hammet, Andrew; Preiss, Thomas; Basrai, Munira A.; Heierhorst, Jörg

    2013-01-01

    During its natural life cycle, budding yeast (Saccharomyces cerevisiae) has to adapt to drastically changing environments, but how environmental-sensing pathways are linked to adaptive gene expression changes remains incompletely understood. Here, we describe two closely related yeast hEST1A-B (SMG5-6)–like proteins termed Esl1 and Esl2 that contain a 14-3-3–like domain and a putative PilT N-terminus ribonuclease domain. We found that, unlike their metazoan orthologs, Esl1 and Esl2 were not involved in nonsense-mediated mRNA decay or telomere maintenance pathways. However, in genome-wide expression array analyses, absence of Esl1 and Esl2 led to more than two-fold deregulation of ∼50 transcripts, most of which were expressed inversely to the appropriate metabolic response to environmental nutrient supply; for instance, normally glucose-repressed genes were derepressed in esl1Δ esl2Δ double mutants during growth in a high-glucose environment. Likewise, in a genome-wide synthetic gene array screen, esl1Δ esl2Δ double mutants were synthetic sick with null mutations for Rim8 and Dfg16, which form the environmental-sensing complex of the Rim101 pH response gene expression pathway. Overall, these results suggest that Esl1 and Esl2 contribute to the regulation of adaptive gene expression responses of environmental sensing pathways. PMID:23893744

  13. Role of protein kinase C family in the cerebellum-dependent adaptive learning of horizontal optokinetic response eye movements in mice.

    Science.gov (United States)

    Shutoh, Fumihiro; Katoh, Akira; Ohki, Masafumi; Itohara, Shigeyoshi; Tonegawa, Susumu; Nagao, Soichi

    2003-07-01

    Among the subtypes of the Ca2+-dependent protein kinase C (PKC), which play a crucial role in long-term depression (LTD), both alpha and gamma are expressed in the cerebellar floccular Purkinje cells. To reveal the functional differences of PKC subtypes, we examined the adaptability of ocular reflexes of PKCgamma mutant mice, which show mild ataxia and normal LTD. In mutant mice, gains of the horizontal optokinetic eye response (HOKR) were reduced. Adaptation of the HOKR was not affected but its retinal slip dependency was altered in mutant mice. Sustained 1-h sinusoidal screen oscillation, which induced a relatively large amount of retinal slips in both mutant and wild-type mice, increased the HOKR gain in wild-type mice but not in mutant mice. In contrast, exposure to 1 h of sustained slower screen oscillations, which induced relatively small retinal slips in mutant and wild-type mice, increased the HOKR gain in both mutant and wild-type mice. Adaptation of the HOKR of the mutant mice to slow screen oscillation and those of wild-type mice to fast and slow screen oscillations were all abolished by local applications of a PKC inhibitor (chelerythrine) within the flocculi. Electrophysiological and anatomical studies showed no appreciable changes in the sources and magnitudes of climbing fibre inputs, which mediate retinal slip signals to the flocculus in the mutant mice. These results suggest that PKCgamma has a modulatory role in determining retinal slip dependency, and other PKC subtypes, e.g. PKCalpha, may play a crucial role in the adaptation of the HOKR.

  14. 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

    the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background...

  15. Lysine(63)-linked ubiquitylation of PIN2 auxin carrier protein governs hormonally controlled adaptation of Arabidopsis root growth

    Czech Academy of Sciences Publication Activity Database

    Leitner, J.; Petrášek, Jan; Tomanov, K.; Retzer, K.; Pařezová, Markéta; Korbei, B.; Bachmair, A.; Zažímalová, Eva; Luschnig, Ch.

    2012-01-01

    Roč. 109, č. 21 (2012), s. 8322-8327 ISSN 0027-8424 R&D Projects: GA ČR(CZ) GAP305/11/2476 Institutional research plan: CEZ:AV0Z50380511 Keywords : PLASMA-MEMBRANE PROTEIN * EFFLUX CARRIER * INTRACELLULAR TRAFFICKING Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.737, year: 2012

  16. 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

    Heterologous protein production 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 to characterize the physiological impact of erythropoietin production, and discover production bottlenecks, ...

  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. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    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......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  20. Tick-Host Range Adaptation: Changes in Protein Profiles in Unfed Adult Ixodes scapularis and Amblyomma americanum Saliva Stimulated to Feed on Different Hosts

    Directory of Open Access Journals (Sweden)

    Lucas Tirloni

    2017-12-01

    Full Text Available Understanding the molecular basis of how ticks adapt to feed on different animal hosts is central to understanding tick and tick-borne disease (TBD epidemiology. There is evidence that ticks differentially express specific sets of genes when stimulated to start feeding. This study was initiated to investigate if ticks such as Ixodes scapularis and Amblyomma americanum that are adapted to feed on multiple hosts utilized the same sets of proteins to prepare for feeding. We exposed I. scapularis and A. americanum to feeding stimuli of different hosts (rabbit, human, and dog by keeping unfed adult ticks enclosed in a perforated microfuge in close contact with host skin, but not allowing ticks to attach on host. Our data suggest that ticks of the same species differentially express tick saliva proteins (TSPs when stimulated to start feeding on different hosts. SDS-PAGE and silver staining analysis revealed unique electrophoretic profiles in saliva of I. scapularis and A. americanum that were stimulated to feed on different hosts: rabbit, human, and dog. LC-MS/MS sequencing and pairwise analysis demonstrated that I. scapularis and A. americanum ticks expressed unique protein profiles in their saliva when stimulated to start feeding on different hosts: rabbit, dog, or human. Specifically, our data revealed TSPs that were unique to each treatment and those that were shared between treatments. Overall, we identified a total of 276 and 340 non-redundant I. scapularis and A. americanum TSPs, which we have classified into 28 functional classes including: secreted conserved proteins (unknown functions, proteinase inhibitors, lipocalins, extracellular matrix/cell adhesion, heme/iron metabolism, signal transduction and immunity-related proteins being the most predominant in saliva of unfed ticks. With exception of research on vaccines against Rhipicephalus microplus, which its natural host, cattle, research on vaccine against other ticks relies feeding ticks

  1. A 7-day high protein hypocaloric diet promotes cellular metabolic adaptations and attenuates lean mass loss in healthy males

    Directory of Open Access Journals (Sweden)

    Matthew Furber

    2017-08-01

    Full Text Available Mitochondrial quantity and density are associated with increased oxidative metabolism. It has been demonstrated that a hypocaloric high fat/low carbohydrate (HF/LC diet can up-regulate transcriptional markers of mitochondrial biogenesis; this was yet to be explored in vivo subsequent to a high protein/low carbohydrate (HP/LC diet. Thus the aims of the study were to explore such diets on transcriptional markers or mitochondrial biogenesis, body composition and resting metabolic rate (RMR. Forty-five healthy male participants were randomly assigned one of four intervention diets: eucaloric high protein low carbohydrate (PRO-EM, hypocaloric high protein low carbohydrate (PRO-ER, eucaloric high carbohydrate (CHO-EM or hypocaloric high carbohydrate (CHO-ER. The macronutrient ratio of the high protein diet and high carbohydrate diets was 40:30:30% and 10:60:30% (PRO:CHO:FAT respectively. Energy intake for the hypocaloric diets were calculated to match resting metabolic rate. Participants visited the laboratory on 3 occasions each separated by 7 days. On each visit body composition, resting metabolic rate and a muscle biopsy from the vastus lateralis was collected. Prior to visit 1 and 2 habitual diet was consumed which was used as a control, between visit 2 and 3 the intervention diet was consumed continuously for 7-days. No group × time effect was observed, however in the PRO-ER group a significant increase in AMPK, PGC-1α, SIRT1 and SIRT3 mRNA expression was observed post diet intervention groups (p < 0.05. No change was observed in any of the transcriptional markers in the other 3 groups. Despite ∼30% reduction in calorie intake no difference in lean mass (LM loss was observed between the PRO-ER and CHO-EM groups. The results from this study suggest that a 7-day a high protein low carbohydrate hypocaloric diet increased AMPK, SIRT1 and PGC-1 α mRNA expression at rest, and also suggest that increased dietary protein may attenuate LM mass

  2. 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

  3. Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.

    Directory of Open Access Journals (Sweden)

    Giuseppina Rea

    2011-01-01

    Full Text Available Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues

  4. Muscle ion transporters and antioxidative proteins have different adaptive potential in arm than in leg skeletal muscle with exercise training

    DEFF Research Database (Denmark)

    Mohr, Magni; Nielsen, Tobias Schmidt; Weihe, Pál

    2017-01-01

    It was evaluated whether upper-body compared to lower-body musculature exhibits a different phenotype in relation to capacity for handling reactive oxygen species (ROS), H(+), La(-), Na(+), K(+) and also whether it differs in adaptive potential to exercise training. Eighty-three sedentary...... premenopausal women aged 45 ± 6 years (mean ± SD) were randomized into a high-intensity intermittent swimming group (HIS, n = 21), a moderate-intensity swimming group (MOS, n = 21), a soccer group (SOC, n = 21), or a control group (CON, n = 20). Intervention groups completed three weekly training sessions...... for 15 weeks, and pre- and postintervention biopsies were obtained from deltoideus and vastus lateralis muscle. Before training, monocarboxylate transporter 4 (MCT4), Na(+)/K(+) pump α2, and superoxide dismutase 2 (SOD2) expressions were lower (P

  5. Identification of S-Nitrosylated (SNO) Proteins inEntamoeba histolyticaAdapted to Nitrosative Stress: Insights into the Role of SNO Actin andIn vitroVirulence.

    Science.gov (United States)

    Trebicz-Geffen, Meirav; Shahi, Preeti; Nagaraja, Shruti; Vanunu, Shai; Manor, Shiran; Avrahami, Amit; Ankri, Serge

    2017-01-01

    We have recently reported that Entamoeba histolytica trophozoites can adapt to toxic levels of the nitric oxide (NO) donor, S-nitrosoglutathione (GSNO). Even if the consequences of this adaptation on the modulation of gene expression in NO-adapted trophozoites (NAT) have been previously explored, insight on S-nitrosylated (SNO) proteins in NAT is missing. Our study aims to fill this knowledge gap by performing a screening of SNO proteins in NAT. Employing SNO resin-assisted capture (RAC), we identified 242 putative SNO proteins with key functions in calcium binding, enzyme modulation, redox homeostasis, and actin cytoskeleton. Of the SNO proteins in NAT, proteins that are associated with actin family cytoskeleton protein are significantly enriched. Here we report that the formation of actin filaments (F-actin) is impaired in NAT. Consequently, the ability of NAT to ingest erythrocytes and their motility and their cytopathic activity are impaired. These phenotypes can be imitated by treating control parasite with cytochalasin D (CytD), a drug that binds to F-actin polymer and prevent polymerization of actin monomers. Removal of GSNO from the culture medium of NAT restored the sensitivity of the parasite to nitrosative stress (NS) and its ability to form F-actin formation and its virulence. These results establish the central role of NO in shaping the virulence of the parasite through its effect on F-actin formation and highlight the impressive ability of this parasite to adapt to NS.

  6. Structural models of intrinsically disordered and calcium-bound folded states of a protein adapted for secretion

    OpenAIRE

    O’Brien, Darragh P.; Hernandez, Belen; Durand, Dominique; Hourdel, Véronique; Sotomayor-Pérez, Ana-Cristina; Vachette, Patrice; Ghomi, Mahmoud; Chamot-Rooke, Julia; Ladant, Daniel; Brier, Sébastien; Chenal, Alexandre

    2016-01-01

    International audience; Many Gram-negative bacteria use Type I secretion systems, T1SS, to secrete virulence factors that contain calcium-binding Repeat-in-ToXin (RTX) motifs. Here, we present structural models of an RTX protein, RD, in both its intrinsically disordered calcium-free Apo-state and its folded calcium-bound Holo-state. Apo-RD behaves as a disordered polymer chain comprising several statistical elements that exhibit local rigidity with residual secondary structure. Holo-RD is a f...

  7. The p36 Isoform of Murine Cytomegalovirus m152 Protein Suffices for Mediating Innate and Adaptive Immune Evasion

    OpenAIRE

    Fink, Annette; Renzaho, Angeliqué; Reddehase, Matthias J.; Lemmermann, Niels A. W.

    2013-01-01

    The MHC-class I (MHC-I)-like viral (MHC-Iv) m152 gene product of murine cytomegalovirus (mCMV) was the first immune evasion molecule described for a member of the β-subfamily of herpesviruses as a paradigm for analogous functions of human cytomegalovirus proteins. Notably, by interacting with classical MHC-I molecules and with MHC-I-like RAE1 family ligands of the activatory natural killer (NK) cell receptor NKG2D, it inhibits presentation of antigenic peptides to CD8 T cells and the NKG2D-d...

  8. A Fasciola hepatica-derived fatty acid binding protein induces protection against schistosomiasis caused by Schistosoma bovis using the adjuvant adaptation (ADAD) vaccination system.

    Science.gov (United States)

    Vicente, Belén; López-Abán, Julio; Rojas-Caraballo, José; Pérez del Villar, Luis; Hillyer, George V; Martínez-Fernández, Antonio R; Muro, Antonio

    2014-10-01

    Several efforts have been made to identify anti-schistosomiasis vaccine candidates and new vaccination systems. The fatty acid binding protein (FAPB) has been shown to induce a high level of protection in trematode infection. The adjuvant adaptation (ADAD) vaccination system was used in this study, including recombinant FABP, a natural immunomodulator and saponins. Mice immunised with the ADAD system were able to up-regulate proinflammatory cytokines (IL-1 and IL-6) and induce high IgG2a levels. Moreover, there was a significant reduction in worm burden, egg liver and hepatic lesion in vaccinated mice in two independent experiments involving Schistosoma bovis infected mice. The foregoing data shows that ADAD system using FABP provide a good alternative for triggering an effective immune response against animal schistosomiasis. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Atrial Fibrillation Activates AMP-Dependent Protein Kinase and its Regulation of Cellular Calcium Handling: Potential Role in Metabolic Adaptation and Prevention of Progression.

    Science.gov (United States)

    Harada, Masahide; Tadevosyan, Artavazd; Qi, Xiaoyan; Xiao, Jiening; Liu, Tao; Voigt, Niels; Karck, Matthias; Kamler, Markus; Kodama, Itsuo; Murohara, Toyoaki; Dobrev, Dobromir; Nattel, Stanley

    2015-07-07

    Atrial fibrillation (AF) is associated with metabolic stress, which activates adenosine monophosphate-regulated protein kinase (AMPK). This study sought to examine AMPK response to AF and associated metabolic stress, along with consequences for atrial cardiomyocyte Ca(2+) handling. Calcium ion (Ca(2+)) transients (CaTs) and cell shortening (CS) were measured in dog and human atrial cardiomyocytes. AMPK phosphorylation and AMPK association with Ca(2+)-handling proteins were evaluated by immunoblotting and immunoprecipitation. CaT amplitude and CS decreased at 4-min glycolysis inhibition (GI) but returned to baseline at 8 min, suggesting cellular adaptation to metabolic stress, potentially due to AMPK activation. GI increased AMPK-activating phosphorylation, and an AMPK inhibitor, compound C (CompC), abolished the adaptation of CaT and CS to GI. The AMPK activator 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) increased CaT amplitude and CS, restoring CompC-induced CaT and CS decreases. CompC decreased L-type calcium channel current (ICa,L), along with ICa,L-triggered CaT amplitude and sarcoplasmic reticulum (SR) Ca(2+) content under voltage clamp conditions in dog cells and suppressed CaT and ICa,L in human cardiomyocytes. Small interfering ribonucleic acid-based AMPK knockdown decreased CaT amplitude in neonatal rat cardiomyocytes. L-type Ca(2+) channel α subunits coimmunoprecipitated with AMPKα. Atrial AMPK-activating phosphorylation was enhanced by 1 week of electrically maintained AF in dogs; fractional AMPK phosphorylation was increased in paroxysmal AF and reduced in longstanding persistent AF patients. AMPK is activated by metabolic stress and AF, and helps maintain the intactness of atrial ICa,L, Ca(2+) handling, and cell contractility. AMPK contributes to the atrial compensatory response to AF-related metabolic stress; AF-related metabolic responses may be an interesting new therapeutic target. Copyright © 2015 American College of Cardiology

  10. Progress in the development of Fasciola hepatica vaccine using recombinant fatty acid binding protein with the adjuvant adaptation system ADAD.

    Science.gov (United States)

    López-Abán, J; Casanueva, P; Nogal, J; Arias, M; Morrondo, P; Diez-Baños, P; Hillyer, G V; Martínez-Fernández, A R; Muro, A

    2007-04-30

    Fatty acid binding proteins (FABP) have been designed as a potential vaccine against fasciolosis. In this work, the immunoprophylaxis of the recombinant Fh15 FABP from F. hepatica (Fh15) in adjuvant/immunomodulator ADAD system was evaluated using mice and sheep challenged with F. hepatica. The ADAD system combines the Fh15 antigen with an immunomodulator (hydroalcoholic extract of Polypodium leucotomos; PAL) and/or an adjuvant (saponins of Quillaja saponaria; Qs) in a water/oil emulsion (30/70) with a non-mineral oil (Montanide). All the infected control mice died by 41-48 days post-infection. The mice vaccinated with ADAD only with PAL+Fh15 present a survival rate of 40-50% and those vaccinated with ADAD containing PAL+Qs+Fh15 had a survival rate of 50-62.5%. IgG1 antibodies were lower in surviving mice in comparison with non-surviving mice. The sheep vaccinated with ADAD PAL+Qs+Fh15 showed lower fluke recovery (43%), less hepatic lesions and higher post-infection daily weight gain than F. hepatica infected control animals. Thus, the ADAD system using recombinant fatty acid binding proteins from F. hepatica could be a good option to develop vaccines against F. hepatica.

  11. 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.

  12. Adaptive immune stimulation is required to obtain high protection with fatty acid binding protein vaccine candidate against Fasciola hepatica in Balb/C mice.

    Science.gov (United States)

    López-Abán, Julio; Esteban, Ana; Vicente, Belén; Rojas-Caraballo, José; del Olmo, Esther; Martínez-Fernández, Antonio R; Hillyer, George V; Muro, Antonio

    2012-06-01

    Fascioliasis is a parasitic disease that mainly affects cattle and sheep, causing significant economic losses with a great impact in developing countries. Human fascioliasis is becoming more important with the high endemicity in some countries of the world. Previous studies have shown the importance of Fasciola hepatica fatty acid binding proteins (FABP) as protective molecules against fascioliasis in various animal models including mice, rabbits, and sheep. Our studies have shown the protective efficacy of recombinant FABP (rFh15) when the protein is formulated in the adjuvant adaptation system (ADAD), using either natural or synthetic immunomodulators. The ADAD system is most effective when it is used 5 days before each dose of specific vaccine antigen. The results showed survival rates of up to 50% with less severe hepatic lesions and high levels of IgG2a or IFNγ in immunized mice, using the ADAD system, compared to survival rates of 13% with no hepatic lesion reduction and high levels of IgG1 and IL-4 in those mice immunized with the simplified mode (ADADs).

  13. Inhibitory function of adapter-related protein complex 2 alpha 1 subunit in the process of nuclear translocation of human immunodeficiency virus type 1 genome

    International Nuclear Information System (INIS)

    Kitagawa, Yukiko; Kameoka, Masanori; Shoji-Kawata, Sanae; Iwabu, Yukie; Mizuta, Hiroyuki; Tokunaga, Kenzo; Fujino, Masato; Natori, Yukikazu; Yura, Yoshiaki; Ikuta, Kazuyoshi

    2008-01-01

    The transfection of human cells with siRNA against adapter-related protein complex 2 alpha 1 subunit (AP2α) was revealed to significantly up-regulate the replication of human immunodeficiency virus type 1 (HIV-1). This effect was confirmed by cell infection with vesicular stomatitis virus G protein-pseudotyped HIV-1 as well as CXCR4-tropic and CCR5-tropic HIV-1. Viral adsorption, viral entry and reverse transcription processes were not affected by cell transfection with siRNA against AP2α. In contrast, viral nuclear translocation as well as the integration process was significantly up-regulated in cells transfected with siRNA against AP2α. Confocal fluorescence microscopy revealed that a subpopulation of AP2α was not only localized in the cytoplasm but was also partly co-localized with lamin B, importin β and Nup153, implying that AP2α negatively regulates HIV-1 replication in the process of nuclear translocation of viral DNA in the cytoplasm or the perinuclear region. We propose that AP2α may be a novel target for disrupting HIV-1 replication in the early stage of the viral life cycle

  14. Crystallization and X-ray diffraction analysis of SpaE, a basal pilus protein from the gut-adapted Lactobacillus rhamnosus GG.

    Science.gov (United States)

    Mishra, Arjun K; Megta, Abhin Kumar; Palva, Airi; von Ossowski, Ingemar; Krishnan, Vengadesan

    2017-06-01

    SpaE is the predicted basal pilin subunit in the sortase-dependent SpaFED pilus from the gut-adapted and commensal Lactobacillus rhamnosus GG. Thus far, structural characterization of the cell-wall-anchoring basal pilins has remained difficult and has been limited to only a few examples from pathogenic genera and species. To gain a further structural understanding of the molecular mechanisms that are involved in the anchoring and assembly of sortase-dependent pili in less harmful bacteria, L. rhamnosus GG SpaE for crystallization was produced by recombinant expression in Escherichia coli. Although several attempts to crystallize the SpaE protein were unsuccessful, trigonal crystals that diffracted to a resolution of 3.1 Å were eventually produced using PEG 3350 as a precipitant and high protein concentrations. Further optimization with a combination of additives led to the generation of SpaE crystals in an orthorhombic form that diffracted to a higher resolution of 1.5 Å. To expedite structure determination by SAD phasing, selenium-substituted (orthorhombic) SpaE crystals were grown and X-ray diffraction data were collected to 1.8 Å resolution.

  15. The Modular Adaptive Ribosome.

    Directory of Open Access Journals (Sweden)

    Anupama Yadav

    Full Text Available The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5'UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.

  16. Involvement of co-repressor LUH and the adapter proteins SLK1 and SLK2 in the regulation of abiotic stress response genes in Arabidopsis.

    Science.gov (United States)

    Shrestha, Barsha; Guragain, Bhuwan; Sridhar, Vaniyambadi V

    2014-02-24

    During abiotic stress many genes that are important for growth and adaptation to stress are expressed at elevated levels. However, the mechanisms that keep the stress responsive genes from expressing under non stress conditions remain elusive. Recent genetic characterization of the co-repressor LEUNIG_HOMOLOG (LUH) and transcriptional adaptor proteins SEUSS-LIKE1 (SLK1) and SLK2 have been proposed to function redundantly in diverse developmental processes; however their function in the abiotic stress response is unknown. Moreover, the molecular functions of LUH, SLK1 and SLK2 remain obscure. Here, we show the molecular function of LUH, SLK1 and SLK2 and the role of this complex in the abiotic stress response. The luh, slk1 and slk2 mutant plants shows enhanced tolerance to salt and osmotic stress conditions. SLK1 and SLK2 interact physically with the LUFS domain in LUH forming SLK1-LUH and SLK2-LUH co-repressor complexes to inhibit the transcription. LUH has repressor activity, whereas SLK1 and SLK2 function as adaptors to recruit LUH, which in turn recruits histone deacetylase to the target sequences to repress transcription. The stress response genes RD20, MYB2 and NAC019 are expressed at elevated levels in the luh, slk1 and slk2 mutant plants. Furthermore, these stress response genes are associated with decreased nucleosome density and increased acetylation levels at H3K9 and H3K14 in the luh, slk1 and slk2 mutant plants. Our results indicate that SLK1, SLK2 and LUH form a co-repressor complex. LUH represses by means of an epigenetic process involving histone modification to facilitate the condensation of chromatin thus preventing transcription at the target genes.

  17. Acute and Long-Term Impact of High-Protein Diets on Endocrine and Metabolic Function, Body Composition, and Exercise-Induced Adaptations.

    Science.gov (United States)

    Morales, Flor E; Tinsley, Grant M; Gordon, Paul M

    2017-01-01

    High-protein diets have been shown to improve body composition through alterations in satiety, muscle protein synthesis, and the thermic effect of food. Given these findings, the purpose of this review is to discuss the integration of the specific hormonal and metabolic effects of high-protein diets following both acute and long-term usage, especially with regard to body composition. Full-text articles were obtained through PubMed by using the terms "high-protein diet and body composition," "high-protein diet and exercise," "high-protein diet risk," "high-protein diet side effects," "protein quality PDCAAS," "RDA for protein," and "daily protein recommendation." Articles were initially screened according to their title and abstract; careful evaluation of the full manuscripts was then used to identify relevant articles. The higher satiety exerted by high-protein diets is generated through increments in anorexigenic, as well as decrements in orexigenic hormones. Improvements in muscle mass are achieved by activation of muscle protein synthesis acting through the mTOR pathway. High thermic effect of food is caused due to necessary deamination, gluconeogenesis, and urea synthesis caused by high-protein diets. Interestingly, high-protein diets in both hypo- and normocaloric conditions have shown to improve body composition, whereas in combination with hypercaloric conditions does not seem to increase fat mass, when the excess energy comes from protein. High protein diets effectively improve body composition by acting through different pathways.

  18. 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

  19. Development of a dual luciferase activity and fluorescamine protein assay adapted to a 384 micro-well plate format: Reducing variability in human luciferase transactivation cell lines aimed at endocrine active substances.

    Science.gov (United States)

    Brennan, Jennifer C; Tillitt, Donald E

    2018-03-01

    There is a need to adapt cell bioassays to 384-well and 1536-well formats instead of the traditional 96-well format as high-throughput screening (HTS) demands increase. However, the sensitivity and performance of the bioassay must be re-verified in these higher micro-well plates, and verification of cell health must also be HT (high-throughput). We have adapted two commonly used human breast luciferase transactivation cell bioassays, the recently re-named estrogen agonist/antagonist screening VM7Luc4E2 cell bioassay (previously designated BG1Luc4E2) and the androgen/glucocorticoid screening MDA-kb2 cell bioassay, to 384-well formats for HTS of endocrine-active substances (EASs). This cost-saving adaptation includes a fast, accurate, and easy measurement of protein amount in each well via the fluorescamine assay with which to normalize luciferase activity of cell lysates without requiring any transfer of the cell lysates. Here we demonstrate that by accounting for protein amount in the cell lysates, antagonistic agents can easily be distinguished from cytotoxic agents in the MDA-kb2 and VM7Luc4E2 cell bioassays. Additionally, we demonstrate via the fluorescamine assay improved interpretation of luciferase activity in wells along the edge of the plate (the so-called "edge effect"), thereby increasing usable wells to the entire plate, not just interior wells. Published by Elsevier Ltd.

  20. Development of a dual luciferase activity and fluorescamine protein assay adapted to a 384 micro-well plate format: Reducing variability in human luciferase transactivation cell lines aimed at endocrine active substances

    Science.gov (United States)

    Brennan, Jennifer; Tillitt, Donald E.

    2018-01-01

    There is a need to adapt cell bioassays to 384-well and 1536-well formats instead of the traditional 96-well format as high-throughput screening (HTS) demands increase. However, the sensitivity and performance of the bioassay must be re-verified in these higher micro-well plates, and verification of cell health must also be HT (high-throughput). We have adapted two commonly used human breast luciferase transactivation cell bioassays, the recently re-named estrogen agonist/antagonist screening VM7Luc4E2 cell bioassay (previously designated BG1Luc4E2) and the androgen/glucocorticoid screening MDA-kb2 cell bioassay, to 384-well formats for HTS of endocrine-active substances (EASs). This cost-saving adaptation includes a fast, accurate, and easy measurement of protein amount in each well via the fluorescamine assay with which to normalize luciferase activity of cell lysates without requiring any transfer of the cell lysates. Here we demonstrate that by accounting for protein amount in the cell lysates, antagonistic agents can easily be distinguished from cytotoxic agents in the MDA-kb2 and VM7Luc4E2 cell bioassays. Additionally, we demonstrate via the fluorescamine assay improved interpretation of luciferase activity in wells along the edge of the plate (the so-called “edge effect”), thereby increasing usable wells to the entire plate, not just interior wells.

  1. The endothelial adaptor molecule TSAd is required for VEGF-induced angiogenic sprouting through junctional c-Src activation

    NARCIS (Netherlands)

    Gordon, Emma J; Fukuhara, Daisuke; Weström, Simone; Padhan, Narendra; Sjöström, Elisabet O; van Meeteren, Laurens; He, Liqun; Orsenigo, Fabrizio; Dejana, Elisabetta; Bentley, Katie; Spurkland, Anne; Claesson-Welsh, Lena

    2016-01-01

    Activation of vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2) by VEGF binding is critical for vascular morphogenesis. In addition, VEGF disrupts the endothelial barrier by triggering the phosphorylation and turnover of the junctional molecule VE-cadherin, a process mediated by the

  2. 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...... 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 lighting ceases...

  3. 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

    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 ...

  4. An optimized xylene-free protein extraction method adapted to formalin-fixed paraffin embedded tissue sections for western blot analysis.

    Science.gov (United States)

    Mansour, Anthony G; Khalil, Pamela Abou; Bejjani, Noha; Chatila, Rajaa; Dagher-Hamalian, Carole; Faour, Wissam H

    2017-03-01

    Deparaffinization of formalin-fixed paraffin embedded (FFPE) tissues with xylene currently remains a major challenge to the biomedical community. We developed an efficient xylene-free protocol to isolate proteins from archived FFPE human tissue sections. A total of 79 different types of FFPE tissue sections of 8 µm thickness were obtained from various archived FFPE specimens. Deparaffinization was conducted by gently washing each section with around 1 ml of hot distilled water (≈80°C). The deparaffinized tissues were homogenized in lysis buffer, and the isolated proteins were quantified and efficiently resolved using western blot analysis for the presence of Protein kinase B (PKB/AKT) and β-actin. Moreover, a significant amount of proteins was successfully isolated with an average of 2.31 µg/µl. The migration pattern of AKT and β-actin obtained from the specimens was similar to the positive control obtained from protein lysates prepared from in vitro cultured MDA231 cancer cell lines. AKT was successfully identified in all specimens, and β-actin protein was resolved with an efficiency higher than 80%. The entire extraction procedure requires only 20 minutes. This newly developed technique is an efficient, safe, cost-effective, and rapid method to isolate proteins from FFPE tissue sections adequate for molecular analysis.

  5. 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 distributed...

  6. 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...

  7. Adaptation Stories

    International Development Research Centre (IDRC) Digital Library (Canada)

    By Reg'

    formed a real foundation for endogenous, and, therefore, sustainable, strategies for adaptation to climate change. The stories reinforce what we already knew: that successful adaptation must come from the people who are living on the front lines, facing the many problems caused by climate change and climate variation.

  8. Adaptation to a high protein, carbohydrate-free diet induces a marked reduction of fatty acid synthesis and lipogenic enzymes in rat adipose tissue that is rapidly reverted by a balanced diet.

    Science.gov (United States)

    Brito, S M R C; Moura, M A F; Kawashita, N H; Festuccia, W T L; Garófalo, M A R; Kettelhut, I C; Migliorini, R H

    2005-06-01

    We have previously shown that in vivo lipogenesis is markedly reduced in liver, carcass, and in 4 different depots of adipose tissue of rats adapted to a high protein, carbohydrate-free (HP) diet. In the present work, we investigate the activity of enzymes involved in lipogenesis in the epididymal adipose tissue (EPI) of rats adapted to an HP diet before and 12 h after a balanced diet was introduced. Rats fed an HP diet for 15 days showed a 60% reduction of EPI fatty acid synthesis in vivo that was accompanied by 45%-55% decreases in the activities of pyruvate dehydrogenase complex, ATP-citrate lyase, acetyl-CoA carboxylase, glucose-6-phosphate dehydrogenase, and malic enzyme. Reversion to a balanced diet for 12 h resulted in a normalization of in vivo EPI lipogenesis, and in a restoration of acetyl-CoA carboxylase activity to levels that did not differ significantly from control values. The activities of ATP-citrate lyase and pyruvate dehydrogenase complex increased to about 75%-86% of control values, but the activities of glucose-6-phosphate dehydrogenase and malic enzyme remained unchanged 12 h after diet reversion. The data indicate that in rats, the adjustment of adipose tissue lipogenic activity is an important component of the metabolic adaptation to different nutritional conditions.

  9. 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...

  10. Toothbrush Adaptations.

    Science.gov (United States)

    Exceptional Parent, 1987

    1987-01-01

    Suggestions are presented for helping disabled individuals learn to use or adapt toothbrushes for proper dental care. A directory lists dental health instructional materials available from various organizations. (CB)

  11. Ambiguous Adaptation

    DEFF Research Database (Denmark)

    Møller Larsen, Marcus; Lyngsie, Jacob

    2017-01-01

    intense relational mechanisms provide an effective means for contingency adaptation and therefore reduce the probability of premature termination. However, in situations where relationships are already governed by longer duration contracts, we argue that investments in relational mechanism create...

  12. Ambiguous Adaptation

    DEFF Research Database (Denmark)

    Møller Larsen, Marcus; Lyngsie, Jacob

    We investigate why some exchange relationships terminate prematurely. We argue that investments in informal governance structures induce premature termination in relationships already governed by formal contracts. The formalized adaptive behavior of formal governance structures and the flexible...... and reciprocal adaptation of informal governance structure create ambiguity in situations of contingencies, which, subsequently, increases the likelihood of premature relationship termination. Using a large sample of exchange relationships in the global service provider industry, we find support for a hypothesis...

  13. 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...

  14. 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....

  15. Radio-adaptive response

    International Nuclear Information System (INIS)

    Ikushima, T.

    1992-01-01

    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)

  16. 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

  17. Protein: MPA1 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available MPA1 TLR signaling molecules MAVS IPS1, KIAA1271, VISA VISA_(gene) Mitochondrial antiviral-signaling pr...otein CARD adapter inducing interferon beta, Interferon beta promoter stimulator protein... 1, Putative NF-kappa-B-activating protein 031N, Virus-induced-signaling adapter 9606 Homo sapiens Q7Z434 57506 2VGQ 57506 ...

  18. Strategies of biochemical adaptation for hibernation in a South American marsupial, Dromiciops gliroides: 2. Control of the Akt pathway and protein translation machinery.

    Science.gov (United States)

    Luu, Bryan E; Wijenayake, Sanoji; Zhang, Jing; Tessier, Shannon N; Quintero-Galvis, Julian F; Gaitán-Espitia, Juan Diego; Nespolo, Roberto F; Storey, Kenneth B

    2017-12-13

    When faced with harsh environmental conditions, the South American marsupial, monito del monte (Dromiciops gliroides), reduces its body temperature and uses either daily torpor or multiday hibernation to survive. This study used ELISA and multiplex assays to characterize the responses to hibernation by three regulatory components of protein translation machinery [p-eIF2α(S51), p-eIF4E(S209), p-4EBP(Thr37/46)] and eight targets involved in upstream signaling control of translation [p-IGF-1R(Tyr1135/1136), PTEN(S380), p-Akt(S473), p-GSK-3α(S21), p-GSK-3β(S9), p-TSC2(S939), p-mTOR(S2448), and p70S6K(T412)]. Liver, brain and kidney were analyzed comparing control and hibernation (4days continuous torpor) conditions. In the liver, increased phosphorylation of IGF-1R, Akt, GSK-3β, TSC2, mTOR, eIF2α, and 4EBP (1.60-1.98 fold compared to control) occurred during torpor suggesting that the regulatory phosphorylation cascade and protein synthesis remained active during torpor. However, responses by brain and kidney differed; torpor resulted in increased phosphorylation of GSK-3β (2.15-4.17 fold) and TSC2 (2.03-3.65 fold), but phosphorylated Akt decreased (to 34-62% of control levels). Torpor also led to an increase in phosphorylated eIF2α (1.4 fold) content in the brain. These patterns of differential protein phosphorylation in brain and kidney were indicative of suppression of protein translation but also could suggest an increase in antioxidant and anti-apoptotic signaling during torpor. Previous studies of liver metabolism in hibernating eutherian mammals have shown that Akt kinase and its downstream signaling components play roles in facilitating hypometabolism by suppressing energy expensive anabolic processes during torpor. However, the results in this study reveal differences between eutherian and marsupial hibernators, suggesting alternative actions of liver Akt during torpor. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Inverse modulation of the energy sensor Snf1-related protein kinase 1 on hypoxia adaptation and salt stress tolerance in Arabidopsis thaliana.

    Science.gov (United States)

    Im, Jong Hee; Cho, Young-Hee; Kim, Geun-Don; Kang, Geun-Ho; Hong, Jung-Woo; Yoo, Sang-Dong

    2014-10-01

    Terrestrial plants are exposed to complex stresses of high salt-induced abscisic acid (ABA) and submergence-induced hypoxia when seawater floods fields. Many studies have investigated plant responses to individual stress conditions, but not so much for coupled or sequentially imposed stresses. We examined molecular regulatory mechanisms of gene expression underlying the cellular responses involved in crosstalk between salt and hypoxia stresses. Salt/ABA- and AtMYC2-dependent induction of a synthetic ABA-responsive element and the native RD22 promoters were utilized in our cell-based functional assays. Such promoter-based reporter induction was largely inhibited by hypoxia and hypoxia-inducible AKIN10 activity. Biochemical analyses showed that AKIN10 negatively modulates AtMYC2 protein accumulation via proteasome activity upon AKIN10 kinase activity-dependent protein modification. Further genetic analysis using transgenic plants expressing AKIN10 provided evidence that AKIN10 activity undermined AtMYC2-dependent salt tolerance. Our findings unravel a novel molecular interaction between the key signalling constituents leading crosstalk between salt and hypoxia stresses in Arabidopsis thaliana under the detrimental condition of submergence in saltwater. © 2014 John Wiley & Sons Ltd.

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

    Directory of Open Access Journals (Sweden)

    Ha Duc Chu

    2016-01-01

    Full Text Available 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.

  1. Strategic Adaptation

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    2015-01-01

    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 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....... 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....

  2. 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....

  3. 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.

  4. Is adaptation. Truly an adaptation?

    Directory of Open Access Journals (Sweden)

    Thais Flores Nogueira Diniz

    2006-04-01

    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.

  5. Fluorescent protein-mediated colour polymorphism in reef corals: multicopy genes extend the adaptation/acclimatization potential to variable light environments.

    Science.gov (United States)

    Gittins, John R; D'Angelo, Cecilia; Oswald, Franz; Edwards, Richard J; Wiedenmann, Jörg

    2015-01-01

    The genomic framework that enables corals to adjust to unfavourable conditions is crucial for coral reef survival in a rapidly changing climate. We have explored the striking intraspecific variability in the expression of coral pigments from the green fluorescent protein (GFP) family to elucidate the genomic basis for the plasticity of stress responses among reef corals. We show that multicopy genes can greatly increase the dynamic range over which corals can modulate transcript levels in response to the light environment. Using the red fluorescent protein amilFP597 in the coral Acropora millepora as a model, we demonstrate that its expression increases with light intensity, but both the minimal and maximal gene transcript levels vary markedly among colour morphs. The pigment concentration in the tissue of different morphs is strongly correlated with the number of gene copies with a particular promoter type. These findings indicate that colour polymorphism in reef corals can be caused by the environmentally regulated expression of multicopy genes. High-level expression of amilFP597 is correlated with reduced photodamage of zooxanthellae under acute light stress, supporting a photoprotective function of this pigment. The cluster of light-regulated pigment genes can enable corals to invest either in expensive high-level pigmentation, offering benefits under light stress, or to rely on low tissue pigment concentrations and use the conserved resources for other purposes, which is preferable in less light-exposed environments. The genomic framework described here allows corals to pursue different strategies to succeed in habitats with highly variable light stress levels. In summary, our results suggest that the intraspecific plasticity of reef corals' stress responses is larger than previously thought. © 2014 The Authors Molecular Ecology Published by John Wiley & Sons Ltd.

  6. Adaptation is...

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC

    vital sector is under threat. While it is far from the only development challenge facing local farmers, extreme variations in the climate of West Africa in the past several decades have dealt the region a bad hand. Drought and flood now follow each other in succession. Adaptation is... “The floods spoiled our harvests and we.

  7. Ambiguous Adaptation

    DEFF Research Database (Denmark)

    Møller Larsen, Marcus; Lyngsie, Jacob

    and reciprocal adaptation of informal governance structure create ambiguity in situations of contingencies, which, subsequently, increases the likelihood of premature relationship termination. Using a large sample of exchange relationships in the global service provider industry, we find support for a hypothesis...

  8. Adaptation Insights

    International Development Research Centre (IDRC) Digital Library (Canada)

    be given greater access to relevant information to help them adapt their farming practices and socio- economic strategies to climate change? To address this challenge, the project “InfoClim,” led by Senegal's. Ecological Monitoring Centre. (CSE) with support from the. CCAA program, aims at improving the access of farmers ...

  9. Adaptive Lighting

    DEFF Research Database (Denmark)

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

    2015-01-01

    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 lighting ceases...

  10. 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.

  11. The addition of a new immunomodulator with the adjuvant adaptation ADAD system using fatty acid binding proteins increases the protection against Fasciola hepatica.

    Science.gov (United States)

    López-Abán, J; Nogal-Ruiz, J J; Vicente, B; Morrondo, P; Diez-Baños, P; Hillyer, G V; Martínez-Fernández, A R; Feliciano, A San; Muro, A

    2008-05-06

    Fatty acid binding proteins (FABP) have shown protective immune response against Fasciola hepatica infection. We evaluated the protection induced by the Fh12 FABP from F. hepatica (Fh12) combined with the new immunomodulator the lipidic aminoalcohol OA0012 in the ADAD system in mice and sheep. In this work we introduced a lipidic aminoalcohol OA0012 as immunomodulator alone or in combination with the hydroalcoholic extract of Phlebodium pseudoaureum; PAL. Mice vaccinated with ADAD containing OA0012+Fh12 or OA0012+Qs+Fh12 had survival rates of 40-50%. Sheep ADAD-vaccinated with OA0012+Qs+Fh12 showed lower fluke recovery, less hepatic lesions and higher post-infection daily weight gain than F. hepatica infected control animals. Sheep ADAD-vaccinated with OA0012 combined PAL and Qs+Fh12 showed lower fluke recovery (42%), lower adult worms count (57%) lower faecal egg count (38%), less hepatic lesions and higher post-infection daily weight gain than F. hepatica infected control animals. Thus, the addition of a new immunomodulator of synthesis to ADAD system with FABPs increased the protection against F. hepatica.

  12. The role of 3D structure and protein conformation on the innate and adaptive immune responses to silk-based biomaterials.

    Science.gov (United States)

    Bhattacharjee, Maumita; Schultz-Thater, Elke; Trella, Emanuele; Miot, Sylvie; Das, Sanskrita; Loparic, Marko; Ray, Alok R; Martin, Ivan; Spagnoli, Giulio C; Ghosh, Sourabh

    2013-11-01

    We have investigated monocyte and T cell responsiveness to silk based biomaterials of different physico-chemical characteristics. Here we report that untransformed CD14+ human monocytes respond to overnight exposure to silk fibroin-based biomaterials in tridimensional form by IL-1β and IL-6, but not IL-10 gene expression and protein production. In contrast, fibroin based materials in bidimensional form are unable to stimulate monocyte responsiveness. The elicitation of these effects critically requires contact between biomaterials and responding cells, is not sustained and becomes undetectable in longer term cultures. We also observed that NF-κβ and p38 MAP kinase play key roles in monocyte activation by silk-based biomaterials. On the other hand, fibroin based materials, irrespective of their physico-chemical characteristics appeared to be unable to induce the activation of peripheral blood T cells from healthy donors, as evaluated by the expression of activation markers and IFN-γ gene. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  13. 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.

  14. Adaptive sampler

    Science.gov (United States)

    Watson, B.L.; Aeby, I.

    1980-08-26

    An adaptive data compression device for compressing data is described. The device has a frequency content, including a plurality of digital filters for analyzing the content of the data over a plurality of frequency regions, a memory, and a control logic circuit for generating a variable rate memory clock corresponding to the analyzed frequency content of the data in the frequency region and for clocking the data into the memory in response to the variable rate memory clock.

  15. Adaptive positioner

    International Nuclear Information System (INIS)

    Labrador Pavon, I.

    1993-01-01

    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

  16. Adaptable positioner

    International Nuclear Information System (INIS)

    Labrador Pavon, I.

    1993-01-01

    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) 22 fig. 6 ref

  17. ADAPTATION EVALUATION

    Directory of Open Access Journals (Sweden)

    Björn PETERS, M.Sc.

    2001-01-01

    Full Text Available Twenty subjects with lower limb disabilities participated in a simulator study. The purpose of the study was to investigate how an Adaptive Cruise Control (ACC system together with two different hand controls for accelerator and brake influenced workload, comfort and driving behaviour and to further develop a method to evaluate vehicle adaptations for drivers with disabilities. The installed ACC system could maintain a constant speed selected and set by the driver and it also adapted speed in order to keep a safe distance to a leading vehicle. Furthermore, it included a stop-and-go function. Two common types of hand controls for accelerator and brake were used. The hand controls were different both with respect to function, single or dual levers, and position, on the steering column or between the front seats. The subjects were all experienced drivers of adapted cars equipped with hand controls. All subjects drove 100km at two occasions, with and without the ACC system available but with the same hand control. Subjective workload was found to be significantly lower and performance better for the ACC condition. The difference in speed variation between manual and ACC supported driving increased with the distance driven which seems to support the previous finding. The subjects thought they could control both speed and distance to leading vehicles better while the ACC was available. ACC driving did not influence reaction time, speed level, lateral position or variation in lateral position. Headway during car following situations was shorter for the ACC condition compared to manual driving. The ACC was well received, trusted and wanted. It was concluded that the ACC system substantially decreased workload, increased comfort and did not influence safety negatively. The only difference found between the two types of hand controls was that drivers using the dual lever system had less variation in lateral position. The applied evaluation method proved

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

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

    Full Text Available 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 network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

  19. Adaptive management

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...... 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...

  20. ADAPTATION TO PROTEIN DEFICIENCY: CORTISOL, THYROXINE ...

    African Journals Online (AJOL)

    On the other hand, the average plasrna glucose level in the letliargrc malnourished pigs was much lower than in the other two groups and it is cclnceivable that this low glucose level. I-rthargic. (L). 4,3 (3,9 - 4.6). 143 (81 - lzs) e(8,14). I .5 (0,6 - 2,9). 86 (42 I 5e). 4s (33 s4). 1,5 (1,4 - 1,8) s2 (37 - s8). Probability. (P). CvsM+L.

  1. Targeting proteins for degradation.

    Science.gov (United States)

    Schrader, Erin K; Harstad, Kristine G; Matouschek, Andreas

    2009-11-01

    Protein degradation plays a central role in many cellular functions. Misfolded and damaged proteins are removed from the cell to avoid toxicity. The concentrations of regulatory proteins are adjusted by degradation at the appropriate time. Both foreign and native proteins are digested into small peptides as part of the adaptive immune response. In eukaryotic cells, an ATP-dependent protease called the proteasome is responsible for much of this proteolysis. Proteins are targeted for proteasomal degradation by a two-part degron, which consists of a proteasome binding signal and a degradation initiation site. Here we describe how both components contribute to the specificity of degradation.

  2. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. 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

  4. Supporting Adaptive and Adaptable Hypermedia Presentation Semantics

    NARCIS (Netherlands)

    D.C.A. Bulterman (Dick); L. Rutledge (Lloyd); L. Hardman (Lynda); J.R. van Ossenbruggen (Jacco)

    1999-01-01

    textabstractHaving the content of a presentation adapt to the needs, resources and prior activities of a user can be an important benefit of electronic documents. While part of this adaptation is related to the encodings of individual data streams, much of the adaptation can/should be guided by the

  5. Proteomic analysis of endothelial cold-adaptation

    Directory of Open Access Journals (Sweden)

    Zieger Michael AJ

    2011-12-01

    Full Text Available Abstract Background Understanding how human cells in tissue culture adapt to hypothermia may aid in developing new clinical procedures for improved ischemic and hypothermic protection. Human coronary artery endothelial cells grown to confluence at 37°C and then transferred to 25°C become resistant over time to oxidative stress and injury induced by 0°C storage and rewarming. This protection correlates with an increase in intracellular glutathione at 25°C. To help understand the molecular basis of endothelial cold-adaptation, isolated proteins from cold-adapted (25°C/72 h and pre-adapted cells were analyzed by quantitative proteomic methods and differentially expressed proteins were categorized using the DAVID Bioinformatics Resource. Results Cells adapted to 25°C expressed changes in the abundance of 219 unique proteins representing a broad range of categories such as translation, glycolysis, biosynthetic (anabolic processes, NAD, cytoskeletal organization, RNA processing, oxidoreductase activity, response-to-stress and cell redox homeostasis. The number of proteins that decreased significantly with cold-adaptation exceeded the number that increased by 2:1. Almost half of the decreases were associated with protein metabolic processes and a third were related to anabolic processes including protein, DNA and fatty acid synthesis. Changes consistent with the suppression of cytoskeletal dynamics provided further evidence that cold-adapted cells are in an energy conserving state. Among the specific changes were increases in the abundance and activity of redox proteins glutathione S-transferase, thioredoxin and thioredoxin reductase, which correlated with a decrease in oxidative stress, an increase in protein glutathionylation, and a recovery of reduced protein thiols during rewarming from 0°C. Increases in S-adenosylhomocysteine hydrolase and nicotinamide phosphoribosyltransferase implicate a central role for the methionine

  6. Serological and genetic characterisation of bovine respiratory syncytial virus (BRSV) indicates that Danish isolates belong to the intermediate subgroup: no evidence of a selective effect on the variability of G protein nucleotide sequence by prior cell culture adaption and passages in cell culture

    DEFF Research Database (Denmark)

    Larsen, Lars Erik; Uttenthal, Åse; Arctander, P.

    1998-01-01

    , respectively. Phylogenetic analysis showed that the Danish isolates formed three lineages within a separate branch of the phylogenetic tree. Nevertheless, the Danish isolates were closely related to the 220-69Bel isolate, the prototype of the intermediate antigenic subgroup. The sequencing of the extracellular...... part of the G gene of additional 11 field BRSV viruses, processed directly from lung samples without prior adaption to cell culture growth. revealed sequence variabilities in the range obtained with the propagated virus. In addition, several passages in cell culture and in calves had no major impact...... on the nucleotide sequence of the G protein. These findings indicated that the previously established variabilities of the G protein of RS virus isolates were not attributable to mutations induced during the propagation of the virus. The reactivity of the Danish isolates with G protein-specific MAbs were similar...

  7. Adaptation illustrations: Chapter 4

    Science.gov (United States)

    Maria Janowiak; Patricia Butler; Chris Swanston; Matt St. Pierre; Linda. Parker

    2012-01-01

    In this chapter, we demonstrate how the Adaptation Workbook (Chapter 3) can be used with the Adaptation Strategies and Approaches (Chapter 2) to develop adaptation tactics for two real-world management issues. The two illustrations in this chapter are intended to provide helpful tips to managers completing the Adaptation Workbook, as well as to show how the anticipated...

  8. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  9. 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…

  10. 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...... test set, the results are important as a proof of existence of differences and of the need for adaptation. The fact that there are individual differences makes the results significant for the development of games and interaction. It indicates that it is necessary to adapt the game and interaction......, if we desire to make the most appropriate game and interaction for the individual. Hence, we investigate adaptation as an important issue for playware. With simple playware games, we show that the adaptation will speed the game up and down to find the appropriate level that matches the reaction speed...

  11. Adapting to climate change

    Science.gov (United States)

    Constance I. Millar; Christopher W. Swanston; David L. Peterson

    2014-01-01

    Federal agencies have led the development of adaptation principles and tools in forest ecosystems over the past decade. Successful adaptation efforts generally require organizations to: (1) develop science-management partnerships, (2) provide education on climate change science, (3) provide a toolkit of methods and processes for vulnerability assessment and adaptation...

  12. Adaptation to climate change

    NARCIS (Netherlands)

    Carmin, J.; Tierney, K.; Chu, E.; Hunter, L.M.; Roberts, J.T.; Shi, L.; Dunlap, R.E.; Brulle, R.J.

    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

  13. Cold adaptation in marine organisms.

    Science.gov (United States)

    Johnston, I A

    1990-01-30

    Animals from polar seas exhibit numerous so called resistance adaptations that serve to maintain homeostasis at low temperature and prevent lethal freezing injury. Specialization to temperatures at or below 0 degrees C is associated with an inability to survive at temperatures above 3-8 degrees C. Polar fish synthesize various types of glycoproteins or peptides to lower the freezing point of most extracellular fluid compartments in a non-colligative manner. Antifreeze production is seasonal in boreal species and is often initiated by environmental cues other than low temperature, particularly short day lengths. Most of the adaptations that enable intertidal invertebrates to survive freezing are associated with their ability to withstand ariel exposure. Unique adaptations for freezing avoidance include the synthesis of low molecular mass ice-nucleating proteins that control and induce extracellular ice-formation. Marine poikilotherms also exhibit a range of capacity adaptations that increase the rate of some physiological processes so as to partially compensate for the effects of low temperature. However, the rate of embryonic development in a diverse range of marine organisms shows no evidence of temperature compensation. This results in a significant lengthening of the time from fertilization to hatching in polar, relative to temperate, species. Some aspects of the physiology of polar marine species, such as low metabolic and slow growth rates, probably result from a combination of low temperature and other factors such as the highly seasonal nature of food supplies. Although neuromuscular function shows a partial capacity adaptation in Antarctic fish, maximum swimming speeds are lower than for temperate and tropical species, particularly for early stages in the life history.

  14. Plant growth, metabolism and adaptation in relation to stress conditions. XXVII. Can ascorbic acid modify the adverse effects of NaCl and mannitol on amino acids, nucleic acids and protein patterns in Vicia faba seedlings?

    Science.gov (United States)

    Younis, M E; Hasaneen, M N A; Kazamel, A M S

    2009-03-01

    The adverse effects of either NaCl or mannitol on amino acids, protein patterns and nucleic acids in Vicia faba seeds were investigated. The exogenous addition of 4 mM ascorbic acid to the stressing media in which the broad bean seeds were germinated in combination with either the ionic (NaCl) or osmotic (mannitol) stressor induced significant protective changes in the total amount and in the relative composition of amino acids in general and in proline, glycine, glutamic, aspartic, alanine and serine in particular. It also induced changes in nucleic acids (RNA and DNA) content. These changes occurred throughout the entire period of the experiments (12 days). Separate administration of NaCl or mannitol enhanced the occurrence of particular novel proteins that were not detected in control bean seeds (water medium). Protein banding patterns of broad bean seedlings treated with NaCl or mannitol in combination with 4 mM ascorbic acid showed different de novo protein bands, with different molecular weights, at different stages of seedlings growth, with lower levels or a nearly complete absence of the major stress proteins. The pattern of changes for amino acids and nucleic acids and the range of protein bands extracted from the variously treated broad bean seedlings indicate a positive role of ascorbic acid in the alleviation of the damage effects induced by NaCl and mannitol. The importance of this role in the stress tolerance of broad beans is discussed.

  15. Thermal hysteresis proteins.

    Science.gov (United States)

    Barrett, J

    2001-02-01

    Extreme environments present a wealth of biochemical adaptations. Thermal hysteresis proteins (THPs) have been found in vertebrates, invertebrates, plants, bacteria and fungi and are able to depress the freezing point of water (in the presence of ice crystals) in a non-colligative manner by binding to the surface of nascent ice crystals. The THPs comprise a disparate group of proteins with a variety of tertiary structures and often no common sequence similarities or structural motifs. Different THPs bind to different faces of the ice crystal, and no single mechanism has been proposed to account for THP ice binding affinity and specificity. Experimentally THPs have been used in the cryopreservation of tissues and cells and to induce cold tolerance in freeze susceptible organisms. THPs represent a remarkable example of parallel and convergent evolution with different proteins being adapted for an anti-freeze role.

  16. Adaptive protection scheme

    Directory of Open Access Journals (Sweden)

    R. Sitharthan

    2016-09-01

    Full Text Available This paper aims at modelling an electronically coupled distributed energy resource with an adaptive protection scheme. The electronically coupled distributed energy resource is a microgrid framework formed by coupling the renewable energy source electronically. Further, the proposed adaptive protection scheme provides a suitable protection to the microgrid for various fault conditions irrespective of the operating mode of the microgrid: namely, grid connected mode and islanded mode. The outstanding aspect of the developed adaptive protection scheme is that it monitors the microgrid and instantly updates relay fault current according to the variations that occur in the system. The proposed adaptive protection scheme also employs auto reclosures, through which the proposed adaptive protection scheme recovers faster from the fault and thereby increases the consistency of the microgrid. The effectiveness of the proposed adaptive protection is studied through the time domain simulations carried out in the PSCAD⧹EMTDC software environment.

  17. 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.

  18. Adaptation as organism design

    OpenAIRE

    Gardner, Andy

    2009-01-01

    The problem of adaptation is to explain the apparent design of organisms. Darwin solved this problem with the theory of natural selection. However, population geneticists, whose responsibility it is to formalize evolutionary theory, have long neglected the link between natural selection and organismal design. Here, I review the major historical developments in theory of organismal adaptation, clarifying what adaptation is and what it is not, and I point out future avenues for research.

  19. The purpose of adaptation

    OpenAIRE

    Gardner, Andy

    2017-01-01

    A central feature of Darwin’s theory of natural selection is that it explains the purpose of biological adaptation. Here, I: emphasise the scientific importance of understanding what adaptations are for, in terms of facilitating the derivation of empirically-testable predictions; discuss the population genetical basis for Darwin’s theory of the purpose of adaptation, with reference to the “fundamental theorem of natural selection”; and show that a deeper understanding of the purpose of adapta...

  20. 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......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...

  1. Quantifying the Adaptive Cycle.

    Directory of Open Access Journals (Sweden)

    David G Angeler

    Full Text Available 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.

  2. 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...

  3. Adaptive optics in microscopy.

    Science.gov (United States)

    Booth, Martin J

    2007-12-15

    The imaging properties of optical microscopes are often compromised by aberrations that reduce image resolution and contrast. Adaptive optics technology has been employed in various systems to correct these aberrations and restore performance. This has required various departures from the traditional adaptive optics schemes that are used in astronomy. This review discusses the sources of aberrations, their effects and their correction with adaptive optics, particularly in confocal and two-photon microscopes. Different methods of wavefront sensing, indirect aberration measurement and aberration correction devices are discussed. Applications of adaptive optics in the related areas of optical data storage, optical tweezers and micro/nanofabrication are also reviewed.

  4. 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.

  5. Crystal structure of Δ(185-243)ApoA-I suggests a mechanistic framework for the protein adaptation to the changing lipid load in good cholesterol: from flatland to sphereland via double belt, belt buckle, double hairpin and trefoil/tetrafoil.

    Science.gov (United States)

    Gursky, Olga

    2013-01-09

    Apolipoprotein A-I (apoA-I) is the major protein of plasma high-density lipoproteins (HDLs), macromolecular assemblies of proteins and lipids that remove cell cholesterol and protect against atherosclerosis. HDL heterogeneity, large size (7.7-12 nm), and ability to exchange proteins have prevented high-resolution structural analysis. Low-resolution studies showed that two apoA-I molecules form an antiparallel α-helical "double belt" around an HDL particle. The atomic-resolution structure of the C-terminal truncated lipid-free Δ(185-243)apoA-I, determined recently by Mei and Atkinson, provides unprecedented new insights into HDL structure-function. It allows us to propose a molecular mechanism for the adaptation of the full-length protein to increasing lipid load during cholesterol transport. ApoA-I conformations on small, midsize, and large HDLs are proposed based on the tandem α-helical repeats and the crystal structure of Δ(185-243)apoA-I and are validated by comparison with extensive biophysical data reported by many groups. In our models, the central half of the double belt ("constant" segment 66-184) is structurally conserved while the N- and C-terminal half ("variable" segments 1-65 and 185-243) rearranges upon HDL growth. This includes incremental unhinging of the N-terminal bundle around two flexible regions containing G39 and G65 to elongate the belt, along with concerted swing motion of the double belt around G65-P66 and G185-G186 hinges that are aligned on various-size particles, to confer two-dimensional surface curvature to spherical HDLs. The proposed conformational ensemble integrates and improves several existing HDL models. It helps provide a structural framework necessary to understand functional interactions with over 60 other HDL-associated proteins and, ultimately, improve the cardioprotective function of HDL. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Crystal Structure of Δ(185–243)apoA-I Suggests a Mechanistic Framework for the Protein Adaptation to the Changing Lipid Load in Good Cholesterol: From Flatland to Sphereland via Double Belt, Belt-Buckle, Double Hairpin and Trefoil/Tetrafoil

    Science.gov (United States)

    Gursky, Olga

    2012-01-01

    ApoA-I is the major protein of plasma high-density lipoproteins (HDL), macromolecular assemblies of proteins and lipids that remove cell cholesterol and protect against atherosclerosis. HDL heterogeneity, large size (7.7–12 nm) and ability to exchange proteins have prevented high-resolution structural analysis. Low-resolution studies showed that two apoA-I molecules form an antiparallel α-helical “double belt” around an HDL particle. Atomic-resolution structure of the C-terminal truncated lipid-free Δ(185–243)apoA-I, determined recently by Mei and Atkinson, provides unprecedented new insights into HDL structure-function. It allows us to propose a molecular mechanism for the adaptation of the full-length protein to increasing lipid load during cholesterol transport. ApoA-I conformations on the small, mid-size and large HDL are proposed based on the tandem α-helical repeats and the crystal structure of Δ(185–243)apoA-I, and are validated by comparison with extensive biophysical data reported by many groups. In our models, the central half of the double belt (“constant” segment 66–184) is structurally conserved while the N- and C-terminal half (“variable” segments 1–65 and 185–243) re-arranges upon HDL growth. This includes incremental unhinging of the N-terminal bundle around two flexible regions containing G39 and G65 to elongate the belt, along with concerted swing motion of the double belt around G65-P66 and G185–G186 hinges that are aligned on various-size particles, to confer 2D surface curvature to spherical HDL. The proposed conformational ensemble integrates and improves several existing HDL models. It helps provide a structural framework necessary to understand functional interactions with over 60 other HDL-associated proteins and, ultimately, improve cardioprotective function of HDL. PMID:23041415

  7. Cold adaptation of enzyme reaction rates.

    Science.gov (United States)

    Bjelic, Sinisa; Brandsdal, Bjørn O; Aqvist, Johan

    2008-09-23

    A major issue for organisms living at extreme temperatures is to preserve both stability and activity of their enzymes. Cold-adapted enzymes generally have a reduced thermal stability, to counteract freezing, and show a lower enthalpy and a more negative entropy of activation compared to mesophilic and thermophilic homologues. Such a balance of thermodynamic activation parameters can make the reaction rate decrease more linearly, rather than exponentially, as the temperature is lowered, but the structural basis for rate optimization toward low working temperatures remains unclear. In order to computationally address this problem, it is clear that reaction simulations rather than standard molecular dynamics calculations are needed. We have thus carried out extensive computer simulations of the keto-enol(ate) isomerization steps in differently adapted citrate synthases to explore the structure-function relationships behind catalytic rate adaptation to different temperatures. The calculations reproduce the absolute rates of the psychrophilic and mesophilic enzymes at 300 K, as well as the lower enthalpy and more negative entropy of activation of the cold-adapted enzyme, where the latter simulation result is obtained from high-precision Arrhenius plots. The overall catalytic effect originates from electrostatic stabilization of the transition state and enolate and the reduction of reorganization free energy. The simulations, however, show psychrophilic, mesophilic, and hyperthermophilic citrate synthases to have increasingly stronger electrostatic stabilization of the transition state, while the energetic penalty in terms of internal protein interactions follows the reverse order with the cold-adapted enzyme having the most favorable energy term. The lower activation enthalpy and more negative activation entropy observed for cold-adapted enzymes are found to be associated with a decreased protein stiffness. The origin of this effect is, however, not localized to the

  8. 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.

  9. Management for adaptation

    Science.gov (United States)

    John Innes; Linda A. Joyce; Seppo Kellomaki; Bastiaan Louman; Aynslie Ogden; Ian Thompson; Matthew Ayres; Chin Ong; Heru Santoso; Brent Sohngen; Anita Wreford

    2009-01-01

    This chapter develops a framework to explore examples of adaptation options that could be used to ensure that the ecosystem services provided by forests are maintained under future climates. The services are divided into broad areas within which managers can identify specific management goals for individual forests or landscapes. Adaptation options exist for the major...

  10. Detachable caster adapter

    Science.gov (United States)

    Mohr, R. J.

    1969-01-01

    Detachable caster adapter moves heavy welding tables when fork lift trucks are not practical. A support saddle on the adapter, connected to the caster platform by means of a hinge, fits the leg of the welding table, but can be modified to fit other leg configurations.

  11. Human pathogen avoidance adaptations

    NARCIS (Netherlands)

    Tybur, J.M.; Lieberman, D.

    2016-01-01

    Over the past few decades, researchers have become increasingly interested in the adaptations guiding the avoidance of disease-causing organisms. Here we discuss the latest developments in this area, including a recently developed information-processing model of the adaptations underlying pathogen

  12. Adaptation investments and homeownership

    DEFF Research Database (Denmark)

    Hansen, Jørgen Drud; Skak, Morten

    2008-01-01

    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...

  13. Adaptation investments and homeownership

    DEFF Research Database (Denmark)

    Hansen, Jørgen Drud; Skak, Morten

    2008-01-01

    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...

  14. Introduction: Adapting Idols

    NARCIS (Netherlands)

    Joost Bruin; dr. Koos Zwaan

    2012-01-01

    Introduction book Adapting Idols Since the first series of Pop Idol aired in the UK just over a decade ago, Idols television shows have been broadcast in more than forty countries all over the world. In all those countries the global Idols format has been adapted to local cultures and production

  15. Adaptive noise cancellation

    International Nuclear Information System (INIS)

    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. (author)

  16. Turbine system and adapter

    Energy Technology Data Exchange (ETDEWEB)

    Hogberg, Nicholas Alvin; Garcia-Crespo, Andres Jose

    2017-05-30

    A turbine system and adapter are disclosed. The adapter includes a turbine attachment portion having a first geometry arranged to receive a corresponding geometry of a wheelpost of a turbine rotor, and a bucket attachment portion having a second geometry arranged to receive a corresponding geometry of a root portion of a non-metallic turbine bucket. Another adapter includes a turbine attachment portion arranged to receive a plurality of wheelposts of a turbine rotor, and a bucket attachment portion arranged to receive a plurality of non-metallic turbine buckets having single dovetail configuration root portions. The turbine system includes a turbine rotor wheel configured to receive metal buckets, at least one adapter secured to at least one wheelpost on the turbine rotor wheel, and at least one non-metallic bucket secured to the at least one adapter.

  17. 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.

  18. Adaptive Processes in Hearing

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Christensen-Dalsgaard, Jakob; Tranebjærg, Lisbeth

    2018-01-01

    induced by hearing impairment and the compensation provided by hearing devices. These devices themselves are now able to adapt to the listener’s individual environment, attentional state, and behavior. These topics related to auditory adaptation, in the broad sense of the term, were central to the 6th......Our auditory environment is constantly changing and evolving over time, requiring us to rapidly adapt to a complex dynamic sensory input. This adaptive ability of our auditory system can be observed at different levels, from individual cell responses to complex neural mechanisms and behavior...... International Symposium on Auditory and Audiological Research held in Nyborg, Denmark, in August 2017. The symposium addressed adaptive processes in hearing from different angles, together with a wide variety of other auditory and audiological topics. The papers in this special issue result from some...

  19. Adaptive signal processor

    Energy Technology Data Exchange (ETDEWEB)

    Walz, H.V.

    1980-07-01

    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 ..mu..sec. 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.

  20. Adaptive signal processor

    International Nuclear Information System (INIS)

    Walz, H.V.

    1980-07-01

    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

  1. Transition and adaptation

    DEFF Research Database (Denmark)

    Andrade, Stefan Bastholm

    2015-01-01

    This article analyses how Danish farm families adapted to harsh and changing conditions in the period after the great western agricultural crisis in the early 1980s. Drawing on Bourdieu's concepts of habitus and adaptation, I analyse the creation and consolidation of different class fractions...... their agricultural production annually from 1980–2008. The result is a five-farmer typology that, together with logit regression models including background covariates, reveals how the farm families' adaptation strategies relate to educational level, financial situation, family composition and whether the farmer can...... amongst farm families due to different adaptation strategies. The data contain information about the population of self-employed farmers and their families who were between 30–35 years old in 1980 (n = 9,123). Using sequence analysis, I examine farm families' adaptation strategies for maintaining...

  2. 75 FR 57859 - Specially Adapted Housing and Special Home Adaptation

    Science.gov (United States)

    2010-09-23

    ... Home Adaptation AGENCY: Department of Veterans Affairs. ACTION: Final rule. SUMMARY: The Department of... specially adapted housing and special home adaptation grants. This final rule incorporates certain... regulations pertaining to eligibility for specially adapted housing (SAH) grants and special home adaptation...

  3. [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. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  4. Symmetry Adapted Basis Sets

    DEFF Research Database (Denmark)

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

    In theoretical physics, theoretical chemistry and engineering, one often wishes to solve partial differential equations subject to a set of boundary conditions. This gives rise to eigenvalue problems of which some solutions may be very difficult to find. For example, the problem of finding...... 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...

  5. 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

  6. 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...

  7. Fuzzy controller adaptation

    Science.gov (United States)

    Myravyova, E. A.; Sharipov, M. I.; Radakina, D. S.

    2017-10-01

    During writing this work, the fuzzy controller with a double base of rules was studied, which was applied for the synthesis of the automated control system. A method for fuzzy controller adaptation has been developed. The adaptation allows the fuzzy controller to automatically compensate for parametric interferences that occur at the control object. Specifically, the fuzzy controller controlled the outlet steam temperature in the boiler unit BKZ-75-39 GMA. The software code was written in the programming support environment Unity Pro XL designed for fuzzy controller adaptation.

  8. 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.

  9. Transformer: an adaptation framework supporting contextual adaptation behavior composition

    OpenAIRE

    Gui, Ning; De Florio, Vincenzo; Holvoet, Tom

    2013-01-01

    As software systems today increasingly operate in changing and complex environments, they are expected to dynamically adapt to the changing environments sometimes with multiple co-existing adaptation goals. This paper proposes an adaptation framework to facilitate adaptation with multiple concerns by using reusable and composable adaptation modules. Rather than using one-size-fits-all approach, in this framework, system global adaptation behavior is generated by contextually fusin...

  10. 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...

  11. Exploring adaptive program behavior

    DEFF Research Database (Denmark)

    Bonnichsen, Lars Frydendal; Probst, Christian W.

    Modern computer systems are increasingly complex, with ever changing bottlenecks. This makes it difficult to ensure consistent performance when porting software, or even running it. Adaptivity, ie, switching between program variations, and dynamic recompilation have been suggested as solutions. B...

  12. 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...

  13. Adaptive optics in ophthalmology

    Science.gov (United States)

    Iroshnikov, Nikita G.; Larichev, Andrey V.

    2006-09-01

    We present the experimental implementation of ophthalmic diagnostic systems with adaptive optics compensation of human eye aberration. The systems feature high speed operation and utilize deformable bimorph mirrors for wavefront correction. The results of aberration measurements and correction are discussed.

  14. Adaptation and Influence

    DEFF Research Database (Denmark)

    Paster, Thomas

    on influence. These two dimensions - adaptation and influence - result in four ideal types: business-dominated social compromise, imposed social compromise, business dominance, and political confrontation. Examples from German welfare state history illustrate these four types. The paper suggests...

  15. Exploring Adaptive Program Behavior

    DEFF Research Database (Denmark)

    Bonnichsen, Lars Frydendal; Probst, Christian W.

    Modern computer systems are increasingly complex, with ever changing bottlenecks. This makes it difficult to ensure consistent performance when porting software, or even running it. Adaptivity, ie, switching between program variations, and dynamic recompilation have been suggested as solutions. B...

  16. 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...

  17. Adaptive Trajectory Design

    Data.gov (United States)

    National Aeronautics and Space Administration — Adaptive Trajectory Design (ATD) is an original concept for quick and efficient end-to-end trajectory designs using proven piece-wise dynamical methods. With ongoing...

  18. Adaptive multiresolution methods

    Directory of Open Access Journals (Sweden)

    Schneider Kai

    2011-12-01

    Full Text Available These lecture notes present adaptive multiresolution schemes for evolutionary PDEs in Cartesian geometries. The discretization schemes are based either on finite volume or finite difference schemes. The concept of multiresolution analyses, including Harten’s approach for point and cell averages, is described in some detail. Then the sparse point representation method is discussed. Different strategies for adaptive time-stepping, like local scale dependent time stepping and time step control, are presented. Numerous numerical examples in one, two and three space dimensions validate the adaptive schemes and illustrate the accuracy and the gain in computational efficiency in terms of CPU time and memory requirements. Another aspect, modeling of turbulent flows using multiresolution decompositions, the so-called Coherent Vortex Simulation approach is also described and examples are given for computations of three-dimensional weakly compressible mixing layers. Most of the material concerning applications to PDEs is assembled and adapted from previous publications [27, 31, 32, 34, 67, 69].

  19. Adaptive Spectral Doppler Estimation

    DEFF Research Database (Denmark)

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

    2009-01-01

    . The methods can also provide better quality of the estimated power spectral density (PSD) of the blood signal. Adaptive spectral estimation techniques are known to pro- vide good spectral resolution and contrast even when the ob- servation window is very short. The 2 adaptive techniques are tested......In this paper, 2 adaptive spectral estimation techniques are analyzed for spectral Doppler ultrasound. The purpose is to minimize the observation window needed to estimate the spectrogram to provide a better temporal resolution and gain more flexibility when designing the data acquisition sequence...... and compared with the averaged periodogram (Welch’s method). The blood power spectral capon (BPC) method is based on a standard minimum variance technique adapted to account for both averaging over slow-time and depth. The blood amplitude and phase estimation technique (BAPES) is based on finding a set...

  20. ABC transporters in adaptive immunity.

    Science.gov (United States)

    Seyffer, Fabian; Tampé, Robert

    2015-03-01

    ABC transporters ubiquitously found in all kingdoms of life move a broad range of solutes across membranes. Crystal structures of four distinct types of ABC transport systems have been solved, shedding light on different conformational states within the transport process. Briefly, ATP-dependent flipping between inward- and outward-facing conformations allows directional transport of various solutes. The heterodimeric transporter associated with antigen processing TAP1/2 (ABCB2/3) is a crucial element of the adaptive immune system. The ABC transport complex shuttles proteasomal degradation products into the endoplasmic reticulum. These antigenic peptides are loaded onto major histocompatibility complex class I molecules and presented on the cell surface. We detail the functional modules of TAP, its ATPase and transport cycle, and its interaction with and modulation by other cellular components. In particular, we emphasize how viral factors inhibit TAP activity and thereby prevent detection of the infected host cell by cytotoxic T-cells. Merging functional details on TAP with structural insights from related ABC transporters refines the understanding of solute transport. Although human ABC transporters are extremely diverse, they still may employ conceptually related transport mechanisms. Appropriately, we delineate a working model of the transport cycle and how viral factors arrest TAP in distinct conformations. Deciphering the transport cycle of human ABC proteins is the major issue in the field. The defined peptidic substrate, various inhibitory viral factors, and its role in adaptive immunity provide unique tools for the investigation of TAP, making it an ideal model system for ABC transporters in general. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Climate Change Adaptation Approaches

    Science.gov (United States)

    2011-05-11

    US Army Corps of Engineers BUILDING STRONG® Climate Change Adaptation Approaches Presented at the E2S2 Symposium May 11th, 2011 New Orleans, LA...COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Climate Change Adaptation Approaches 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...10/09).  One of the four priorities is to maintain readiness in the face of climate change .  Addressing Climate Change Risk and Vulnerability: a

  2. 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.

  3. 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.

  4. Interfacial Protein-Protein Associations

    OpenAIRE

    Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2013-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for ...

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

    International Nuclear Information System (INIS)

    Berkhout, F.; Hertin, J.; Gann, D.M.

    2006-01-01

    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

  6. On the role of electrostatics on protein-protein interactions

    Science.gov (United States)

    Zhang, Zhe; Witham, Shawn; Alexov, Emil

    2011-01-01

    The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity. PMID:21572182

  7. On the role of electrostatics in protein-protein interactions

    Science.gov (United States)

    Zhang, Zhe; Witham, Shawn; Alexov, Emil

    2011-06-01

    The role of electrostatics in protein-protein interactions and binding is reviewed in this paper. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and the basic electrostatic effects occurring upon the formation of the complex are discussed. The effect of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated which indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartments. The similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity.

  8. Adaptation to nicotine feeding in Myzus persicae.

    Science.gov (United States)

    Ramsey, John S; Elzinga, Dezi A; Sarkar, Pooja; Xin, Yi-Ran; Ghanim, Murad; Jander, Georg

    2014-08-01

    Lineages of the generalist hemipteran herbivore Myzus persicae (green peach aphid) that have expanded their host range to include tobacco often have elevated nicotine tolerance. The tobacco-adapted M. persicae lineage used in this study was able to reproduce on nicotine-containing artificial diets at concentrations that were 15-fold higher than those that were lethal to a non-adapted M. persicae lineage. Fecundity of the nicotine-tolerant M. persicae lineage was increased by 100 μM nicotine in artificial diet, suggesting that this otherwise toxic alkaloid can serve as a feeding stimulant at low concentrations. This lineage also was pre-adapted to growth on tobacco, exhibiting no drop in fecundity when it was moved onto tobacco from a different host plant. Although growth of the non-tobacco-adapted M. persicae lineage improved after three generations on tobacco, this higher reproductive rate was not associated with increased nicotine tolerance. Myzus persicae gene expression microarrays were used to identify transcripts that are up-regulated in response to nicotine in the tobacco-adapted lineage. Induced expression was found for CYP6CY3, which detoxifies nicotine in M. persicae, other genes encoding known classes of detoxifying enzymes, and genes encoding secreted M. persicae salivary proteins.

  9. 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

  10. 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.

  11. 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.

  12. Training adaptive teams.

    Science.gov (United States)

    Gorman, Jamie C; Cooke, Nancy J; Amazeen, Polemnia G

    2010-04-01

    We report an experiment in which three training approaches are compared with the goal of training adaptive teams. Cross-training is an established method in which team members are trained with the goal of building shared knowledge. Perturbation training is a new method in which team interactions are constrained to provide new coordination experiences during task acquisition. These two approaches, and a more traditional procedural approach, are compared. Assigned to three training conditions were 26 teams. Teams flew nine simulated uninhabited air vehicle missions; three were critical tests of the team's ability to adapt to novel situations. Team performance, response time to novel events, and shared knowledge were measured. Perturbation-trained teams significantly outperformed teams in the other conditions in two out of three critical test missions. Cross-training resulted in significant increases in shared teamwork knowledge and highest mean performance in one critical test. Procedural training led to the least adaptive teams. Perturbation training allows teams to match coordination variability during training to demands for coordination variability during posttraining performance. Although cross-training has adaptive benefits, it is suggested that process-oriented approaches, such as perturbation training, can lead to more adaptive teams. Perturbation training is amenable to simulation-based training, where perturbations provide interaction experiences that teams can transfer to novel, real-world situations.

  13. Biophysics of protein evolution and evolutionary protein biophysics

    Science.gov (United States)

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  14. Novel polymorphisms in UTR and coding region of inducible heat shock protein 70.1 gene in tropically adapted Indian zebu cattle (Bos indicus) and riverine buffalo (Bubalus bubalis).

    Science.gov (United States)

    Sodhi, M; Mukesh, M; Kishore, A; Mishra, B P; Kataria, R S; Joshi, B K

    2013-09-25

    Due to evolutionary divergence, cattle (taurine, and indicine) and buffalo are speculated to have different responses to heat stress condition. Variation in candidate genes associated with a heat-shock response may provide an insight into the dissimilarity and suggest targets for intervention. The present work was undertaken to characterize one of the inducible heat shock protein genes promoter and coding regions in diverse breeds of Indian zebu cattle and buffaloes. The genomic DNA from a panel of 117 unrelated animals representing 14 diversified native cattle breeds and 6 buffalo breeds were utilized to determine the complete sequence and gene diversity of HSP70.1 gene. The coding region of HSP70.1 gene in Indian zebu cattle, Bos taurus and buffalo was similar in length (1,926 bp) encoding a HSP70 protein of 641 amino acids with a calculated molecular weight (Mw) of 70.26 kDa. However buffalo had a longer 5' and 3' untranslated region (UTR) of 204 and 293 nucleotides respectively, in comparison to Indian zebu cattle and Bos taurus wherein length of 5' and 3'-UTR was 172 and 286 nucleotides, respectively. The increased length of buffalo HSP70.1 gene compared to indicine and taurine gene was due to two insertions each in 5' and 3'-UTR. Comparative sequence analysis of cattle (taurine and indicine) and buffalo HSP70.1 gene revealed a total of 54 gene variations (50 SNPs and 4 INDELs) among the three species in the HSP70.1 gene. The minor allele frequencies of these nucleotide variations varied from 0.03 to 0.5 with an average of 0.26. Among the 14 B. indicus cattle breeds studied, a total of 19 polymorphic sites were identified: 4 in the 5'-UTR and 15 in the coding region (of these 2 were non-synonymous). Analysis among buffalo breeds revealed 15 SNPs throughout the gene: 6 at the 5' flanking region and 9 in the coding region. In bubaline 5'-UTR, 2 additional putative transcription factor binding sites (Elk-1 and C-Re1) were identified, other than three common sites

  15. Multi-modal exercise training and protein-pacing enhances physical performance adaptations independent of growth hormone and BDNF but may be dependent on IGF-1 in exercise-trained men.

    Science.gov (United States)

    Ives, Stephen J; Norton, Chelsea; Miller, Vincent; Minicucci, Olivia; Robinson, Jake; O'Brien, Gabe; Escudero, Daniela; Paul, Maia; Sheridan, Caitlin; Curran, Kathryn; Rose, Kayla; Robinson, Nathaniel; He, Feng; Arciero, Paul J

    2017-02-01

    Protein-pacing (P; 5-6meals/day @ 2.0g/kgBW/day) and multi-mode exercise (RISE; resistance, interval, stretching, endurance) training (PRISE) improves muscular endurance, strength, power and arterial health in exercise-trained women. The current study extends these findings by examining PRISE on fitness, growth hormone (GH), insulin-like growth factor-1 (IGF-1), and brain-derived neurotrophic factor (BDNF) response, cardiometabolic health, and body composition in exercise-trained men. Twenty active males (>4daysexercise/week) completed either: PRISE (n=11) or RISE (5-6meals/day @ 1.0g/kgBW/day; n=9) for 12weeks. Muscular strength (1-repetition maximum bench and leg press, 1-RM BP, and 1-RM LP), endurance (sit-ups, SU; push-ups, PU), power (squat jump, SJ, and bench throw, BT), flexibility (sit-and-reach, SR), aerobic performance (5km cycling time-trial, TT), GH, IGF-1, BDNF, augmentation index, (AIx), and body composition, were assessed at weeks 0 (pre) and 13 (post). At baseline, no differences existed between groups except for GH (RISE, 230±13 vs. PRISE, 382±59pg/ml, pexercise intervention improved 1-RM, SJ, BT, PU, SU, SR, 5km-TT, GH, AIx, BP, and body composition in both groups (time, pExercise-trained men consuming a P diet combined with multi-component exercise training (PRISE) enhance muscular power, strength, aerobic performance, and flexibility which are not likely related to GH or BDNF but possibly to IGF-1 response. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  16. 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...... to the premise that “fit” between an organization’s external context and its internal structure may enhance performance, but also to the suggestion that the adaptation process may be asymmetric (Moon et al., 2004). Further, the paper contributes to practice by highlighting both the opportunities and risks...

  17. 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...... of the home choose ownership. This article analyses the consumer's optimization. The model provides an explanation for the observation that homeowners typically live in larger dwelling units than tenants. It also provides and explanation for a high price on housing services tending to reduce homeownership...

  18. Adaptive dynamical networks

    Science.gov (United States)

    Maslennikov, O. V.; Nekorkin, V. I.

    2017-10-01

    Dynamical networks are systems of active elements (nodes) interacting with each other through links. Examples are power grids, neural structures, coupled chemical oscillators, and communications networks, all of which are characterized by a networked structure and intrinsic dynamics of their interacting components. If the coupling structure of a dynamical network can change over time due to nodal dynamics, then such a system is called an adaptive dynamical network. The term ‘adaptive’ implies that the coupling topology can be rewired; the term ‘dynamical’ implies the presence of internal node and link dynamics. The main results of research on adaptive dynamical networks are reviewed. Key notions and definitions of the theory of complex networks are given, and major collective effects that emerge in adaptive dynamical networks are described.

  19. Engineering Adaptive Web Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    2007-01-01

    Information and services on the web are accessible for everyone. Users of the web differ in their background, culture, political and social environment, interests and so on. Ambient intelligence was envisioned as a concept for systems which are able to adapt to user actions and needs....... 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...

  20. 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.

  1. Adapt or Become Extinct!

    DEFF Research Database (Denmark)

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

    2011-01-01

    The High-Performance Computing ecosystem consists of a large variety of execution platforms that demonstrate a wide diversity in hardware characteristics such as CPU architecture, memory organization, interconnection network, accelerators, etc. This environment also presents a number of hard boun...... 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....

  2. 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...

  3. Engineering Adaptive Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    . The different requirements might be satisfied by different variants of features maintained and provided by Web applications. An adaptive Web application can be seen as a family of Web applications where application instances are those generated for particular user based on his characteristics relevant...... 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...

  4. 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...

  5. 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

  6. SpotADAPT

    DEFF Research Database (Denmark)

    Kaulakiene, Dalia; Thomsen, Christian; Pedersen, Torben Bach

    2015-01-01

    by Amazon Web Services (AWS). The users aiming for the spot market are presented with many instance types placed in multiple datacenters in the world, and thus it is difficult to choose the optimal deployment. In this paper, we propose the framework SpotADAPT (Spot-Aware (re-)Deployment of Analytical...... execution within boundaries). Moreover, during the execution of the workload, SpotADAPT suggests a redeployment if the current spot instance gets terminated by Amazon or a better deployment becomes possible due to fluctuations of the spot prices. The approach is evaluated using the actual execution times...

  7. Learning and Domain Adaptation

    Science.gov (United States)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  8. 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...

  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. Hybrid Adaptive Flight Control with Model Inversion Adaptation

    Science.gov (United States)

    Nguyen, Nhan

    2011-01-01

    This study investigates a hybrid adaptive flight control method as a design possibility for a flight control system that can enable an effective adaptation strategy to deal with off-nominal flight conditions. The hybrid adaptive control blends both direct and indirect adaptive control in a model inversion flight control architecture. The blending of both direct and indirect adaptive control provides a much more flexible and effective adaptive flight control architecture than that with either direct or indirect adaptive control alone. The indirect adaptive control is used to update the model inversion controller by an on-line parameter estimation of uncertain plant dynamics based on two methods. The first parameter estimation method is an indirect adaptive law based on the Lyapunov theory, and the second method is a recursive least-squares indirect adaptive law. The model inversion controller is therefore made to adapt to changes in the plant dynamics due to uncertainty. As a result, the modeling error is reduced that directly leads to a decrease in the tracking error. In conjunction with the indirect adaptive control that updates the model inversion controller, a direct adaptive control is implemented as an augmented command to further reduce any residual tracking error that is not entirely eliminated by the indirect adaptive control.

  11. Proteins engineering

    International Nuclear Information System (INIS)

    2000-01-01

    At the - Departement d'Ingenierie et d'etudes de proteines (Deip) of the CEA more than seventy researchers are working hard to understand the function of proteins. For that they use the molecular labelling technique (F.M.)

  12. 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 ...

  13. Adaptation and mitigation

    Science.gov (United States)

    Constance I. Millar; Kenneth E. Skog; Duncan C. McKinley; Richard A. Birdsey; Christopher W. Swanston; Sarah J. Hines; Christopher W. Woodall; Elizabeth D. Reinhardt; David L. Peterson; James M. Vose

    2012-01-01

    Forest ecosystems respond to natural climatic variability and human-caused climate change in ways that are adverse as well as beneficial to the biophysical environment and to society. Adaptation refers to responses or adjustments made—whether passive, reactive, or anticipatory—to climatic variability and change (Carter et al. 1994). Many adjustments occur whether...

  14. CLIMATE CHANGE ADAPTATION

    International Development Research Centre (IDRC) Digital Library (Canada)

    Cathy Egan

    change exacerbates shocks and stresses. The capacity of communities to adapt can be improved if they have access to economic and physical resources, as well as to technology, information, infra- structure, and institutions. Public policies can help provide these resources. But what happens if the policies themselves have ...

  15. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    living in the future could occur, if built spaces could evolve and adapt alongside inhabitants. As such, present study explores the interdisciplinary possibilities in utilizing computational power to co-create with users and generate designs based on human input. We argue that this could lead...

  16. 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...

  17. Creating Adaptive Policies

    International Development Research Centre (IDRC) Digital Library (Canada)

    Signs of the imperative for adaptive policy-making are coming from all sectors of our economy including healthcare, transportation, business, information technology, energy, international development, agriculture and natural resources management, to name but a few. We highlight these examples in the following sections ...

  18. The governance of adaptation

    NARCIS (Netherlands)

    Huitema, Dave; Adger, William Neil; Berkhout, Frans; Massey, Eric; Mazmanian, Daniel; Munaretto, Stefania; Plummer, Ryan; Termeer, Katrien

    2016-01-01

    The governance of climate adaptation involves the collective efforts of multiple societal actors to address problems, or to reap the benefits, associated with impacts of climate change. Governing involves the creation of institutions, rules and organizations, and the selection of normative

  19. ADAM: ADaptive Autonomous Machine

    NARCIS (Netherlands)

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

    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

  20. Adaptive sequential controller

    Energy Technology Data Exchange (ETDEWEB)

    El-Sharkawi, Mohamed A. (Renton, WA); Xing, Jian (Seattle, WA); Butler, Nicholas G. (Newberg, OR); Rodriguez, Alonso (Pasadena, CA)

    1994-01-01

    An adaptive sequential controller (50/50') for controlling a circuit breaker (52) or other switching device to substantially eliminate transients on a distribution line caused by closing and opening the circuit breaker. The device adaptively compensates for changes in the response time of the circuit breaker due to aging and environmental effects. A potential transformer (70) provides a reference signal corresponding to the zero crossing of the voltage waveform, and a phase shift comparator circuit (96) compares the reference signal to the time at which any transient was produced when the circuit breaker closed, producing a signal indicative of the adaptive adjustment that should be made. Similarly, in controlling the opening of the circuit breaker, a current transformer (88) provides a reference signal that is compared against the time at which any transient is detected when the circuit breaker last opened. An adaptive adjustment circuit (102) produces a compensation time that is appropriately modified to account for changes in the circuit breaker response, including the effect of ambient conditions and aging. When next opened or closed, the circuit breaker is activated at an appropriately compensated time, so that it closes when the voltage crosses zero and opens when the current crosses zero, minimizing any transients on the distribution line. Phase angle can be used to control the opening of the circuit breaker relative to the reference signal provided by the potential transformer.

  1. Adaptive sequential controller

    Science.gov (United States)

    El-Sharkawi, Mohamed A.; Xing, Jian; Butler, Nicholas G.; Rodriguez, Alonso

    1994-01-01

    An adaptive sequential controller (50/50') for controlling a circuit breaker (52) or other switching device to substantially eliminate transients on a distribution line caused by closing and opening the circuit breaker. The device adaptively compensates for changes in the response time of the circuit breaker due to aging and environmental effects. A potential transformer (70) provides a reference signal corresponding to the zero crossing of the voltage waveform, and a phase shift comparator circuit (96) compares the reference signal to the time at which any transient was produced when the circuit breaker closed, producing a signal indicative of the adaptive adjustment that should be made. Similarly, in controlling the opening of the circuit breaker, a current transformer (88) provides a reference signal that is compared against the time at which any transient is detected when the circuit breaker last opened. An adaptive adjustment circuit (102) produces a compensation time that is appropriately modified to account for changes in the circuit breaker response, including the effect of ambient conditions and aging. When next opened or closed, the circuit breaker is activated at an appropriately compensated time, so that it closes when the voltage crosses zero and opens when the current crosses zero, minimizing any transients on the distribution line. Phase angle can be used to control the opening of the circuit breaker relative to the reference signal provided by the potential transformer.

  2. Time to adapt

    International Nuclear Information System (INIS)

    Parry, M.

    2008-01-01

    As every month goes by it becomes increasingly clear that we will need to adapt to climate change. Of course, early action needs to be taken to mitigate it by reducing emissions of greenhouse gases, but this must be complemented by investment in adaptation in the places most affected. The sooner we put resources into adaptation the less damage will be sustained. The latest assessment by the Intergovernmental Panel on Climate Change (IPCC) came to the new conclusion that the effects of climate change are occurring now. The Earth has already warmed by 0.5 degrees C due to increases in atmospheric greenhouse gases, and we can observe the effects of this on every continent - most troublingly the current drying and warming in Africa's Sahelian region, and the effects of sea-level rise on coastal flood plains and small islands. Inevitably, some adaptation is also occurring now but little of this is planned and almost no additional resources have yet been deployed toward it. Some further warming is inevitable. Even if we were to cut emissions both immediately and so enormously that greenhouse gas concentrations in the atmosphere are stabilised at current levels - an impossible task - a temperature increase of a further 0.6 degrees C would still be inevitable due to thermal lag of the oceans and atmosphere. So 1.1 degrees C of climate change is the very least that we should plan for. The impacts from such an increase will probably include: reduced water availability - with consequent falls in agricultural productivity - in the dry tropics; increased coastal flooding; and increased morbidity and mortality from heat waves and droughts. Adaptation is the only way of avoiding or reducing these

  3. Molecular adaptations to concurrent training.

    Science.gov (United States)

    de Souza, E O; Tricoli, V; Roschel, H; Brum, P C; Bacurau, A V N; Ferreira, J C B; Aoki, M S; Neves, M; Aihara, A Y; da Rocha Correa Fernandes, A; Ugrinowitsch, C

    2013-03-01

    This study investigated the chronic effects of concurrent training (CT) on morphological and molecular adaptations. 37 men (age=23.7±5.5 year) were divided into 4 groups: interval (IT), strength (ST) and concurrent (CT) training and a control group (C) and underwent 8 weeks of training. Maximum strength (1RM) and muscle cross-sectional area (CSA) were evaluated before and after training. Muscle samples were obtained before the training program and 48 h after the last training session. VO2max improved in 5±0.95% and 15±1.3% (pre- to post-test) in groups CT and IT, respectively, when compared to C. Time to exhaustion (TE) improved from pre- to post-test when compared to C (CT=6.1±0.58%; IT=8.3±0.88%; ST=3.2±0.66%). 1RM increased from pre-to post-test only in ST and CT groups (ST=18.5±3.16%; CT=17.6±3.01%). Similarly, ST and CT groups increased quadriceps CSA from pre-to post-test (6.2±1.4%; 7.8±1.66%). The p70S6K1 total protein content increased after CT. The ST group showed increased Akt phosphorylation at Ser473 (45.0±3.3%) whereas AMPK phosphorylation at Thr172 increased only in IT group, (100±17.6%). In summary, our data suggest that despite the differences in molecular adaptations between training regimens, CT did not blunt muscle strength and hypertrophy increments when compared with ST. © Georg Thieme Verlag KG Stuttgart · New York.

  4. Extensive X-linked adaptive evolution in central chimpanzees

    DEFF Research Database (Denmark)

    Hvilsom, Christina; Qian, Yu; Bataillon, Thomas

    2012-01-01

    Surveying genome-wide coding variation within and among species gives unprecedented power to study the genetics of adaptation, in particular the proportion of amino acid substitutions fixed by positive selection. Additionally, contrasting the autosomes and the X chromosome holds information...... on the dominance of beneficial (adaptive) and deleterious mutations. Here we capture and sequence the complete exomes of 12 chimpanzees and present the largest set of protein-coding polymorphism to date. We report extensive adaptive evolution specifically targeting the X chromosome of chimpanzees with as much...... as 30% of all amino acid replacements being adaptive. Adaptive evolution is barely detectable on the autosomes except for a few striking cases of recent selective sweeps associated with immunity gene clusters. We also find much stronger purifying selection than observed in humans, and in contrast...

  5. 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.

  6. Cancer cell adaptation to chemotherapy

    International Nuclear Information System (INIS)

    Di Nicolantonio, Federica; Johnson, Penny; Somers, Shaw S; Toh, Simon; Higgins, Bernie; Lamont, Alan; Gulliford, Tim; Hurren, Jeremy; Yiangou, Constantinos; Cree, Ian A; Mercer, Stuart J; Knight, Louise A; Gabriel, Francis G; Whitehouse, Pauline A; Sharma, Sanjay; Fernando, Augusta; Glaysher, Sharon; Di Palma, Silvana

    2005-01-01

    Tumor resistance to chemotherapy may be present at the beginning of treatment, develop during treatment, or become apparent on re-treatment of the patient. The mechanisms involved are usually inferred from experiments with cell lines, as studies in tumor-derived cells are difficult. Studies of human tumors show that cells adapt to chemotherapy, but it has been largely assumed that clonal selection leads to the resistance of recurrent tumors. Cells derived from 47 tumors of breast, ovarian, esophageal, and colorectal origin and 16 paired esophageal biopsies were exposed to anticancer agents (cisplatin; 5-fluorouracil; epirubicin; doxorubicin; paclitaxel; irinotecan and topotecan) in short-term cell culture (6 days). Real-time quantitative PCR was used to measure up- or down-regulation of 16 different resistance/target genes, and when tissue was available, immunohistochemistry was used to assess the protein levels. In 8/16 paired esophageal biopsies, there was an increase in the expression of multi-drug resistance gene 1 (MDR1) following epirubicin + cisplatin + 5-fluorouracil (ECF) chemotherapy and this was accompanied by increased expression of the MDR-1 encoded protein, P-gp. Following exposure to doxorubicin in vitro, 13/14 breast carcinomas and 9/12 ovarian carcinomas showed >2-fold down-regulation of topoisomerase IIα (TOPOIIα). Exposure to topotecan in vitro, resulted in >4-fold down-regulation of TOPOIIα in 6/7 colorectal tumors and 8/10 ovarian tumors. This study suggests that up-regulation of resistance genes or down-regulation in target genes may occur rapidly in human solid tumors, within days of the start of treatment, and that similar changes are present in pre- and post-chemotherapy biopsy material. The molecular processes used by each tumor appear to be linked to the drug used, but there is also heterogeneity between individual tumors, even those with the same histological type, in the pattern and magnitude of response to the same drugs. Adaptation

  7. Cancer cell adaptation to chemotherapy

    Directory of Open Access Journals (Sweden)

    Higgins Bernie

    2005-07-01

    Full Text Available Abstract Background Tumor resistance to chemotherapy may be present at the beginning of treatment, develop during treatment, or become apparent on re-treatment of the patient. The mechanisms involved are usually inferred from experiments with cell lines, as studies in tumor-derived cells are difficult. Studies of human tumors show that cells adapt to chemotherapy, but it has been largely assumed that clonal selection leads to the resistance of recurrent tumors. Methods Cells derived from 47 tumors of breast, ovarian, esophageal, and colorectal origin and 16 paired esophageal biopsies were exposed to anticancer agents (cisplatin; 5-fluorouracil; epirubicin; doxorubicin; paclitaxel; irinotecan and topotecan in short-term cell culture (6 days. Real-time quantitative PCR was used to measure up- or down-regulation of 16 different resistance/target genes, and when tissue was available, immunohistochemistry was used to assess the protein levels. Results In 8/16 paired esophageal biopsies, there was an increase in the expression of multi-drug resistance gene 1 (MDR1 following epirubicin + cisplatin + 5-fluorouracil (ECF chemotherapy and this was accompanied by increased expression of the MDR-1 encoded protein, P-gp. Following exposure to doxorubicin in vitro, 13/14 breast carcinomas and 9/12 ovarian carcinomas showed >2-fold down-regulation of topoisomerase IIα (TOPOIIα. Exposure to topotecan in vitro, resulted in >4-fold down-regulation of TOPOIIα in 6/7 colorectal tumors and 8/10 ovarian tumors. Conclusion This study suggests that up-regulation of resistance genes or down-regulation in target genes may occur rapidly in human solid tumors, within days of the start of treatment, and that similar changes are present in pre- and post-chemotherapy biopsy material. The molecular processes used by each tumor appear to be linked to the drug used, but there is also heterogeneity between individual tumors, even those with the same histological type, in the

  8. Adaptive response to high LET radiations

    International Nuclear Information System (INIS)

    Dam, Annamaria; Bogdandi, E. Noemi; Polonyi, Istvan; Sardy, M. Marta; Balashazy, Imre; Palfalvy, Jozsef

    2001-01-01

    The biological consequences of exposure to ionizing radiation include gene mutation, chromosome aberrations, cellular transformation and cell death. These effects are attributed to the DNA damaging effects of the irradiation resulting in irreversible changes during DNA replication or during the processing of the DNA damage by enzymatic repair processes. These repair processes could initiate some adaptive mechanisms in the cell, which could lead to radioadaptive response (RAR). Adaptive responses have typically been detected by exposing cells to a low radiation dose (1-50 mGy) and then challenging the cells with a higher dose of radiation (2-4 Gy) and comparing the outcome to that seen with the challenge dose only. For adaptive response to be seen the challenge dose must be delivered within 24 hour of the inducing dose. Radio-adaptation is extensively studied for low LET radiation. Nevertheless, few data are available for high LET radiation at very low doses and dose rate. Our study was aimed to investigate the radioadaptive response to low-dose neutron irradiation by detection of the genotoxic damage i.e.: hprt-mutant colonies induced. Altered protein synthesis was also studied to identify stress proteins may responsible for radio-adaptation. New alpha particle irradiator system was also built up to study the biological effects of low dose alpha irradiation. The experiments were carried out on monolayers of human melanoma and CHO (Chines Hamster Ovary) cells irradiated by neutrons produced in the biological irradiation channel of the Research Reactor of Budapest Neutron Center. Cells were exposed to 0.5-50 mGy neutron doses with dose rates of 1.59-10 mGy/min. The challenge doses of 2-4 Gy gamma rays were administrated within 1-48 hours after priming treatment. The induced mutants at hprt locus were selected by adding 6-thioguanine and allow to grow for 10 days for expression of the phenotype. The protein synthesis was studied by PAGE, the molecular mass of specific

  9. 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

  10. Protein Structure Prediction with Visuospatial Analogy

    Science.gov (United States)

    Davies, Jim; Glasgow, Janice; Kuo, Tony

    We show that visuospatial representations and reasoning techniques can be used as a similarity metric for analogical protein structure prediction. Our system retrieves pairs of α-helices based on contact map similarity, then transfers and adapts the structure information to an unknown helix pair, showing that similar protein contact maps predict similar 3D protein structure. The success of this method provides support for the notion that changing representations can enable similarity metrics in analogy.

  11. 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.

  12. 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.

  13. RODOS database adapter

    International Nuclear Information System (INIS)

    Xie Gang

    1995-11-01

    Integrated data management is an essential aspect of many automatical information systems such as RODOS, a real-time on-line decision support system for nuclear emergency management. In particular, the application software must provide access management to different commercial database systems. This report presents the tools necessary for adapting embedded SQL-applications to both HP-ALLBASE/SQL and CA-Ingres/SQL databases. The design of the database adapter and the concept of RODOS embedded SQL syntax are discussed by considering some of the most important features of SQL-functions and the identification of significant differences between SQL-implementations. Finally fully part of the software developed and the administrator's and installation guides are described. (orig.) [de

  14. Science with Adaptive Optics

    CERN Document Server

    Brandner, Wolfgang; ESO Workshop

    2005-01-01

    The field of Adaptive Optics (AO) for astronomy has matured in recent years, and diffraction-limited image resolution in the near-infrared is now routinely achieved by ground-based 8 to 10m class telescopes. This book presents the proceedings of the ESO Workshop on Science with Adaptive Optics held in the fall of 2003. The book provides an overview on AO instrumentation, data acquisition and reduction strategies, and covers observations of the sun, solar system objects, circumstellar disks, substellar companions, HII regions, starburst environments, late-type stars, the galactic center, active galaxies, and quasars. The contributions present a vivid picture of the multitude of science topics being addressed by AO in observational astronomy.

  15. 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...

  16. Designing Adaptive Web Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    2008-01-01

    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......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......-based applications aim to leave some of their features at the design stage in the form of variables which are dependent on several criteria. The resolution of the variables is called adaptation and can be seen from two perspectives: adaptation by humans to the changed requirements of stakeholders and dynamic system...

  17. 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...

  18. Adaptations in Play

    DEFF Research Database (Denmark)

    Jørgensen, Ida Kathrine Hammeleff

    2017-01-01

    In the long history of board games, certain games have been passed on in generations and have evolved and been shaped to fit different cultural and religious contexts and functions (Parlett 1999). More recently we have seen popular board games being repackaged to fit pop-cultural themes retrieved...... from television or cinema (Woods 2012). Furthermore, since the early days of digital games, tabletop games have served as a source of inspiration for many video-game designers, and more recently we have seen the occurrence of tabletop game adaptations of popular video-games such as StarCraft (Blizzard...... Studies. New Challenges, New Directions. Edited by Jørgen Bruhn, Anne Gjelsvik and Eirik Frisvold Hanssen. London: Bloomsbury. Hutcheon, L. 2006. A Theory of Adaptation. New York: Routledge Parlett, D. 1999. The Oxford History of Board Games. Oxford: Oxford University Press. Wittgenstein, L. 1958...

  19. Plant protein for food: opportunities and bottlenecks

    Directory of Open Access Journals (Sweden)

    Chardigny Jean-Michel

    2016-07-01

    Full Text Available Dietary proteins represent a key issue for the future regarding worldwide food security. Besides animal sources, plant proteins represent an opportunity to mainly contribute to protein demand. Whether some plant protein sources could appear as deficient in some essential amino acids, mixtures from different sources could represent opportunities to further propose adapted supply regarding specific demand. Such opportunities includes legumes as well as by-products of oil processing, i.e. canola and sunflower cakes. The nutritional benefits of such new sources are still under investigation considering benefits and limits like allergenicity. Finally, consumer behavior and acceptability remains the final bottleneck for developing new protein sources.

  20. Adaptive Context Tree Weighting

    OpenAIRE

    O'Neill, Alexander; Hutter, Marcus; Shao, Wen; Sunehag, Peter

    2012-01-01

    We describe an adaptive context tree weighting (ACTW) algorithm, as an extension to the standard context tree weighting (CTW) algorithm. Unlike the standard CTW algorithm, which weights all observations equally regardless of the depth, ACTW gives increasing weight to more recent observations, aiming to improve performance in cases where the input sequence is from a non-stationary distribution. Data compression results show ACTW variants improving over CTW on merged files from standard compres...

  1. 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.

  2. 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.

  3. Adaptive Metric Dimensionality Reduction

    OpenAIRE

    Gottlieb, Lee-Ad; Kontorovich, Aryeh; Krauthgamer, Robert

    2013-01-01

    We study adaptive data-dependent dimensionality reduction in the context of supervised learning in general metric spaces. Our main statistical contribution is a generalization bound for Lipschitz functions in metric spaces that are doubling, or nearly doubling. On the algorithmic front, we describe an analogue of PCA for metric spaces: namely an efficient procedure that approximates the data's intrinsic dimension, which is often much lower than the ambient dimension. Our approach thus leverag...

  4. 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.

  5. Effect of Metformin on Potassium-adapted and Non- adapted ...

    African Journals Online (AJOL)

    Purpose: To assess the effects of potassium adaptation on some biochemical parameters in diabetic rats treated with metformin. Methods: Diabetes was induced via intraperitoneal administration of streptozotocin in potassium- adapted and non-adapted rats and, then metformin (350 mg/kg) was administered orally.

  6. Modular protein switches derived from antibody mimetic proteins.

    Science.gov (United States)

    Nicholes, N; Date, A; Beaujean, P; Hauk, P; Kanwar, M; Ostermeier, M

    2016-02-01

    Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. 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. Copyright © 2013. Published by Elsevier Ltd.

  8. 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.

  9. 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...

  10. Adaptive building skin structures

    International Nuclear Information System (INIS)

    Del Grosso, A E; Basso, P

    2010-01-01

    The concept of adaptive and morphing structures has gained considerable attention in the recent years in many fields of engineering. In civil engineering very few practical applications are reported to date however. Non-conventional structural concepts like deployable, inflatable and morphing structures may indeed provide innovative solutions to some of the problems that the construction industry is being called to face. To give some examples, searches for low-energy consumption or even energy-harvesting green buildings are amongst such problems. This paper first presents a review of the above problems and technologies, which shows how the solution to these problems requires a multidisciplinary approach, involving the integration of architectural and engineering disciplines. The discussion continues with the presentation of a possible application of two adaptive and dynamically morphing structures which are proposed for the realization of an acoustic envelope. The core of the two applications is the use of a novel optimization process which leads the search for optimal solutions by means of an evolutionary technique while the compatibility of the resulting configurations of the adaptive envelope is ensured by the virtual force density method

  11. The Adaptation Finance Gap Report

    DEFF Research Database (Denmark)

    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...... 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...... and highlights challenges associated with measuring progress towards fulfilling the adaptation finance gap, while informing national and international efforts to advance adaptation. It analyses the ‘adaptation finance gap’ against the background of the provisions laid out in the Paris Agreement, and benefits...

  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. Protein intrinsic disorder in plants.

    Science.gov (United States)

    Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

    2013-09-12

    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 signaling 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 cannot 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.

  14. 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.

  15. Protein Extractability

    African Journals Online (AJOL)

    Results showed that protein extractability was dependent on pH, type of salt, salt concentrations and extraction time. Salts extracted more proteins from the moringa seed flour than water. Maximum extraction of protein was. 85.06% and 84.72% with 0.5 M CaCl and 0.75 M NaCl respectively. On varying the pH, maximum ...

  16. Efficient adaptive fuzzy control scheme

    NARCIS (Netherlands)

    Papp, Z.; Driessen, B.J.F.

    1995-01-01

    The paper presents an adaptive nonlinear (state-) feedback control structure, where the nonlinearities are implemented as smooth fuzzy mappings defined as rule sets. The fine tuning and adaption of the controller is realized by an indirect adaptive scheme, which modifies the parameters of the fuzzy

  17. 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

  18. 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.

  19. 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

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

    DEFF Research Database (Denmark)

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

    2001-01-01

    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......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...

  1. Molecular adaptation within the coat protein-encoding gene of ...

    Indian Academy of Sciences (India)

    Oliver J. E., Freer J., Andersen R. L., Cox K. D., Robinson T. L. and Fuchs M. 2009 Genetic diversity of Prunus necrotic ringspot virus isolates within a cherry orchard in New York. Plant Dis. 93,. 599–606. Pearson W. R. and Lipman D. J. 1988 Improved tools for biologi- cal sequence comparison. Proc. Natl. Acad. Sci. USA 85 ...

  2. Molecular adaptation within the coat protein-encoding gene of ...

    Indian Academy of Sciences (India)

    Sour cherry var. MuskatnajaPrazskaja. Holovousy, Czech Republic. AF170161. PS 7/11. Sour cherry var. MuskatnajaPrazskaja. Holovousy, Czech Republic. AF170160. 06-54. Prune var. Anna Spath. Holovousy, Czech Republic. EF565262. PlmCl.fri1. Plum cv. Friar. Chile. S78312. PV-96. Prunus mahaleb. Germany.

  3. Molecular adaptation within the coat protein-encoding gene of ...

    Indian Academy of Sciences (India)

    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 ...

  4. Molecular adaptation within the coat protein-encoding gene of ...

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used ... The domain part of the email address of all email addresses used by the office of Indian Academy of Sciences, including those of the staff, the journals, ...

  5. Adaptive nonlinear flight control

    Science.gov (United States)

    Rysdyk, Rolf Theoduor

    1998-08-01

    Research under supervision of Dr. Calise and Dr. Prasad at the Georgia Institute of Technology, School of Aerospace Engineering. has demonstrated the applicability of an adaptive controller architecture. The architecture successfully combines model inversion control with adaptive neural network (NN) compensation to cancel the inversion error. The tiltrotor aircraft provides a specifically interesting control design challenge. The tiltrotor aircraft is capable of converting from stable responsive fixed wing flight to unstable sluggish hover in helicopter configuration. It is desirable to provide the pilot with consistency in handling qualities through a conversion from fixed wing flight to hover. The linear model inversion architecture was adapted by providing frequency separation in the command filter and the error-dynamics, while not exiting the actuator modes. This design of the architecture provides for a model following setup with guaranteed performance. This in turn allowed for convenient implementation of guaranteed handling qualities. A rigorous proof of boundedness is presented making use of compact sets and the LaSalle-Yoshizawa theorem. The analysis allows for the addition of the e-modification which guarantees boundedness of the NN weights in the absence of persistent excitation. The controller is demonstrated on the Generic Tiltrotor Simulator of Bell-Textron and NASA Ames R.C. The model inversion implementation is robustified with respect to unmodeled input dynamics, by adding dynamic nonlinear damping. A proof of boundedness of signals in the system is included. The effectiveness of the robustification is also demonstrated on the XV-15 tiltrotor. The SHL Perceptron NN provides a more powerful application, based on the universal approximation property of this type of NN. The SHL NN based architecture is also robustified with the dynamic nonlinear damping. A proof of boundedness extends the SHL NN augmentation with robustness to unmodeled actuator

  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 intrusion data system

    International Nuclear Information System (INIS)

    Johnson, C.S.

    1976-01-01

    An Adaptive Intrusion Data System (AIDS) was developed to collect data from intrusion alarm sensors as part of an evaluation system to improve sensor performance. AIDS is a unique digital data compression, storage, and formatting system. It also incorporates capability for video selection and recording for assessment of the sensors monitored by the system. The system is software reprogrammable to numerous configurations that may be utilized for the collection of environmental, bi-level, analog and video data. The output of the system is digital tapes formatted for direct data reduction on a CDC 6400 computer, and video tapes containing timed tagged information that can be correlated with the digital data

  9. 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....... They are the result of acooperation between Søren Molin, professor in the group, and his brother, JanMolin, professor at Department of Organization and Industrial Sociology atCopenhagen Business School. The cooperation arises from the recognition that bothmicrobial ecology and sociology/organization theory works...

  10. Low power adaptive synchronizer

    Energy Technology Data Exchange (ETDEWEB)

    Sadowski, Greg

    2018-02-20

    A circuit adapts to the occurrence of metastable states. The circuit inhibits passing of the metastable state to circuits that follow, by clock gating the output stage. In order to determine whether or not to gate the clock of the output stage, two detect circuits may be used. One circuit detects metastability and another circuit detects metastability resolved to a wrong logic level. The results from one or both detector circuits are used to gate the next clock cycle if needed, waiting for the metastable situation to be resolved.

  11. 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....

  12. Agente adaptable y aprendizaje

    Directory of Open Access Journals (Sweden)

    Arturo Angel Lara Rivero

    2013-05-01

    Full Text Available En este trabajo se contrasta el concepto de agente programado con el de agente complejo adaptable, se presenta una nueva visión ligada al aprendizaje y la estructura del agente. La imagen del agente se analiza considerando los modelos internos, la práctica, el concepto de rutina y la influencia en su comportamiento, y la importancia del aprendizaje ex ante y ex post. Por último se muestra que la resolución de problemas está sujeta a restricciones del agente y se describen las formas de explorar el espacio de soluciones mediante tres tipos de exploración: exhaustiva, aleatoria y selectiva.

  13. Skeletal adaptations to bipedalism

    Directory of Open Access Journals (Sweden)

    Vasiljević Perica

    2014-01-01

    Full Text Available Bipedalism is the main characteristic of humans. During evolutin bipedalism emerged probably as an adaptation to a changing environment. Major changes in skeletal system included femur, pelvis, skull and spine. The significance of bipedal locomotion: Bipedalism freed the forelimbs for carrying objects, creation and usage of tools. In the upright position animals have a broader view of the environment and the early detection of predators is crucial for survival. Bipedal locomotion makes larger distances easier to pass, which is very important in the migration of hominids.

  14. Practical adaptive quantum tomography

    Science.gov (United States)

    Granade, Christopher; Ferrie, Christopher; Flammia, Steven T.

    2017-11-01

    We introduce a fast and accurate heuristic for adaptive tomography that addresses many of the limitations of prior methods. Previous approaches were either too computationally intensive or tailored to handle special cases such as single qubits or pure states. By contrast, our approach combines the efficiency of online optimization with generally applicable and well-motivated data-processing techniques. We numerically demonstrate these advantages in several scenarios including mixed states, higher-dimensional systems, and restricted measurements. http://cgranade.com complete data and source code for this work are available online [1], and can be previewed at https://goo.gl/koiWxR.

  15. Renal adaptation during hibernation.

    Science.gov (United States)

    Jani, Alkesh; Martin, Sandra L; Jain, Swati; Keys, Daniel; Edelstein, Charles L

    2013-12-01

    Hibernators periodically undergo profound physiological changes including dramatic reductions in metabolic, heart, and respiratory rates and core body temperature. This review discusses the effect of hypoperfusion and hypothermia observed during hibernation on glomerular filtration and renal plasma flow, as well as specific adaptations in renal architecture, vasculature, the renin-angiotensin system, and upregulation of possible protective mechanisms during the extreme conditions endured by hibernating mammals. Understanding the mechanisms of protection against organ injury during hibernation may provide insights into potential therapies for organ injury during cold storage and reimplantation during transplantation.

  16. 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

  17. Protein politics

    NARCIS (Netherlands)

    Vijver, Marike

    2005-01-01

    This study is part of the program of the interdisciplinary research group Profetas (protein foods, environment, technology and society). Profetas consists of technological, environmental and socio-economic research projects on protein food systems which result in the development of scenarios and

  18. Whey Protein

    Science.gov (United States)

    ... Fraction de Lactosérum, Fraction de Petit-Lait, Goat Milk Whey, Goat Whey, Isolat de Protéine de Lactosérum, Isolat de Protéine de Petit-Lait, Lactosérum de Lait de Chèvre, MBP, Milk Protein, Milk Protein Isolate, Mineral Whey Concentrate, Proteínas ...

  19. Protein adhesives

    Science.gov (United States)

    Charles R. Frihart; Linda F. Lorenz

    2018-01-01

    Nature uses a wide variety of chemicals for providing adhesion internally (e.g., cell to cell) and externally (e.g., mussels to ships and piers). This adhesive bonding is chemically and mechanically complex, involving a variety of proteins, carbohydrates, and other compounds.Consequently,the effect of protein structures on adhesive properties is only partially...

  20. Possible adaptive growth responses of Chromolaena odorata during ...

    African Journals Online (AJOL)

    The changes in morphological and crude protein content of Chromolaena odorata to heavy metal-induced stress were investigated. This was with a view to providing information on the test plant adaptation potential during remediation of contaminated with . Stems of C. odorata were planted in soils treated with Cd (as CdCl) ...

  1. 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.

  2. Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

    NARCIS (Netherlands)

    Bruggeman, F.J.; de Haan, J.; Hardin, H.M.; Bouwman, J.G.; Rossell Aragort, S.L.; van Eunen, K.; Bakker, B.M.; Westerhoff, H.V.

    2006-01-01

    Cells adapt to changes in their environment by the concerted action of many different regulatory mechanisms. Examples of such mechanisms are feedback inhibition by intermediates of metabolism, covalent modification of enzymes and changes in the abundance of mRNAs and proteins. These mechanisms act

  3. Time-dependent hierarchical regulation analysis: deciphering cellular adaptation.

    NARCIS (Netherlands)

    Bruggeman, F.J.; Haan, J; Hardin, H.M.; Bouwman, J.; Rossell, S.; van Eunen, K.; Bakker, B.M.; Westerhoff, H.V.

    2006-01-01

    Cells adapt to changes in their environment by the concerted action of many different regulatory mechanisms. Examples of such mechanisms are feedback inhibition by intermediates of metabolism, covalent modification of enzymes and changes in the abundance of mRNAs and proteins. These mechanisms act

  4. Adaptation of microorganisms and their transport systems to high temperatures

    NARCIS (Netherlands)

    Tolner, B; Poolman, B.; Konings, W.N

    1997-01-01

    Growth of Bacteria and Archaea has been observed at temperatures up to 95 and 110 degrees C, respectively. These thermophiles are adapted to environments of high temperature by changes in the membrane lipid composition, higher thermostabilities of the (membrane) proteins, higher turnover rates of

  5. Plasma membrane disruption: repair, prevention, adaptation

    Science.gov (United States)

    McNeil, Paul L.; Steinhardt, Richard A.

    2003-01-01

    Many metazoan cells inhabit mechanically stressful environments and, consequently, their plasma membranes are frequently disrupted. Survival requires that the cell rapidly repair or reseal the disruption. Rapid resealing is an active and complex structural modification that employs endomembrane as its primary building block, and cytoskeletal and membrane fusion proteins as its catalysts. Endomembrane is delivered to the damaged plasma membrane through exocytosis, a ubiquitous Ca2+-triggered response to disruption. Tissue and cell level architecture prevent disruptions from occurring, either by shielding cells from damaging levels of force, or, when this is not possible, by promoting safe force transmission through the plasma membrane via protein-based cables and linkages. Prevention of disruption also can be a dynamic cell or tissue level adaptation triggered when a damaging level of mechanical stress is imposed. Disease results from failure of either the preventive or resealing mechanisms.

  6. 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.

  7. 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

  8. Face adaptation improves gender discrimination.

    Science.gov (United States)

    Yang, Hua; Shen, Jianhong; Chen, Juan; Fang, Fang

    2011-01-01

    Adaptation to a visual pattern can alter the sensitivities of neuronal populations encoding the pattern. However, the functional roles of adaptation, especially in high-level vision, are still equivocal. In the present study, we performed three experiments to investigate if face gender adaptation could affect gender discrimination. Experiments 1 and 2 revealed that adapting to a male/female face could selectively enhance discrimination for male/female faces. Experiment 3 showed that the discrimination enhancement induced by face adaptation could transfer across a substantial change in three-dimensional face viewpoint. These results provide further evidence suggesting that, similar to low-level vision, adaptation in high-level vision could calibrate the visual system to current inputs of complex shapes (i.e. face) and improve discrimination at the adapted characteristic. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. Adaptive Playware in Physical Games

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop; Thorsteinsson, Arnar Tumi

    2011-01-01

    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...... of the individual player. The appropriate level will change with game/interaction complexity, and adaptation finds the appropriate level for the individual player, even in multi-player games....

  10. 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...

  11. Homeoviscous adaptation and the regulation of membrane lipids

    DEFF Research Database (Denmark)

    Ernst, Robert; Ejsing, Christer S; Antonny, Bruno

    2016-01-01

    Biological membranes are complex and dynamic assemblies of lipids and proteins. Poikilothermic organisms including bacteria, fungi, reptiles, and fish do not control their body temperature and must adapt their membrane lipid composition in order to maintain membrane fluidity in the cold. This ada......Biological membranes are complex and dynamic assemblies of lipids and proteins. Poikilothermic organisms including bacteria, fungi, reptiles, and fish do not control their body temperature and must adapt their membrane lipid composition in order to maintain membrane fluidity in the cold...... such as neurons maintain unique lipid compositions with specific physicochemical properties. To date little is known about the sensory mechanisms regulating the acyl chain profile in such specialized cells or during adaptive responses. Here we summarize our current understanding of lipid metabolic networks...

  12. The PDZ domain as a complex adaptive system.

    Directory of Open Access Journals (Sweden)

    Alexei Kurakin

    2007-09-01

    Full Text Available Specific protein associations define the wiring of protein interaction networks and thus control the organization and functioning of the cell as a whole. Peptide recognition by PDZ and other protein interaction domains represents one of the best-studied classes of specific protein associations. However, a mechanistic understanding of the relationship between selectivity and promiscuity commonly observed in the interactions mediated by peptide recognition modules as well as its functional meaning remain elusive. To address these questions in a comprehensive manner, two large populations of artificial and natural peptide ligands of six archetypal PDZ domains from the synaptic proteins PSD95 and SAP97 were generated by target-assisted iterative screening (TAIS of combinatorial peptide libraries and by synthesis of proteomic fragments, correspondingly. A comparative statistical analysis of affinity-ranked artificial and natural ligands yielded a comprehensive picture of known and novel PDZ ligand specificity determinants, revealing a hitherto unappreciated combination of specificity and adaptive plasticity inherent to PDZ domain recognition. We propose a reconceptualization of the PDZ domain in terms of a complex adaptive system representing a flexible compromise between the rigid order of exquisite specificity and the chaos of unselective promiscuity, which has evolved to mediate two mutually contradictory properties required of such higher order sub-cellular organizations as synapses, cell junctions, and others--organizational structure and organizational plasticity/adaptability. The generalization of this reconceptualization in regard to other protein interaction modules and specific protein associations is consistent with the image of the cell as a complex adaptive macromolecular system as opposed to clockwork.

  13. Adaptation, allometry, and hypertension.

    Science.gov (United States)

    Weder, A B; Schork, N J

    1994-08-01

    Essential hypertension is a "disease of civilization" but has a clear genetic component. From an evolutionary perspective, persistence in the human genome of elements capable of raising blood pressure presupposes their adaptive significance. Recently, two hypotheses that explicitly appeal to selectionist arguments, the "slavery" and "thrifty gene" theories, have been forwarded. We find neither completely successful, and we advance an alternative explanation of the adaptive importance of genes responsible for hypertension. We propose that blood pressure rises during childhood and adolescence to subserve homeostatic needs of the organism. Specifically, we contend that blood pressure is a flexible element in the repertoire of renal homeostatic mechanisms serving to match renal function to growth. The effect of modern diet and lifestyle on human growth stimulates earlier and more vigorous development, straining biologically necessary relationships between renal and general somatic growth and requiring compensation via homeostatic mechanisms preserved during evolution. Prime among such mechanisms is blood pressure, which rises as a compensation to maintain renal function in the face of greater growth. Since virtually all members of acculturated societies share in the modern lifestyle, the demands imposed by accelerated growth and development result in a populational shift to higher blood pressures, with a consequent increase in the prevalence of hypertension. We propose that hypertension is the product of maladaptation of highly genetically conserved mechanisms subserving important biological homeostatic needs. Elucidation of the mechanisms underlying hypertension will require approaches that examine the developmental processes linking growth to blood pressure.

  14. Adaptability and climate change

    International Nuclear Information System (INIS)

    Sprague, M.W.

    1991-01-01

    The potential social, economic and environmental impacts of climate change are reviewed, with emphasis on agricultural implications. Impact analyses must be done on the scale of watersheds or river basins. For agriculture, climate change effects on water resources are likely to be more important than temperature changes, and climatic variability is also equally important. Another set of critical climatic variables are the frequencies, magnitudes and timing of extreme events such as floods, droughts, etc. A carbon dioxide enriched atmosphere will increase water use efficiency and confer increased tolerance to drought, salinity and air pollution. Better understanding and accounting is required for the effects of increased carbon dioxide on all plant life, including crops. Adaptability of agriculture to change must be taken into account in predicting impacts of climate change, with technological innovation and infrastructure giving agriculture a dynamic nature. Limitations and adaptations must be considered when formulating public policy, to ensure that marginal costs do not exceed marginal benefits. Monoculture plantation forests may be the most efficient sinks of atmospheric carbon dioxide, yet widespread reliance on them may harm biological diversity. Actions the U.S. is currently taking under a no-regrets policy are summarized

  15. Exploring guideline adaptation strategy for Turkey: Is "ADAPTE" feasible or does it need adaptation as well?

    Science.gov (United States)

    Ayhan Baser, Duygu; Kahveci, Rabia; Baydar Artantas, Aylin; Yasar, İlknur; Aksoy, Hilal; Koc, Esra Meltem; Kasim, İsmail; Kunnamo, Ilkka; Özkara, Adem

    2018-02-01

    Clinical Practice Guidelines are mostly developed by 3 methods; namely, de novo, adoption, and adaptation. Nonpublished studies and authors experience shows that most guidelines in Turkey are either by adoption or by adaptation. There is no available local tool for adaptation, so the process is not standardized and most of the time not explicitly defined. The objective of this study is to search for international guideline adaptation tools and test their feasibility in Turkish context, to serve a final goal of developing a unique local strategic tool for guideline adaptation. The methodological design of this study includes selection of an international tool for Clinical Practice Guideline adaptation, piloting this tool with selected Turkish guidelines, identifying the feasibility of this tool and exploring the needs for adaptation of the tool, drawing recommendations for adaptation of the strategies, and validation of the process by local experts. The study from planning phase to finalizing the guidance, including pilot studies and panel but excluding translation of ADAPTE, lasted 18 months. Nine researchers were involved in the adaptation process and 15 more experts were involved in the validation panel. Following the suggestions of the research team on modifications and validation through the expert panel; 2 steps of the ADAPTE toolkit were rejected, 2 steps were accepted by modification, 7 steps were accepted by additional recommendations. In addition, 2 tools were suggested to be added to the toolkit. This is the first study on adaptation of guidelines in Turkey. Pilot adaptation of 2 guidelines with ADAPTE revealed that ADAPTE is a useful and feasible tool in Turkish setting, but might require certain changes in recommendations and revision of tools. © 2017 John Wiley & Sons, Ltd.

  16. Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis

    Science.gov (United States)

    Venev, Sergey V; Zeldovich, Konstantin B

    2018-01-01

    Abstract Prokaryotes evolved to thrive in an extremely diverse set of habitats, and their proteomes bear signatures of environmental conditions. Although correlations between amino acid usage and environmental temperature are well-documented, understanding of the mechanisms of thermal adaptation remains incomplete. Here, we couple the energetic costs of protein folding and protein homeostasis to build a microscopic model explaining both the overall amino acid composition and its temperature trends. Low biosynthesis costs lead to low diversity of physical interactions between amino acid residues, which in turn makes proteins less stable and drives up chaperone activity to maintain appropriate levels of folded, functional proteins. Assuming that the cost of chaperone activity is proportional to the fraction of unfolded client proteins, we simulated thermal adaptation of model proteins subject to minimization of the total cost of amino acid synthesis and chaperone activity. For the first time, we predicted both the proteome-average amino acid abundances and their temperature trends simultaneously, and found strong correlations between model predictions and 402 genomes of bacteria and archaea. The energetic constraint on protein evolution is more apparent in highly expressed proteins, selected by codon adaptation index. We found that in bacteria, highly expressed proteins are similar in composition to thermophilic ones, whereas in archaea no correlation between predicted expression level and thermostability was observed. At the same time, thermal adaptations of highly expressed proteins in bacteria and archaea are nearly identical, suggesting that universal energetic constraints prevail over the phylogenetic differences between these domains of life. PMID:29106597

  17. 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...

  18. Adaptive mutations alter antibody structure and dynamics during affinity maturation.

    Science.gov (United States)

    Adhikary, Ramkrishna; Yu, Wayne; Oda, Masayuki; Walker, Ross C; Chen, Tingjian; Stanfield, Robyn L; Wilson, Ian A; Zimmermann, Jörg; Romesberg, Floyd E

    2015-03-24

    While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.

  19. Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

    OpenAIRE

    Ogura, Masako; Perez, J. Christian; Mittl, Peer R. E; Lee, Hae-Kyung; Dailide, Geidrius; Tan, Shumin; Ito, Yoshiyuki; Secka, Ousman; Dailidiene, Daiva; Putty, Kalyani; Berg, Douglas E; Kalia, Awdhesh

    2007-01-01

    Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs t...

  20. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

    Science.gov (United States)

    Gretchen H. Roffler; Stephen J. Amish; Seth Smith; Ted Cosart; Marty Kardos; Michael K. Schwartz; Gordon Luikart

    2016-01-01

    Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding...

  1. Adaptive resummation of Markovian quantum dynamics

    International Nuclear Information System (INIS)

    Lucas, Felix

    2014-01-01

    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.

  2. Cross-Adaptation: Heat and Cold Adaptation to Improve Physiological and Cellular Responses to Hypoxia.

    Science.gov (United States)

    Gibson, Oliver R; Taylor, Lee; Watt, Peter W; Maxwell, Neil S

    2017-09-01

    To prepare for extremes of heat, cold or low partial pressures of oxygen (O 2 ), humans can undertake a period of acclimation or acclimatization to induce environment-specific adaptations, e.g. heat acclimation (HA), cold acclimation (CA), or altitude training. While these strategies are effective, they are not always feasible due to logistical impracticalities. Cross-adaptation is a term used to describe the phenomenon whereby alternative environmental interventions, e.g. HA or CA, may be a beneficial alternative to altitude interventions, providing physiological stress and inducing adaptations observable at altitude. HA can attenuate physiological strain at rest and during moderate-intensity exercise at altitude via adaptations allied to improved O 2 delivery to metabolically active tissue, likely following increases in plasma volume and reductions in body temperature. CA appears to improve physiological responses to altitude by attenuating the autonomic response to altitude. While no cross-acclimation-derived exercise performance/capacity data have been measured following CA, post-HA improvements in performance underpinned by aerobic metabolism, and therefore dependent on O 2 delivery at altitude, are likely. At a cellular level, heat shock protein responses to altitude are attenuated by prior HA, suggesting that an attenuation of the cellular stress response and therefore a reduced disruption to homeostasis at altitude has occurred. This process is known as cross-tolerance. The effects of CA on markers of cross-tolerance is an area requiring further investigation. Because much of the evidence relating to cross-adaptation to altitude has examined the benefits at moderate to high altitudes, future research examining responses at lower altitudes should be conducted, given that these environments are more frequently visited by athletes and workers. Mechanistic work to identify the specific physiological and cellular pathways responsible for cross-adaptation between

  3. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

    DEFF Research Database (Denmark)

    Blagoev, B.; Kratchmarova, I.; Ong, S.E.

    2003-01-01

    employ stable isotopic amino acids in cell culture (SILAC) to differentially label proteins in EGF-stimulated versus unstimulated cells. Combined cell lysates were affinity-purified over the SH2 domain of the adapter protein Grb2 (GST-SH2 fusion protein) that specifically binds phosphorylated EGFR...... and Src homologous and collagen (Shc) protein. We identified 228 proteins, of which 28 were selectively enriched upon stimulation. EGFR and Shc, which interact directly with the bait, had large differential ratios. Many signaling molecules specifically formed complexes with the activated EGFR-Shc, as did...

  4. Organizing signal transduction through A-kinase anchoring proteins (AKAPs).

    Science.gov (United States)

    Logue, Jeremy S; Scott, John D

    2010-11-01

    A fundamental role for protein-protein interactions in the organization of signal transduction pathways is evident. Anchoring, scaffolding and adapter proteins function to enhance the precision and directionality of these signaling events by bringing enzymes together. The cAMP signaling pathway is organized by A-kinase anchoring proteins. This family of proteins assembles enzyme complexes containing the cAMP-dependent protein kinase, phosphoprotein phosphatases, phosphodiesterases and other signaling effectors to optimize cellular responses to cAMP and other second messengers. Selected A-kinase anchoring protein signaling complexes are highlighted in this minireview. © 2010 The Authors Journal compilation © 2010 FEBS.

  5. Computational identification of adaptive mutants using the VERT system

    Directory of Open Access Journals (Sweden)

    Winkler James

    2012-04-01

    Full Text Available Background Evolutionary dynamics of microbial organisms can now be visualized using the Visualizing Evolution in Real Time (VERT system, in which several isogenic strains expressing different fluorescent proteins compete during adaptive evolution and are tracked using fluorescent cell sorting to construct a population history over time. Mutations conferring enhanced growth rates can be detected by observing changes in the fluorescent population proportions. Results Using data obtained from several VERT experiments, we construct a hidden Markov-derived model to detect these adaptive events in VERT experiments without external intervention beyond initial training. Analysis of annotated data revealed that the model achieves consensus with human annotation for 85-93% of the data points when detecting adaptive events. A method to determine the optimal time point to isolate adaptive mutants is also introduced. Conclusions The developed model offers a new way to monitor adaptive evolution experiments without the need for external intervention, thereby simplifying adaptive evolution efforts relying on population tracking. Future efforts to construct a fully automated system to isolate adaptive mutants may find the algorithm a useful tool.

  6. Adaptive Immunity to Fungi

    Science.gov (United States)

    Wüthrich, Marcel; Deepe, George S.; Klein, Bruce

    2013-01-01

    Only a handful of the more than 100,000 fungal species on our planet cause disease in humans, yet the number of life-threatening fungal infections in patients has recently skyrocketed as a result of advances in medical care that often suppress immunity intensely. This emerging crisis has created pressing needs to clarify immune defense mechanisms against fungi, with the ultimate goal of therapeutic applications. Herein, we describe recent insights in understanding the mammalian immune defenses deployed against pathogenic fungi. The review focuses on adaptive immune responses to the major medically important fungi and emphasizes how dendritic cells and subsets in various anatomic compartments respond to fungi, recognize their molecular patterns, and signal responses that nurture and shape the differentiation of T cell subsets and B cells. Also emphasized is how the latter deploy effector and regulatory mechanisms that eliminate these nasty invaders while also constraining collateral damage to vital tissue. PMID:22224780

  7. Innate and adaptive immunosenescence.

    Science.gov (United States)

    Agarwal, Shradha; Busse, Paula J

    2010-03-01

    To review the effect of increasing age on the immune system and some of its clinical implications. MEDLINE and PubMed searches were performed cross-referencing the keywords immunosenescence, aging, and immunity. Articles were reviewed for additional citations. Articles were reviewed and selected based on relevance to subject matter. The study of immunosenescence is complex and not completely understood. Aging affects both the innate and adaptive arms of the immune response. With increased age, there may be a decrease in phagocytosis, alteration of cellular migration, changes in cell populations and numbers, and a decreased ability to produce specific antibodies. Clinically, these changes potentially increase morbidity and mortality in elderly individuals through an increased rate of infections, malignancy, and autoimmunity. The process of aging is accompanied by diverse changes in immunity. Several therapeutic approaches are under investigation, including cytokine therapy, hormonal replacement, antioxidant supplementation, and caloric restriction, to attenuate or potentially reverse immunosenescence.

  8. Capabilities for Strategic Adaptation

    DEFF Research Database (Denmark)

    Distel, Andreas Philipp

    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...... are in terms of their constituent elements, where these capabilities come from, and how their effectiveness can be fostered. Thus, the dissertation’s aim is to address these gaps by advancing our understanding of the multilevel aspects and micro-foundations of dynamic capabilities. In doing so, it focuses...... on capabilities for sensing and seizing new business opportunities and reconfiguring corporate resources. More specifically, the dissertation examines the role of key organization members, such as knowledge workers and top managers, in defining and building these capabilities. Moreover, it investigates how...

  9. Mobile, Flexible, and Adaptable

    DEFF Research Database (Denmark)

    Agergaard, Jytte; Thao, Thi Vu

    2011-01-01

    Industrialisation and urban growth are constitutive aspects of Vietnam's new economy and are important driving forces behind increasing rural-to-urban migration. Growth in informal sector employment is a significant aspect of this development, which has provided for both male and female migrants......, although they generally are engaged in different occupations. Based on a case study among porters at Hanoi's Long Bien Market, this paper examines rural-to-urban migrants' gendered migration practices. Two interrelated aspects of gendered migration practices are in focus: the role of migration networks...... of the female porters demonstrate a particular way of adapting to the migration process. Also, it is emphasised how women's flexible practices are facilitated by women's own village-based networks. It is suggested that ‘in-betweenness’, which stands for the simultaneous and overlapping presence of urban...

  10. 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...

  11. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  12. Protein deamidation

    OpenAIRE

    Robinson, Noah E.

    2002-01-01

    A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically ...

  13. Adaptive Playware in Physical Games

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop; Thorsteinsson, Arnar Tumi

    2011-01-01

    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...... 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...... 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. Adaptation and Natural Selection revisited.

    Science.gov (United States)

    Sober, E; Wilson, D S

    2011-02-01

    In Adaptation and Natural Selection, George C. Williams linked the distinction between group and individual adaptation with the distinction between group and individual selection. Williams' Principle, as we will call it, says that adaptation at a level requires selection at that level. This is a necessary but not a sufficient condition; for example, group adaptation requires group selection, but the fact that group selection influences a trait's evolution does not suffice for the resulting trait frequency to be a group adaptation. What more is required? In this paper, we describe an answer to this question that has been developed in multilevel selection theory. We also discuss an alternative framework for defining units of adaptation that violates Williams' Principle. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  15. Sulfated glycopeptide nanostructures for multipotent protein activation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sungsoo S.; Fyrner, Timmy; Chen, Feng; Álvarez, Zaida; Sleep, Eduard; Chun, Danielle S.; Weiner, Joseph A.; Cook, Ralph W.; Freshman, Ryan D.; Schallmo, Michael S.; Katchko, Karina M.; Schneider, Andrew D.; Smith, Justin T.; Yun, Chawon; Singh, Gurmit; Hashmi, Sohaib Z.; McClendon, Mark T.; Yu, Zhilin; Stock, Stuart R.; Hsu, Wellington K.; Hsu, Erin L.; Stupp , Samuel I. (NWU)

    2017-06-19

    Biological systems have evolved to utilize numerous proteins with capacity to bind polysaccharides for the purpose of optimizing their function. A well-known subset of these proteins with binding domains for the highly diverse sulfated polysaccharides are important growth factors involved in biological development and tissue repair. We report here on supramolecular sulfated glycopeptide nanostructures, which display a trisulfated monosaccharide on their surfaces and bind five critical proteins with different polysaccharide-binding domains. Binding does not disrupt the filamentous shape of the nanostructures or their internal β-sheet backbone, but must involve accessible adaptive configurations to interact with such different proteins. The glycopeptide nanostructures amplified signalling of bone morphogenetic protein 2 significantly more than the natural sulfated polysaccharide heparin, and promoted regeneration of bone in the spine with a protein dose that is 100-fold lower than that required in the animal model. These highly bioactive nanostructures may enable many therapies in the future involving proteins.

  16. Protein blotting with direct blotting electrophoresis.

    Science.gov (United States)

    Beck, S

    1988-05-01

    Direct blotting electrophoresis, a method designed to be of general application for the separation and electroblotting of macromolecules, has been adapted to produce protein blots suitable for subsequent processing by standard techniques such as dye staining or immunological detection. After their separation in a very short gel the protein bands are electrophoresed out of the gel onto an immobilizing matrix. The matrix which is moved across the bottom of the gel by a conveyor belt binds these proteins with high affinity. Once the protein samples have been loaded onto the gel and electrophoresis has been started, no further intervention is needed until the blot is completed. The total expenditure of time for such a direct blot is less than 4 h for a mixture of proteins in the molecular weight range of 14-70 kDa. The staining sensitivity of directly blotted proteins is about 200 ng protein per band as revealed by India ink staining.

  17. Molecular mechanisms of spatial protein quality control.

    Science.gov (United States)

    Alberti, Simon

    2012-01-01

    Evidence is now accumulating that damaged proteins are not randomly distributed but often concentrated in microscopically visible and functionally distinct inclusion bodies. How misfolded proteins are organized into these compartments, however, is still unknown. We have recently begun to investigate stress-inducible protein quality control (PQC) bodies in yeast cells. Surprisingly, we found that protein misfolding and aggregation were not sufficient to trigger body formation under mild heat stress conditions. Rather, compartment assembly also required the concerted action of molecular chaperones, protein-sorting factors and protein-sequestration factors, thus defining a minimal machinery for spatial PQC. Expression of this machinery was limited to times of acute stress through rapid changes in mRNA abundance and a proteasomal feedback mechanism. These findings demonstrate that yeast cells can control the amount of soluble misfolded proteins through regulated phase transitions in the cytoplasm, thus allowing them to rapidly adapt to changing environmental conditions.

  18. Legal foundations of adaptive licensing.

    Science.gov (United States)

    Oye, K; Baird, L G; Chia, A; Hocking, S; Hutt, P B; Lee, D; Norwalk, L; Salvatore, V

    2013-09-01

    In April 2012, MIT's Center for Biomedical Innovation and the European Medicines Agency (EMA) cosponsored a workshop on legal foundations of adaptive pharmaceuticals licensing. Past and present attorneys from the US Food and Drug Administration (FDA), the EMA, and Health Sciences Agency Singapore (HSA) found that existing statutes provided authority for adaptive licensing (AL). By contrast, an attorney from Health Canada identified gaps in authority. Reimbursement during initial phases of adaptive approaches to licensing was deemed consistent with existing statutes in all jurisdictions.

  19. Adaptive Mesh Refinement in CTH

    International Nuclear Information System (INIS)

    Crawford, David

    1999-01-01

    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. Adaptive unmanned aerial vechile control

    OpenAIRE

    Bernotaitis, Vilimantas

    2016-01-01

    This thesis analyzes unmanned aerial vehicles and its adaptivity - their structures, operational principles and components. Also analyzing algorithms of adaptive neural networks and their usage in unmanned aerial vehicles. The main objective of this thesis is to analyze structures, control systems of unmanned aerial vehicles and their abilities to adapt to changing environment. This thesis contains analysis of already used solutions and their drawbacks. As research made in this thesis shown t...

  1. Adapting Playware to Rehabilitation Practices

    DEFF Research Database (Denmark)

    Nielsen, Camilla Balslev; Lund, Henrik Hautop

    2011-01-01

    We describe how playware and games may become adaptive to the interaction of the individual user and how therapists use this adaptation property to apply modular interactive tiles in rehabilitation practices that demand highly individualized training. Therapists may use the interactive modular...... patients modulating exercises and difficulty levels. We also find that in physical games there are individual differences in patient interaction capabilities and styles, and that modularity allows the therapist to adapt exercises to the individual patient’s capabilities....

  2. 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

  3. 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

  4. Email Adaptation for Conflict Handling

    DEFF Research Database (Denmark)

    Lee, Joyce Yi‐Hui; Panteli, Niki; Bülow, Anne Marie

    2018-01-01

    This paper explores the context of email‐based communication in anestablished but fragile, inter‐organisational partnership, which wasoften overlain with conflict. Drawing upon adaptation theory, thisstudy explores how participants adapt to the use of email to handleconflict. Extensive data were...... the leanness of email in managing conflict, we found that underthe described conflict situation the very leanness of emailwas appreciated and thus, exploited by those concerned tomanage the conflict situation. Specifically, we identified 4 keyconflict‐triggered adaptation strategies, namely......, interactionavoidance, disempowering, blame‐protection, and image‐shelteringthat drove the ways in which email was adapted to maintainorganisational partnerships under conflict....

  5. Adaptive Wireless Transceiver, Phase I

    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...

  6. Redox meets protein trafficking.

    Science.gov (United States)

    Bölter, Bettina; Soll, Jürgen; Schwenkert, Serena

    2015-09-01

    After the engulfment of two prokaryotic organisms, the thus emerged eukaryotic cell needed to establish means of communication and signaling to properly integrate the acquired organelles into its metabolism. Regulatory mechanisms had to evolve to ensure that chloroplasts and mitochondria smoothly function in accordance with all other cellular processes. One essential process is the post-translational import of nuclear encoded organellar proteins, which needs to be adapted according to the requirements of the plant. The demand for protein import is constantly changing depending on varying environmental conditions, as well as external and internal stimuli or different developmental stages. Apart from long-term regulatory mechanisms such as transcriptional/translation control, possibilities for short-term acclimation are mandatory. To this end, protein import is integrated into the cellular redox network, utilizing the recognition of signals from within the organelles and modifying the efficiency of the translocon complexes. Thereby, cellular requirements can be communicated throughout the whole organism. This article is part of a Special Issue entitled: Chloroplast Biogenesis. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. 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.

  8. Computerized adaptive testing item selection in computerized adaptive learning systems

    NARCIS (Netherlands)

    Eggen, Theodorus Johannes Hendrikus Maria; Eggen, T.J.H.M.; Veldkamp, B.P.

    2012-01-01

    Item selection methods traditionally developed for computerized adaptive testing (CAT) are explored for their usefulness in item-based computerized adaptive learning (CAL) systems. While in CAT Fisher information-based selection is optimal, for recovering learning populations in CAL systems item

  9. Temporal specificity of the initial adaptive response in motor adaptation.

    Directory of Open Access Journals (Sweden)

    Wilsaan M Joiner

    2017-07-01

    Full Text Available Repeated exposure to a novel physical environment eventually leads to a mature adaptive response whereby feedforward changes in motor output mirror both the amplitude and temporal structure of the environmental perturbations. However, adaptive responses at the earliest stages of learning have been found to be not only smaller, but systematically less specific in their temporal structure compared to later stages of learning. This observation has spawned a lively debate as to whether the temporal structure of the initial adaptive response is, in fact, stereotyped and non-specific. To settle this debate, we directly measured the adaptive responses to velocity-dependent and position-dependent force-field perturbations (vFFs and pFFs at the earliest possible stage of motor learning in humans-after just a single-movement exposure. In line with previous work, we found these earliest stage adaptive responses to be more similar than the perturbations that induced them. However, the single-trial adaptive responses for vFF and pFF perturbations were clearly distinct, and the disparity between them reflected the difference between the temporal structure of the perturbations that drove them. Critically, we observed these differences between single-trial adaptive responses when vFF and pFF perturbations were randomly intermingled from one trial to the next within the same block, indicating perturbation response specificity at the single trial level. These findings demonstrate that the initial adaptive responses to physical perturbations are not stereotyped. Instead, the neural plasticity in sensorimotor areas is sensitive to the temporal structure of a movement perturbation even at the earliest stage in learning. This insight has direct implications for the development of computational models of early-stage motor adaptation and the evolution of this adaptive response with continued training.

  10. Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants.

    Science.gov (United States)

    Hackenberg, Dieter; McKain, Michael R; Lee, Soon Goo; Roy Choudhury, Swarup; McCann, Tyler; Schreier, Spencer; Harkess, Alex; Pires, J Chris; Wong, Gane Ka-Shu; Jez, Joseph M; Kellogg, Elizabeth A; Pandey, Sona

    2017-10-01

    Signaling pathways regulated by heterotrimeric G-proteins exist in all eukaryotes. The regulator of G-protein signaling (RGS) proteins are key interactors and critical modulators of the Gα protein of the heterotrimer. However, while G-proteins are widespread in plants, RGS proteins have been reported to be missing from the entire monocot lineage, with two exceptions. A single amino acid substitution-based adaptive coevolution of the Gα:RGS proteins was proposed to enable the loss of RGS in monocots. We used a combination of evolutionary and biochemical analyses and homology modeling of the Gα and RGS proteins to address their expansion and its potential effects on the G-protein cycle in plants. Our results show that RGS proteins are widely distributed in the monocot lineage, despite their frequent loss. There is no support for the adaptive coevolution of the Gα:RGS protein pair based on single amino acid substitutions. RGS proteins interact with, and affect the activity of, Gα proteins from species with or without endogenous RGS. This cross-functional compatibility expands between the metazoan and plant kingdoms, illustrating striking conservation of their interaction interface. We propose that additional proteins or alternative mechanisms may exist which compensate for the loss of RGS in certain plant species. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  11. Plant Cell Adaptive Responses to Microgravity

    Science.gov (United States)

    Kordyum, Elizabeth; Kozeko, Liudmyla; Talalaev, Alexandr

    Microgravity is an abnormal environmental condition that plays no role in the functioning of biosphere. Nevertheless, the chronic effect of microgravity in space flight as an unfamiliar factor does not prevent the development of adaptive reactions at the cellular level. In real microgravity in space flight under the more or less optimal conditions for plant growing, namely temperature, humidity, CO2, light intensity and directivity in the hardware angiosperm plants perform an “reproductive imperative”, i.e. they flower, fruit and yield viable seeds. It is known that cells of a multicellular organism not only take part on reactions of the organism but also carry out processes that maintain their integrity. In light of these principles, the problem of the identification of biochemical, physiological and structural patterns that can have adaptive significance at the cellular and subcellular level in real and simulated microgravity is considered. Cytological studies of plants developing in real and simulated microgravity made it possible to establish that the processes of mitosis, cytokinesis, and tissue differentiation of vegetative and generative organs are largely normal. At the same time, under microgravity, essential reconstruction in the structural and functional organization of cell organelles and cytoskeleton, as well as changes in cell metabolism and homeostasis have been described. In addition, new interesting data concerning the influence of altered gravity on lipid peroxidation intensity, the level of reactive oxygen species, and antioxidant system activity, just like on the level of gene expression and synthesis of low-molecular and high-molecular heat shock proteins were recently obtained. So, altered gravity caused time-dependent increasing of the HSP70 and HSP90 levels in cells, that may indicate temporary strengthening of their functional loads that is necessary for re-establish a new cellular homeostasis. Relative qPCR results showed that

  12. Statistical Physics of Adaptation

    Directory of Open Access Journals (Sweden)

    Nikolay Perunov

    2016-06-01

    Full Text Available 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.

  13. 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 ...

  14. Stimuli-Adaptable Materials

    DEFF Research Database (Denmark)

    Frankær, Sarah Maria Grundahl

    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......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...

  15. Adaptive optics photoacoustic microscopy.

    Science.gov (United States)

    Jiang, Minshan; Zhang, Xiangyang; Puliafito, Carmen A; Zhang, Hao F; Jiao, Shuliang

    2010-10-11

    We have developed an adaptive optics photoacoustic microscope (AO-PAM) for high-resolution imaging of biological tissues, especially the retina. To demonstrate the feasibility of AO-PAM we first designed the AO system to correct the wavefront errors of the illuminating light of PAM. The aberrations of the optical system delivering the illuminating light to the sample in PAM was corrected with a close-loop AO system consisting of a 141-element MEMS-based deformable mirror (DM) and a Shack-Hartmann (SH) wavefront sensor operating at 15 Hz. The photoacoustic signal induced by the illuminating laser beam was detected by a custom-built needle ultrasonic transducer. When the wavefront errors were corrected by the AO system, the lateral resolution of PAM was measured to be better than 2.5 µm using a low NA objective lens. We tested the system on imaging ex vivo ocular samples, e.g., the ciliary body and retinal pigment epithelium (RPE) of a pig eye. The AO-PAM images showed significant quality improvement. For the first time we were able to resolve single RPE cells with PAM.

  16. Protein Crystallizability.

    Science.gov (United States)

    Smialowski, Pawel; Wong, Philip

    2016-01-01

    Obtaining diffracting quality crystals remains a major challenge in protein structure research. We summarize and compare methods for selecting the best protein targets for crystallization, construct optimization and crystallization condition design. Target selection methods are divided into algorithms predicting the chance of successful progression through all stages of structural determination (from cloning to solving the structure) and those focusing only on the crystallization step. We tried to highlight pros and cons of different approaches examining the following aspects: data size, redundancy and representativeness, overfitting during model construction, and results evaluation. In summary, although in recent years progress was made and several sequence properties were reported to be relevant for crystallization, the successful prediction of protein crystallization behavior and selection of corresponding crystallization conditions continue to challenge structural researchers.

  17. Error signals driving locomotor adaptation

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    anaesthesia (n = 5) instead of repetitive nerve stimulation. Foot anaesthesia reduced ankle adaptation to external force perturbations during walking. Our results suggest that cutaneous input plays a role in force perception, and may contribute to the 'error' signal involved in driving walking adaptation when...

  18. 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

  19. Disciplinary Literacy: "Adapt" Not Adopt

    Science.gov (United States)

    Gillis, Victoria

    2014-01-01

    This article argues that every teacher is not a teacher of literacy, but instead posits that teachers in content areas must adapt literacy strategies to the content being taught and to the context in which that teaching occurs. Examples of adaptations of a literacy strategy for use in English/language arts, mathematics, science, and social studies…

  20. Adaptation Research in Rehabilitation Counseling

    Science.gov (United States)

    Parker, Randall M.

    2007-01-01

    This paper reviews current research concerning psychosocial adaptation to chronic illness and disability and presents recommendations for future development of theories in this area. First, those who craft or adapt theories must use nondisabling, respectful, and empowering language. Rehabilitation professionals must avoid terms that connote…

  1. Adaptive Management of Environmental Flows

    Science.gov (United States)

    Webb, J. Angus; Watts, Robyn J.; Allan, Catherine; Conallin, John C.

    2018-03-01

    Adaptive management enables managers to work with complexity and uncertainty, and to respond to changing biophysical and social conditions. Amid considerable uncertainty over the benefits of environmental flows, governments are embracing adaptive management as a means to inform decision making. This Special Issue of Environmental Management presents examples of adaptive management of environmental flows and addresses claims that there are few examples of its successful implementation. It arose from a session at the 11th International Symposium on Ecohydraulics held in Australia, and is consequently dominated by papers from Australia. We classified the papers according to the involvement of researchers, managers and the local community in adaptive management. Five papers report on approaches developed by researchers, and one paper on a community-led program; these case studies currently have little impact on decision making. Six papers provide examples involving water managers and researchers, and two papers provide examples involving water managers and the local community. There are no papers where researchers, managers and local communities all contribute equally to adaptive management. Successful adaptive management of environmental flows occurs more often than is perceived. The final paper explores why successes are rarely reported, suggesting a lack of emphasis on reflection on management practices. One major challenge is to increase the documentation of successful adaptive management, so that benefits of learning extend beyond the project where it takes place. Finally, moving towards greater involvement of all stakeholders is critical if we are to realize the benefits of adaptive management for improving outcomes from environmental flows.

  2. 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

  3. 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…

  4. [The adaptation to contact lenses].

    Science.gov (United States)

    Koos, D; Koos, M J

    1992-01-01

    The indications of contact lens adaptation in optical purpose are widely large, starting, with refractive errors [correction of vices], unilateral and bilateral aphakia, myopia, anisometropia and astigmatism, together with the use of contact lens in esthetic purpose. We have been presented the adaptation techniques, the supervise, and maintenance of contact lens.

  5. 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 ...

  6. 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...

  7. Adaptive Municipal e-forms

    NARCIS (Netherlands)

    Kuiper, P.M.; van Dijk, Elisabeth M.A.G.; Boerma, A.K.; Weibelzahl, S.; Cristea, A.

    2006-01-01

    Adaptation of electronic forms seems to be a step forward to reduce the burden for people who fill in forms. Municipalities more and more offer eforms online that can be used to request a municipal product or service. To create adaptive e-forms that satisfy the need of end-users, involvement of

  8. Cultural Adaptation in Outdoor Programming

    Science.gov (United States)

    Fabrizio, Sheila M.; Neill, James

    2005-01-01

    Outdoor programs often intentionally provide a different culture and the challenge of working out how to adapt. Failure to adapt, however, can cause symptoms of culture shock, including homesickness, negative personal behavior, and interpersonal conflict. This article links cross-cultural and outdoor programming literature and provides case…

  9. 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…

  10. Adaptivity in Professional Printing Systems

    NARCIS (Netherlands)

    Verriet, J.H.; Basten, T; Hamberg, R.; Reckers, F.J.; Somers, L.

    2013-01-01

    There is a constant pressure on developers of embedded systems to simultaneously increase system functionality and to decrease development costs. Aviable way to obtain a better system performance with the same physical hardware is adaptivity: a system should be able to adapt itself to dynamically

  11. The adaptation to climate change

    International Nuclear Information System (INIS)

    Van Gameren, Valentine; Weikmans, Romain; Zaccai, Edwin

    2014-01-01

    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

  12. A robust adaptive robot controller

    NARCIS (Netherlands)

    Berghuis, Harry; Berghuis, Harry; Ortega, Romeo; Nijmeijer, Henk

    1993-01-01

    A globally convergent adaptive control scheme for robot motion control with the following features is proposed. First, the adaptation law possesses enhanced robustness with respect to noisy velocity measurements. Second, the controller does not require the inclusion of high gain loops that may

  13. An Adaptive Course Generation Framework

    Science.gov (United States)

    Li, Frederick W. B.; Lau, Rynson W. H.; Dharmendran, Parthiban

    2010-01-01

    Existing adaptive e-learning methods are supported by student (user) profiling for capturing student characteristics, and course structuring for organizing learning materials according to topics and levels of difficulties. Adaptive courses are then generated by extracting materials from the course structure to match the criteria specified in the…

  14. Adaptation of thermal power plants

    NARCIS (Netherlands)

    Bogmans, Christian W.J.; Dijkema, Gerard P.J.; Vliet, van Michelle T.H.

    2017-01-01

    When does climate change information lead to adaptation? We analyze thermal power plant adaptation by means of investing in water-saving (cooling) technology to prevent a decrease in plant efficiency and load reduction. A comprehensive power plant investment model, forced with downscaled climate

  15. Mainstreaming Climate Change Adaptation into

    African Journals Online (AJOL)

    2017-10-02

    Oct 2, 2017 ... consistent with this view is the UNDP-UNEP concept which describes mainstreaming in climate change adaptation as the iterative process of integrating climate change adaptation into development policy-making, planning, budgeting, implementation and monitoring processes at national, sector and ...

  16. 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.

  17. 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...

  18. Error adaptation in mental arithmetic.

    Science.gov (United States)

    Desmet, Charlotte; Imbo, Ineke; De Brauwer, Jolien; Brass, Marcel; Fias, Wim; Notebaert, Wim

    2012-01-01

    Until now, error and conflict adaptation have been studied extensively using simple laboratory tasks. A common finding is that responses slow down after errors. According to the conflict monitoring theory, performance should also improve after an error. However, this is usually not observed. In this study, we investigated whether the characteristics of the experimental paradigms normally used could explain this absence. More precisely, these paradigms have in common that behavioural adaptation has little room to be expressed. We therefore studied error and conflict adaptation effects in a task that encounters the richness of everyday life's behavioural adaptation--namely, mental arithmetic, where multiple solution strategies are available. In accordance with our hypothesis, we observed that post-error accuracy increases after errors in mental arithmetic. No support for conflict adaptation in mental arithmetic was found. Implications for current theories of conflict and error monitoring are discussed.

  19. Strategy for Climate Change Adaptation

    DEFF Research Database (Denmark)

    Rasmussen, Torben Valdbjørn

    2014-01-01

    . 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...

  20. What Drives Business Model Adaptation?

    DEFF Research Database (Denmark)

    Saebi, Tina; Lien, Lasse B.; Foss, Nicolai Juul

    2017-01-01

    Business models change as managers not only innovate business models, but also engage in more mundane adaptation in response to external changes, such as changes in the level or composition of demand. However, little is known about what causes such business model adaptation. We employ threat......-rigidity as well as prospect theory to examine business model adaptation in response to external threats and opportunities. Additionally, drawing on the behavioural theory of the firm, we argue that the past strategic orientation of a firm creates path dependencies that influence the propensity of the firm...... to adapt its business model. We test our hypotheses on a sample of 1196 Norwegian companies, and find that firms are more likely to adapt their business model under conditions of perceived threats than opportunities, and that strategic orientation geared towards market development is more conducive...

  1. 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.

  2. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks.

    Science.gov (United States)

    Chakraborty, Sandip; Alvarez-Ponce, David

    2016-01-01

    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.

  3. 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.

  4. 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. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  5. The Drosophila CLAMP protein associates with diverse proteins on chromatin.

    Science.gov (United States)

    Urban, Jennifer A; Urban, John M; Kuzu, Guray; Larschan, Erica N

    2017-01-01

    Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP). More recently, we established that CLAMP has non-sex-specific roles as an essential protein that regulates chromatin accessibility at promoters genome-wide. To identify associations between CLAMP and other factors in both male and female cells, we used two complementary mass spectrometry approaches. We demonstrate that CLAMP associates with the transcriptional regulator complex Negative Elongation Factor (NELF) in both sexes and determine that CLAMP reduces NELF recruitment to several target genes. In sum, we have identified many new CLAMP-associated factors and provide a resource for further study of this little understood essential protein.

  6. 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...... 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...

  7. Pupylation: proteasomal targeting by a protein modifier in bacteria.

    Science.gov (United States)

    Burns, Kristin E; Darwin, K Heran

    2012-01-01

    Proteins targeted for degradation by the mycobacterial proteasome are covalently modified with prokaryotic ubiquitin-like protein (Pup) in a process termed "pupylation." Despite its name, Pup is only ubiquitin-like in function and not sequence or structure. Furthermore, the enzymology of pupylation appears to be distinct from protein modification by ubiquitin (Ub) and other ubiquitin-like proteins (Ubls). Nonetheless, we have adapted methods established in the Ub field for the production of reagents to isolate, identify, and analyze pupylated proteins in mycobacteria. These methods can be modified to study specific pupylated proteins in various Pup-bearing bacteria or to identify posttranslational modifiers in other prokaryotes.

  8. Protein nanoparticles for therapeutic protein delivery.

    Science.gov (United States)

    Herrera Estrada, L P; Champion, J A

    2015-06-01

    Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

  9. Adaptive Augmenting Control and Launch Vehicle Adaptive Control Flight Experiments

    Data.gov (United States)

    National Aeronautics and Space Administration — Researchers at NASA Armstrong are working to further the development of an adaptive augmenting control algorithm (AAC). The AAC was developed to improve the...

  10. 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.

  11. Model and Adaptive Operations of an Adaptive Component

    Science.gov (United States)

    Wei, Le; Zhao, Qiuyun; Shu, Hongping

    In order to keep up with the dynamical and open internet environment and in terms of component, an adaptive component model which is based on event mechanism and policy binding is proposed. Components of the model can sense external changes and give the explicit description of the external environment. According to preset policy, component also can take adaptive operations such as adding, deleting, replacing and updating when necessary, and adjust the behavior and structure of the internetware to provide better services.

  12. Data-Reusing Adaptive Filtering Algorithms with Adaptive Error Constraint

    OpenAIRE

    Young-Seok Choi

    2016-01-01

    We present a family of data-reusing and affine projection algorithms. For identification of a noisy linear finite impulse response channel, a partial knowledge of a channel, especially noise, can be used to improve the performance of the adaptive filter. Motivated by this fact, the proposed scheme incorporates an estimate of a knowledge of noise. A constraint, called the adaptive noise constraint, estimates an unknown information of noise. By imposing this constraint on a...

  13. 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

  14. Recombinant protein production technology

    Science.gov (United States)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  15. Farming System Evolution and Adaptive Capacity: Insights for Adaptation Support

    Directory of Open Access Journals (Sweden)

    Jami L. Dixon

    2014-02-01

    Full Text Available Studies of climate impacts on agriculture and adaptation often provide current or future assessments, ignoring the historical contexts farming systems are situated within. We investigate how historical trends have influenced farming system adaptive capacity in Uganda using data from household surveys, semi-structured interviews, focus-group discussions and observations. By comparing two farming systems, we note three major findings: (1 similar trends in farming system evolution have had differential impacts on the diversity of farming systems; (2 trends have contributed to the erosion of informal social and cultural institutions and an increasing dependence on formal institutions; and (3 trade-offs between components of adaptive capacity are made at the farm-scale, thus influencing farming system adaptive capacity. To identify the actual impacts of future climate change and variability, it is important to recognize the dynamic nature of adaptation. In practice, areas identified for further adaptation support include: shift away from one-size-fits-all approach the identification and integration of appropriate modern farming method; a greater focus on building inclusive formal and informal institutions; and a more nuanced understanding regarding the roles and decision-making processes of influential, but external, actors. More research is needed to understand farm-scale trade-offs and the resulting impacts across spatial and temporal scales.

  16. Sampling Random Bioinformatics Puzzles using Adaptive Probability Distributions

    DEFF Research Database (Denmark)

    Have, Christian Theil; Appel, Emil Vincent; Bork-Jensen, Jette

    2016-01-01

    We present a probabilistic logic program to generate an educational puzzle that introduces the basic principles of next generation sequencing, gene finding and the translation of genes to proteins following the central dogma in biology. In the puzzle, a secret "protein word" must be found by asse...... and the randomness of the generation process, sampling may fail to generate a satisfactory puzzle. To avoid failure we employ a strategy using adaptive probabilities which change in response to previous steps of generative process, thus minimizing the risk of failure....

  17. Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.

    Science.gov (United States)

    Sojo, Victor; Dessimoz, Christophe; Pomiankowski, Andrew; Lane, Nick

    2016-11-01

    Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exterior-facing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared with water-soluble proteins in closely related species of archaea and bacteria. These patterns are consistent across the whole tree of life, and in each of the three domains of archaea, bacteria, and eukaryotes. Our findings point to a fundamental evolutionary principle: membrane proteins evolve faster due to stronger adaptive selection in changing environments, whereas cytosolic proteins are under more stringent purifying selection in the homeostatic interior of the cell. This effect should be strongest in prokaryotes, weaker in unicellular eukaryotes (with intracellular membranes), and weakest in multicellular eukaryotes (with extracellular homeostasis). We demonstrate that this is indeed the case. Similarly, we show that extracellular water-soluble proteins exhibit an even stronger pattern of low homology than membrane proteins. These striking differences in conservation of membrane proteins versus water-soluble proteins have important implications for evolution and medicine. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Externalizing Research Through Adaptive Frameworks

    DEFF Research Database (Denmark)

    Vedel, Jane Bjørn; Irwin, Alan; Høngaard Andersen, Peter

    2013-01-01

    Adaptive approaches to collaborations between industry and academic research institutions can enable both parties to achieve their goals more effectively. Here, we discuss our experience with such approaches and suggest recommendations for addressing the associated management challenges....

  19. Training Adaptability in Digital Skills

    National Research Council Canada - National Science Library

    Hess-Kosa, Kathleen

    2001-01-01

    .... As outlined in this Phase I report, Aptima and the Group for Organizational Effectiveness (gOE) have lain the groundwork for an innovative, computer-based, digital-skills training package designed to increase the adaptability of digital skills...

  20. Terrain Adaptive Reconfiguration of Mobility

    Data.gov (United States)

    National Aeronautics and Space Administration — Develop an algorithm (and software) to automatically adapt a reconfigurable robot to different types of terrains for improved mobility, that compared to SOA:...

  1. 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...

  2. Human whole body cold adaptation.

    NARCIS (Netherlands)

    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

  3. Genetic Algorithms for Case Adaptation

    International Nuclear Information System (INIS)

    Salem, A.M.; Mohamed, A.H.

    2008-01-01

    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

  4. 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.

  5. Military Adaptation to Climate Change

    Science.gov (United States)

    2011-05-01

    of Defense United States of America Environment, Energy Security and Sustainability Symposium (May 9-12, 2011) Military Adaptation to Climate Change ...2011 2. REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Military Adaptation to Climate Change 5a. CONTRACT NUMBER... climate change . …” Remarks at the Halifax International Security Forum, Halifax, Nova Scotia Nov 2009 2010 Quadrennial Defense Review For the first

  6. Adaptive control for chaotic systems

    Energy Technology Data Exchange (ETDEWEB)

    Hua Changchun E-mail: cch@ysu.edu.cn; Guan Xinping

    2004-10-01

    Control problem of chaotic system is investigated via adaptive method. A fairly simple adaptive controller is constructed, which can control chaotic systems to unstable fixed points. The precise mathematical models of chaotic systems need not be known and only the fixed points and the dimensions of chaotic systems are required to be known. Simulations on controlling different chaotic systems are investigated and the results show the validity and feasibility of the proposed controller.

  7. 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....

  8. 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

  9. Adapting agriculture to climate change.

    Science.gov (United States)

    Howden, S Mark; Soussana, Jean-François; Tubiello, Francesco N; Chhetri, Netra; Dunlop, Michael; Meinke, Holger

    2007-12-11

    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 existing agricultural systems, often variations of existing climate risk management. We show that implementation of these options is likely to have substantial benefits under moderate climate change for some cropping systems. However, there are limits to their effectiveness under more severe climate changes. Hence, more systemic changes in resource allocation need to be considered, such as targeted diversification of production systems and livelihoods. We argue that achieving increased adaptation action will necessitate integration of climate change-related issues with other risk factors, such as climate variability and market risk, and with other policy domains, such as sustainable development. Dealing with the many barriers to effective adaptation will require a comprehensive and dynamic policy approach covering a range of scales and issues, for example, from the understanding by farmers of change in risk profiles to the establishment of efficient markets that facilitate response strategies. Science, too, has to adapt. Multidisciplinary problems require multidisciplinary solutions, i.e., a focus on integrated rather than disciplinary science and a strengthening of the interface with decision makers. A crucial component of this approach is the implementation of adaptation assessment frameworks that are relevant, robust, and easily operated by all stakeholders, practitioners, policymakers, and scientists.

  10. Fair adaptation to climate change

    International Nuclear Information System (INIS)

    Paavola, Jouni; Adger, W. Neil

    2006-01-01

    This article identifies social justice dilemmas associated with the necessity to adapt to climate change, examines how they are currently addressed by the climate change regime, and proposes solutions to overcome prevailing gaps and ambiguities. We argue that the key justice dilemmas of adaptation include responsibility for climate change impacts, the level and burden sharing of assistance to vulnerable countries for adaptation, distribution of assistance between recipient countries and adaptation measures, and fair participation in planning and making decisions on adaptation. We demonstrate how the climate change regime largely omits responsibility but makes a general commitment to assistance. However, the regime has so far failed to operationalise assistance and has made only minor progress towards eliminating obstacles for fair participation. We propose the adoption of four principles for fair adaptation in the climate change regime. These include avoiding dangerous climate change, forward-looking responsibility, putting the most vulnerable first and equal participation of all. We argue that a safe maximum standard of 400-500 ppm of CO 2 concentrations in the atmosphere and a carbon tax of $20-50 per carbon equivalent ton could provide the initial instruments for operationalising the principles. (author)

  11. 3D adaptive optics in a light sheet microscope.

    Science.gov (United States)

    Bourgenot, Cyril; Saunter, Christopher D; Taylor, Jonathan M; Girkin, John M; Love, Gordon D

    2012-06-04

    We report on a single plane illumination microscope (SPIM) incorporating adaptive optics in the imaging arm. We show how aberrations can occur from the sample mounting tube and quantify the aberrations both experimentally and computationally. A wavefront sensorless approach was taken to imaging a green fluorescent protein (GFP) labelled transgenic zebrafish. We show improvements in image quality whilst recording a 3D "z-stack" and show how the aberrations come from varying depths in the fish.

  12. Optical Control over Monomeric and Multimeric Protein Hybrids

    NARCIS (Netherlands)

    Putri, Rindia Maharani

    2017-01-01

    Living materials are based on proteins that adapt and change in structure and function continuously when in use; cellular microtubules, ATP synthases and ribosomes are but a few examples. Breathing life into semi-synthetic materials would allow improved understanding over protein regulation and

  13. Directional Darwinian Selection in proteins.

    Science.gov (United States)

    McClellan, David A

    2013-01-01

    Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

  14. Meiosis evolves: adaptation to external and internal environments.

    Science.gov (United States)

    Bomblies, Kirsten; Higgins, James D; Yant, Levi

    2015-10-01

    306 I. 306 II. 307 III. 312 IV. 317 V. 318 319 References 319 SUMMARY: Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we found evidence of two especially potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole-genome duplication and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge are likely to involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of meiosis gene evolution suggests that the structural components of meiosis coevolve as adaptive modules that may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species probably reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  15. Aquaporin Protein-Protein Interactions

    Directory of Open Access Journals (Sweden)

    Jennifer Virginia Roche

    2017-10-01

    Full Text Available Aquaporins are tetrameric membrane-bound channels that facilitate transport of water and other small solutes across cell membranes. In eukaryotes, they are frequently regulated by gating or trafficking, allowing for the cell to control membrane permeability in a specific manner. Protein–protein interactions play crucial roles in both regulatory processes and also mediate alternative functions such as cell adhesion. In this review, we summarize recent knowledge about aquaporin protein–protein interactions; dividing the interactions into three types: (1 interactions between aquaporin tetramers; (2 interactions between aquaporin monomers within a tetramer (hetero-tetramerization; and (3 transient interactions with regulatory proteins. We particularly focus on the structural aspects of the interactions, discussing the small differences within a conserved overall fold that allow for aquaporins to be differentially regulated in an organism-, tissue- and trigger-specific manner. A deep knowledge about these differences is needed to fully understand aquaporin function and regulation in many physiological processes, and may enable design of compounds targeting specific aquaporins for treatment of human disease.

  16. Protein immobilization strategies for protein biochips

    NARCIS (Netherlands)

    Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

    2007-01-01

    In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

  17. Coevolution of gene expression among interacting proteins

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, Hunter B.; Hirsh, Aaron E.; Wall, Dennis P.; Eisen,Michael B.

    2004-03-01

    Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate previously uncharacterized coevolution of gene expression, adding a different dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein protein interactions.

  18. 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).

  19. Molecular mechanism of radioadaptive response: A cross-adaptive response for enhanced repair of DNA damage in adapted cells

    International Nuclear Information System (INIS)

    Takaji Ikushima

    1997-01-01

    The radioadaptive response (RAR) has been attributed to the induction of a repair mechanism by low doses of ionizing radiation, but the molecular nature of the mechanism is not yet elucidated. We have characterized RAR in a series of experiments in cultured Chinese hamster V79 cells. A 4-h interval is required for the full expression of RAR, which decays with the progression of cell proliferation. Treatments with inhibitors of poly(ADP-ribose) polymerase, protein- or RNA synthesis, and protein kinase C suppress the RAR expression. The RAR cross-reacts on clastogenic lesions induced by other physical and chemical DNA-damaging agents. The presence of newly synthesised proteins has been detected during the expression period. Experiments performed using single-cell gel electrophoresis provided more direct evidence for a faster and enhaced DNA repair rate in adapted cells. Here, using single-cell gel electrophoresis, a cross-adaptive response has been demonstrated for enhanced repair of DNA damage induced by neocarzinostatin in radio-adapted cells. (author)

  20. 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.